Microbial community composition and diversity in Caspian Sea sediments

Mahmoudi, Nagissa; Robeson, Michael S.; Castro, Hector F.; Fortney, Julian L.; Techtmann, Stephen M.; Joyner, Dominique C.; Paradis, Charles J.; Pfiffner, Susan M.; Hazen, Terry C.

doi:10.1093/femsec/fiu013

Microbial community composition and diversity in Caspian Sea sediments

Journal Article · Thu Dec 04 23:00:00 EST 2014 · FEMS Microbiology Ecology (Online)

DOI:https://doi.org/10.1093/femsec/fiu013· OSTI ID:1625318

Mahmoudi, Nagissa ^[1]; Robeson, Michael S. ^[2]; Castro, Hector F. ^[3]; Fortney, Julian L. ^[4]; Techtmann, Stephen M. ^[4]; Joyner, Dominique C. ^[4]; Paradis, Charles J. ^[5]; Pfiffner, Susan M. ^[6]; Hazen, Terry C. ^[7]

Univ. of Tennessee, Knoxville, TN (United States). Dept. of Civil and Environmental Engineering; Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology; DOE/OSTI
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioSciences Division
Univ. of Tennessee, Knoxville, TN (United States). Dept. of Chemistry
Univ. of Tennessee, Knoxville, TN (United States). Dept. of Civil and Environmental Engineering; Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology
Univ. of Tennessee, Knoxville, TN (United States). Dept. of Earth and Planetary Sciences
Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology
Univ. of Tennessee, Knoxville, TN (United States). Dept. of Civil and Environmental Engineering; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioSciences Division; Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Earth and Planetary Sciences; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Microbiology

The Caspian Sea is heavily polluted due to industrial and agricultural effluents as well as extraction of oil and gas reserves. Microbial communities can influence the fate of contaminants and nutrients. However, insight into the microbial ecology of the Caspian Sea significantly lags behind other marine systems. Here we describe microbial biomass, diversity and composition in sediments collected from three sampling stations in the Caspian Sea. Illumina sequencing of 16S rRNA genes revealed the presence of a number of known bacterial and archaeal heterotrophs suggesting that organic carbon is a primary factor shaping microbial communities. Surface sediments collected from bottom waters with low oxygen levels were dominated by Gammaproteobacteria while surface sediments collected from bottom waters under hypoxic conditions were dominated by Deltaproteobacteria, specifically sulfate-reducing bacteria. Thaumarchaeota was dominant across all surface sediments indicating that nitrogen cycling in this system is strongly influenced by ammonia-oxidizing archaea. This study provides a baseline assessment that may serve as a point of reference as this system changes or as the efficacy of new remediation efforts are implemented.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC); University of Tennessee; BP America

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1625318

Journal Information:: FEMS Microbiology Ecology (Online), Journal Name: FEMS Microbiology Ecology (Online) Journal Issue: 1 Vol. 91; ISSN 1574-6941

Publisher:: Federation of European Microbiological SocietiesCopyright Statement

Country of Publication:: United States

Language:: English

References (85)

Bacterial Community Composition in Different Sediments from the Eastern Mediterranean Sea: a Comparison of Four 16S Ribosomal DNA Clone Libraries Polymenakou, Paraskevi N.; Bertilsson, Stefan; Tselepides, Anastasios Microbial Ecology, Vol. 50, Issue 3 https://doi.org/10.1007/s00248-005-0005-6	journal	October 2005
Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review Zelles, L. Biology and Fertility of Soils, Vol. 29, Issue 2 https://doi.org/10.1007/s003740050533	journal	May 1999
The Effects of Hypoxia on Sediment Nitrogen Cycling in the Baltic Sea Jäntti, Helena; Hietanen, Susanna AMBIO, Vol. 41, Issue 2 https://doi.org/10.1007/s13280-011-0233-6	journal	January 2012
Pathways of organic carbon oxidation in three continental margin sediments Canfield, D. E.; Jørgensen, B. B.; Fossing, H. Marine Geology, Vol. 113, Issue 1-2 https://doi.org/10.1016/0025-3227(93)90147-n	journal	July 1993
Assessing microbial carbon sources and potential PAH degradation using natural abundance 14C analysis Mahmoudi, Nagissa; Fulthorpe, Roberta R.; Burns, Leanne Environmental Pollution, Vol. 175 https://doi.org/10.1016/j.envpol.2012.12.020	journal	April 2013
Organochlorinated compounds in Caspian Sea sediments de Mora, Stephen; Villeneuve, Jean-Pierre; Reza Sheikholeslami, Mohammad Marine Pollution Bulletin, Vol. 48, Issue 1-2 https://doi.org/10.1016/j.marpolbul.2003.10.001	journal	January 2004
Isolation and characterization of crude-oil-degrading bacteria from the Persian Gulf and the Caspian Sea Hassanshahian, Mehdi; Emtiazi, Giti; Cappello, Simone Marine Pollution Bulletin, Vol. 64, Issue 1 https://doi.org/10.1016/j.marpolbul.2011.11.006	journal	January 2012
Communities of sediment ammonia-oxidizing bacteria along a coastal pollution gradient in the East China Sea Hou, Manhua; Xiong, Jinbo; Wang, Kai Marine Pollution Bulletin, Vol. 86, Issue 1-2 https://doi.org/10.1016/j.marpolbul.2014.07.031	journal	September 2014
Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea Musat, Niculina; Werner, Ursula; Knittel, Katrin Systematic and Applied Microbiology, Vol. 29, Issue 4 https://doi.org/10.1016/j.syapm.2005.12.006	journal	June 2006
Hypoxia: from molecular responses to ecosystem responses Wu, Rudolf S. S. Marine Pollution Bulletin, Vol. 45, Issue 1-12 https://doi.org/10.1016/s0025-326x(02)00061-9	journal	September 2002
Aliphatic and aromatic hydrocarbons in coastal caspian Sea sediments Tolosa, Imma; de Mora, Stephen; Sheikholeslami, Mohammad Reza Marine Pollution Bulletin, Vol. 48, Issue 1-2 https://doi.org/10.1016/s0025-326x(03)00255-8	journal	January 2004
Geophysical evidence for gas hydrates in the deep water of the South Caspian Basin, Azerbaijan Diaconescu, C. C.; Kieckhefer, R. M.; Knapp, J. H. Marine and Petroleum Geology, Vol. 18, Issue 2 https://doi.org/10.1016/s0264-8172(00)00061-1	journal	February 2001
Rapid Degradation of Deepwater Horizon Spilled Oil by Indigenous Microbial Communities in Louisiana Saltmarsh Sediments Mahmoudi, Nagissa; Porter, Teresita M.; Zimmerman, Andrew R. Environmental Science & Technology, Vol. 47, Issue 23 https://doi.org/10.1021/es4036072	journal	November 2013
Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys Werner, Jeffrey J.; Zhou, Dennis; Caporaso, J. Gregory The ISME Journal, Vol. 6, Issue 7 https://doi.org/10.1038/ismej.2011.186	journal	December 2011
Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments Kubo, Kyoko; Lloyd, Karen G.; F. Biddle, Jennifer The ISME Journal, Vol. 6, Issue 10 https://doi.org/10.1038/ismej.2012.37	journal	May 2012
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill Mason, Olivia U.; Hazen, Terry C.; Borglin, Sharon The ISME Journal, Vol. 6, Issue 9 https://doi.org/10.1038/ismej.2012.59	journal	June 2012
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A. The ISME Journal, Vol. 6, Issue 8 https://doi.org/10.1038/ismej.2012.8	journal	March 2012
Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses Meng, Jun; Xu, Jun; Qin, Dan The ISME Journal, Vol. 8, Issue 3 https://doi.org/10.1038/ismej.2013.174	journal	October 2013
Archaea predominate among ammonia-oxidizing prokaryotes in soils Leininger, S.; Urich, T.; Schloter, M. Nature, Vol. 442, Issue 7104 https://doi.org/10.1038/nature04983	journal	August 2006
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing Bokulich, Nicholas A.; Subramanian, Sathish; Faith, Jeremiah J. Nature Methods, Vol. 10, Issue 1 https://doi.org/10.1038/nmeth.2276	journal	December 2012
UPARSE: highly accurate OTU sequences from microbial amplicon reads Edgar, Robert C. Nature Methods, Vol. 10, Issue 10 https://doi.org/10.1038/nmeth.2604	journal	August 2013
Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function Fuerst, John A.; Sagulenko, Evgeny Nature Reviews Microbiology, Vol. 9, Issue 6 https://doi.org/10.1038/nrmicro2578	journal	May 2011
Deep-sea striving Walker, Alan Nature Reviews Microbiology, Vol. 11, Issue 6 https://doi.org/10.1038/nrmicro3037	journal	May 2013
Global patterns in bacterial diversity Lozupone, C. A.; Knight, R. Proceedings of the National Academy of Sciences, Vol. 104, Issue 27 https://doi.org/10.1073/pnas.0611525104	journal	June 2007
Comparison of Oil Degrading Microbial Communities in Sediments from the Persian Gulf and Caspian Sea Hassanshahian, Mehdi; Emtiazi, Giti; Kermanshahi, Rouha Kasra Soil and Sediment Contamination: An International Journal, Vol. 19, Issue 3 https://doi.org/10.1080/15320381003695215	journal	April 2010
PyNAST: a flexible tool for aligning sequences to a template alignment Caporaso, J. G.; Bittinger, K.; Bushman, F. D. Bioinformatics, Vol. 26, Issue 2 https://doi.org/10.1093/bioinformatics/btp636	journal	November 2009
Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks Huson, Daniel H.; Scornavacca, Celine Systematic Biology, Vol. 61, Issue 6 https://doi.org/10.1093/sysbio/sys062	journal	September 2012
High abundance of JS-1- and Chloroflexi -related Bacteria in deeply buried marine sediments revealed by quantitative, real-time PCR Blazejak, Anna; Schippers, Axel FEMS Microbiology Ecology, Vol. 72, Issue 2 https://doi.org/10.1111/j.1574-6941.2010.00838.x	journal	May 2010
Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria Hazen, Terry C.; Dubinsky, Eric A.; DeSantis, Todd Z. Science, Vol. 330, Issue 6001 https://doi.org/10.1126/science.1195979	journal	August 2010
Physiology and Diversity of Ammonia-Oxidizing Archaea Stahl, David A.; de la Torre, José R. Annual Review of Microbiology, Vol. 66, Issue 1 https://doi.org/10.1146/annurev-micro-092611-150128	journal	October 2012
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome McDonald, Daniel; Clemente, Jose C.; Kuczynski, Justin GigaScience, Vol. 1, Issue 1 https://doi.org/10.1186/2047-217x-1-7	journal	July 2012
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data McMurdie, Paul J.; Holmes, Susan PLoS ONE, Vol. 8, Issue 4 https://doi.org/10.1371/journal.pone.0061217	journal	April 2013
Large-Scale Distribution and Activity of Prokaryotes in Deep-Sea Surface Sediments of the Mediterranean Sea and the Adjacent Atlantic Ocean Giovannelli, Donato; Molari, Massimiliano; d’Errico, Giuseppe PLoS ONE, Vol. 8, Issue 8 https://doi.org/10.1371/journal.pone.0072996	journal	August 2013
Human and Environmental Impacts on River Sediment Microbial Communities Gibbons, Sean M.; Jones, Edwin; Bearquiver, Angelita PLoS ONE, Vol. 9, Issue 5 https://doi.org/10.1371/journal.pone.0097435	journal	May 2014
Quantification of microbial communities in subsurface marine sediments of the Black Sea and off Namibia Schippers, Axel; Kock, Dagmar; Hoeft, Carmen Lausanne : Frontiers Research Foundation https://doi.org/10.15488/459	text	January 2012
Overview of Hypoxia around the World Diaz, Robert J. Journal of Environment Quality, Vol. 30, Issue 2 https://doi.org/10.2134/jeq2001.302275x	journal	January 2001
Phycisphaera mikurensis gen. nov., sp. nov., isolated from a marine alga, and proposal of Phycisphaeraceae fam. nov., Phycisphaerales ord. nov. and Phycisphaerae classis nov. in the phylum Planctomycetes Fukunaga, Yukiyo; Kurahashi, Midori; Sakiyama, Yayoi The Journal of General and Applied Microbiology, Vol. 55, Issue 4 https://doi.org/10.2323/jgam.55.267	journal	January 2009
Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones Peng, Xuefeng; Jayakumar, Amal; Ward, Bess B. Frontiers in Microbiology, Vol. 4 https://doi.org/10.3389/fmicb.2013.00177	journal	January 2013
Microbial Communities of Deep-Sea Methane Seeps at Hikurangi Continental Margin (New Zealand) Ruff, S. Emil; Ramette, Alban Nicolas; Arnds, Julia Public Library of Science https://doi.org/10.7892/boris.91374	text	January 2013
The Influence of Water Column Hypoxia on the Behaviour of Manganese and Iron in Sandy Coastal Marine Sediment Kristiansen, K. D.; Kristensen, E.; Jensen, E. M. H. Estuarine, Coastal and Shelf Science, Vol. 55, Issue 4 https://doi.org/10.1006/ecss.2001.0934	journal	October 2002
Recent studies on bacterial populations and processes in subseafloor sediments: A review Parkes, R. John; Cragg, Barry A.; Wellsbury, Peter Hydrogeology Journal, Vol. 8, Issue 1 https://doi.org/10.1007/PL00010971	journal	March 2000
Pathways of organic carbon oxidation in three continental margin sediments Canfield, D. E.; Jørgensen, B. B.; Fossing, H. Marine Geology, Vol. 113, Issue 1-2 https://doi.org/10.1016/0025-3227(93)90147-N	journal	July 1993
Eutrophication of Marine Waters: Effects on Benthic Microbial Communities Meyer-Reil, Lutz-Arend; Köster, Marion Marine Pollution Bulletin, Vol. 41, Issue 1-6 https://doi.org/10.1016/S0025-326X(00)00114-4	journal	January 2000
Hypoxia: from molecular responses to ecosystem responses Wu, Rudolf S. S. Marine Pollution Bulletin, Vol. 45, Issue 1-12 https://doi.org/10.1016/S0025-326X(02)00061-9	journal	September 2002
Aliphatic and aromatic hydrocarbons in coastal caspian Sea sediments Tolosa, Imma; de Mora, Stephen; Sheikholeslami, Mohammad Reza Marine Pollution Bulletin, Vol. 48, Issue 1-2 https://doi.org/10.1016/S0025-326X(03)00255-8	journal	January 2004
An assessment of metal contamination in coastal sediments of the Caspian Sea de Mora, Stephen; Sheikholeslami, Mohammad Reza; Wyse, Eric Marine Pollution Bulletin, Vol. 48, Issue 1-2 https://doi.org/10.1016/S0025-326X(03)00285-6	journal	January 2004
Identification of a novel alkenone in Black Sea sediments Xu, L.; Reddy, C. M.; Farrington, J. W. Organic Geochemistry, Vol. 32, Issue 5 https://doi.org/10.1016/S0146-6380(01)00019-5	journal	May 2001
Geophysical evidence for gas hydrates in the deep water of the South Caspian Basin, Azerbaijan Diaconescu, C. C.; Kieckhefer, R. M.; Knapp, J. H. Marine and Petroleum Geology, Vol. 18, Issue 2 https://doi.org/10.1016/S0264-8172(00)00061-1	journal	February 2001
The oil and gas resource base of the Caspian region Effimoff, Igor Journal of Petroleum Science and Engineering, Vol. 28, Issue 4 https://doi.org/10.1016/S0920-4105(00)00075-9	journal	December 2000
Analysis of deep-water exchange in the Caspian Sea based on environmental tracers Peeters, F.; Kipfer, R.; Achermann, D. Deep Sea Research Part I: Oceanographic Research Papers, Vol. 47, Issue 4 https://doi.org/10.1016/S0967-0637(99)00066-7	journal	April 2000
Hypoxia by degrees: Establishing definitions for a changing ocean Hofmann, A. F.; Peltzer, E. T.; Walz, P. M. Deep Sea Research Part I: Oceanographic Research Papers, Vol. 58, Issue 12 https://doi.org/10.1016/j.dsr.2011.09.004	journal	December 2011
A descriptive account of benthic macrofauna and sediment from an area of planned petroleum exploration in the southern Caspian Sea Parr, T. D.; Tait, R. D.; Maxon, C. L. Estuarine, Coastal and Shelf Science, Vol. 71, Issue 1-2 https://doi.org/10.1016/j.ecss.2006.07.018	journal	January 2007
Determination of phospholipid fatty acid structures and stable carbon isotope compositions of deep-sea sediments of the Northwest Pacific, ODP site 1179 Mills, Christopher T.; Dias, Robert F.; Graham, Dennis Marine Chemistry, Vol. 98, Issue 2-4 https://doi.org/10.1016/j.marchem.2005.10.001	journal	February 2006
River inflow and salinity changes in the Caspian Sea during the last 5500 years Leroy, S. A. G.; Marret, F.; Gibert, E. Quaternary Science Reviews, Vol. 26, Issue 25-28 https://doi.org/10.1016/j.quascirev.2007.09.012	journal	December 2007
Mineralization of organic matter in the sea bed—the role of sulphate reduction Jørgensen, Bo Barker Nature, Vol. 296, Issue 5858 https://doi.org/10.1038/296643a0	journal	April 1982
Predominant archaea in marine sediments degrade detrital proteins Lloyd, Karen G.; Schreiber, Lars; Petersen, Dorthe G. Nature, Vol. 496, Issue 7444 https://doi.org/10.1038/nature12033	journal	March 2013
Insights into the phylogeny and coding potential of microbial dark matter Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander Nature, Vol. 499, Issue 7459 https://doi.org/10.1038/nature12352	journal	July 2013
QIIME allows analysis of high-throughput community sequencing data Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse Nature Methods, Vol. 7, Issue 5 https://doi.org/10.1038/nmeth.f.303	journal	April 2010
Feast and famine — microbial life in the deep-sea bed Jørgensen, Bo Barker; Boetius, Antje Nature Reviews Microbiology, Vol. 5, Issue 10 https://doi.org/10.1038/nrmicro1745	journal	October 2007
Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean Francis, C. A.; Roberts, K. J.; Beman, J. M. Proceedings of the National Academy of Sciences, Vol. 102, Issue 41, p. 14683-14688 https://doi.org/10.1073/pnas.0506625102	journal	September 2005
Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin Inagaki, F.; Nunoura, T.; Nakagawa, S. Proceedings of the National Academy of Sciences, Vol. 103, Issue 8 https://doi.org/10.1073/pnas.0511033103	journal	February 2006
Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru Biddle, J. F.; Lipp, J. S.; Lever, M. A. Proceedings of the National Academy of Sciences, Vol. 103, Issue 10 https://doi.org/10.1073/pnas.0600035103	journal	February 2006
Archaeal nitrification in the ocean Wuchter, C.; Abbas, B.; Coolen, M. J. L. Proceedings of the National Academy of Sciences, Vol. 103, Issue 33 https://doi.org/10.1073/pnas.0600756103	journal	August 2006
Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea McCarren, J.; Becker, J. W.; Repeta, D. J. Proceedings of the National Academy of Sciences, Vol. 107, Issue 38 https://doi.org/10.1073/pnas.1010732107	journal	August 2010
Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge Jorgensen, S. L.; Hannisdal, B.; Lanzen, A. Proceedings of the National Academy of Sciences, Vol. 109, Issue 42 https://doi.org/10.1073/pnas.1207574109	journal	October 2012
Bacterial abundance and composition in marine sediments beneath the Ross Ice Shelf, Antarctica Carr, S. A.; Vogel, S. W.; Dunbar, R. B. Geobiology, Vol. 11, Issue 4 https://doi.org/10.1111/gbi.12042	journal	May 2013
Non-parametric multivariate analyses of changes in community structure Clarke, K. R. Austral Ecology, Vol. 18, Issue 1 https://doi.org/10.1111/j.1442-9993.1993.tb00438.x	journal	March 1993
Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation Leloup, Julie; Fossing, Henrik; Kohls, Katharina Environmental Microbiology, Vol. 11, Issue 5 https://doi.org/10.1111/j.1462-2920.2008.01855.x	journal	May 2009
Distribution of candidate division JS1 and other Bacteria in tidal sediments of the German Wadden Sea using targeted 16S rRNA gene PCR-DGGE: Candidate division JS1 and other Bacteria in tidal sediments Webster, Gordon; Yarram, Laura; Freese, Elke FEMS Microbiology Ecology, Vol. 62, Issue 1 https://doi.org/10.1111/j.1574-6941.2007.00372.x	journal	October 2007
Prokaryotic biodiversity and activity in the deep subseafloor biosphere: Diversity and activity in the deep subseafloor biosphere Fry, John C.; Parkes, R. John; Cragg, Barry A. FEMS Microbiology Ecology, Vol. 66, Issue 2 https://doi.org/10.1111/j.1574-6941.2008.00566.x	journal	November 2008
Bacterial diversity of water and sediment in the Changjiang estuary and coastal area of the East China Sea Feng, Bi-Wei; Li, Xiao-Ran; Wang, Jin-Hui FEMS Microbiology Ecology, Vol. 70, Issue 2 https://doi.org/10.1111/j.1574-6941.2009.00772.x	journal	November 2009
Enrichment and cultivation of prokaryotes associated with the sulphate-methane transition zone of diffusion-controlled sediments of Aarhus Bay, Denmark, under heterotrophic conditions: Enrichment of prokaryotes associated with the SMTZ Webster, Gordon; Sass, Henrik; Cragg, Barry A. FEMS Microbiology Ecology, Vol. 77, Issue 2 https://doi.org/10.1111/j.1574-6941.2011.01109.x	journal	May 2011
Distributions of Microbial Activities in Deep Subseafloor Sediments D'Hondt, S. Science, Vol. 306, Issue 5705 https://doi.org/10.1126/science.1101155	journal	December 2004
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy Wang, Q.; Garrity, G. M.; Tiedje, J. M. Applied and Environmental Microbiology, Vol. 73, Issue 16 https://doi.org/10.1128/AEM.00062-07	journal	June 2007
Variations in Archaeal and Bacterial Diversity Associated with the Sulfate-Methane Transition Zone in Continental Margin Sediments (Santa Barbara Basin, California) Harrison, B. K.; Zhang, H.; Berelson, W. Applied and Environmental Microbiology, Vol. 75, Issue 6 https://doi.org/10.1128/AEM.01812-08	journal	January 2009
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB DeSantis, T. Z.; Hugenholtz, P.; Larsen, N. Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072 https://doi.org/10.1128/AEM.03006-05	journal	July 2006
Comparative Analysis of Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in Anoxic Marine Sediments Orphan, V. J.; Hinrichs, K. -U.; Ussler, W. Applied and Environmental Microbiology, Vol. 67, Issue 4 https://doi.org/10.1128/AEM.67.4.1922-1934.2001	journal	April 2001
Microbial Communities from Methane Hydrate-Bearing Deep Marine Sediments in a Forearc Basin Reed, David W.; Fujita, Yoshiko; Delwiche, Mark E. Applied and Environmental Microbiology, Vol. 68, Issue 8 https://doi.org/10.1128/AEM.68.8.3759-3770.2002	journal	August 2002
Microbial Communities Associated with Geological Horizons in Coastal Subseafloor Sediments from the Sea of Okhotsk Inagaki, Fumio; Suzuki, Masae; Takai, Ken Applied and Environmental Microbiology, Vol. 69, Issue 12 https://doi.org/10.1128/AEM.69.12.7224-7235.2003	journal	December 2003
Widespread Occurrence of a Novel Division of Bacteria Identified by 16S rRNA Gene Sequences Originally Found in Deep Marine Sediments Webster, Gordon; Parkes, R. John; Fry, John C. Applied and Environmental Microbiology, Vol. 70, Issue 9 https://doi.org/10.1128/AEM.70.9.5708-5713.2004	journal	September 2004
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities Lozupone, C.; Knight, R. Applied and Environmental Microbiology, Vol. 71, Issue 12 https://doi.org/10.1128/AEM.71.12.8228-8235.2005	journal	December 2005
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome McDonald, Daniel; Clemente, Jose C.; Kuczynski, Justin GigaScience, Vol. 1, Issue 1 https://doi.org/10.1186/2047-217X-1-7	journal	July 2012
Microbial Communities of Deep-Sea Methane Seeps at Hikurangi Continental Margin (New Zealand) Ruff, S. Emil; Arnds, Julia; Knittel, Katrin PLoS ONE, Vol. 8, Issue 9 https://doi.org/10.1371/journal.pone.0072627	journal	September 2013
The Caspian Lake: History, biota, structure, and function Dumont, H. J. Limnology and Oceanography, Vol. 43, Issue 1 https://doi.org/10.4319/lo.1998.43.1.0044	journal	January 1998

Cited By (20)

Stimulation of carbon nanomaterials on syntrophic oxidation of butyrate in sediment enrichments and a defined coculture Zhang, Wei; Zhang, Jianchao; Lu, Yahai Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-30745-7	journal	August 2018
Faecal pollution affects abundance and diversity of aquatic microbial community in anthropo-zoogenically influenced lotic ecosystems Paruch, Lisa; Paruch, Adam M.; Eiken, Hans Geir Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-56058-x	journal	December 2019
Comparison of Thaumarchaeotal populations from four deep sea basins Techtman, Stephen M.; Mahmoudi, Nagissa; Whitt, Kendall T. FEMS Microbiology Ecology, Vol. 93, Issue 11 https://doi.org/10.1093/femsec/fix128	journal	October 2017
Aquatic microbial diversity associated with faecal pollution of Norwegian waterbodies characterized by 16S rRNA gene amplicon deep sequencing Paruch, Lisa; Paruch, Adam M.; Eiken, Hans Geir Microbial Biotechnology, Vol. 12, Issue 6 https://doi.org/10.1111/1751-7915.13461	journal	July 2019
Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay Mori, Fumiaki; Umezawa, Yu; Kondo, Ryuji Microbes and Environments, Vol. 33, Issue 4 https://doi.org/10.1264/jsme2.me18092	journal	January 2018
Sulfur-Oxidizing Bacteria Mediate Microbial Community Succession and Element Cycling in Launched Marine Sediment Ihara, Hideyuki; Hori, Tomoyuki; Aoyagi, Tomo Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00152	journal	February 2017
Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea Zhang, Yu; Wang, Xungong; Zhen, Yu Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02133	journal	November 2017
Temperature Driven Changes in Benthic Bacterial Diversity Influences Biogeochemical Cycling in Coastal Sediments Hicks, Natalie; Liu, Xuan; Gregory, Richard Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01730	journal	August 2018
Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment Black, Ellen M.; Chimenti, Michael S.; Just, Craig L. PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3536	journal	July 2017
Bacterial diversity in deep-sea sediments under influence of asphalt seep at the São Paulo Plateau Queiroz, Luciano Lopes; Bendia, Amanda Gonçalves; Duarte, Rubens Tadeu Delgado Antonie van Leeuwenhoek, Vol. 113, Issue 5 https://doi.org/10.1007/s10482-020-01384-8	journal	January 2020
Microbial diversity of sediments from an inactive hydrothermal vent field, Southwest Indian Ridge Yang, Zhifeng; Xiao, Xiang; Zhang, Yu Marine Life Science & Technology, Vol. 2, Issue 1 https://doi.org/10.1007/s42995-019-00007-0	journal	October 2019
Archaeal communities in sponge, sediment and water from marine lakes and open water habitats Polónia, Ana Rita Moura; Cleary, Daniel Francis Richard Marine Biology Research, Vol. 15, Issue 3 https://doi.org/10.1080/17451000.2019.1633469	journal	March 2019
Bacterial diversity in deep-sea sediments under influence of asphalt seep at the São Paulo Plateau Queiroz, Luciano Lopes; Gonçalves Bendia, Amanda; Duarte, Rubens Tadeu Delgado Antonie van Leeuwenhoek https://doi.org/10.1101/753616	posted_content	December 2019
Sequential bioavailability of sedimentary organic matter to heterotrophic bacteria: Sequential bioavailability of sedimentary organic matter Mahmoudi, Nagissa; Beaupré, Steven R.; Steen, Andrew D. Environmental Microbiology, Vol. 19, Issue 7 https://doi.org/10.1111/1462-2920.13745	journal	May 2017
Genome biology of a novel lineage of planctomycetes widespread in anoxic aquatic environments Spring, Stefan; Bunk, Boyke; Spröer, Cathrin Environmental Microbiology, Vol. 20, Issue 7 https://doi.org/10.1111/1462-2920.14253	journal	July 2018
Nitrate addition stimulates microbial decomposition of organic matter in salt marsh sediments Bulseco, Ashley N.; Giblin, Anne E.; Tucker, Jane Global Change Biology, Vol. 25, Issue 10 https://doi.org/10.1111/gcb.14726	journal	July 2019
Microcosm evaluation of the impact of oil contamination and chemical dispersant addition on bacterial communities and sediment remediation of an estuarine port environment Louvado, A.; Coelho, F. J. R. C.; Oliveira, V. Journal of Applied Microbiology, Vol. 127, Issue 1 https://doi.org/10.1111/jam.14261	journal	March 2019
Hydrocarbon Degradation in Caspian Sea Sediment Cores Subjected to Simulated Petroleum Seepage in a Newly Designed Sediment-Oil-Flow-Through System Mishra, Sonakshi; Wefers, Peggy; Schmidt, Mark Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00763	journal	April 2017
Microbial Community Response to Simulated Petroleum Seepage in Caspian Sea Sediments Stagars, Marion H.; Mishra, Sonakshi; Treude, Tina Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00764	journal	April 2017
Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities Miller, John I.; Techtmann, Stephen; Fortney, Julian Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00995	journal	May 2019

Similar Records

Microbial ecology and biogeochemistry of hypersaline sediments in Orca Basin

Journal Article · Tue Apr 21 00:00:00 EDT 2020 · PLoS ONE · OSTI ID:1629786

Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia

Journal Article · Tue May 05 00:00:00 EDT 2015 · Geobiology · OSTI ID:1265359

Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia

Journal Article · Tue May 05 00:00:00 EDT 2015 · Geobiology · OSTI ID:1401624

Related Subjects

54 ENVIRONMENTAL SCIENCES
59 BASIC BIOLOGICAL SCIENCES
Caspian Sea
Illumina
Microbiology
PLFA
archaea
bacteria
marine sediments

Microbial community composition and diversity in Caspian Sea sediments

Citation Formats

References (85)

Cited By (20)

Similar Records

Related Subjects