Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns

Click to copy article linkArticle link copied!

This article references 94 other publications.

1. 1

   Hubbell, S. P. The Unified Neutral Theory of Biodiversity and Biogeography; Princeton University Press, 2001.

   Google Scholar

   There is no corresponding record for this reference.
2. 2

   Wang, J.; Shen, J.; Wu, Y.; Tu, C.; Soininen, J.; Stegen, J. C.; He, J.; Liu, X.; Zhang, L.; Zhang, E. Phylogenetic Beta Diversity in Bacterial Assemblages across Ecosystems: Deterministic versus Stochastic Processes. ISME J. 2013, 7, 1310– 1321,  DOI: 10.1038/ismej.2013.30

   Google Scholar

   2

   Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

   Wang, Jianjun; Shen, Ji; Wu, Yucheng; Tu, Chen; Soininen, Janne; Stegen, James C.; He, Jizheng; Liu, Xingqi; Zhang, Lu; Zhang, Enlou

   ISME Journal (2013), 7 (7), 1310-1321CODEN: IJSOCF; ISSN:1751-7362. (Nature Publishing Group)

   Increasing evidence has emerged for non-random spatial distributions of microbes, but knowledge of the processes that cause variation in microbial assemblage among ecosystems is lacking. For instance, some studies showed that deterministic processes such as habitat specialization are important, while other studies hold that bacterial communities are assembled by stochastic forces. Here we examine the relative influence of deterministic and stochastic processes for bacterial communities from subsurface environments, stream biofilm, lake water, lake sediment and soil using pyrosequencing of the 16S rRNA gene. We show that there is a general pattern in phylogenetic signal in species ecol. niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community compn. The phylogenetic dissimilarities among-habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within-habitat types, the highest phylogenetic turnover rate through space was obsd. in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups. For three sample groups, spatial distance reflected unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial Mantel results based on obsd. beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight that bacteria show strong habitat assocns. that have likely emerged through evolutionary adaptation.
3. 3

   Graham, E. B.; Crump, A. R.; Resch, C. T.; Fansler, S.; Arntzen, E.; Kennedy, D. W.; Fredrickson, J. K.; Stegen, J. C. Deterministic Influences Exceed Dispersal Effects on Hydrologically-Connected Microbiomes. Environ. Microbiol. 2017, 19, 1552– 1567,  DOI: 10.1111/1462-2920.13720

   Google Scholar

   3

   Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes

   Graham, Emily B.; Crump, Alex R.; Resch, Charles T.; Fansler, Sarah; Arntzen, Evan; Kennedy, David W.; Fredrickson, Jim K.; Stegen, James C.

   Environmental Microbiology (2017), 19 (4), 1552-1567CODEN: ENMIFM; ISSN:1462-2912. (Wiley-Blackwell)

   Summary : Subsurface groundwater-surface water mixing zones (hyporheic zones) have enhanced biogeochem. activity, but assembly processes governing subsurface microbiomes remain a crit. uncertainty in understanding hyporheic biogeochem. To address this obstacle, we investigated (a) biogeog. patterns in attached and waterborne microbiomes across three hydrol.-connected, physicochem.-distinct zones (inland hyporheic, nearshore hyporheic and river); (b) assembly processes that generated these patterns; (c) groups of organisms that corresponded to deterministic changes in the environment; and (d) correlations between these groups and hyporheic metab. All microbiomes remained dissimilar through time, but consistent presence of similar taxa suggested dispersal and/or common selective pressures among zones. Further, we demonstrated a pronounced impact of deterministic assembly in all microbiomes as well as seasonal shifts from heterotrophic to autotrophic microorganisms assocd. with increases in groundwater discharge. The abundance of one statistical cluster of organisms increased with active biomass and respiration, revealing organisms that may strongly influence hyporheic biogeochem. Based on our results, we propose a conceptualization of hyporheic zone metab. in which increased org. carbon concns. during surface water intrusion support heterotrophy, which succumbs to autotrophy under groundwater discharge. These results provide new opportunities to enhance microbially-explicit ecosystem models describing hyporheic zone biogeochem. and its influence over riverine ecosystem function.
4. 4

   Chase, J. M. Drought Mediates the Importance of Stochastic Community Assembly. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 17430– 17434,  DOI: 10.1073/pnas.0704350104

   Google Scholar

   4

   Drought mediates the importance of stochastic community assembly

   Chase, Jonathan M.

   Proceedings of the National Academy of Sciences of the United States of America (2007), 104 (44), 17430-17434CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

   Historically, the biodiversity and compn. of species in a locality was thought to be influenced primarily by deterministic factors. In such cases, species' niches create differential responses to environmental conditions and interspecific interactions, which combine to det. that locality's biodiversity and species compn. More recently, proponents of the neutral theory have placed a premium on how stochastic factors, such as birth, death, colonization, and extinction (termed "ecol. drift") influence diversity and species compn. in a locality independent of their niches. Here, I develop the hypothesis that the relative importance of stochastic ecol. drift and/or priority effects depend on the harshness of the ecol. filter in those habitats. I established long-term exptl. ponds to explore the relative importance of community assembly history and drought on patterns of community compositional similarity among ponds that were otherwise similar in their environmental conditions. I show considerable site-to-site variation in pond community compn. in the absence of drought that likely resulted from a combination of stochastic ecol. drift and priority effects. However, in ponds that experienced drought, I found much higher similarity among communities that likely resulted from niche-selection filtering out species from the regional pool that could not tolerate such environmental harshness. These results implicate the crit. role for understanding the processes of community assembly when examg. patterns of biodiversity at different spatial scales.
5. 5

   Van Der Gast, C. J.; Ager, D.; Lilley, A. K. Temporal Scaling of Bacterial Taxa Is Influenced by Both Stochastic and Deterministic Ecological Factors. Environ. Microbiol. 2008, 10, 1411– 1418,  DOI: 10.1111/j.1462-2920.2007.01550.x

   Google Scholar

   5

   Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors

   van der Gast Christopher J; Ager Duane; Lilley Andrew K

   Environmental microbiology (2008), 10 (6), 1411-8 ISSN:.

   Microorganisms operate at a range of spatial and temporal scales acting as key drivers of ecosystem properties. Therefore, many key questions in microbial ecology require the consideration of both spatial and temporal scales. Spatial scaling, in particular the species-area relationship (SAR), has a long history in ecology and has recently been addressed in microbial ecology. However, the temporal analogue of the SAR, the species-time relationship, has received far less attention even in the science of general ecology. Here we focus upon the role of temporal scaling in microbial ecological patterns by coupling molecular characterization of bacterial communities in discrete island (bioreactor) systems with a macroecological approach. Our findings showed that the temporal scaling exponent (slope), and therefore taxa turnover of the bacterial taxa-time relationship decreased as selective pressure (industrial wastewater concentration) increased. Also, as the concentration of industrial wastewater increased across the bioreactors, we observed a gradual switch from stochastic community assembly to more deterministic (niche)-based considerations. The identification of broad-scale statistical patterns is particularly relevant to microbial ecology, as it is frequently difficult to identify individual species or their functions. In this study, we identify wide-reaching statistical patterns of diversity and show that they are shaped by the prevalent underlying ecological factors.
6. 6

   Pagaling, E.; Strathdee, F.; Spears, B. M.; Cates, M. E.; Allen, R. J.; Free, A. Community History Affects the Predictability of Microbial Ecosystem Development. ISME J. 2014, 8, 19– 30,  DOI: 10.1038/ismej.2013.150

   Google Scholar

   6

   Community history affects the predictability of microbial ecosystem development

   Pagaling Eulyn; Strathdee Fiona; Spears Bryan M; Cates Michael E; Allen Rosalind J; Free Andrew

   The ISME journal (2014), 8 (1), 19-30 ISSN:.

   Microbial communities mediate crucial biogeochemical, biomedical and biotechnological processes, yet our understanding of their assembly, and our ability to control its outcome, remain poor. Existing evidence presents conflicting views on whether microbial ecosystem assembly is predictable, or inherently unpredictable. We address this issue using a well-controlled laboratory model system, in which source microbial communities colonize a pristine environment to form complex, nutrient-cycling ecosystems. When the source communities colonize a novel environment, final community composition and function (as measured by redox potential) are unpredictable, although a signature of the community's previous history is maintained. However, when the source communities are pre-conditioned to their new habitat, community development is more reproducible. This situation contrasts with some studies of communities of macro-organisms, where strong selection under novel environmental conditions leads to reproducible community structure, whereas communities under weaker selection show more variability. Our results suggest that the microbial rare biosphere may have an important role in the predictability of microbial community development, and that pre-conditioning may help to reduce unpredictability in the design of microbial communities for biotechnological applications.
7. 7

   Langenheder, S.; Lindström, E. S.; Tranvik, L. J. Structure and Function of Bacterial Communities Emerging from Different Sources under Identical Conditions Structure and Function of Bacterial Communities Emerging from Different Sources under Identical Conditions. Appl. Environ. Microbiol. 2006, 72, 212– 220,  DOI: 10.1128/aem.72.1.212-220.2006

   Google Scholar

   7

   Structure and function of bacterial communities emerging from different sources under identical conditions

   Langenheder, Silke; Lindstroem, Eva S.; Tranvik, Lars J.

   Applied and Environmental Microbiology (2006), 72 (1), 212-220CODEN: AEMIDF; ISSN:0099-2240. (American Society for Microbiology)

   The aim of this study was to compare two major hypotheses concerning the formation of bacterial community compn. (BCC) at the local scale, i.e., whether BCC is detd. by the prevailing local environmental conditions or by "metacommunity processes.". A batch culture expt. where bacteria from eight distinctly different aquatic habitats were regrown under identical conditions was performed to test to what extent similar communities develop under similar selective pressure. Differently composed communities emerged from different inoculum communities, as detd. by terminal restriction fragment length polymorphism anal. of the 16S rRNA gene. There was no indication that similarity increased between communities upon growth under identical conditions compared to that for growth at the ambient sampling sites. This suggests that the history and distribution of taxa within the source communities were stronger regulating factors of BCC than the environmental conditions. Moreover, differently composed communities were different with regard to specific functions, such as enzyme activities, but maintained similar broad-scale functions, such as biomass prodn. and respiration.
8. 8

   Lee, S.-H.; Sorensen, J. W.; Grady, K. L.; Tobin, T. C.; Shade, A. Divergent Extremes but Convergent Recovery of Bacterial and Archaeal Soil Communities to an Ongoing Subterranean Coal Mine Fire. ISME J. 2017, 11, 1447– 1459,  DOI: 10.1038/ismej.2017.1

   Google Scholar

   8

   Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire

   Lee Sang-Hoon; Sorensen Jackson W; Grady Keara L; Shade Ashley; Lee Sang-Hoon; Tobin Tammy C; Shade Ashley

   The ISME journal (2017), 11 (6), 1447-1459 ISSN:.

   Press disturbances are stressors that are extended or ongoing relative to the generation times of community members, and, due to their longevity, have the potential to alter communities beyond the possibility of recovery. They also provide key opportunities to investigate ecological resilience and to probe biological limits in the face of prolonged stressors. The underground coal mine fire in Centralia, Pennsylvania has been burning since 1962 and severely alters the overlying surface soils by elevating temperatures and depositing coal combustion pollutants. As the fire burns along the coal seams to disturb new soils, previously disturbed soils return to ambient temperatures, resulting in a chronosequence of fire impact. We used 16S rRNA gene sequencing to examine bacterial and archaeal soil community responses along two active fire fronts in Centralia, and investigated the influences of assembly processes (selection, dispersal and drift) on community outcomes. The hottest soils harbored the most variable and divergent communities, despite their reduced diversity. Recovered soils converged toward similar community structures, demonstrating resilience within 10-20 years and exhibiting near-complete return to reference communities. Measured soil properties (selection), local dispersal, and neutral community assembly models could not explain the divergences of communities observed at temperature extremes, yet beta-null modeling suggested that communities at temperature extremes follow niche-based processes rather than null. We hypothesize that priority effects from responsive seed bank transitions may be key in explaining the multiple equilibria observed among communities at extreme temperatures. These results suggest that soils generally have an intrinsic capacity for robustness to varied disturbances, even to press disturbances considered to be 'extreme', compounded, or incongruent with natural conditions.
9. 9

   Liang, J.-L.; Li, X.-J.; Shu, H.-Y.; Wang, P.; Kuang, J.-L.; Liu, J.; Zhang, M.-M.; Shu, W.-S.; Huang, L.-N. Fine-Scale Spatial Patterns in Microbial Community Composition in an Acid Mine Drainage. FEMS Microbiol. Ecol. 2017, 93, 1– 8,  DOI: 10.1093/femsec/fix124

   Google Scholar

   9

   Methane-metabolizing microbial communities in sediments of the Haima cold seep area, northwest slope of the South China Sea

   Niu, Mingyang; Fan, Xibei; Zhuang, Guangchao; Liang, Qianyong; Wang, Fengping

   FEMS Microbiology Ecology (2017), 93 (9), 1-13CODEN: FMECEZ; ISSN:1574-6941. (Oxford University Press)

   Cold seeps are widespread chemosynthetic ecosystems in the deep-sea environment, and cold seep microbial communities of the South China Sea are poorly constrained. Here we report on the archaeal communities, particularly those involved in methane metabolization, in sediments of a newly discovered cold seep (named 'Haima') on the northwest slope of the South China Sea. Archaeal diversity, abundance and distribution were investigated in two piston cores collected from a seep area (QDN-14B) and a non-seep control site (QDN-31B). Geochem. investigation of the QDN-14B core identified an estd. sulfate-methane transition zone (Estd. SMTZ) at 300-400 cm below sea floor (cmbsf), where a high abundance of anaerobic methane-oxidizing archaea (ANME) occurred, as revealed by anal. of the 16S rRNA gene and the gene (mcrA) encoding the α-subunit of the key enzyme methyl-coenzyme M reductase. ANME-2a/b was predominant in the upper and middle layers of the estd. SMTZ, whereas ANME-1b outcompeted ANME-2 in the sulfate-depleted bottom layers of the estd. SMTZ and the methanogenic zone. Fine-scale phylogenetic anal. further divided the ANME-1b group into three subgroups with different distribution patterns: ANME-1bI, ANME-1bII and ANME-1bIII. Multivariate analyses indicated that dissolved inorg. carbon and sulfate may be important factors controlling the compn. of the methane-metabolizing community. Our study on ANME niche sepn. and interactions with other archaeal groups improves our understanding of the metabolic diversity and flexibility of ANME, and the findings further suggest that ANME subgroups may have evolved diversified/specified metabolic capabilities other than syntrophic anaerobic oxidn. of methane coupled with sulfate redn. in marine sediments.
10. 10

    Dini-Andreote, F.; Stegen, J. C.; van Elsas, J. D.; Salles, J. F. Disentangling Mechanisms That Mediate the Balance between Stochastic and Deterministic Processes in Microbial Succession. Proc. Natl. Acad. Sci. U.S.A. 2015, 112, E1326– E1332,  DOI: 10.1073/pnas.1414261112

    Google Scholar

    10

    Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession

    Dini-Andreote, Francisco; Stegen, James C.; van Elsas, Jan Dirk; Salles, Joana Falcao

    Proceedings of the National Academy of Sciences of the United States of America (2015), 112 (11), E1326-E1332CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

    Ecol. succession and the balance between stochastic and deterministic processes are two major themes within microbial ecol., but these conceptual domains have mostly developed independent of each other. Here we provide a framework that integrates shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. Synthesizing previous work, we devised a conceptual model that links ecosystem development to alternative hypotheses related to shifts in ecol. assembly processes. Conceptual model hypotheses were tested by coupling spatiotemporal data on soil bacterial communities with environmental conditions in a salt marsh chronosequence spanning 105 years of succession. Analyses within successional stages showed community compn. to be initially governed by stochasticity, but as succession proceeded, there was a progressive increase in deterministic selection correlated with increasing sodium concn. Analyses of community turnover among successional stages-which provide a larger spatiotemporal scale relative to within stage analyses-revealed that changes in the concn. of soil org. matter were the main predictor of the type and relative influence of determinism. Taken together, these results suggest scale-dependency in the mechanisms underlying selection. To better understand mechanisms governing these patterns, we developed an ecol. simulation model that revealed how changes in selective environments cause shifts in the stochastic/deterministic balance. Finally, we propose an extended-and exptl. testable-conceptual model integrating ecol. assembly processes with primary and secondary succession. This framework provides a priori hypotheses for future expts., thereby facilitating a systematic approach to understand assembly and succession in microbial communities across ecosystems.
11. 11

    Vass, M.; Langenheder, S. The Legacy of the Past: Effects of Historical Processes on Microbial Metacommunities. Aquat. Microb. Ecol. 2017, 79, 13– 19,  DOI: 10.3354/ame01816

    Google Scholar

    There is no corresponding record for this reference.
12. 12

    Andersson, M. G. I.; Berga, M.; Lindström, E. S.; Langenheder, S. The Spatial Structure of Bacterial Communities Is Influenced by Historical Environmental Conditions. Ecology 2014, 95, 1134– 1140,  DOI: 10.1890/13-1300.1

    Google Scholar

    12

    The spatial structure of bacterial communities is influenced by historical environmental conditions

    Andersson Martin G I; Berga Merce; Lindstrom Eva S; Langenheder Silke

    Ecology (2014), 95 (5), 1134-40 ISSN:0012-9658.

    The spatial structure of ecological communities, including that of bacteria, is often influenced by species sorting by contemporary environmental conditions. Moreover, historical processes, i.e., ecological and evolutionary events that have occurred at some point in the past, such as dispersal limitation, drift, priority effects, or selection by past environmental conditions, can be important, but are generally investigated much less. Here, we conducted a field study using 16 rock pools, where we specifically compared the importance of past vs. contemporary environmental conditions for bacterial community structure by correlating present differences in bacterial community composition among pools to environmental conditions measured on the same day, as well as to those measured 2, 4, 6, and 8 d earlier. The results prove that selection by past environmental conditions exists, since we were able to show that bacterial communities are, to a greater extent, an imprint of past compared to contemporary environmental conditions. We suggest that this is the result of a combination of different mechanisms, including priority effects that cause rapid adaptation to new environmental conditions of taxa that have been initially selected by past environmental conditions, and slower rates of turnover in community composition compared to environmental conditions.
13. 13

    Bargiela, R.; Mapelli, F.; Rojo, D.; Chouaia, B.; Tornés, J.; Borin, S.; Richter, M.; Del Pozo, M. V.; Cappello, S.; Gertler, C.; Genovese, M.; Denaro, R.; Martínez-Martínez, M.; Fodelianakis, S.; Amer, R. A.; Bigazzi, D.; Han, X.; Chen, J.; Chernikova, T. N.; Golyshina, O. V.; Mahjoubi, M.; Jaouanil, A.; Benzha, F.; Magagnini, M.; Hussein, E.; Al-Horani, F.; Cherif, A.; Blaghen, M.; Abdel-Fattah, Y. R.; Kalogerakis, N.; Barbas, C.; Malkawi, H. I.; Golyshin, P. N.; Yakimov, M. M.; Daffonchio, D.; Ferrer, M. Bacterial Population and Biodegradation Potential in Chronically Crude Oil-Contaminated Marine Sediments Are Strongly Linked to Temperature. Sci. Rep. 2015, 5, 11651,  DOI: 10.1038/srep11651

    Google Scholar

    13

    Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature

    Bargiela, Rafael; Mapelli, Francesca; Rojo, David; Chouaia, Bessem; Tornes, Jesus; Borin, Sara; Richter, Michael; Del Pozo, Mercedes V.; Cappello, Simone; Gertler, Christoph; Genovese, Maria; Denaro, Renata; Martinez-Martinez, Monica; Fodelianakis, Stilianos; Amer, Ranya A.; Bigazzi, David; Han, Xifang; Chen, Jianwei; Chernikova, Tatyana N.; Golyshina, Olga V.; Mahjoubi, Mouna; Jaouanil, Atef; Benzha, Fatima; Magagnini, Mirko; Hussein, Emad; Al-Horani, Fuad; Cherif, Ameur; Blaghen, Mohamed; Abdel-Fattah, Yasser R.; Kalogerakis, Nicolas; Barbas, Coral; Malkawi, Hanan I.; Golyshin, Peter N.; Yakimov, Michail M.; Daffonchio, Daniele; Ferrer, Manuel

    Scientific Reports (2015), 5 (), 11651CODEN: SRCEC3; ISSN:2045-2322. (Nature Publishing Group)

    Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geog. constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geog. sepd. oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compns. and their biodegrdn. potential were primarily assocd. (P < 0.05) with both temp. and chem. diversity. Furthermore, we obsd. a link between temp. and chem. and biol. diversity that was stronger in chronically polluted sites than in pristine ones where accidental oil spills occurred. We propose that low temp. increases bacterial richness while decreasing catabolic diversity and that chronic pollution promotes catabolic diversification. Our results further suggest that the bacterial populations in chronically polluted sites may respond more promptly in degrading petroleum after accidental oil spills.
14. 14

    Nemergut, D. R.; Schmidt, S. K.; Fukami, T.; O’Neill, S. P.; Bilinski, T. M.; Stanish, L. F.; Knelman, J. E.; Darcy, J. L.; Lynch, R. C.; Wickey, P.; Ferrenberg, S. Patterns and Processes of Microbial Community Assembly. Microbiol. Mol. Biol. Rev. 2013, 77, 342– 356,  DOI: 10.1128/mmbr.00051-12

    Google Scholar

    14

    Patterns and processes of microbial community assembly

    Nemergut Diana R; Schmidt Steven K; Fukami Tadashi; O'Neill Sean P; Bilinski Teresa M; Stanish Lee F; Knelman Joseph E; Darcy John L; Lynch Ryan C; Wickey Phillip; Ferrenberg Scott

    Microbiology and molecular biology reviews : MMBR (2013), 77 (3), 342-56 ISSN:.

    Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183-206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.
15. 15

    Graham, E. B.; Knelman, J. E.; Schindlbacher, A.; Siciliano, S.; Breulmann, M.; Yannarell, A.; Beman, J. M.; Abell, G.; Philippot, L.; Prosser, J.; Foulquier, A.; Yuste, J. C.; Glanville, H. C.; Jones, D. L.; Angel, R.; Salminen, J.; Newton, R. J.; Bürgmann, H.; Ingram, L. J.; Hamer, U.; Siljanen, H. M. P.; Peltoniemi, K.; Potthast, K.; Bañeras, L.; Hartmann, M.; Banerjee, S.; Yu, R. Q.; Nogaro, G.; Richter, A.; Koranda, M.; Castle, S. C.; Goberna, M.; Song, B.; Chatterjee, A.; Nunes, O. C.; Lopes, A. R.; Cao, Y.; Kaisermann, A.; Hallin, S.; Strickland, M. S.; Garcia-Pausas, J.; Barba, J.; Kang, H.; Isobe, K.; Papaspyrou, S.; Pastorelli, R.; Lagomarsino, A.; Lindström, E. S.; Basiliko, N.; Nemergut, D. R. Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?. Front. Microbiol. 2016, 7, 214,  DOI: 10.3389/fmicb.2016.00214

    Google Scholar

    15

    Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

    Graham Emily B; Knelman Joseph E; Schindlbacher Andreas; Siciliano Steven; Breulmann Marc; Yannarell Anthony; Beman J M; Abell Guy; Philippot Laurent; Prosser James; Foulquier Arnaud; Yuste Jorge C; Glanville Helen C; Jones Davey L; Angel Roey; Richter Andreas; Salminen Janne; Newton Ryan J; Burgmann Helmut; Ingram Lachlan J; Hamer Ute; Siljanen Henri M P; Peltoniemi Krista; Potthast Karin; Baneras Lluis; Hartmann Martin; Banerjee Samiran; Yu Ri-Qing; Nogaro Geraldine; Koranda Marianne; Castle Sarah C; Goberna Marta; Song Bongkeun; Chatterjee Amitava; Nunes Olga C; Lopes Ana R; Cao Yiping; Kaisermann Aurore; Hallin Sara; Strickland Michael S; Garcia-Pausas Jordi; Barba Josep; Kang Hojeong; Isobe Kazuo; Papaspyrou Sokratis; Pastorelli Roberta; Lagomarsino Alessandra; Lindstrom Eva S; Basiliko Nathan; Nemergut Diana R

    Frontiers in microbiology (2016), 7 (), 214 ISSN:1664-302X.

    Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.
16. 16

    Bier, R. L.; Bernhardt, E. S.; Boot, C. M.; Graham, E. B.; Hall, E. K.; Lennon, J. T.; Nemergut, D. R.; Osborne, B. B.; Ruiz-González, C.; Schimel, J. P.; Waldrop, M. P.; Wallenstein, M. D. Linking Microbial Community Structure and Microbial Processes: An Empirical and Conceptual Overview. FEMS Microbiol. Ecol. 2015, 91, fiv113,  DOI: 10.1093/femsec/fiv113

    Google Scholar

    There is no corresponding record for this reference.
17. 17

    Gadd, G. M. Metals, Minerals and Microbes: Geomicrobiology and Bioremediation. Microbiology 2010, 156, 609– 643,  DOI: 10.1099/mic.0.037143-0

    Google Scholar

    17

    Metals, minerals and microbes: geomicrobiology and bioremediation

    Gadd, Geoffrey Michael

    Microbiology (Reading, United Kingdom) (2010), 156 (3), 609-643CODEN: MROBEO; ISSN:1350-0872. (Society for General Microbiology)

    A review. Microbes play key geoactive roles in the biosphere, particularly in the areas of element biotransformations and biogeochem. cycling, metal and mineral transformations, decompn., bioweathering, and soil and sediment formation. All kinds of microbes, including prokaryotes and eukaryotes and their symbiotic assocns. with each other and 'higher organisms', can contribute actively to geol. phenomena, and central to many such geomicrobial processes are transformations of metals and minerals. Microbes have a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissoln. or deterioration. Such mechanisms are important components of natural biogeochem. cycles for metals as well as assocd. elements in biomass, soil, rocks and minerals, e.g. sulfur and phosphorus, and metalloids, actinides and metal radionuclides. Apart from being important in natural biosphere processes, metal and mineral transformations can have beneficial or detrimental consequences in a human context. Bioremediation is the application of biol. systems to the clean-up of org. and inorg. pollution, with bacteria and fungi being the most important organisms for reclamation, immobilization or detoxification of metallic and radionuclide pollutants. Some biominerals or metallic elements deposited by microbes have catalytic and other properties in nanoparticle, cryst. or colloidal forms, and these are relevant to the development of novel biomaterials for technol. and antimicrobial purposes. On the neg. side, metal and mineral transformations by microbes may result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and assocd. metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment, all with immense social and economic consequences. The ubiquity and importance of microbes in biosphere processes make geomicrobiol. one of the most important concepts within microbiol., and one requiring an interdisciplinary approach to define environmental and applied significance and underpin exploitation in biotechnol.
18. 18

    Handley, K. M.; Wrighton, K. C.; Miller, C. S.; Wilkins, M. J.; Kantor, R. S.; Thomas, B. C.; Williams, K. H.; Gilbert, J. A.; Long, P. E.; Banfield, J. F. Disturbed Subsurface Microbial Communities Follow Equivalent Trajectories despite Different Structural Starting Points. Environ. Microbiol. 2015, 17, 622– 636,  DOI: 10.1111/1462-2920.12467

    Google Scholar

    18

    Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points

    Handley, Kim M.; Wrighton, Kelly C.; Miller, Christopher S.; Wilkins, Michael J.; Kantor, Rose S.; Thomas, Brian C.; Williams, Kenneth H.; Gilbert, Jack A.; Long, Philip E.; Banfield, Jillian F.

    Environmental Microbiology (2015), 17 (3), 622-636CODEN: ENMIFM; ISSN:1462-2912. (Wiley-Blackwell)

    Summary : Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide exptl. evidence for niche vs. neutral and founding community effects during a bioremediation-related org. carbon disturbance. Subsurface sediment, partitioned into 22 flow-through columns, was stimulated in situ by the addn. of acetate as a carbon and electron donor source. This drove the system into a new transient biogeochem. state characterized by iron redn. and enriched Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After approx. 1 mo, conditions favored sulfate redn., and were accompanied by a substantial increase in the relative abundance of Desulfobulbus, Desulfosporosinus, Desulfitobacterium and Desulfotomaculum. Two subsets of four to five columns each were switched from acetate to lactate amendment during either iron (earlier) or sulfate (later) redn. Hence, subsets had significantly different founding communities. All lactate treatments exhibited lower relative abundances of Desulfotomaculum and Bacteroidetes, enrichments of Clostridiales and Psychrosinus species, and a temporal succession from highly abundant Clostridium sensu stricto to Psychrosinus. Regardless of starting point, lactate-switch communities followed comparable structural trajectories, whereby convergence was evident 9 to 16 days after each switch, and significant after 29 to 34 days of lactate addn. Results imply that neither the founding community nor neutral processes influenced succession following perturbation. Reconstructed 16S rRNA gene data is accessible via the GenBank accession nos. KC716084-KC731398.
19. 19

    Handley, K. M.; Piceno, Y. M.; Hu, P.; Tom, L. M.; Mason, O. U.; Andersen, G. L.; Jansson, J. K.; Gilbert, J. A. Metabolic and Spatio-Taxonomic Response of Uncultivated Seafloor Bacteria Following the Deepwater Horizon Oil Spill. ISME J. 2017, 11, 2569– 2583,  DOI: 10.1038/ismej.2017.110

    Google Scholar

    19

    Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill

    Handley, K. M.; Piceno, Y. M.; Hu, P.; Tom, L. M.; Mason, O. U.; Andersen, G. L.; Jansson, J. K.; Gilbert, J. A.

    ISME Journal (2017), 11 (11), 2569-2583CODEN: IJSOCF; ISSN:1751-7362. (Nature Research)

    The release of 700 million liters of oil into the Gulf of Mexico over a few months in 2010 produced dramatic changes in the microbial ecol. of the water and sediment. Here, we reconstructed the genomes of 57 widespread uncultivated bacteria from post-spill deep-sea sediments, and recovered their gene expression pattern across the seafloor. These genomes comprised a common collection of bacteria that were enriched in heavily affected sediments around the wellhead. Although rare in distal sediments, some members were still detectable at sites up to 60 km away. Many of these genomes exhibited phylogenetic clustering indicative of common trait selection by the environment, and within half we identified 264 genes assocd. with hydrocarbon degrdn. Alkane degrdn. ability was near ubiquitous among candidate hydrocarbon degraders, whereas just three harbored elaborate gene inventories for the degrdn. of alkanes and arom. and polycyclic arom. hydrocarbons (PAHs). Differential gene expression profiles revealed a spill-promoted microbial sulfur cycle alongside gene upregulation assocd. with PAH degrdn. Gene expression assocd. with alkane degrdn. was widespread, although active alkane degrader identities changed along the pollution gradient. Analyses suggest that a broad metabolic capacity to respond to oil inputs exists across a large array of usually rare indigenous deep-sea bacteria.
20. 20

    Joye, S.; Kleindienst, S.; Gilbert, J.; Handley, K.; Weisenhorn, P.; Overholt, W.; Kostka, J. Responses of Microbial Communities to Hydrocarbon Exposures. Oceanography 2016, 29, 136– 149,  DOI: 10.5670/oceanog.2016.78

    Google Scholar

    There is no corresponding record for this reference.
21. 21

    Jeanbille, M.; Gury, J.; Duran, R.; Tronczynski, J.; Ghiglione, J.-F.; Agogué, H.; Saïd, O. B.; Taïb, N.; Debroas, D.; Garnier, C.; Auguet, J.-C. Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments. Front. Microbiol. 2016, 7, 1303,  DOI: 10.3389/fmicb.2016.01303

    Google Scholar

    21

    Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments

    Jeanbille Mathilde; Gury Jerome; Duran Robert; Tronczynski Jacek; Ghiglione Jean-Francois; Agogue Helene; Said Olfa Ben; Taib Najwa; Debroas Didier; Garnier Cedric; Auguet Jean-Christophe

    Frontiers in microbiology (2016), 7 (), 1303 ISSN:1664-302X.

    Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of particle size distribution was strong on eukaryotic diversity. Similarly to alpha-diversity, beta-diversity patterns were strongly influenced by the environmental filter, while PAHs had no influence on the prokaryotic community structure and a weak impact on the eukaryotic community structure at the continental scale. However, at the regional scale, PAHs became the main driver shaping the structure of bacterial and eukaryotic communities. These patterns were not found for PICRUSt predicted prokaryotic functions, thus indicating some degree of functional redundancy. Eukaryotes presented a greater potential for their use as PAH contamination biomarkers, owing to their stronger response at both regional and continental scales.
22. 22

    Allison, S. D.; Martiny, J. B. H. Resistance, Resilience, and Redundancy in Microbial Communities. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 11512– 11519,  DOI: 10.1073/pnas.0801925105

    Google Scholar

    22

    Resistance, resilience, and redundancy in microbial communities

    Allison, Steven D.; Martiny, Jennifer B. H.

    Proceedings of the National Academy of Sciences of the United States of America (2008), 105 (Suppl. 1), 11512-11519CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

    A review. Although it is generally accepted that plant community compn. is key for predicting rates of ecosystem processes in the face of global change, microbial community compn. is often ignored in ecosystem modeling. To address this issue, we review recent expts. and assess whether microbial community compn. is resistant, resilient, or functionally redundant in response to four different disturbances. We find that the compn. of most microbial groups is sensitive and not immediately resilient to disturbance, regardless of taxonomic breadth of the group or the type of disturbance. Other studies demonstrate that changes in compn. are often assocd. with changes in ecosystem process rates. Thus, changes in microbial communities due to disturbance may directly affect ecosystem processes. Based on these relationships, we propose a simple framework to incorporate microbial community compn. into ecosystem process models. We conclude that this effort would benefit from more empirical data on the links among microbial phylogeny, physiol. traits, and disturbance responses. These relationships will det. how readily microbial community compn. can be used to predict the responses of ecosystem processes to global change.
23. 23

    Zhou, J.; Ning, D. Stochastic Community Assembly: Does It Matter in Microbial Ecology?. Microbiol. Mol. Biol. Rev. 2017, 81, e00002  DOI: 10.1128/MMBR.00002-17

    Google Scholar

    There is no corresponding record for this reference.
24. 24

    Huang, X.; Shi, J.; Cui, C.; Yin, H.; Zhang, R.; Ma, X.; Zhang, X. Biodegradation of Phenanthrene by Rhizobium Petrolearium SL-1. J. Appl. Microbiol. 2016, 121, 1616– 1626,  DOI: 10.1111/jam.13292

    Google Scholar

    24

    Biodegradation of phenanthrene by Rhizobium petrolearium SL-1

    Huang, X.; Shi, J.; Cui, C.; Yin, H.; Zhang, R.; Ma, X.; Zhang, X.

    Journal of Applied Microbiology (2016), 121 (6), 1616-1626CODEN: JAMIFK; ISSN:1364-5072. (Wiley-Blackwell)

    We aimed to investigate the phenanthrene degrdn. characteristics and possible phenanthrene degrdn. pathways of Rhizobium petrolearium SL-1. Using high-performance liq. chromatog. (HPLC), UV-visible and gas chromatog.-mass spectrometry (GC-MS) anal., the phenanthrene-degrading properties and metabolites of Rh. petrolearium SL-1 were analyzed, and then combined with genome-based anal. to elucidate the possible biodegrdn. pathway of phenanthrene in Rh. petrolearium SL-1. The results of the analyses showed that phenanthrene (100 mg l-1) was completely degraded by strain SL-1 at 35°C, 0·02% salinity and pH 9.0 within 3 days. A wide range of polycyclic arom. hydrocarbons, including naphthalene, fluorene, anthracene and pyrene, could also be degraded by this strain. Based on the identified metabolites, the utilization of probable intermediates and the presence of putative phenanthrene catabolic genes, we concluded that phenanthrene was degraded via two different routes, namely the 'naphthalene' and the 'phthalic acid' routes. Significance and Impact of the Study : For the first time, this study shows the degrdn. pathway of phenanthrene by a Rhizobium strain. Because of its excellent stress resistance, metabolic versatility, high degrdn. efficiency and potential application in phytoremediation, Rh. petrolearium SL-1 is a potential candidate for the bioremediation of polycyclic arom. hydrocarbons-contaminated areas. The genomic sequence of Rh. petrolearium SL-1 was deposited in the European Nucleotide Archive (http://www.ebi.ac.uk/ena) under the accession no. ERP014329.
25. 25

    Syutsubo, K.; Kishira, H.; Harayama, S. Development of Specific Oligonucleotide Probes for the Identification and in Situ Detection of Hydrocarbon-Degrading Alcanivorax Strains. Environ. Microbiol. 2001, 3, 371– 379,  DOI: 10.1046/j.1462-2920.2001.00204.x

    Google Scholar

    25

    Development of specific oligonucleotide probes for the identification and in situ detection of hydrocarbon-degrading Alcanivorax strains

    Syutsubo, Kazuaki; Kishira, Hideo; Harayama, Shigeaki

    Environmental Microbiology (2001), 3 (6), 371-379CODEN: ENMIFM; ISSN:1462-2912. (Blackwell Science Ltd.)

    The genus Alcanivorax comprises diverse hydrocarbon-degrading marine bacteria. Novel 16S rRNA-targeted oligonucleotide DNA probes (ALV735 and ALV735-b) were developed to quantify two subgroups of the Alcanivorax/Fundibacter group by fluorescence in situ hybridization (FISH), and the conditions for the single-mismatch discrimination of the probes were optimized. The specificity of the probes was improved further using a singly mismatched oligonucleotide as a competitor. The growth of Alcanivorax cells in crude oil-contaminated sea water under the biostimulation condition was investigated by FISH with the probe ALV735, which targeted the main cluster of the Alcanivorax/Fundibacter group. The size of the Alcanivorax population increased with increasing incubation time and accounted for 91% of the 4,6-diamidino-2-phenylindole (DAPI) count after incubation for 2 wk. The probes developed in this study are useful for detecting Alcanivorax populations in petroleum hydrocarbon-degrading microbial consortia.
26. 26

    Röling, W. F. M.; Milner, M. G.; Jones, D. M. Robust Hydrocarbon Degradation and Dynamics of Bacterial Communities during Nutrient-Enhanced Oil Spill Bioremediation. Appl. Environ. Microbiol. 2002, 68, 5537– 5548,  DOI: 10.1128/AEM.68.11.5537-5548.2002

    Google Scholar

    26

    Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation

    Roling, Wilfred F. M.; Milner, Michael G.; Jones, D. Martin; Lee, Kenneth; Daniel, Fabien; Swannell, Richard J. P.; Head, Ian M.

    Applied and Environmental Microbiology (2002), 68 (11), 5537-5548CODEN: AEMIDF; ISSN:0099-2240. (American Society for Microbiology)

    Degrdn. of oil on beaches is, in general, limited by the supply of inorg. nutrients. In order to obtain a more systematic understanding of the effects of nutrient addn. on oil spill bioremediation, beach sediment microcosms contaminated with oil were treated with different levels of inorg. nutrients. Oil biodegrdn. was assessed respirometrically and on the basis of changes in oil compn. Bacterial communities were compared by numerical anal. of denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified 16S rRNA genes and cloning and sequencing of PCR-amplified 16S rRNA genes. Nutrient amendment over a wide range of concns. significantly improved oil degrdn., confirming that N and P limited degrdn. over the concn. range tested. However, the extent and rate of oil degrdn. were similar for all microcosms, indicating that, in this expt., it was the addn. of inorg. nutrients rather than the precise amt. that was most important operationally. Very different microbial communities were selected in all of the microcosms. Similarities between DGGE profiles of replicate samples from a single microcosm were high (95%±5%), but similarities between DGGE profiles from replicate microcosms receiving the same level of inorg. nutrients (68%±5%) were not significantly higher than those between microcosms subjected to different nutrient amendments (63%±7%). It is apparent that the different communities selected cannot be attributed to the level of inorg. nutrients present in different microcosms. Bioremediation treatments dramatically reduced the diversity of the bacterial community. The decrease in diversity could be accounted for by a strong selection for bacteria belonging to the alkane-degrading Alcanivorax/Fundibacter group. On the basis of Shannon-Weaver indexes, rapid recovery of the bacterial community diversity to preoiling levels of diversity occurred. However, although the overall diversity was similar, there were considerable qual. differences in the community structure before and after the bioremediation treatments.
27. 27

    Hazen, T. C.; Dubinsky, E. A.; DeSantis, T. Z.; Andersen, G. L.; Piceno, Y. M.; Singh, N.; Jansson, J. K.; Probst, A.; Borglin, S. E.; Fortney, J. L.; Stringfellow, W. T.; Bill, M.; Conrad, M. E.; Tom, L. M.; Chavarria, K. L.; Alusi, T. R.; Lamendella, R.; Joyner, D. C.; Spier, C.; Baelum, J.; Auer, M.; Zemla, M. L.; Chakraborty, R.; Sonnenthal, E. L.; D’haeseleer, P.; Holman, H.-Y. N.; Osman, S.; Lu, Z.; Van Nostrand, J. D.; Deng, Y.; Zhou, J.; Mason, O. U. Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria. Science 2010, 330, 204– 208,  DOI: 10.1126/science.1195979

    Google Scholar

    27

    Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria

    Hazen, Terry C.; Dubinsky, Eric A.; De Santis, Todd Z.; Andersen, Gary L.; Piceno, Yvette M.; Singh, Navjeet; Jansson, Janet K.; Probst, Alexander; Borglin, Sharon E.; Fortney, Julian L.; Stringfellow, William T.; Bill, Markus; Conrad, Mark E.; Tom, Lauren M.; Chavarria, Krystle L.; Alusi, Thana R.; Lamendella, Regina; Joyner, Dominique C.; Spier, Chelsea; Baelum, Jacob; Auer, Manfred; Zemla, Marcin L.; Chakraborty, Romy; Sonnenthal, Eric L.; D'haeseleer, Patrik; Holman, Hoi-Ying N.; Osman, Shariff; Lu, Zhenmei; Van Nostrand, Joy D.; Deng, Ye; Zhou, Jizhong; Mason, Olivia U.

    Science (Washington, DC, United States) (2010), 330 (6001), 204-208CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

    Biol. effects and expected fate of the vast amt. of oil in the Gulf of Mexico from the Deepwater Horizon blow-out are unknown due to the depth and magnitude of this event. The dispersed hydrocarbon plume stimulated deep-sea indigenous γ-Proteobacteria which are closely related to known petroleum degraders. Hydrocarbon-degrading genes coincided with the concn. of various oil pollutants. Hydrocarbon compn. changes with distance from the source and incubation expts. with environmental isolates demonstrated faster-than-expected hydrocarbon biodegrdn. rates at 5°. Based on these results, the potential exists for intrinsic bioremediation of the oil plume in the deep-water column without substantial O2 drawdown.
28. 28

    Redmond, M. C.; Valentine, D. L. Natural Gas and Temperature Structured a Microbial Community Response to the Deepwater Horizon Oil Spill. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 20292– 20297,  DOI: 10.1073/pnas.1108756108

    Google Scholar

    28

    Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill

    Redmond, Molly C.; Valentine, David L.

    Proceedings of the National Academy of Sciences of the United States of America (2012), 109 (50), 20292-20297, S20292/1-S20292/5CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)

    Microbial communities present in the Gulf of Mexico rapidly responded to the Deepwater Horizon oil spill. In deep water plumes, these communities were initially dominated by members of Oceanospirillales, Colwellia, and Cycloclasticus. None of these groups were abundant in surface oil slick samples, and Colwellia was much more abundant in oil-degrading enrichment cultures incubated at 4° than at room temp., suggesting that the colder temps. at plume depth favored the development of these communities. These groups decreased in abundance after the well was capped in July, but the addn. of hydrocarbons in lab. incubations of deep waters from the Gulf of Mexico stimulated Colwellia's growth. Colwellia was the primary organism that incorporated 13C from ethane and propane in stable isotope probing expts., and given its abundance in environmental samples at the time that ethane and propane oxidn. rates were high, it is likely that Colwellia was active in ethane and propane oxidn. in situ. Colwellia also incorporated 13C benzene, and Colwellia's abundance in crude oil enrichments without natural gas suggests that it has the ability to consume a wide range of hydrocarbon compds. or their degrdn. products. However, the fact that ethane and propane alone were capable of stimulating the growth of Colwellia, and to a lesser extent, Oceanospirillales, suggests that high natural gas content of this spill may have provided an advantage to these organisms.
29. 29

    Fuentes, S.; Barra, B.; Caporaso, J. G.; Seeger, M. From Rare to Dominant: A Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation. Appl. Environ. Microbiol. 2016, 82, 888– 896,  DOI: 10.1128/aem.02625-15

    Google Scholar

    29

    From rare to dominant: a fine-tuned soil bacterial bloom during petroleum hydrocarbon bioremediation

    Fuentes, Sebastian; Barra, Barbara; Caporaso, J. Gregory; Seeger, Michael

    Applied and Environmental Microbiology (2016), 82 (3), 888-896CODEN: AEMIDF; ISSN:1098-5336. (American Society for Microbiology)

    Hydrocarbons are worldwide-distributed pollutants that disturb various ecosystems. The aim of this study was to characterize the short-lapse dynamics of soil microbial communities in response to hydrocarbon pollution and different bioremediation treatments. Replicate diesel-spiked soil microcosms were inoculated with either a defined bacterial consortium or a hydrocarbonoclastic bacterial enrichment and incubated for 12 wk. The microbial community dynamics was followed weekly in microcosms using Illumina 16S rRNA gene sequencing. Both the bacterial consortium and enrichment enhanced hydrocarbon degrdn. in diesel-polluted soils. A pronounced and rapid bloom of a native gammaproteobacterium was obsd. in all dieselpolluted soils. A unique operational taxonomic unit (OTU) related to the Alkanindiges genus represented ∼0.1% of the sequences in the original community but surprisingly reached>60% after 6 wk. Despite this Alkanindiges-related bloom, inoculated strains were maintained in the community and may explain the differences in hydrocarbon degrdn. This study shows the detailed dynamics of a soil bacterial bloom in response to hydrocarbon pollution, resembling microbial blooms obsd. in marine environments. Rare community members presumably act as a reservoir of ecol. functions in high-diversity environments, such as soils. This rare-to-dominant bacterial shift illustrates the potential role of a rare biosphere facing drastic environmental disturbances. Addnl., it supports the concept of "conditionally rare taxa," in which rareness is a temporary state conditioned by environmental constraints.
30. 30

    Head, I. M.; Jones, D. M.; Röling, W. F. M. Marine Microorganisms Make a Meal of Oil. Nat. Rev. Microbiol. 2006, 4, 173– 182,  DOI: 10.1038/nrmicro1348

    Google Scholar

    30

    Marine microorganisms make a meal of oil

    Head, Ian M.; Jones, D. Martin; Roeling, Wilfred F. M.

    Nature Reviews Microbiology (2006), 4 (3), 173-182CODEN: NRMACK; ISSN:1740-1526. (Nature Publishing Group)

    A review concerning marine bacterial biodegrdn. of petroleum as a C and energy source is given. Topics discussed include: crude oil compn.; global players in hydrocarbon degrdn.; community dynamics and nutrients (do different treatments have a systematic effect on biodegrdn. and assocd. microbial communities, can results of small-scale lab. expts. be extrapolated to the field and how do community dynamics compare in different environmental settings); ecol. of in-situ hydrocarbon biodegrdn. (systems biol., resource ratio theory, predation effect, importance of interactions); and hydrocarbon degrdn. in the genomic age.
31. 31

    Yakimov, M. M.; Timmis, K. N.; Golyshin, P. N. Obligate Oil-Degrading Marine Bacteria. Curr. Opin. Biotechnol. 2007, 18, 257– 266,  DOI: 10.1016/j.copbio.2007.04.006

    Google Scholar

    31

    Obligate oil-degrading marine bacteria

    Yakimov, Michail M.; Timmis, Kenneth N.; Golyshin, Peter N.

    Current Opinion in Biotechnology (2007), 18 (3), 257-266CODEN: CUOBE3; ISSN:0958-1669. (Elsevier Ltd.)

    A review is given. Over the past few years, a new and ecophysiol. unusual group of marine hydrocarbon-degrading bacteria, the obligate hydrocarbonoclastic bacteria (OHCB), has been recognized and shown to play a significant role in the biol. removal of petroleum hydrocarbons from polluted marine waters. The introduction of oil or oil constituents into seawater leads to successive blooms of a relatively limited no. of indigenous marine bacterial genera (Alcanivorax, Marinobacter, Thallassolituus, Cycloclasticus, Oleispira and a few others (the OHCB)) which are present at low or undetectable levels before the polluting event. The types of OHCB that bloom depend on the latitude/temp., salinity, redox and other prevailing phys.-chem. factors. These blooms result in the rapid degrdn. of many oil constituents, a process that can be accelerated further by supplementation with limiting nutrients. Genome sequencing and functional genomic anal. of Alcanivorax borkumensis, the paradigm of OHCB, has provided significant insights into the genomic basis of the efficiency and versatility of its hydrocarbon utilization, the metabolic routes underlying its special hydrocarbon diet, and its ecol. success. These and other studies have revealed the potential of OHCB for multiple biotechnol. applications that include not only oil pollution mitigation, but also biopolymer prodn. and biocatalysis.
32. 32

    Rojo, F. Degradation of Alkanes by Bacteria. Environ. Microbiol. 2009, 11, 2477– 2490,  DOI: 10.1111/j.1462-2920.2009.01948.x

    Google Scholar

    32

    Degradation of alkanes by bacteria

    Rojo, Fernando

    Environmental Microbiology (2009), 11 (10), 2477-2490CODEN: ENMIFM; ISSN:1462-2912. (Wiley-Blackwell)

    A review. Pollution of soil and water environments by crude oil has been, and is still today, an important problem. Crude oil is a complex mixt. of thousands of compds. Among them, alkanes constitute the major fraction. Alkanes are satd. hydrocarbons of different sizes and structures. Although they are chem. very inert, most of them can be efficiently degraded by several microorganisms. This review summarizes current knowledge on how microorganisms degrade alkanes, focusing on the biochem. pathways used and on how the expression of pathway genes is regulated and integrated within cell physiol.
33. 33

    Andreoni, V.; Gianfreda, L. Bioremediation and Monitoring of Aromatic-Polluted Habitats. Appl. Microbiol. Biotechnol. 2007, 76, 287– 308,  DOI: 10.1007/s00253-007-1018-5

    Google Scholar

    33

    Bioremediation and monitoring of aromatic-polluted habitats

    Andreoni, Vincenza; Gianfreda, Liliana

    Applied Microbiology and Biotechnology (2007), 76 (2), 287-308CODEN: AMBIDG; ISSN:0175-7598. (Springer)

    A review. Bioremediation may restore contaminated soils through the broad biodegradative capabilities evolved by microorganisms towards undesirable org. compds. Understanding bioremediation and its effectiveness is rapidly advancing, bringing available mol. approaches for examg. the presence and expression of the key genes involved in microbial processes. These methods are continuously improving and require further development and validation of primer- and probe-based analyses and expansion of databases for alternative microbial markers. Phylogenetic marker approaches provide tools to det. which organisms are present or generally active in a community; functional gene markers provide only information concerning the distribution or transcript levels (DNA [DNA]- or mRNA [mRNA]-based approaches) of specific gene populations across environmental gradients. Stable isotope probing methods offer great potential to identify microorganisms that metabolize and assimilate specific substrates in environmental samples, incorporating usually a rare isotope (i.e., 13C) into their DNA and RNA. DNA and RNA in situ characterization allows the detn. of the species actually involved in the processes being measured. DNA microarrays may analyze the expression of thousands of genes in a soil simultaneously. A global anal. of which genes are being expressed under various conditions in contaminated soils will reveal the metabolic status of microorganisms and indicate environmental modifications accelerating bioremediation.
34. 34

    BODC Marine Environment Monitoring and Assessment National (MERMAN) database. https://www.bodc.ac.uk/projects/data_management/uk/merman/assessments_and_data_access/csemp/ (accessed 25 Jul 2018).

    Google Scholar

    There is no corresponding record for this reference.
35. 35

    Woodhead, R. J.; Law, R. J.; Matthiessen, P. Polycyclic Aromatic Hydrocarbons in Surface Sediments Around England and Wales, and Their Possible Biological Significance. Mar. Pollut. Bull. 1999, 38, 773– 790,  DOI: 10.1016/s0025-326x(99)00039-9

    Google Scholar

    35

    Polycyclic aromatic hydrocarbons in surface sediments around England and Wales, and their possible biological significance

    Woodhead, R. J.; Law, R. J.; Matthiessen, P.

    Marine Pollution Bulletin (1999), 38 (9), 773-790CODEN: MPNBAZ; ISSN:0025-326X. (Elsevier Science Ltd.)

    Concns. of polycyclic arom. hydrocarbons (PAH) were detd. in sediments taken at offshore, coastal and estuarine sites around the UK during 1993-1996. In all, 99 samples were taken from 80 locations, including 48 of the stations established under the UK National Monitoring Program. Fifteen individual parent PAH compds. were detd. using a method incorporating an ultrasonication extn. step, followed by online clean-up and HPLC with fluorescence detection. The highest concns. of 4-6-ring PAH were at a site within Milford Haven, and derive primarily from combustion sources within the estuary. High concns. of these compds. were also in the industrialized estuaries of the Rivers Tyne, Wear and Tees (NE England), and these estuaries also yielded the highest concns. of the low-mol. wt. (MW) PAH. An ecotoxicol. assessment indicates that the estuaries of the English northeast coast (Tyne, Wear and Tees) and Milford Haven contain PAH-contaminated sediments at some sites which are likely to be acutely toxic to certain sediment dwellers. A wider range of industrialized estuaries appears to contain enough PAH in sediments to cause chronic effects, including the induction of neoplastic liver disease in fish.
36. 36

    Northcott, G. L.; Jones, K. C. Spiking Hydrophobic Organic Compounds into Soil and Sediment: A Review and Critique of Adopted Procedures. Environ. Toxicol. Chem. 2000, 19, 2418– 2430,  DOI: 10.1002/etc.5620191005

    Google Scholar

    36

    Spiking hydrophobic organic compounds into soil and sediment: a review and critique of adopted procedures

    Northcott, Grant L.; Jones, Kevin C.

    Environmental Toxicology and Chemistry (2000), 19 (10), 2418-2430CODEN: ETOCDK; ISSN:0730-7268. (SETAC Press)

    A review with 124 refs. Studies on the fate and effects of org. pollutants in soil and sediment are often carried out under lab. conditions and often require the study compd. to be introduced, or spiked, into the test substrate. The procedures adopted to spike relatively large amts. of hydrophobic org. compds. into soil and sediment can introduce interferences into expts. that have the potential to dominate the process(es) under investigation. This review identifies and discusses key factors of spiking procedures that can introduce significant interferences to expts. These include soil or sediment drying and rewetting, effects of carrier solvents, and the homogeneity of spike distribution. The persistence of solvents, and therefore their contribution to soil and sediment org. carbon, is discussed with ref. to potential effects on the partitioning behavior of spiked compds. The spiking procedures used in 64 published articles and the information supplied by authors are reported. In general, authors should report more detailed information regarding the procedural aspects of compd. spiking. The std. operating procedures need to be validated and recommended for spiking org. compds. into soil and sediment by recommended organizations. As an aid to this process, a no. of practices to observe when spiking org. compds. into soil and sediment is recommended.
37. 37

    Caporaso, J. G.; Lauber, C. L.; Walters, W. A.; Berg-Lyons, D.; Huntley, J.; Fierer, N.; Owens, S. M.; Betley, J.; Fraser, L.; Bauer, M.; Gormley, N.; Gilbert, J. A.; Smith, G.; Knight, R. Ultra-High-Throughput Microbial Community Analysis on the Illumina HiSeq and MiSeq Platforms. ISME J. 2012, 6, 1621– 1624,  DOI: 10.1038/ismej.2012.8

    Google Scholar

    37

    Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

    Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.; Berg-Lyons, Donna; Huntley, James; Fierer, Noah; Owens, Sarah M.; Betley, Jason; Fraser, Louise; Bauer, Markus; Gormley, Niall; Gilbert, Jack A.; Smith, Geoff; Knight, Rob

    ISME Journal (2012), 6 (8), 1621-1624CODEN: IJSOCF; ISSN:1751-7362. (Nature Publishing Group)

    DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-assocd. and free-living environments. A crit. question as more sequencing platforms become available is whether biol. conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biol. results, and addnl. that biol. conclusions are consistent across sequencing platforms (the HiSeq2000 vs. the MiSeq) and across the sequenced regions of amplicons. The ISME Journal (2012) 6, 1621-1624; doi:10.1038/ismej.2012.8; published online 8 March 2012.
38. 38

    Krueger, F. Trim Galore!: A Wrapper Tool Around Cutadapt and FastQC to Consistently Apply Quality and Adapter Trimming to FastQ Files , 2015.

    Google Scholar

    There is no corresponding record for this reference.
39. 39

    Rognes, T.; Flouri, T.; Nichols, B.; Quince, C.; Mahé, F. VSEARCH: A Versatile Open Source Tool for Metagenomics. PeerJ 2016, 4, e2584  DOI: 10.7717/peerj.2584

    Google Scholar

    There is no corresponding record for this reference.
40. 40

    Aigle, A.; Prosser, J. I.; Gubry-Rangin, C. The Application of High-Throughput Sequencing Technology to Analysis of AmoA Phylogeny and Environmental Niche Specialisation of Terrestrial Bacterial Ammonia-Oxidisers. Environ. Microbiome 2019, 14, 3,  DOI: 10.1186/s40793-019-0342-6

    Google Scholar

    40

    The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers

    Aigle Axel; Prosser James I; Gubry-Rangin Cecile

    Environmental microbiome (2019), 14 (1), 3 ISSN:.

    BACKGROUND: Characterisation of microbial communities increasingly involves use of high throughput sequencing methods (e.g. MiSeq Illumina) that amplify relatively short sequences of 16S rRNA or functional genes, the latter including ammonia monooxygenase subunit A (amoA), a key functional gene for ammonia oxidising bacteria (AOB) and archaea (AOA). The availability of these techniques, in combination with developments in phylogenetic methodology, provides the potential for better analysis of microbial niche specialisation. This study aimed to develop an approach for sequencing of bacterial and archaeal amoA genes amplified from soil using bioinformatics pipelines developed for general analysis of functional genes and employed sequence data to reassess phylogeny and niche specialisation in terrestrial bacterial ammonia oxidisers. RESULTS: amoA richness and community composition differed with bioinformatics approaches used but analysis of MiSeq sequences was reliable for both archaeal and bacterial amoA genes and was used for subsequent assessment of potential niche specialisation of soil bacteria ammonia oxidisers. Prior to ecological analysis, phylogenetic analysis of Nitrosospira, which dominates soil AOB, was revisited using a phylogenetic analysis of 16S rRNA and amoA genes in available AOB genomes. This analysis supported congruence between phylogenies of the two genes and increased previous phylogenetic resolution, providing support for additional gene clusters of potential ecological significance. Analysis of environmental sequences using these new sequencing, bioinformatics and phylogenetic approaches demonstrated, for the first time, similar niche specialisation in AOB to that in AOA, indicating pH as a key ecological factor controlling the composition of soil ammonia oxidiser communities. CONCLUSIONS: This study presents the first bioinformatics pipeline for optimal analysis of Illumina MiSeq sequencing of a functional gene and is adaptable to any amplicon size (even genes larger than 500 bp). The pipeline was used to provide an up-to-date phylogenetic analysis of terrestrial betaproteobacterial amoA genes and to demonstrate the importance of soil pH for their niche specialisation and is broadly applicable to other ecosystems and diverse microbiomes.
41. 41

    Schloss, P. D.; Westcott, S. L.; Ryabin, T.; Hall, J. R.; Hartmann, M.; Hollister, E. B.; Lesniewski, R. a.; Oakley, B. B.; Parks, D. H.; Robinson, C. J.; Sahl, J. W.; Stres, B.; Thallinger, G. G.; Van Horn, D. J.; Weber, C. F. Introducing Mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Appl. Environ. Microbiol. 2009, 75, 7537– 7541,  DOI: 10.1128/aem.01541-09

    Google Scholar

    41

    Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities

    Schloss, Patrick D.; Westcott, Sarah L.; Ryabin, Thomas; Hall, Justine R.; Hartmann, Martin; Hollister, Emily B.; Lesniewski, Ryan A.; Oakley, Brian B.; Parks, Donovan H.; Robinson, Courtney J.; Sahl, Jason W.; Stres, Blaz; Thallinger, Gerhard G.; Van Horn, David J.; Weber, Carolyn F.

    Applied and Environmental Microbiology (2009), 75 (23), 7537-7541CODEN: AEMIDF; ISSN:0099-2240. (American Society for Microbiology)

    Mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calc. distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This anal. of more than 222,000 sequences was completed in less than 2 h with a laptop computer.
42. 42

    Quast, C.; Pruesse, E.; Yilmaz, P.; Gerken, J.; Schweer, T.; Yarza, P.; Peplies, J.; Glöckner, F. O. The SILVA Ribosomal RNA Gene Database Project: Improved Data Processing and Web-Based Tools. Nucleic Acids Res. 2012, 41, D590– D596,  DOI: 10.1093/nar/gks1219

    Google Scholar

    There is no corresponding record for this reference.
43. 43

    Perez Calderon, L. J.; Vossen, K.; Potts, L. D.; Gallego, A.; Anderson, J. A.; Witte, U. Advective Pore-Water Transport of Hydrocarbons in North East Scotland Coastal Sands. Environ. Sci. Pollut. Res. 2018, 25, 28445– 28459,  DOI: 10.1007/s11356-018-2815-3

    Google Scholar

    43

    Advective pore-water transport of hydrocarbons in North East Scotland coastal sands

    Perez Calderon, Luis J.; Vossen, Kathrin; Potts, Lloyd D.; Gallego, Alejandro; Anderson, James A.; Witte, Ursula

    Environmental Science and Pollution Research (2018), 25 (28), 28445-28459CODEN: ESPLEC; ISSN:0944-1344. (Springer)

    In the current study, oil spills in the marine environment can cause ecosystem-level impacts. Dispersant application as an oil spill response measure leads to the widespread distribution of hydrocarbons in the water column and marine sediments. The North Sea is an area of intense hydrocarbon prodn. and is at risk of oil spills, which are of concern to its benthic ecosystem due to its sediments high permeability. Here, entrainment of hydrocarbons via pore-water advection into permeable North Sea sands and the assocd. effect of Superdispersant-25, a com. oil dispersant, were evaluated in a lab. Centrally stirred chambers that induce advective pore-water fluxes in sediments were filled with sediment, seawater and mixts. of oil and Superdispersant-25. Dispersant application had contrasting effects on hydrocarbon interactions with sediment: (1) it reduced accumulation of hydrocarbons in surface sediments and (2) facilitated the entrainment of hydrocarbons up to 8 cm deep into sediments by increasing hydrocarbon soly. in seawater and its subsequent washout or pumping into sediment by pore-water movement. Results here show that dispersant application can have counter-intuitive effects on hydrocarbon interactions with marine sediments and highlight the need for further research in this area to make better informed decision in an oil spill response scenario.
44. 44

    R Core Team R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, 2017.

    Google Scholar

    There is no corresponding record for this reference.
45. 45

    Wickham, H.; Chang, W. Ggplot2: Elegant Graphics for Data Analysis; Springer-Verlag: New York, 2009.

    Google Scholar

    There is no corresponding record for this reference.
46. 46

    Oksanen, J.; Blanchet, F. G.; Friendly, M.; Kindt, R.; Legendre, P.; Mcglinn, D.; Minchin, P. R.; O ’hara, R. B.; Simpson, G. L.; Solymos, P.; Henry, M.; Stevens, H.; Szoecs, E.; Wagner, H.; Oksanen, M. J. Package “Vegan.” 2018.

    Google Scholar

    There is no corresponding record for this reference.
47. 47

    Pinheiro, J.; Bates, D.; DebRoy, S.; Sarkar, D. R. C. T. Nlme: Linear and Nonlinear Mixed Effects Models , 2021.

    Google Scholar

    There is no corresponding record for this reference.
48. 48

    Searle, S. R.; Speed, F. M.; Milliken, G. A. Population Marginal Means in the Linear Model: An Alternative to Least Squares Means. Am. Statistician 1980, 34, 216– 221,  DOI: 10.1080/00031305.1980.10483031

    Google Scholar

    There is no corresponding record for this reference.
49. 49

    Oksanen, J.; Blanchet, F. G.; Friendly, M.; Kindt, R.; Legendre, P.; McGlinn, D.; Minchin, P. R.; O’Hara, R. B.; Simpson, G. L.; Solymos, P.; Stevens, M. H. H.; Szoecs, E.; Wagner, H. Vegan: Community Ecology Package , 2017.

    Google Scholar

    There is no corresponding record for this reference.
50. 50

    Bray, J. R.; Curtis, J. T. An Ordination of the Upland Forest Communities of Southern Wisconsin. Ecol. Monogr. 1957, 27, 325– 349,  DOI: 10.2307/1942268

    Google Scholar

    There is no corresponding record for this reference.
51. 51

    Katoh, K.; Rozewicki, J.; Yamada, K. D. MAFFT Online Service: Multiple Sequence Alignment, Interactive Sequence Choice and Visualization. Briefings Bioinf. 2019, 20, 1160– 1166,  DOI: 10.1093/bib/bbx108

    Google Scholar

    51

    MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

    Katoh, Kazutaka; Rozewicki, John; Yamada, Kazunori D.

    Briefings in Bioinformatics (2019), 20 (4), 1160-1166CODEN: BBIMFX; ISSN:1477-4054. (Oxford University Press)

    A review. This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge nos. of biol. sequences are available and the need for MSAs with large nos. of sequences is increasing. To ext. biol. relevant information from such data, sophistication of algorithms is necessary but not sufficient. Intuitive and interactive tools for exptl. biologists to semiautomatically handle large data are becoming important. We are working on development of MAFFT toward these two directions. Here, we explain (i) the Web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and MSAs.
52. 52

    Nguyen, L.-T.; Schmidt, H. A.; von Haeseler, A.; Minh, B. Q. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Mol. Biol. Evol. 2015, 32, 268– 274,  DOI: 10.1093/molbev/msu300

    Google Scholar

    52

    IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies

    Nguyen, Lam-Tung; Schmidt, Heiko A.; von Haeseler, Arndt; Minh, Bui Quang

    Molecular Biology and Evolution (2015), 32 (1), 268-274CODEN: MBEVEO; ISSN:0737-4038. (Oxford University Press)

    Large phylogenomics data sets require fast tree inference methods, esp. for max.-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for addnl. approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, resp. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
53. 53

    Kembel, S. An Introduction to the Picante Package. R Proj 2010, 1– 16

    Google Scholar

    There is no corresponding record for this reference.

    No. April

54. 54

    Stegen, J. C.; Lin, X.; Fredrickson, J. K.; Chen, X.; Kennedy, D. W.; Murray, C. J.; Rockhold, M. L.; Konopka, A. Quantifying Community Assembly Processes and Identifying Features That Impose Them. ISME J. 2013, 7, 2069– 2079,  DOI: 10.1038/ismej.2013.93

    Google Scholar

    54

    Quantifying community assembly processes and identifying features that impose them

    Stegen James C; Lin Xueju; Fredrickson Jim K; Chen Xingyuan; Kennedy David W; Murray Christopher J; Rockhold Mark L; Konopka Allan

    The ISME journal (2013), 7 (11), 2069-79 ISSN:.

    Spatial turnover in the composition of biological communities is governed by (ecological) Drift, Selection and Dispersal. Commonly applied statistical tools cannot quantitatively estimate these processes, nor identify abiotic features that impose these processes. For interrogation of subsurface microbial communities distributed across two geologically distinct formations of the unconfined aquifer underlying the Hanford Site in southeastern Washington State, we developed an analytical framework that advances ecological understanding in two primary ways. First, we quantitatively estimate influences of Drift, Selection and Dispersal. Second, ecological patterns are used to characterize measured and unmeasured abiotic variables that impose Selection or that result in low levels of Dispersal. We find that (i) Drift alone consistently governs ∼25% of spatial turnover in community composition; (ii) in deeper, finer-grained sediments, Selection is strong (governing ∼60% of turnover), being imposed by an unmeasured but spatially structured environmental variable; (iii) in shallower, coarser-grained sediments, Selection is weaker (governing ∼30% of turnover), being imposed by vertically and horizontally structured hydrological factors;(iv) low levels of Dispersal can govern nearly 30% of turnover and be caused primarily by spatial isolation resulting from limited exchange between finer and coarser-grain sediments; and (v) highly permeable sediments are associated with high levels of Dispersal that homogenize community composition and govern over 20% of turnover. We further show that our framework provides inferences that cannot be achieved using preexisting approaches, and suggest that their broad application will facilitate a unified understanding of microbial communities.
55. 55

    Parada, A. E.; Needham, D. M.; Fuhrman, J. A. Every Base Matters : Assessing Small Subunit RRNA Primers for Marine Microbiomes with Mock Communities , Time Series and Global Field Samples. Environ. Microbiol. 2016, 18, 1403– 1414,  DOI: 10.1111/1462-2920.13023

    Google Scholar

    55

    Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

    Parada, Alma E.; Needham, David M.; Fuhrman, Jed A.

    Environmental Microbiology (2016), 18 (5), 1403-1414CODEN: ENMIFM; ISSN:1462-2912. (Wiley-Blackwell)

    Summary : Microbial community anal. via high-throughput sequencing of amplified 16S rRNA genes is an essential microbiol. tool. We found the popular primer pair 515F (515F-C) and 806R greatly underestimated (e.g. SAR11) or overestimated (e.g. Gammaproteobacteria) common marine taxa. We evaluated marine samples and mock communities (contg. 11 or 27 marine 16S clones), showing alternative primers 515F-Y (5'-GTGYCAGCMGCCGCGGTAA) and 926R (5'-CCGYCAATTYMTTTRAGTTT) yield more accurate ests. of mock community abundances, produce longer amplicons that can differentiate taxa unresolvable with 515F-C/806R, and amplify eukaryotic 18S rRNA. Mock communities amplified with 515F-Y/926R yielded closer obsd. community compn. vs. expected (r2 = 0.95) compared with 515F-Y/806R (r2 ∼ 0.5). Unexpectedly, biases with 515F-Y/806R against SAR11 in field samples (∼4-10-fold) were stronger than in mock communities (∼2-fold). Correcting a mismatch to Thaumarchaea in the 515F-C increased their apparent abundance in field samples, but not as much as using 926R rather than 806R. With plankton samples rich in eukaryotic DNA (> 1μm size fraction), 18S sequences averaged ∼17% of all sequences. A single mismatch can strongly bias amplification, but even perfectly matched primers can exhibit preferential amplification. We show that beyond in silico predictions, testing with mock communities and field samples is important in primer selection.
56. 56

    Berga, M.; Székely, A. J.; Langenheder, S. Effects of Disturbance Intensity and Frequency on Bacterial Community Composition and Function. PLoS One 2012, 7, e36959  DOI: 10.1371/journal.pone.0036959

    Google Scholar

    56

    Effects of disturbance intensity and frequency on bacterial community composition and function

    Berga, Merce; Szekely, Anna J.; Langenheder, Silke

    PLoS One (2012), 7 (5), e36959CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)

    Disturbances influence community structure and ecosystem functioning. Bacteria are key players in ecosystems and it is therefore crucial to understand the effect of disturbances on bacterial communities and how they respond to them, both compositionally and functionally. The main aim of this study was to test the effect of differences in disturbance strength on bacterial communities. For this, the authors implemented two independent short-term expts. with dialysis bags contg. natural bacterial communities, which were transplanted between ambient and 'disturbed' incubation tanks, manipulating either the intensity or the frequency of a salinity disturbance. They followed changes in community compn. by terminal restriction fragment anal. (T-RFLP) and measured various community functions (bacterial prodn., carbon substrate utilization profiles and rates) directly after and after a short period of recovery under ambient conditions. Increases in disturbance strength resulted in gradually stronger changes in bacterial community compn. and functions. In the disturbance intensity expt., the sensitivity to the disturbance and the ability of recovery differed between different functions. In the disturbance frequency expt., effects on the different functions were more consistent and recovery was not obsd. Moreover, in case of the intensity expt., there was also a time lag in the responses of community compn. and functions, with functional responses being faster than compositional ones. To summarize, this study shows that disturbance strength has the potential to change the functional performance and compn. of bacterial communities. It further highlights that the overall effects, rates of recovery and the degree of congruence in the response patterns of community compn. and functioning along disturbance gradients depend on the type of function and the character of the disturbance.
57. 57

    Shade, A.; Read, J. S.; Welkie, D. G.; Kratz, T. K.; Wu, C. H.; McMahon, K. D. Resistance, Resilience and Recovery: Aquatic Bacterial Dynamics after Water Column Disturbance. Environ. Microbiol. 2011, 13, 2752– 2767,  DOI: 10.1111/j.1462-2920.2011.02546.x

    Google Scholar

    57

    Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance

    Shade, Ashley; Read, Jordan S.; Welkie, David G.; Kratz, Timothy K.; Wu, Chin H.; McMahon, Katherine D.

    Environmental Microbiology (2011), 13 (10), 2752-2767CODEN: ENMIFM; ISSN:1462-2912. (Wiley-Blackwell)

    For lake microbes, water column mixing acts as a disturbance because it homogenizes thermal and chem. gradients known to define the distributions of microbial taxa. Our first objective was to isolate hypothesized drivers of lake bacterial response to water column mixing. To accomplish this, we designed an enclosure expt. with three treatments to independently test key biogeochem. changes induced by mixing: oxygen addn. to the hypolimnion, nutrient addn. to the epilimnion, and full water column mixing. We used mol. fingerprinting to observe bacterial community dynamics in the treatment and control enclosures, and in ambient lake water. We found that oxygen and nutrient amendments simulated the phys.-chem. water column environment following mixing and resulted in similar bacterial communities to the mixing treatment, affirming that these were important drivers of community change. These results demonstrate that specific environmental changes can replicate broad disturbance effects on microbial communities. Our second objective was to characterize bacterial community stability by quantifying community resistance, recovery and resilience to an episodic disturbance. The communities in the nutrient and oxygen amendments changed quickly (had low resistance), but generally matched the control compn. by the 10th day after treatment, exhibiting resilience. These results imply that aquatic bacterial assemblages are generally stable in the face of disturbance.
58. 58

    Sjöstedt, J.; Langenheder, S.; Kritzberg, E.; Karlsson, C. M. G.; Lindström, E. S. Repeated Disturbances Affect Functional but Not Compositional Resistance and Resilience in an Aquatic Bacterioplankton Community. Environ. Microbiol. Rep. 2018, 10, 493– 500,  DOI: 10.1111/1758-2229.12656

    Google Scholar

    58

    Repeated disturbances affect functional but not compositional resistance and resilience in an aquatic bacterioplankton community

    Sjostedt Johanna; Langenheder Silke; Lindstrom Eva S; Sjostedt Johanna; Kritzberg Emma; Karlsson Christofer M G

    Environmental microbiology reports (2018), 10 (4), 493-500 ISSN:.

    Disturbances are believed to be one of the main factors influencing variations in community diversity and functioning. Here we investigated if exposure to a pH press disturbance affected the composition and functional performance of a bacterial community and its resistance, recovery and resilience to a second press disturbance (salt addition). Lake bacterial assemblages were initially exposed to reduced pH in six mesocosms whereas another six mesocosms were kept as reference. Seven days after the pH disturbance, three tanks from each treatment were exposed to a salt disturbance. Both bacterial production and enzyme activity were negatively affected by the salt treatment, regardless if the communities had been subject to a previous disturbance or not. However, cell-specific enzyme activity had a higher resistance in communities pre-exposed to the pH disturbance compared to the reference treatment. In contrast, for cell-specific bacterial production resistance was not affected, but recovery was faster in the communities that had previously been exposed to the pH disturbance. Over time, bacterial community composition diverged among treatments, in response to both pH and salinity. The difference in functional recovery, resilience and resistance may depend on differences in community composition caused by the pH disturbance, niche breadth or acquired stress resistance.
59. 59

    Drury, B.; Rosi-Marshall, E.; Kelly, J. J. Wastewater Treatment Effluent Reduces the Abundance and Diversity of Benthic Bacterial Communities in Urban and Suburban Rivers. Appl. Environ. Microbiol. 2013, 79, 1897– 1905,  DOI: 10.1128/aem.03527-12

    Google Scholar

    59

    Wastewater treatment effluent reduces the abundance and diversity of benthic bacterial communities in urban and suburban rivers

    Drury, Bradley; Rosi-Marshall, Emma; Kelly, John J.

    Applied and Environmental Microbiology (2013), 79 (6), 1897-1905CODEN: AEMIDF; ISSN:0099-2240. (American Society for Microbiology)

    In highly urbanized areas, wastewater treatment plant (WWTP) effluent can represent a significant component of freshwater ecosystems. As it is impossible for the compn. of WWTP effluent to match the compn. of the receiving system, the potential exists for effluent to significantly impact the chem. and biol. characteristics of the receiving ecosystem. We assessed the impacts of WWTP effluent on the size, activity, and compn. of benthic microbial communities by comparing two distinct field sites in the Chicago metropolitan region: a highly urbanized river receiving effluent from a large WWTP and a suburban river receiving effluent from a much smaller WWTP. At sites upstream of effluent input, the urban and suburban rivers differed significantly in chem. characteristics and in the compn. of their sediment bacterial communities. Although effluent resulted in significant increases in inorg. nutrients in both rivers, surprisingly, it also resulted in significant decreases in the population size and diversity of sediment bacterial communities. Tag pyrosequencing of bacterial 16S rRNA genes revealed significant effects of effluent on sediment bacterial community compn. in both rivers, including decreases in abundances of Deltaproteobacteria, Desulfococcus, Dechloromonas, and Chloroflexi sequences and increases in abundances of Nitrospirae and Sphingobacteriales sequences. The overall effect of the WWTP inputs was that the two rivers, which were distinct in chem. and biol. properties upstream of the WWTPs, were almost indistinguishable downstream. These results suggest that WWTP effluent has the potential to reduce the natural variability that exists among river ecosystems and indicate that WWTP effluent may contribute to biotic homogenization.
60. 60

    Li, D.; Yang, M.; Li, Z.; Qi, R.; He, J.; Liu, H. Change of Bacterial Communities in Sediments along Songhua River in Northeastern China after a Nitrobenzene Pollution Event. FEMS Microbiol. Ecol. 2008, 65, 494– 503,  DOI: 10.1111/j.1574-6941.2008.00540.x

    Google Scholar

    60

    Change of bacterial communities in sediments along Songhua River in Northeastern China after a nitrobenzene pollution event

    Li, Dong; Yang, Min; Li, Zonglai; Qi, Rong; He, Jizheng; Liu, Huijuan

    FEMS Microbiology Ecology (2008), 65 (3), 494-503CODEN: FMECEZ; ISSN:0168-6496. (Wiley-Blackwell)

    More than 100 tons of nitrobenzene and related compds. were released into Songhua River due to the explosion of an aniline prodn. factory in Nov., 2005. Sediment samples were taken from the heavily polluted drainage canal, one upstream and three downstream river sites. The change of bacterial community structures along the river was studied by denaturing gradient gel electrophoresis (DGGE) and cloning and sequencing of 16S rRNA genes with five clone libraries constructed and 101 sequences acquired representing 172 clones. Both DGGE profiles and sequences of 16S rRNA genes from clone libraries demonstrated that the contaminated drainage canal and three downstream river sites were similar in that all had Betaproteobacteria, mainly grouped into Comamonadaceae, as the dominant group of bacteria, and all sites had Firmicutes, primarily as Clostridium spp. These results suggest that these latter two groups of bacteria may play potential roles in degrdn. and detoxification of nitrobenzene in the present contaminated river environments.
61. 61

    Lamendella, R.; Strutt, S.; Borglin, S.; Chakraborty, R.; Tas, N.; Mason, O. U.; Hultman, J.; Prestat, E.; Hazen, T. C.; Jansson, J. K. Assessment of the Deepwater Horizon Oil Spill Impact on Gulf Coast Microbial Communities. Front. Microbiol. 2014, 5, 130,  DOI: 10.3389/fmicb.2014.00130

    Google Scholar

    61

    Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities

    Lamendella Regina; Strutt Steven; Borglin Sharon; Chakraborty Romy; Tas Neslihan; Prestat Emmanuel; Mason Olivia U; Hultman Jenni; Hazen Terry C; Jansson Janet K

    Frontiers in microbiology (2014), 5 (), 130 ISSN:1664-302X.

    One of the major environmental concerns of the Deepwater Horizon oil spill in the Gulf of Mexico was the ecological impact of the oil that reached shorelines of the Gulf Coast. Here we investigated the impact of the oil on the microbial composition in beach samples collected in June 2010 along a heavily impacted shoreline near Grand Isle, Louisiana. Successional changes in the microbial community structure due to the oil contamination were determined by deep sequencing of 16S rRNA genes. Metatranscriptomics was used to determine expression of functional genes involved in hydrocarbon degradation processes. In addition, potential hydrocarbon-degrading Bacteria were obtained in culture. The 16S data revealed that highly contaminated samples had higher abundances of Alpha- and Gammaproteobacteria sequences. Successional changes in these classes were observed over time, during which the oil was partially degraded. The metatranscriptome data revealed that PAH, n-alkane, and toluene degradation genes were expressed in the contaminated samples, with high homology to genes from Alteromonadales, Rhodobacterales, and Pseudomonales. Notably, Marinobacter (Gammaproteobacteria) had the highest representation of expressed genes in the samples. A Marinobacter isolated from this beach was shown to have potential for transformation of hydrocarbons in incubation experiments with oil obtained from the Mississippi Canyon Block 252 (MC252) well; collected during the Deepwater Horizon spill. The combined data revealed a response of the beach microbial community to oil contaminants, including prevalence of Bacteria endowed with the functional capacity to degrade oil.
62. 62

    Cohan, F. M.; Koeppel, A. F. The Origins of Ecological Diversity in Prokaryotes. Curr. Biol. 2008, 18, R1024– R1034,  DOI: 10.1016/j.cub.2008.09.014

    Google Scholar

    62

    The Origins of Ecological Diversity in Prokaryotes

    Cohan, Frederick M.; Koeppel, Alexander F.

    Current Biology (2008), 18 (21), R1024-R1034CODEN: CUBLE2; ISSN:0960-9822. (Cell Press)

    A review. The urkingdoms and major divisions of prokaryotes are enormously diverse in their metabolic capabilities and membrane architectures. These ancient differences likely have a strong influence on the kinds of ecol. adaptations that may evolve today. Some ecol. transitions have been identified as having occurred primarily in the distant past, including transitions between saline and non-saline habitats. At the microevolutionary level, the likely existence of a billion prokaryotic species challenges microbiologists to det. what might promote rapid speciation in prokaryotes, and to identify the ecol. dimensions upon which new species diverge and by which they may coexist. Rapid speciation in prokaryotes is fostered by several unique properties of prokaryotic genetic exchange, including their propensity to acquire novel gene loci by horizontal genetic transfer, as well as the rarity of their genetic exchange, which allows speciation by ecol. divergence alone, without a requirement for sexual isolation. The ecol. dimensions of prokaryotic speciation may be identified by comparing the ecol. of the most newly divergent, ecol. distinct populations (ecotypes). This program is challenged by our ignorance of the physiol. and ecol. features most likely responsible for adaptive divergence between closely related ecotypes in any given clade. This effort will require development of universal approaches to hypothesize demarcations of ecotypes, and to confirm and characterize their ecol. distinctness, without prior knowledge of a given clade's ecol.
63. 63

    Shahi, A.; Ince, B.; Aydin, S.; Ince, O. Assessment of the Horizontal Transfer of Functional Genes as a Suitable Approach for Evaluation of the Bioremediation Potential of Petroleum-Contaminated Sites: A Mini-Review. Appl. Microbiol. Biotechnol. 2017, 101, 4341– 4348,  DOI: 10.1007/s00253-017-8306-5

    Google Scholar

    63

    Assessment of the horizontal transfer of functional genes as a suitable approach for evaluation of the bioremediation potential of petroleum-contaminated sites: a mini-review

    Shahi, Aiyoub; Ince, Bahar; Aydin, Sevcan; Ince, Orhan

    Applied Microbiology and Biotechnology (2017), 101 (11), 4341-4348CODEN: AMBIDG; ISSN:0175-7598. (Springer)

    Petroleum sludge contains recalcitrant residuals. These compds. because of being toxic to humans and other organism are of the major concerns. Therefore, petroleum sludge should be safely disposed. Physicochem. methods which are used by this sector are mostly expensive and need complex devices. Bioremediation methods because of being eco-friendly and cost-effective overcome most of the limitations of physicochem. treatments. Microbial strains capable to degrade petroleum hydrocarbons are practically present in all soils and sediments and their population d. increases in contact with contaminants. Bacterial strains cannot degrade alone all kinds of petroleum hydrocarbons, rather microbial consortium should collaborate with each other for degrdn. of petroleum hydrocarbon mixts. Horizontal transfer of functional genes between bacteria plays an important role in increasing the metabolic potential of the microbial community. Therefore, selecting a suitable degrading gene and tracking its horizontal transfer would be a useful approach to evaluate the bioremediation process and to assess the bioremediation potential of contaminated sites.
64. 64

    Logares, R.; Lindström, E. S.; Langenheder, S.; Logue, J. B.; Paterson, H.; Laybourn-Parry, J.; Rengefors, K.; Tranvik, L.; Bertilsson, S. Biogeography of Bacterial Communities Exposed to Progressive Long-Term Environmental Change. ISME J. 2013, 7, 937– 948,  DOI: 10.1038/ismej.2012.168

    Google Scholar

    64

    Biogeography of bacterial communities exposed to progressive long-term environmental change

    Logares, Ramiro; Lindstroem, Eva S.; Langenheder, Silke; Logue, Juerg B.; Paterson, Harriet; Laybourn-Parry, Johanna; Rengefors, Karin; Tranvik, Lars; Bertilsson, Stefan

    ISME Journal (2013), 7 (5), 937-948CODEN: IJSOCF; ISSN:1751-7362. (Nature Publishing Group)

    The response of microbial communities to long-term environmental change is poorly understood. Here, we study bacterioplankton communities in a unique system of coastal Antarctic lakes that were exposed to progressive long-term environmental change, using 454 pyrosequencing of the 16S rDNA gene (V3-V4 regions). At the time of formation, most of the studied lakes harbored marine-coastal microbial communities, as they were connected to the sea. During the past 20 000 years, most lakes isolated from the sea, and subsequently they experienced a gradual, but strong, salinity change that eventually developed into a gradient ranging from freshwater (salinity 0) to hypersaline (salinity 100). Our results indicated that present bacterioplankton community compn. was strongly correlated with salinity and weakly correlated with geog. distance between lakes. A few abundant taxa were shared between some lakes and coastal marine communities. Nevertheless, lakes contained a large no. of taxa that were not detected in the adjacent sea. Abundant and rare taxa within saline communities presented similar biogeog., suggesting that these groups have comparable environmental sensitivity. Habitat specialists and generalists were detected among abundant and rare taxa, with specialists being relatively more abundant at the extremes of the salinity gradient. Altogether, progressive long-term salinity change appears to have promoted the diversification of bacterioplankton communities by modifying the compn. of ancestral communities and by allowing the establishment of new taxa.
65. 65

    Pandit, S. N.; Kolasa, J.; Cottenie, K. Contrasts between Habitat Generalists and Specialists: An Empirical Extension to the Basic Metacommunity Framework. Ecology 2009, 90, 2253– 2262,  DOI: 10.1890/08-0851.1

    Google Scholar

    65

    Contrasts between habitat generalists and specialists: an empirical extension to the basic metacommunity framework

    Pandit Shubha N; Kolasa Jurek; Cottenie Karl

    Ecology (2009), 90 (8), 2253-62 ISSN:0012-9658.

    Emergence of the metacommunity concept has made a substantial contribution to better understanding of the community composition and dynamics in a regional context. However, long-term field data for testing of available metacommunity models are still scarce, and the extent to which these models apply to the real world remains unknown. Tests conducted so far have largely sought to fit data on the entire regional set of species to one of several metacommunity models, implicitly assuming that all species operate similarly over the same set of sites. However, species differ in their habitat use. These differences can, in the most general terms, be expressed as a gradient of habitat specialization (ranging from habitat specialists to habitat generalists). We postulate that such differences in habitat specialization will have implications for metacommunity dynamics. Specifically, we predict that specialists respond more to local processes and generalists respond to regional spatial processes. We tested these predictions using natural microcosm communities for which long-term (nine-year) environmental and population dynamics data were available. We used redundancy analysis to determine the proportion of variation explained by environmental and spatial factors. We repeated this analysis to explain variation in the entire regional set of species, in generalist species only, and in specialists only. We further used ANOVA to test for differences in the proportions of explained variation. We found that habitat specialists responded primarily to environmental factors and habitat generalists responded mainly to spatial factors. Thus, from the metacommunity perspective, the dynamics of habitat specialists are best explained by a combination of species sorting and mass effects, while that of habitat generalists are best explained by patch dynamics and neutral models. Consequently, we infer that a natural metacommunity can exhibit complicated dynamics, with some groups of species (e.g., habitat specialists) governed according to environmental processes and other groups (e.g., habitat generalists) governed mainly by dispersal processes.
66. 66

    Kostka, J. E.; Prakash, O.; Overholt, W. A.; Green, S. J.; Freyer, G.; Canion, A.; Delgardio, J.; Norton, N.; Hazen, T. C.; Huettel, M. Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill. Appl. Environ. Microbiol. 2011, 77, 7962– 7974,  DOI: 10.1128/aem.05402-11

    Google Scholar

    66

    Hydrocarbon-degrading bacteria and the bacterial community response in Gulf of Mexico beach sands impacted by the deepwater horizon oil spill

    Kostka, Joel E.; Prakash, Om; Overholt, Will A.; Green, Stefan J.; Freyer, Gina; Canion, Andy; Delgardio, Jonathan; Norton, Nikita; Hazen, Terry C.; Huettel, Markus

    Applied and Environmental Microbiology (2011), 77 (22), 7962-7974CODEN: AEMIDF; ISSN:0099-2240. (American Society for Microbiology)

    A significant portion of oil from the recent Deepwater Horizon (DH) oil spill in the Gulf of Mexico was transported to the shoreline, where it may have severe ecol. and economic consequences. The objectives of this study were (i) to identify and characterize predominant oil-degrading taxa that may be used as model hydrocarbon degraders or as microbial indicators of contamination and (ii) to characterize the in situ response of indigenous bacterial communities to oil contamination in beach ecosystems. This study was conducted at municipal Pensacola Beach, FL, where chem. anal. revealed weathered oil petroleum hydrocarbon (C8 to C40) concns. ranging from 3.1 to 4500 mg kg-1 in beach sands. A total of 24 bacterial strains from 14 genera were isolated from oiled beach sands and confirmed as oil-degrading microorganisms. Isolated bacterial strains were primarily Gammaproteobacteria, including representatives of genera with known oil degraders (Alcanivorax, Marinobacter, Pseudomonas, and Acinetobacter). Sequence libraries generated from oiled sands revealed phylotypes that showed high sequence identity (up to 99%) to rRNA gene sequences from the oil-degrading bacterial isolates. The abundance of bacterial SSU rRNA gene sequences was ∼10-fold higher in oiled (0.44 × 107 to 10.2 × 107 copies g-1) vs. clean (0.024 × 107 to 1.4 × 107 copies g-1) sand. Community anal. revealed a distinct response to oil contamination, and SSU rRNA gene abundance derived from the genus Alcanivorax showed the largest increase in relative abundance in contaminated samples. We conclude that oil contamination from the DH spill had a profound impact on the abundance and community compn. of indigenous bacteria in Gulf beach sands, and our evidence points to members of the Gammaproteobacteria (Alcanivorax, Marinobacter) and Alphaproteobacteria (Rhodobacteraceae) as key players in oil degrdn. there.
67. 67

    Röling, W. F. M.; de Brito Couto, I. R.; Swannell, R. P. J.; Head, I. M. Response of Archaeal Communities in Beach Sediments to Spilled Oil and Bioremediation. Appl. Environ. Microbiol. 2004, 70, 2614– 2620,  DOI: 10.1128/AEM.70.5.2614-2620.2004

    Google Scholar

    67

    Response of Archaeal communities in beach sediments to spilled oil and bioremediation

    Roling Wilfred F M; de Brito Couto Ivana R; Swannell Richard P J; Head Ian M

    Applied and environmental microbiology (2004), 70 (5), 2614-20 ISSN:0099-2240.

    While the contribution of Bacteria to bioremediation of oil-contaminated shorelines is well established, the response of Archaea to spilled oil and bioremediation treatments is unknown. The relationship between archaeal community structure and oil spill bioremediation was examined in laboratory microcosms and in a bioremediation field trial. 16S rRNA gene-based PCR and denaturing gradient gel analysis revealed that the archaeal community in oil-free laboratory microcosms was stable for 26 days. In contrast, in oil-polluted microcosms a dramatic decrease in the ability to detect Archaea was observed, and it was not possible to amplify fragments of archaeal 16S rRNA genes from samples taken from microcosms treated with oil. This was the case irrespective of whether a bioremediation treatment (addition of inorganic nutrients) was applied. Since rapid oil biodegradation occurred in nutrient-treated microcosms, we concluded that Archaea are unlikely to play a role in oil degradation in beach ecosystems. A clear-cut relationship between the presence of oil and the absence of Archaea was not apparent in the field experiment. This may have been related to continuous inoculation of beach sediments in the field with Archaea from seawater or invertebrates and shows that the reestablishment of Archaea following bioremediation cannot be used as a determinant of ecosystem recovery following bioremediation. Comparative 16S rRNA sequence analysis showed that the majority of the Archaea detected (94%) belonged to a novel, distinct cluster of group II uncultured Euryarchaeota, which exhibited less than 87% identity to previously described sequences. A minor contribution of group I uncultured Crenarchaeota was observed.
68. 68

    Newell, S. E.; Eveillard, D.; Mccarthy, M. J.; Gardner, W. S.; Liu, Z.; Ward, B. B. A Shift in the Archaeal Nitrifier Community in Response to Natural and Anthropogenic Disturbances in the Northern Gulf of Mexico. Environ. Microbiol. Rep. 2014, 6, 106– 112,  DOI: 10.1111/1758-2229.12114

    Google Scholar

    68

    A shift in the archaeal nitrifier community in response to natural and anthropogenic disturbances in the northern Gulf of Mexico

    Newell, Silvia E.; Eveillard, Damien; McCarthy, Mark J.; Gardner, Wayne S.; Liu, Zhanfei; Ward, Bess B.

    Environmental Microbiology Reports (2014), 6 (1), 106-112CODEN: EMRNAG; ISSN:1758-2229. (Wiley-Blackwell)

    Summary : The Gulf of Mexico is affected by hurricanes and suffers seasonal hypoxia. The Deepwater Horizon oil spill impacted every trophic level in the coastal region. Despite their importance in bioremediation and biogeochem. cycles, it is difficult to predict the responses of microbial communities to phys. and anthropogenic disturbances. Here, we quantify sediment ammonia-oxidizing archaeal (AOA) community diversity, resistance and resilience, and important geochem. factors after major hurricanes and the oil spill. Dominant AOA archetypes correlated with different geochem. factors, suggesting that different AOA are constrained by distinct parameters. Diversity was lowest after the hurricanes, showing weak resistance to phys. disturbances. However, diversity was highest during the oil spill and coincided with a community shift, suggesting a new alternative stable state sustained for at least 1 yr. The new AOA community was not significantly different from that at the spill site 1 yr after the spill. This sustained shift in nitrifier community structure may be a result of oil exposure.
69. 69

    Pagaling, E.; Vassileva, K.; Mills, C. G.; Bush, T.; Blythe, R. A.; Schwarz-Linek, J.; Strathdee, F.; Allen, R. J.; Free, A. Assembly of Microbial Communities in Replicate Nutrient-Cycling Model Ecosystems Follows Divergent Trajectories, Leading to Alternate Stable States. Environ. Microbiol. 2017, 19, 3374– 3386,  DOI: 10.1111/1462-2920.13849

    Google Scholar

    69

    Assembly of microbial communities in replicate nutrient-cycling model ecosystems follows divergent trajectories, leading to alternate stable states

    Pagaling, Eulyn; Vassileva, Kristin; Mills, Catherine G.; Bush, Timothy; Blythe, Richard A.; Schwarz-Linek, Jana; Strathdee, Fiona; Allen, Rosalind J.; Free, Andrew

    Environmental Microbiology (2017), 19 (8), 3374-3386CODEN: ENMIFM; ISSN:1462-2912. (Wiley-Blackwell)

    We studied in detail the reproducibility of community development in replicate nutrient-cycling microbial microcosms that were set up identically and allowed to develop under the same environmental conditions. Multiple replicate closed microcosms were constructed using pond sediment and water, enriched with cellulose and sulfate, and allowed to develop over several months under const. environmental conditions, after which their microbial communities were characterized using 16S rRNA gene sequencing. Our results show that initially similar microbial communities can follow alternative - yet stable - trajectories, diverging in time in a system size-dependent manner. The divergence between replicate communities increased in time and decreased with larger system size. In particular, notable differences emerged in the heterotrophic degrader communities in our microcosms; one group of steady state communities was enriched with Firmicutes, while the other was enriched with Bacteroidetes. The communities dominated by these two phyla also contained distinct populations of sulfate-reducing bacteria. This biomodality in community compn. appeared to arise during recovery from a low-diversity state that followed initial cellulose degrdn. and sulfate redn.
70. 70

    McGenity, T. J.; Folwell, B. D.; McKew, B. A.; Sanni, G. O. Marine Crude-Oil Biodegradation: A Central Role for Interspecies Interactions. Aquat. Biosyst. 2012, 8, 10,  DOI: 10.1186/2046-9063-8-10

    Google Scholar

    70

    Marine crude-oil biodegradation: a central role for interspecies interactions

    McGenity Terry J; Folwell Benjamin D; McKew Boyd A; Sanni Gbemisola O

    Aquatic biosystems (2012), 8 (1), 10 ISSN:.

    The marine environment is highly susceptible to pollution by petroleum, and so it is important to understand how microorganisms degrade hydrocarbons, and thereby mitigate ecosystem damage. Our understanding about the ecology, physiology, biochemistry and genetics of oil-degrading bacteria and fungi has increased greatly in recent decades; however, individual populations of microbes do not function alone in nature. The diverse array of hydrocarbons present in crude oil requires resource partitioning by microbial populations, and microbial modification of oil components and the surrounding environment will lead to temporal succession. But even when just one type of hydrocarbon is present, a network of direct and indirect interactions within and between species is observed. In this review we consider competition for resources, but focus on some of the key cooperative interactions: consumption of metabolites, biosurfactant production, provision of oxygen and fixed nitrogen. The emphasis is largely on aerobic processes, and especially interactions between bacteria, fungi and microalgae. The self-construction of a functioning community is central to microbial success, and learning how such "microbial modules" interact will be pivotal to enhancing biotechnological processes, including the bioremediation of hydrocarbons.
71. 71

    Leibold, M. A.; McPeek, M. A. Coexistence of the Niche and Neutral Perspectives in Community Ecology. Ecology 2006, 87, 1399– 1410, [1399:COTNAN]2.0.CO;2  DOI: 10.1890/0012-9658(2006)87[1399:cotnan]2.0.co;2

    Google Scholar

    71

    Coexistence of the niche and neutral perspectives in community ecology

    Leibold Mathew A; McPeek Mark A

    Ecology (2006), 87 (6), 1399-410 ISSN:0012-9658.

    The neutral theory for community structure and biodiversity is dependent on the assumption that species are equivalent to each other in all important ecological respects. We explore what this concept of equivalence means in ecological communities, how such species may arise evolutionarily, and how the possibility of ecological equivalents relates to previous ideas about niche differentiation. We also show that the co-occurrence of ecologically similar or equivalent species is not incompatible with niche theory as has been supposed, because niche relations can sometimes favor coexistence of similar species. We argue that both evolutionary and ecological processes operate to promote the introduction and to sustain the persistence of ecologically similar and in many cases nearly equivalent species embedded in highly structured food webs. Future work should focus on synthesizing niche and neutral perspectives rather than dichotomously debating whether neutral or niche models provide better explanations for community structure and biodiversity.
72. 72

    McKew, B. A.; Coulon, F.; Osborn, A. M.; Timmis, K. N.; McGenity, T. J. Determining the Identity and Roles of Oil-Metabolizing Marine Bacteria from the Thames Estuary, UK. Environ. Microbiol. 2007, 9, 165– 176,  DOI: 10.1111/j.1462-2920.2006.01125.x

    Google Scholar

    72

    Determining the identity and roles of oil-metabolizing marine bacteria from the Thames estuary, UK

    McKew, Boyd A.; Coulon, Frederic; Osborn, A. Mark; Timmis, Kenneth N.; McGenity, Terry J.

    Environmental Microbiology (2007), 9 (1), 165-176CODEN: ENMIFM; ISSN:1462-2912. (Blackwell Publishing Ltd.)

    Crude oil is a complex mixt. of different hydrocarbons. While diverse bacterial communities can degrade oil, the specific roles of individual members within such communities remain unclear. To identify the key bacterial taxa involved in aerobic degrdn. of specific hydrocarbons, microcosm expts. were established using seawater from Stanford le Hope, Thames estuary, UK, adjacent to a major oil refinery. In all microcosms, hydrocarbon degrdn. was significant within 10 wk, ranging from > 99% of low-mol.-wt. alkanes (C10-18), 41-84% of high-mol.-wt. alkanes (C20-32) and pristane, and 32-88% of polycyclic arom. hydrocarbons (PAHs). Anal. of 16S rRNA sequences from clone libraries and denaturing gradient gel electrophoresis (DGGE) indicated that, except when incubated with fluorene, PAH-degrading communities were dominated by Cycloclasticus. Moreover, PAH-degrading communities were distinct from those in microcosms contg. alkanes. Degrdn. of the branched alkane, pristane, was carried out almost exclusively by Alcanivorax. Bacteria related to Thalassolituus oleivorans (99-100% identity) were the dominant known alkane degraders in n-alkane (C12-32) microcosms, while Roseobacter-related bacteria were also consistently found in these microcosms. However, in contrast to previous studies, Thalassolituus, rather than Alcanivorax, was dominant in crude oil-enriched microcosms. The communities in n-decane microcosms differed from those in microcosms supplemented with less volatile alkanes, with a phylogenetically distinct species of Thalassolituus out-competing T. oleivorans. These data suggest that the diversity and importance of the genus Thalassolituus is greater than previously established. Overall, these expts. demonstrate how degrdn. of different petroleum hydrocarbons is partitioned between different bacterial taxa, which together as a community can remediate petroleum hydrocarbon-impacted estuarine environments.
73. 73

    Sauret, C.; Christaki, U.; Moutsaki, P.; Hatzianestis, I.; Gogou, A.; Ghiglione, J.-F. Influence of Pollution History on the Response of Coastal Bacterial and Nanoeukaryote Communities to Crude Oil and Biostimulation Assays. Mar. Environ. Res. 2012, 79, 70– 78,  DOI: 10.1016/j.marenvres.2012.05.006

    Google Scholar

    73

    Influence of pollution history on the response of coastal bacterial and nanoeukaryote communities to crude oil and biostimulation assays

    Sauret, Caroline; Christaki, Urania; Moutsaki, Paraskevi; Hatzianestis, Ioannis; Gogou, Alexandra; Ghiglione, Jean-Francois

    Marine Environmental Research (2012), 79 (), 70-78CODEN: MERSDW; ISSN:0141-1136. (Elsevier Ltd.)

    Pollution history has often been proposed to explain site-dependent bioremediation efficiencies, but this hypothesis has been poorly explored. Here, bacteria and their heterotrophic nanoflagellates (HNF) predators originating from pristine and chronically oil-polluted coastal sites were subjected to crude oil ± nutrients or emulsifier amendments. The addn. of crude oil had a more visible effect on bacteria originating from the pristine site with a higher increase in the activity of given OTU and inactivation of other petroleum-sensitive bacteria, as revealed by DNA and RNA-based comparison. Such changes resulted in a delay in microbial growth and in a lower bacterial degrdn. of the more complex hydrocarbons. Biostimulation provoked a selection of different bacterial community assemblages and stirred metabolically active bacteria. This resulted in a clear increase of the peak of bacteria and their HNF predators and higher oil degrdn., irresp. of the pollution history of the site.
74. 74

    Perez Calderon, L. J.; Potts, L. D.; Gontikaki, E.; Gubry-Rangin, C.; Cornulier, T.; Gallego, A.; Anderson, J. A.; Witte, U. Bacterial Community Response in Deep Faroe-Shetland Channel Sediments Following Hydrocarbon Entrainment With and Without Dispersant Addition. Front. Mar. Sci. 2018, 5, 159,  DOI: 10.3389/fmars.2018.00159

    Google Scholar

    There is no corresponding record for this reference.
75. 75

    Liu, Q.; Tang, J.; Liu, X.; Song, B.; Zhen, M.; Ashbolt, N. J. Response of Microbial Community and Catabolic Genes to Simulated Petroleum Hydrocarbon Spills in Soils/Sediments from Different Geographic Locations. J. Appl. Microbiol. 2017, 123, 875– 885,  DOI: 10.1111/jam.13549

    Google Scholar

    75

    Response of microbial community and catabolic genes to simulated petroleum hydrocarbon spills in soils/sediments from different geographic locations

    Liu, Q.; Tang, J.; Liu, X.; Song, B.; Zhen, M.; Ashbolt, N. J.

    Journal of Applied Microbiology (2017), 123 (4), 875-885CODEN: JAMIFK; ISSN:1364-5072. (Wiley-Blackwell)

    Study the response of microbial communities and selected petroleum hydrocarbon (PH)-degrading genes on simulated PH spills in soils/sediments from different geog. locations. Changes in bacterial community and the abundance of PH-degrading genes (alkB, nah and phe) were analyzed by denaturing gradient electrophoresis (DGGE) and qPCR, resp. Degrdn. of alkanes and PAHs in SS and NE materials were greater (P < 0·05) than those in DG and XM. Clay content was neg. correlated with the degrdn. of total alkanes by 112 days and PAHs by 56 days, while total org. carbon content was neg. correlated with initial degrdn. of total alkanes as well as PAHs. Abundances of alkB, nah and phe genes increased 10- to 100-fold and varied by soil type over the incubation period. DGGE fingerprints identified the dominance of α-, β- and γ-Proteobacteria (Gram -ve) and Actinobacteria (Gram +ve) bacteria assocd. with degrdn. of PHs in the materials studied. The geog. divergence resulting from the heterogeneity of physicochem. properties of soils/sediments appeared to influence the abundance of metabolic genes and community structure of microbes capable of degrading PHs. Significance and Impact of the Study : When developing practical in-situ bioremediation approaches for PHs contamination of soils/sediment, appropriate microbial community structures and the abundance of PH-degrading genes appear to be influenced by geog. location.
76. 76

    Jurelevicius, D.; Alvarez, V. M.; Marques, J. M.; de Sousa Lima, L. R. F.; Dias, F. D. A.; Seldin, L. Bacterial Community Response to Petroleum Hydrocarbon Amendments in Freshwater, Marine, and Hypersaline Water-Containing Microcosms. Appl. Environ. Microbiol. 2013, 79, 5927– 5935,  DOI: 10.1128/aem.02251-13

    Google Scholar

    76

    Bacterial community response to petroleum hydrocarbon amendments in freshwater, marine, and hypersaline water-containing microcosms

    Jurelevicius, Diogo; Alvarez, Vanessa Marques; Marques, Joana Montezano; Lima, Laryssa Ribeiro Fonseca de Sousa; Dias, Felipe de Almeida; Seldin, Lucy

    Applied and Environmental Microbiology (2013), 79 (19), 5927-5935CODEN: AEMIDF; ISSN:1098-5336. (American Society for Microbiology)

    Hydrocarbon-degrading bacterial communities from freshwater, marine, and hypersaline Brazilian aquatic ecosystems (with water salinities corresponding to 0.2%, 4%, and 5%, resp.) were enriched with different hydrocarbons (heptadecane, naphthalene, or crude oil). Changes within the different microcosms of bacterial communities were analyzed using cultivation approaches and mol. methods (DNA and RNA extn., followed by genetic fingerprinting and analyses of clone libraries based on the 16S rRNA-coding gene). A redundancy anal. (RDA) of the genetic fingerprint data and a principal component anal. (PCA) of the clone libraries revealed hydrocarbon-enriched bacterial communities specific for each ecosystem studied. However, within the same ecosystem, different bacterial communities were selected according to the petroleum hydrocarbon used. In general, the results demonstrated that Acinetobacter and Cloacibacterium were the dominant genera in freshwater microcosms; the Oceanospirillales order and the Marinobacter, Pseudomonas, and Cycloclasticus genera predominated in marine microcosms; and the Oceanospirillales order and the Marinobacter genus were selected in the different hydrocarbon-contg. microcosms in hypersaline water. Detn. of total petroleum hydrocarbons (TPHs) in all microcosms after 32 days of incubation showed a decrease in the hydrocarbon concn. compared to that for the controls. A total of 50 (41.3%) isolates from the different hydrocarbon-contaminated microcosms were assocd. with the dominant operational taxonomic units (OTUs) obtained from the clone libraries, and their growth in the hydrocarbon contaminating the microcosm from which they were isolated as the sole carbon source was obsd. These data provide insight into the general response of bacterial communities from freshwater, marine, and hypersaline aquatic ecosystems to petroleum hydrocarbon contamination.
77. 77

    Yakimov, M. M.; Denaro, R.; Genovese, M.; Cappello, S.; D’Auria, G.; Chernikova, T. N.; Timmis, K. N.; Golyshin, P. N.; Giluliano, L. Natural Microbial Diversity in Superficial Sediments of Milazzo Harbor (Sicily) and Community Successions during Microcosm Enrichment with Various Hydrocarbons. Environ. Microbiol. 2005, 7, 1426– 1441,  DOI: 10.1111/j.1462-5822.2005.00829.x

    Google Scholar

    77

    Natural microbial diversity in superficial sediments of Milazzo Harbor (Sicily) and community successions during microcosm enrichment with various hydrocarbons

    Yakimov, Michail M.; Denaro, Renata; Genovese, Maria; Cappello, Simone; D'Auria, Giuseppe; Chernikova, Tatyana N.; Timmis, Kenneth N.; Golyshin, Peter N.; Giluliano, Laura

    Environmental Microbiology (2005), 7 (9), 1426-1441CODEN: ENMIFM; ISSN:1462-2912. (Blackwell Publishing Ltd.)

    Hydrocarbon-contaminated superficial sediments collected from the Harbor of Milazzo (Tyrrhenian Sea, northern Sicily), a zone strongly affected by anthropogenic activities, were examd. for in situ biodegradative capacities. A culture-independent mol. phylogenetic approach was used to study the influence of hydrocarbon and nutrient addn. on the activity and diversity of the indigenous microbiota during a microcosm evaluation. The autochthonous microbial community in non-polluted sediments was represented by eubacterial phylotypes grouped within Proteobacteria, CFB and Firmicutes. The archaeal domain was represented by members of Marine Group I of Crenarchaeota. The majority of recovered sequences was affiliated with heterotrophic genera Clostridium and Vibrio, typical members of eutrophic coastal environments. Amendments of hydrocarbons and mineral nutrients to microcosms dramatically changed the initial diversity of the microbial community. Only bacterial phylotypes affiliated with Proteobacteria and CFB division were detected. The decrease in diversity obsd. in several microcosms could be explained by the strong selection for microorganisms belonging to group of marine hydrocarbonoclastic γ-Proteobacteria, namely Alcanivorax, Cycloclasticus, Marinobacter, Marinobacterium/Neptunomonas and Thalassolituus. This study demonstrated that nutrient amendment to hydrocarbon-contaminated superficial sediments enhanced the indigenous microbial biodegrdn. activity and that highly specialized marine hydrocarbonoclastic bacteria, representing a minor fraction in the natural microbial community, play an important role in the biodegrdn. of petroleum hydrocarbons accidentally entering the coastal environment.
78. 78

    Wang, B.; Lai, Q.; Cui, Z.; Tan, T.; Shao, Z. A Pyrene-Degrading Consortium from Deep-Sea Sediment of the West Pacific and Its Key Member Cycloclasticus Sp. P1. Environ. Microbiol. 2008, 10, 1948– 1963,  DOI: 10.1111/j.1462-2920.2008.01611.x

    Google Scholar

    78

    A pyrene-degrading consortium from deep-sea sediment of the West Pacific and its key member Cycloclasticus sp. P1

    Wang, Baojiang; Lai, Qiliang; Cui, Zhisong; Tan, Tianfeng; Shao, Zongze

    Environmental Microbiology (2008), 10 (8), 1948-1963CODEN: ENMIFM; ISSN:1462-2912. (Wiley-Blackwell)

    A pyrene-degrading bacterial consortium was obtained from deep-sea sediments of the Pacific Ocean. The consortium degraded many kinds of polycyclic arom. hydrocarbons (PAHs), including naphthalene, phenanthrene, pyrene, acenaphthene, fluorene, anthracene, fluoranthene, 2-methylnaphthalene and 2,6-dimethylnaphthalene, but it did not grow with chrysene and benzo[α]pyrene. With methods of plate cultivation and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), 72 bacteria belonging to 22 genera were detected from this consortium. Among the detected bacteria, the following genera frequently occurred: Flavobacterium, Cycloclasticus, Novosphingobium, Halomonas, Achromobacter, Roseovarius and Alcanivorax. The first two genera showed the strongest bands in denaturing gradient gel electrophoresis (DGGE) profiles and appeared in all PAH treatments. By now, only one isolated designated P1 was confirmed to be a pyrene degrader. It was identified to be Cycloclasticus spirillensus (100%). Although P1 can degrade pyrene independently, other bacteria, such as Novosphingobium sp. (Band 14), Halomonas sp. (Band 16) and an unidentified bacterium (Band 35), were involved in pyrene degrdn. in some way; they persist in the consortium in the test of diln. to extinction if only the consortium was motivated with pyrene. However, the secondary most important member Flavobacterium sp. evaded from the community at high dilns. As a key member of the consortium, P1 distinguished itself by both cell morphol. and carbon source range among the isolates of this genus. Based on intermediate analyses of pyrene degrdn., P1 was supposed to take an upper pathway different from that previously reported. Together with the results of obtained genes from P1 homol. with those responsible for naphthalene degrdn., its degrdn. to pyrene is supposed to adopt another set of genes unique to presently detected. Summarily, an efficient pyrene-degrading consortium was obtained from the Pacific Ocean sediment, in which Cycloclasticus bacterium played a key role. This is the first report to exploit the diversity of pyrene-degrading bacteria in oceanic environments.
79. 79

    Niepceron, M.; Portet-Koltalo, F.; Merlin, C.; Motelay-Massei, A.; Barray, S.; Bodilis, J. Both Cycloclasticus Spp. and Pseudomonas Spp. as PAH-Degrading Bacteria in the Seine Estuary (France). FEMS Microbiol. Ecol. 2010, 71, 137– 147,  DOI: 10.1111/j.1574-6941.2009.00788.x

    Google Scholar

    79

    Both Cycloclasticus spp. and Pseudomonas spp. as PAH-degrading bacteria in the Seine estuary (France)

    Niepceron, Maite; Portet-Koltalo, Florence; Merlin, Chloe; Motelay-Massei, Anne; Barray, Sylvie; Bodilis, Josselin

    FEMS Microbiology Ecology (2010), 71 (1), 137-147CODEN: FMECEZ; ISSN:0168-6496. (Wiley-Blackwell)

    Like other highly urbanized and industrialized estuaries, the Seine estuary (France) has, for decades, received high inputs of polycyclic arom. hydrocarbons (PAHs). In order to est. the bioremediation potentials and to identify the bacterial species involved in hydrocarbon degrdn., we used microcosms contg. seawater from the Seine estuary supplemented with either naphthalene, phenanthrene, fluorene or pyrene. In the microcosms enriched with naphthalene or phenanthrene, hydrocarbon biodegrdn. was significant within 9 wk (43% or 46%, resp.), as shown by analyses in GC-MS. In similar microcosms incubated also with naphthalene or phenanthrene, anal. of the 16S rRNA gene sequences (DNA and cDNA) with denaturing gradient gel electrophoresis and clone libraries indicated that the PAH-degrading communities were dominated by Cycloclasticus spp., confirming their universal key role in degrdn. of low-mol.-wt. PAHs in marine environments. However, in contrast to previous studies, we found that Pseudomonas spp. also degraded naphthalene and phenanthrene in seawater; this occurred only after 21 days, as was confirmed by real-time PCR. Although this genus has been abundantly described in the literature as a good PAH-degrading bacterial group in soil or in sediment, to our knowledge, this is the first evidence of a significant fitness in PAH degrdn. in seawater.
80. 80

    Li, J.; Zhang, D.; Song, M.; Jiang, L.; Wang, Y.; Luo, C.; Zhang, G. Novel Bacteria Capable of Degrading Phenanthrene in Activated Sludge Revealed by Stable-Isotope Probing Coupled with High-Throughput Sequencing. Biodegradation 2017, 28, 423– 436,  DOI: 10.1007/s10532-017-9806-9

    Google Scholar

    80

    Novel bacteria capable of degrading phenanthrene in activated sludge revealed by stable-isotope probing coupled with high-throughput sequencing

    Li, Jibing; Zhang, Dayi; Song, Mengke; Jiang, Longfei; Wang, Yujie; Luo, Chunling; Zhang, Gan

    Biodegradation (2017), 28 (5-6), 423-436CODEN: BIODEG; ISSN:0923-9820. (Springer)

    The indigenous microorganisms responsible for degrading phenanthrene (PHE) in activated biosludge were identified using DNA-based stable isotope probing. Besides the well-known PHE degraders Burkholderia, Ralstonia, Sinobacteraceae and Arthrobacter, we for the first time linked the taxa Paraburkholderia and Kaistobacter with in situ PHE biodegrdn. Anal. of PAH-RHDα gene detected in the heavy DNA fraction of 13C-PHE treatment suggested the mechanisms of horizontal gene transfer or inter-species hybridization in PAH-RHD gene spread within the microbial community. Addnl., three cultivable PHE degraders, Microbacterium sp. PHE-1, Rhodanobacter sp., PHE-2 and Rhodococcus sp. PHE-3, were isolated from the same activated biosludge. Among them, Rhodanobacter sp.PHE-2 is the first identified strain in its genus with PHE-degrading ability. However, the involvement of these strains in PHE degrdn. in situ was questionable, due to their limited enrichment in the heavy DNA fraction of 13C-PHE treatment and lack of PAH-RHDα gene found in these isolates. Collectively, our findings provide a deeper understanding of the diversity and functions of indigenous microbes in PHE degrdn.
81. 81

    Gutierrez, T.; Singleton, D. R.; Aitken, M. D.; Semple, K. T. Stable Isotope Probing of an Algal Bloom to Identify Uncultivated Members of the Rhodobacteraceae Associated with Low-Molecular-Weight Polycyclic Aromatic Hydrocarbon Degradation. Appl. Environ. Microbiol. 2011, 77, 7856– 7860,  DOI: 10.1128/aem.06200-11

    Google Scholar

    81

    Stable isotope probing of an algal bloom to identify uncultivated members of the Rhodobacteraceae associated with low-molecular-weight polycyclic aromatic hydrocarbon degradation

    Gutierrez, Tony; Singleton, David R.; Aitken, Michael D.; Semple, Kirk T.

    Applied and Environmental Microbiology (2011), 77 (21), 7856-7860CODEN: AEMIDF; ISSN:0099-2240. (American Society for Microbiology)

    Polycyclic arom. hydrocarbon (PAH)-degrading bacteria assocd. with an algal bloom in Tampa Bay, FL, were investigated by stable isotope probing (SIP) with uniformly labeled [13C]naphthalene. The dominant sequences in clone libraries constructed from 13C-enriched bacterial DNA (from naphthalene enrichments) were identified as uncharacterized members of the family Rhodobacteraceae. Quant. PCR primers targeting the 16S rRNA gene of these uncultivated organisms were used to det. their abundance in incubations amended with unlabeled naphthalene and phenanthrene, both of which showed substantial increases in gene copy nos. during the expts. As demonstrated by this work, the application of uniformly 13C-labeled PAHs in SIP expts. can successfully be used to identify novel PAH-degrading bacteria in marine waters.
82. 82

    Kasai, Y.; Kishira, H.; Harayama, S. Bacteria Belonging to the Genus Cycloclasticus Play a Primary Role in the Degradation of Aromatic Hydrocarbons Released in a Marine Environment. Appl. Environ. Microbiol. 2002, 68, 5625– 5633,  DOI: 10.1128/aem.68.11.5625-5633.2002

    Google Scholar

    82

    Bacteria belonging to the genus Cycloclasticus play a primary role in the degradation of aromatic hydrocarbons released in a marine environment

    Kasai, Yuki; Kishira, Hideo; Harayama, Shigeaki

    Applied and Environmental Microbiology (2002), 68 (11), 5625-5633CODEN: AEMIDF; ISSN:0099-2240. (American Society for Microbiology)

    To identify the bacteria that play a major role in the aerobic degrdn. of petroleum polynuclear arom. hydrocarbons (PAHs) in a marine environment, bacteria were enriched from seawater using 2-methylnaphthalene, phenanthrene, or anthracene as a C and energy source. We found that members of the genus Cycloclasticus became predominant in the enrichment cultures. The Cycloclasticus strains isolated could grow on crude oil and degraded PAH components of crude oil, including unsubstituted and substituted naphthalenes, dibenzothiophenes, phenanthrenes, and fluorenes. To deduce the role of Cycloclasticus strains in a coastal zone oil spill, propagation of this bacterial group on oil-coated grains of gravel immersed in seawater was studied in beach-simulating tanks that were 1 m wide by 1.5 m long by 1 m high. The tanks were two-thirds filled with gravel, and seawater was continuously introduced into the tanks; the water level was varied between 30 cm above and 30 cm below the surface of the gravel layer to simulate a 12-h tidal cycle. The no. of Cycloclasticus cells assocd. with the grains was on the order of 103 cells/g of grains before crude oil was added to the tanks and increased to 3 × 106 cells/g of grains after crude oil was added. The no. increased further after 14 days to 108 cells/g of grains when N and P fertilizers were added, while the no. remained 3 × 106 cells/g of grains when no fertilizers were added. PAH degrdn. proceeded parallel with the growth of Cycloclasticus cells on the surfaces of the oil-polluted grains of gravel. These observations suggest that bacteria belonging to the genus Cycloclasticus play an important role in the degrdn. of petroleum PAHs in a marine environment.
83. 83

    Gutierrez, T.; Biddle, J. F.; Teske, A.; Aitken, M. D. Cultivation-Dependent and Cultivation-Independent Characterization of Hydrocarbon-Degrading Bacteria in Guaymas Basin Sediments. Front. Microbiol. 2015, 6, 695,  DOI: 10.3389/fmicb.2015.00695

    Google Scholar

    83

    Cultivation-dependent and cultivation-independent characterization of hydrocarbon-degrading bacteria in Guaymas Basin sediments

    Gutierrez Tony; Biddle Jennifer F; Teske Andreas; Aitken Michael D

    Frontiers in microbiology (2015), 6 (), 695 ISSN:1664-302X.

    Marine hydrocarbon-degrading bacteria perform a fundamental role in the biodegradation of crude oil and its petrochemical derivatives in coastal and open ocean environments. However, there is a paucity of knowledge on the diversity and function of these organisms in deep-sea sediment. Here we used stable-isotope probing (SIP), a valuable tool to link the phylogeny and function of targeted microbial groups, to investigate polycyclic aromatic hydrocarbon (PAH)-degrading bacteria under aerobic conditions in sediments from Guaymas Basin with uniformly labeled [(13)C]-phenanthrene (PHE). The dominant sequences in clone libraries constructed from (13)C-enriched bacterial DNA (from PHE enrichments) were identified to belong to the genus Cycloclasticus. We used quantitative PCR primers targeting the 16S rRNA gene of the SIP-identified Cycloclasticus to determine their abundance in sediment incubations amended with unlabeled PHE and showed substantial increases in gene abundance during the experiments. We also isolated a strain, BG-2, representing the SIP-identified Cycloclasticus sequence (99.9% 16S rRNA gene sequence identity), and used this strain to provide direct evidence of PHE degradation and mineralization. In addition, we isolated Halomonas, Thalassospira, and Lutibacterium sp. with demonstrable PHE-degrading capacity from Guaymas Basin sediment. This study demonstrates the value of coupling SIP with cultivation methods to identify and expand on the known diversity of PAH-degrading bacteria in the deep-sea.
84. 84

    Dubinsky, E. A.; Conrad, M. E.; Chakraborty, R.; Bill, M.; Borglin, S. E.; Hollibaugh, J. T.; Mason, O. U.; Piceno, Y. M.; Reid, F. C.; Stringfellow, W. T.; Tom, L. M.; Hazen, T. C.; Andersen, G. L. Succession of Hydrocarbon-Degrading Bacteria in the Aftermath of the Deepwater Horizon Oil Spill in the Gulf of Mexico. Environ. Sci. Technol. 2013, 47, 10860– 10867,  DOI: 10.1021/es401676y

    Google Scholar

    84

    Succession of Hydrocarbon-Degrading Bacteria in the Aftermath of the Deepwater Horizon Oil Spill in the Gulf of Mexico

    Dubinsky, Eric A.; Conrad, Mark E.; Chakraborty, Romy; Bill, Markus; Borglin, Sharon E.; Hollibaugh, James T.; Mason, Olivia U.; Piceno, Yvette M.; Reid, Francine C.; Stringfellow, William T.; Tom, Lauren M.; Hazen, Terry C.; Andersen, Gary L.

    Environmental Science & Technology (2013), 47 (19), 10860-10867CODEN: ESTHAG; ISSN:0013-936X. (American Chemical Society)

    The Deepwater Horizon oil spill produced large subsurface plumes of dispersed oil and gas in the Gulf of Mexico that stimulated growth of psychrophilic, hydrocarbon degrading bacteria. We tracked succession of plume bacteria before, during and after the 83-day spill to det. the microbial response and biodegrdn. potential throughout the incident. Dominant bacteria shifted substantially over time and were dependent on relative quantities of different hydrocarbon fractions. Unmitigated flow from the wellhead early in the spill resulted in the highest proportions of n-alkanes and cycloalkanes at depth and corresponded with dominance by Oceanospirillaceae and Pseudomonas. Once partial capture of oil and gas began 43 days into the spill, petroleum hydrocarbons decreased, the fraction of arom. hydrocarbons increased, and Colwellia, Cycloclasticus, and Pseudoalteromonas increased in dominance. Enrichment of Methylomonas coincided with pos. shifts in the δ13C values of methane in the plume and indicated significant methane oxidn. occurred earlier than previously reported. Anomalous O depressions persisted at plume depths for over 6 wk after well shut-in and were likely caused by common marine heterotrophs assocd. with degrdn. of high-mol.-wt. org. matter, including Methylophaga. Multiple hydrocarbon-degrading bacteria operated simultaneously throughout the spill, but their relative importance was controlled by changes in hydrocarbon supply.
85. 85

    Sjöstedt, J.; Koch-Schmidt, P.; Pontarp, M.; Canbäck, B.; Tunlid, A.; Lundberg, P.; Hagström, Å.; Riemann, L. Recruitment of Members from the Rare Biosphere of Marine Bacterioplankton Communities after an Environmental Disturbance. Appl. Environ. Microbiol. 2012, 78, 1361– 1369,  DOI: 10.1128/AEM.05542-11

    Google Scholar

    85

    Recruitment of members from the rare biosphere of marine bacterioplankton communities after an environmental disturbance

    Sjostedt Johanna; Koch-Schmidt Per; Pontarp Mikael; Canback Bjorn; Tunlid Anders; Lundberg Per; Hagstrom Ake; Riemann Lasse

    Applied and environmental microbiology (2012), 78 (5), 1361-9 ISSN:.

    A bacterial community may be resistant to environmental disturbances if some of its species show metabolic flexibility and physiological tolerance to the changing conditions. Alternatively, disturbances can change the composition of the community and thereby potentially affect ecosystem processes. The impact of disturbance on the composition of bacterioplankton communities was examined in continuous seawater cultures. Bacterial assemblages from geographically closely connected areas, the Baltic Sea (salinity 7 and high dissolved organic carbon [DOC]) and Skagerrak (salinity 28 and low DOC), were exposed to gradual opposing changes in salinity and DOC over a 3-week period such that the Baltic community was exposed to Skagerrak salinity and DOC and vice versa. Denaturing gradient gel electrophoresis and clone libraries of PCR-amplified 16S rRNA genes showed that the composition of the transplanted communities differed significantly from those held at constant salinity. Despite this, the growth yields (number of cells ml(-1)) were similar, which suggests similar levels of substrate utilization. Deep 454 pyrosequencing of 16S rRNA genes showed that the composition of the disturbed communities had changed due to the recruitment of phylotypes present in the rare biosphere of the original community. The study shows that members of the rare biosphere can become abundant in a bacterioplankton community after disturbance and that those bacteria can have important roles in maintaining ecosystem processes.
86. 86

    Jia, X.; Dini-Andreote, F.; Falcão Salles, J. Community Assembly Processes of the Microbial Rare Biosphere. Trends Microbiol. 2018, 26, 738– 747,  DOI: 10.1016/j.tim.2018.02.011

    Google Scholar

    86

    Community Assembly Processes of the Microbial Rare Biosphere

    Jia, Xiu; Dini-Andreote, Francisco; Falcao Salles, Joana

    Trends in Microbiology (2018), 26 (9), 738-747CODEN: TRMIEA; ISSN:0966-842X. (Elsevier Ltd.)

    Our planet teems with microorganisms that often present a skewed abundance distribution in a local community, with relatively few dominant species coexisting alongside a high no. of rare species. Recent studies have demonstrated that these rare taxa serve as limitless reservoirs of genetic diversity, and perform disproportionate types of functions despite their low abundances. However, relatively little is known about the mechanisms controlling rarity and the processes promoting the development of the rare biosphere. Here, we propose the use of multivariate cut-offs to est. rare species and phylogenetic null models applied to predefined rare taxa to disentangle the relative influences of ecoevolutionary processes mediating the assembly of the rare biosphere. Importantly, the identification of the factors controlling rare species assemblages is crit. for understanding the types of rarity, how the rare biosphere is established, and how rare microorganisms fluctuate over spatiotemporal scales, thus enabling prospective predictions of ecosystem responses.
87. 87

    Shade, A.; Jones, S. E.; Caporaso, J. G.; Handelsman, J.; Knight, R.; Fierer, N.; Gilbert, J. A. Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity. mBio 2014, 5, e01371  DOI: 10.1128/mBio.01371-14

    Google Scholar

    87

    Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity

    Shade, Ashley; Jones, Stuart E.; Caporaso, J. Gregory; Handelsman, Jo; Knight, Rob; Fierer, Noah; Gilbert, Jack A.

    mBio (2014), 5 (4), e01371/1-e01371/10CODEN: MBIOCL; ISSN:2150-7511. (American Society for Microbiology)

    Microbial communities typically contain many rare taxa that make up the majority of the obsd. membership, yet the contribution of this microbial "rare biosphere" to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT made up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amts. of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified "one-hit wonder" CRT that were obsd. at only one time point. Using a case study from a temperate lake, we gained addnl. insights into the ecol. of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amt. to microbial community dynamics than is apparent from their low proportional abundances. This observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time.
88. 88

    Louca, S.; Polz, M. F.; Mazel, F.; Albright, M. B. N.; Huber, J. A.; O’Connor, M. I.; Ackermann, M.; Hahn, A. S.; Srivastava, D. S.; Crowe, S. A.; Doebeli, M.; Parfrey, L. W. Function and Functional Redundancy in Microbial Systems. Nat. Ecol. Evol. 2018, 2, 936– 943,  DOI: 10.1038/s41559-018-0519-1

    Google Scholar

    88

    Function and functional redundancy in microbial systems

    Louca Stilianos; Mazel Florent; O'Connor Mary I; Srivastava Diane S; Doebeli Michael; Parfrey Laura Wegener; Louca Stilianos; O'Connor Mary I; Srivastava Diane S; Doebeli Michael; Parfrey Laura Wegener; Polz Martin F; Mazel Florent; Parfrey Laura Wegener; Mazel Florent; Albright Michaeline B N; Huber Julie A; Ackermann Martin; Ackermann Martin; Hahn Aria S; Crowe Sean A; Crowe Sean A; Crowe Sean A; Doebeli Michael

    Nature ecology & evolution (2018), 2 (6), 936-943 ISSN:.

    Microbial communities often exhibit incredible taxonomic diversity, raising questions regarding the mechanisms enabling species coexistence and the role of this diversity in community functioning. On the one hand, many coexisting but taxonomically distinct microorganisms can encode the same energy-yielding metabolic functions, and this functional redundancy contrasts with the expectation that species should occupy distinct metabolic niches. On the other hand, the identity of taxa encoding each function can vary substantially across space or time with little effect on the function, and this taxonomic variability is frequently thought to result from ecological drift between equivalent organisms. Here, we synthesize the powerful paradigm emerging from these two patterns, connecting the roles of function, functional redundancy and taxonomy in microbial systems. We conclude that both patterns are unlikely to be the result of ecological drift, but are inevitable emergent properties of open microbial systems resulting mainly from biotic interactions and environmental and spatial processes.
89. 89

    Acosta-González, A.; Marqués, S. Bacterial Diversity in Oil-Polluted Marine Coastal Sediments. Curr. Opin. Biotechnol. 2016, 38, 24– 32,  DOI: 10.1016/j.copbio.2015.12.010

    Google Scholar

    89

    Bacterial diversity in oil-polluted marine coastal sediments

    Acosta-Gonzalez, Alejandro; Marques, Silvia

    Current Opinion in Biotechnology (2016), 38 (), 24-32CODEN: CUOBE3; ISSN:0958-1669. (Elsevier B.V.)

    Marine environments harbor a persistent microbial seed which can be shaped by changes of the environmental conditions such as contamination by petroleum components. Oil spills, together with small but continuous discharges of oil from transportation and recreational activities, are important sources of hydrocarbon pollution within the marine realm. Consequently, prokaryotic communities have become well pre-adapted toward oil pollution, and many microorganisms that are exposed to its presence develop an active degradative response. The natural attenuation of oil pollutants, as has been demonstrated in many sites, is modulated according to the intrinsic environmental properties such as the availability of terminal electron acceptors and elemental nutrients, together with the degree of pollution and the type of hydrocarbon fractions present. While dynamics in the bacterial communities in the aerobic zones of coastal sediments are well characterized and the key players in hydrocarbon biodegrdn. have been identified, the subtidal ecol. of the anaerobic community is still not well understood. However, current data suggest common patterns of response in these ecosystems.
90. 90

    Rodriguez-R, L. M.; Overholt, W. A.; Hagan, C.; Huettel, M.; Kostka, J. E.; Konstantinidis, K. T. Microbial Community Successional Patterns in Beach Sands Impacted by the Deepwater Horizon Oil Spill. ISME J. 2015, 9, 1928– 1940,  DOI: 10.1038/ismej.2015.5

    Google Scholar

    90

    Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill

    Rodriguez-R Luis M; Overholt Will A; Hagan Christopher; Huettel Markus; Kostka Joel E; Konstantinidis Konstantinos T

    The ISME journal (2015), 9 (9), 1928-40 ISSN:.

    Although petroleum hydrocarbons discharged from the Deepwater Horizon (DWH) blowout were shown to have a pronounced impact on indigenous microbial communities in the Gulf of Mexico, effects on nearshore or coastal ecosystems remain understudied. This study investigated the successional patterns of functional and taxonomic diversity for over 1 year after the DWH oil was deposited on Pensacola Beach sands (FL, USA), using metagenomic and 16S rRNA gene amplicon techniques. Gamma- and Alphaproteobacteria were enriched in oiled sediments, in corroboration of previous studies. In contrast to previous studies, we observed an increase in the functional diversity of the community in response to oil contamination and a functional transition from generalist populations within 4 months after oil came ashore to specialists a year later, when oil was undetectable. At the latter time point, a typical beach community had reestablished that showed little to no evidence of oil hydrocarbon degradation potential, was enriched in archaeal taxa known to be sensitive to xenobiotics, but differed significantly from the community before the oil spill. Further, a clear succession pattern was observed, where early responders to oil contamination, likely degrading aliphatic hydrocarbons, were replaced after 3 months by populations capable of aromatic hydrocarbon decomposition. Collectively, our results advance the understanding of how natural benthic microbial communities respond to crude oil perturbation, supporting the specialization-disturbance hypothesis; that is, the expectation that disturbance favors generalists, while providing (microbial) indicator species and genes for the chemical evolution of oil hydrocarbons during degradation and weathering.
91. 91

    Stauffert, M.; Cravo-Laureau, C.; Jézéquel, R.; Barantal, S.; Cuny, P.; Gilbert, F.; Cagnon, C.; Militon, C.; Amouroux, D.; Mahdaoui, F.; Bouyssiere, B.; Stora, G.; Merlin, F.-X.; Duran, R. Impact of Oil on Bacterial Community Structure in Bioturbated Sediments. PLoS One 2013, 8, e65347  DOI: 10.1371/journal.pone.0065347

    Google Scholar

    91

    Impact of oil on bacterial community structure in bioturbated sediments

    Stauffert, Magalie; Cravo-Laureau, Cristiana; Jezequel, Ronan; Barantal, Sandra; Cuny, Philippe; Gilbert, Franck; Cagnon, Christine; Militon, Cecile; Amouroux, David; Mahdaoui, Fatima; Bouyssiere, Brice; Stora, Georges; Merlin, Francois-Xavier; Duran, Robert

    PLoS One (2013), 8 (6), e65347CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)

    Oil spills threaten coastlines where biol. processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabs. It is thus essential to consider the bioturbation when detg. the impact of oil on microbial communities. In this study, an exptl. lab. device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions - with tidal cycles and natural seawater - was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addn. of: standardized oil (Blend Arabian Light crude oil, 25.6 mg·g-1 wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addn. of H. diversicolor and its assocd. bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irresp. of the H. diversicolor addn. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries anal. showed an effect of the condition on the bacterial community structure, compn. and dynamics, supported by PerMANOVA anal. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences assocd. to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addn.) revealed two distinct microbial communities characterized by different phylotypes assocd. to known hydrocarbonoclastic bacteria and dominated by Gammaproteobacteria and Deltaproteobacteria. In the oiled-microcosms, the addn. of H. diversicolor reduced the phylotype-richness, sequences assocd. to Actinobacteria, Firmicutes and Plantomycetes were not detected. These observations highlight the influence of the bioturbation on the bacterial community structure without affecting the biodegrdn. capacities.
92. 92

    Cravo-Laureau, C.; Duran, R. Marine Coastal Sediments Microbial Hydrocarbon Degradation Processes: Contribution of Experimental Ecology in the Omics’era. Front. Microbiol. 2014, 5, 39,  DOI: 10.3389/fmicb.2014.00039

    Google Scholar

    92

    Marine coastal sediments microbial hydrocarbon degradation processes: contribution of experimental ecology in the omics'era

    Cravo-Laureau Cristiana; Duran Robert

    Frontiers in microbiology (2014), 5 (), 39 ISSN:1664-302X.

    Coastal marine sediments, where important biological processes take place, supply essential ecosystem services. By their location, such ecosystems are particularly exposed to human activities as evidenced by the recent Deepwater Horizon disaster. This catastrophe revealed the importance to better understand the microbial processes involved on hydrocarbon degradation in marine sediments raising strong interests of the scientific community. During the last decade, several studies have shown the key role played by microorganisms in determining the fate of hydrocarbons in oil-polluted sediments but only few have taken into consideration the whole sediment's complexity. Marine coastal sediment ecosystems are characterized by remarkable heterogeneity, owning high biodiversity and are subjected to fluctuations in environmental conditions, especially to important oxygen oscillations due to tides. Thus, for understanding the fate of hydrocarbons in such environments, it is crucial to study microbial activities, taking into account sediment characteristics, physical-chemical factors (electron acceptors, temperature), nutrients, co-metabolites availability as well as sediment's reworking due to bioturbation activities. Key information could be collected from in situ studies, which provide an overview of microbial processes, but it is difficult to integrate all parameters involved. Microcosm experiments allow to dissect in-depth some mechanisms involved in hydrocarbon degradation but exclude environmental complexity. To overcome these lacks, strategies have been developed, by creating experiments as close as possible to environmental conditions, for studying natural microbial communities subjected to oil pollution. We present here a review of these approaches, their results and limitation, as well as the promising future of applying "omics" approaches to characterize in-depth microbial communities and metabolic networks involved in hydrocarbon degradation. In addition, we present the main conclusions of our studies in this field.
93. 93

    Duran, R.; Cravo-Laureau, C. Role of Environmental Factors and Microorganisms in Determining the Fate of Polycyclic Aromatic Hydrocarbons in the Marine Environment. FEMS Microbiol. Rev. 2016, 40, 814– 830,  DOI: 10.1093/femsre/fuw031

    Google Scholar

    93

    Role of environmental factors and microorganisms in determining the fate of polycyclic aromatic hydrocarbons in the marine environment

    Duran, Robert; Cravo-Laureau, Cristiana

    FEMS Microbiology Reviews (2016), 40 (6), 814-830CODEN: FMREE4; ISSN:1574-6976. (Oxford University Press)

    Polycyclic arom. hydrocarbons (PAHs) are widespread in marine ecosystems and originate from natural sources and anthropogenic activities. PAHs enter the marine environment in two main ways, corresponding to chronic pollution or acute pollution by oil spills. The global PAH fluxes in marine environments are controlled by the microbial degrdn. and the biol. pump, which plays a role in particle settling and in sequestration through bioaccumulation. Due to their low water soly. and hydrophobic nature, PAHs tightly adhere to sediments leading to accumulation in coastal and deep sediments. Microbial assemblages play an important role in detg. the fate of PAHs in water and sediments, supporting the functioning of biogeochem. cycles and the microbial loop. This review summaries the knowledge recently acquired in terms of both chronic and acute PAH pollution. The importance of the microbial ecol. in PAH-polluted marine ecosystems is highlighted as well as the importance of gaining further in-depth knowledge of the environmental services provided by microorganisms.
94. 94

    Dunlevy, S. R.; Singleton, D. R.; Aitken, M. D. Biostimulation Reveals Functional Redundancy of Anthracene-Degrading Bacteria in Polycyclic Aromatic Hydrocarbon-Contaminated Soil. Environ. Eng. Sci. 2013, 30, 697– 705,  DOI: 10.1089/ees.2013.0067

    Google Scholar

    94

    Biostimulation Reveals Functional Redundancy of Anthracene-Degrading Bacteria in Polycyclic Aromatic Hydrocarbon-Contaminated Soil

    Dunlevy, Sage R.; Singleton, David R.; Aitken, Michael D.

    Environmental Engineering Science (2013), 30 (11), 697-705CODEN: EESCF5; ISSN:1092-8758. (Mary Ann Liebert, Inc.)

    Stable-isotope probing was previously used to identify bacterial anthracene-degraders in untreated soil from a former manufd. gas plant site. However, subsequent pyrosequence analyses of total bacterial communities and quantification of 16S rRNA genes indicated that relative abundances of the predominant anthracene-degrading bacteria (designated Anthracene Group 1) diminished as a result of biol. treatment conditions in lab-scale, aerobic bioreactors. This study identified Alphaproteobacterial anthracene-degrading bacteria in bioreactor-treated soil which were dissimilar to those previously identified. The largest group of sequences was from the Alterythrobacter genus while other groups of sequences were assocd. with bacteria within the order Rhizobiales and the genus Bradyrhizobium. Conditions in the bioreactor enriched for organisms capable of degrading anthracene which were not the same as those identified as dominant degraders in the untreated soil. Further, these data suggest that identification of polycyclic arom. hydrocarbon-degrading bacteria in contaminated but untreated soil may be a poor indicator of the most active degraders during biol. treatment.