Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes

Wong, Hon Lun; Visscher, Pieter T.; White, III, Richard Allen; Smith, Daniela -Lee; Patterson, Molly M.; Burns, Brendan P.

doi:10.1038/srep46160

Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes

Journal Article · Tue Apr 11 00:00:00 EDT 2017 · Scientific Reports

DOI:https://doi.org/10.1038/srep46160· OSTI ID:1358501

Wong, Hon Lun ^[1]; Visscher, Pieter T. ^[2]; White, III, Richard Allen ^[3]; Smith, Daniela -Lee ^[1]; Patterson, Molly M. ^[4]; Burns, Brendan P. ^[1]

The Univ. of New South Wales, Sydney (Australia)
Univ. of Connecticut, Storrs, CT (United States); Univ. of New South Wales, Sydney (Australia)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Univ. of Connecticut, Storrs, CT (United States)

Modern microbial mats provide remarkable insights into assembly, function and origin of complex microbial ecosystems. An excellent model of such systems is located in Shark Bay, Australia. Although bacteria have been extensively investigated in these communities, the role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of specific niches associated with this domain. In the present study, high throughput amplicon sequencing was undertaken in conjunction with key biogeochemical properties of two mat types (smooth and pustular). A total of 13,547,552 unfiltered sequences were obtained, and classified sequences were affiliated to three archaeal and candidate phyla, Parvarchaeota, Euryarchaeota and Crenarchaeota. One way analysis of similarity tests (ANOSIM) indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1 %). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota, followed by Thermoplasmata, Class marine benthic group B and Halobacteria. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Conversely, pustular mats were enriched with Halobacteria and Parvarchaeota. The rates of oxygen production/consumption as well as sulphate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic part of mats and was up to seven-fold higher in smooth than in pustular mats. Metabolic cooperation in putative surface anoxic niches is proposed to be key in efficient cycling of key nutrients in these systems.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1358501

Report Number(s):: PNNL-SA--120053

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Vol. 7; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (90)

Formation and breakdown of glycine betaine and trimethylamine in hypersaline environments Oren, Aharon Antonie van Leeuwenhoek, Vol. 58, Issue 4 https://doi.org/10.1007/bf00399342	journal	November 1990
Identification and regulation of novel compatible solutes from hypersaline stromatolite-associated cyanobacteria Goh, Falicia; Barrow, Kevin D.; Burns, Brendan P. Archives of Microbiology, Vol. 192, Issue 12 https://doi.org/10.1007/s00203-010-0634-0	journal	October 2010
Taxonomic and Functional Metagenomic Profiling of the Microbial Community in the Anoxic Sediment of a Sub-saline Shallow Lake (Laguna de Carrizo, Central Spain) Ferrer, Manuel; Guazzaroni, María-Eugenia; Richter, Michael Microbial Ecology, Vol. 62, Issue 4 https://doi.org/10.1007/s00248-011-9903-y	journal	July 2011
Evidence of Novel Phylogenetic Lineages of Methanogenic Archaea from Hypersaline Microbial Mats García-Maldonado, José Q.; Bebout, Brad M.; Everroad, R. Craig Microbial Ecology, Vol. 69, Issue 1 https://doi.org/10.1007/s00248-014-0473-7	journal	August 2014
Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter” Hedlund, Brian P.; Dodsworth, Jeremy A.; Murugapiran, Senthil K. Extremophiles, Vol. 18, Issue 5 https://doi.org/10.1007/s00792-014-0664-7	journal	August 2014
An integrated study reveals diverse methanogens, Thaumarchaeota, and yet-uncultivated archaeal lineages in Armenian hot springs Hedlund, Brian P.; Dodsworth, Jeremy A.; Cole, Jessica K. Antonie van Leeuwenhoek, Vol. 104, Issue 1 https://doi.org/10.1007/s10482-013-9927-z	journal	April 2013
High enrichment of molybdenum in hypersaline microbial mats of Guerrero Negro, Baja California Sur, Mexico Valdivieso-Ojeda, Jacob Alberto; Huerta-Diaz, Miguel Angel; Delgadillo-Hinojosa, Francisco Chemical Geology, Vol. 363 https://doi.org/10.1016/j.chemgeo.2013.11.021	journal	January 2014
Characteristics, distribution and morphogenesis of subtidal microbial systems in Shark Bay, Australia Jahnert, Ricardo J.; Collins, Lindsay B. Marine Geology, Vol. 303-306 https://doi.org/10.1016/j.margeo.2012.02.009	journal	March 2012
A Detailed Phylogeny for the Methanomicrobiales Rouvière, P.; Mandelco, L.; Winker, S. Systematic and Applied Microbiology, Vol. 15, Issue 3 https://doi.org/10.1016/s0723-2020(11)80209-2	journal	August 1992
Determining the specific microbial populations and their spatial distribution within the stromatolite ecosystem of Shark Bay Goh, Falicia; Allen, Michelle A.; Leuko, Stefan The ISME Journal, Vol. 3, Issue 4 https://doi.org/10.1038/ismej.2008.114	journal	December 2008
Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics Burow, Luke C.; Woebken, Dagmar; Marshall, Ian PG The ISME Journal, Vol. 7, Issue 4 https://doi.org/10.1038/ismej.2012.150	journal	November 2012
Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat Kirk Harris, J.; Gregory Caporaso, J.; Walker, Jeffrey J. The ISME Journal, Vol. 7, Issue 1 https://doi.org/10.1038/ismej.2012.79	journal	July 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
Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage Méndez-García, Celia; Mesa, Victoria; Sprenger, Richard R. The ISME Journal, Vol. 8, Issue 6 https://doi.org/10.1038/ismej.2013.242	journal	January 2014
Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics Ruvindy, Rendy; White III, Richard Allen; Neilan, Brett Anthony The ISME Journal, Vol. 10, Issue 1 https://doi.org/10.1038/ismej.2015.87	journal	May 2015
Millimeter‐scale genetic gradients and community‐level molecular convergence in a hypersaline microbial mat Kunin, Victor; Raes, Jeroen; Harris, J. Kirk Molecular Systems Biology, Vol. 4, Issue 1 https://doi.org/10.1038/msb.2008.35	journal	January 2008
Complete nitrification by Nitrospira bacteria Daims, Holger; Lebedeva, Elena V.; Pjevac, Petra Nature, Vol. 528, Issue 7583 https://doi.org/10.1038/nature16461	journal	November 2015
Diversity of halophilic microorganisms: Environments, phylogeny, physiology, and applications Oren, A. Journal of Industrial Microbiology & Biotechnology, Vol. 28, Issue 1 https://doi.org/10.1038/sj.jim.7000176	journal	January 2002
Inner workings of thrombolites: spatial gradients of metabolic activity as revealed by metatranscriptome profiling Mobberley, J. M.; Khodadad, C. L. M.; Visscher, P. T. Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep12601	journal	July 2015
Dimethyl sulphide and methanethiol formation in microbial mats: potential pathways for biogenic signatures Visscher, Pieter T.; Baumgartner, Laura K.; Buckley, Daniel H. Environmental Microbiology, Vol. 5, Issue 4 https://doi.org/10.1046/j.1462-2920.2003.00418.x	journal	April 2003
UCHIME improves sensitivity and speed of chimera detection Edgar, Robert C.; Haas, Brian J.; Clemente, Jose C. Bioinformatics, Vol. 27, Issue 16 https://doi.org/10.1093/bioinformatics/btr381	journal	June 2011
Halococcus hamelinensis sp. nov., a novel halophilic archaeon isolated from stromatolites in Shark Bay, Australia Goh, F. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 6 https://doi.org/10.1099/ijs.0.64180-0	journal	June 2006
Haloferax elongans sp. nov. and Haloferax mucosum sp. nov., isolated from microbial mats from Hamelin Pool, Shark Bay, Australia Allen, M. A.; Goh, F.; Leuko, S. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 4 https://doi.org/10.1099/ijs.0.65360-0	journal	April 2008
Stromatolitic knobs in Storr's Lake (San Salvador, Bahamas): a model system for formation and alteration of laminae Dupraz, C.; Fowler, A.; Tobias, C. Geobiology, Vol. 11, Issue 6 https://doi.org/10.1111/gbi.12063	journal	October 2013
Identification of Desulfobacterales as primary hydrogenotrophs in a complex microbial mat community Burow, L. C.; Woebken, D.; Marshall, I. P. G. Geobiology, Vol. 12, Issue 3 https://doi.org/10.1111/gbi.12080	journal	April 2014
Microbial diversity of extant stromatolites in the hypersaline marine environment of Shark Bay, Australia Burns, Brendan P.; Goh, Falicia; Allen, Michelle Environmental Microbiology, Vol. 6, Issue 10 https://doi.org/10.1111/j.1462-2920.2004.00651.x	journal	October 2004
Vertical distribution of methane metabolism in microbial mats of the Great Sippewissett Salt Marsh Buckley, Daniel H.; Baumgartner, Laura K.; Visscher, Pieter T. Environmental Microbiology, Vol. 10, Issue 4 https://doi.org/10.1111/j.1462-2920.2007.01517.x	journal	April 2008
Microbial diversity in modern marine stromatolites, Highborne Cay, Bahamas Baumgartner, Laura K.; Spear, John R.; Buckley, Daniel H. Environmental Microbiology, Vol. 11, Issue 10 https://doi.org/10.1111/j.1462-2920.2009.01998.x	journal	October 2009
Bacterial, archaeal and eukaryotic diversity of smooth and pustular microbial mat communities in the hypersaline lagoon of Shark Bay Allen, M. A.; Goh, F.; Burns, B. P. Geobiology, Vol. 7, Issue 1 https://doi.org/10.1111/j.1472-4669.2008.00187.x	journal	January 2009
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform Kozich, James J.; Westcott, Sarah L.; Baxter, Nielson T. Applied and Environmental Microbiology, Vol. 79, Issue 17 https://doi.org/10.1128/aem.01043-13	journal	June 2013
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities Schloss, P. D.; Westcott, S. L.; Ryabin, T. Applied and Environmental Microbiology, Vol. 75, Issue 23, p. 7537-7541 https://doi.org/10.1128/aem.01541-09	journal	October 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
Methanogenesis and Sulfate Reduction: Competitive and Noncompetitive Substrates in Estuarine Sediments Oremland, Ronald S.; Polcin, Sandra Applied and Environmental Microbiology, Vol. 44, Issue 6 https://doi.org/10.1128/aem.44.6.1270-1276.1982	journal	January 1982
Metabolism of Acetate, Methanol, and Methylated Amines in Intertidal Sediments of Lowes Cove, Maine † King, Gary M.; Klug, M. J.; Lovley, D. R. Applied and Environmental Microbiology, Vol. 45, Issue 6 https://doi.org/10.1128/aem.45.6.1848-1853.1983	journal	January 1983
Metabolism of Trimethylamine, Choline, and Glycine Betaine by Sulfate-Reducing and Methanogenic Bacteria in Marine Sediments † King, Gary M. Applied and Environmental Microbiology, Vol. 48, Issue 4 https://doi.org/10.1128/aem.48.4.719-725.1984	journal	January 1984
Metabolism of Reduced Methylated Sulfur Compounds in Anaerobic Sediments and by a Pure Culture of an Estuarine Methanogen † Kiene, Ronald P.; Oremland, Ronald S.; Catena, Anthony Applied and Environmental Microbiology, Vol. 52, Issue 5 https://doi.org/10.1128/aem.52.5.1037-1045.1986	journal	January 1986
Methanogenesis from Methylated Amines in a Hypersaline Algal Mat † King, Gary M. Applied and Environmental Microbiology, Vol. 54, Issue 1 https://doi.org/10.1128/aem.54.1.130-136.1988	journal	January 1988
Production and Consumption of Dimethylsulfoniopropionate in Marine Microbial Mats Visscher, Pieter T.; van Gemerden, Hans Applied and Environmental Microbiology, Vol. 57, Issue 11 https://doi.org/10.1128/aem.57.11.3237-3242.1991	journal	January 1991
Higher-level classification of the Archaea: evolution of methanogenesis and methanogens Bapteste, Éric; Brochier, Céline; Boucher, Yan Archaea, Vol. 1, Issue 5 https://doi.org/10.1155/2005/859728	journal	January 2005
RNA-Based Assessment of Diversity and Composition of Active Archaeal Communities in the German Bight Wemheuer, Bernd; Wemheuer, Franziska; Daniel, Rolf Archaea, Vol. 2012 https://doi.org/10.1155/2012/695826	journal	January 2012
Phylogenetic Analysis of a Microbialite-Forming Microbial Mat from a Hypersaline Lake of the Kiritimati Atoll, Central Pacific Schneider, Dominik; Arp, Gernot; Reimer, Andreas PLoS ONE, Vol. 8, Issue 6 https://doi.org/10.1371/journal.pone.0066662	journal	June 2013
Metagenomic Analysis Suggests Modern Freshwater Microbialites Harbor a Distinct Core Microbial Community White, Richard Allen; Chan, Amy M.; Gavelis, Gregory S. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.01531	journal	January 2016
Photosynthesis of benthic microflora measured with high spatial resolution by the oxygen microprofile method: Capabilities and limitations of the method1 Revsbech, Niels Peter; Jorgensen, Bo Barker Limnology and Oceanography, Vol. 28, Issue 4 https://doi.org/10.4319/lo.1983.28.4.0749	journal	July 1983
In situ characterization of sediments: Measurements of oxygen and sulfide profiles with a novel combined needle electrode Visscher, Pieter T.; Beukema, Jan; van Gemerden, Hans Limnology and Oceanography, Vol. 36, Issue 7 https://doi.org/10.4319/lo.1991.36.7.1476	journal	November 1991
Formation and breakdown of glycine betaine and trimethylamine in hypersaline environments Oren, Aharon Antonie van Leeuwenhoek, Vol. 58, Issue 4 https://doi.org/10.1007/BF00399342	journal	November 1990
Heterotrophic bacterial diversity in aquatic microbial mat communities from Antarctica Peeters, Karolien; Verleyen, Elie; Hodgson, Dominic A. Polar Biology, Vol. 35, Issue 4 https://doi.org/10.1007/s00300-011-1100-4	journal	September 2011
Shark Bay stromatolites: Microfabrics and reinterpretation of origins Pamela Reid, R.; James, Noel P.; Macintyre, Ian G. Facies, Vol. 49, Issue 1 https://doi.org/10.1007/s10347-003-0036-8	journal	January 2003
Microbial mats: A joint venture van Gemerden, Hans Marine Geology, Vol. 113, Issue 1-2 https://doi.org/10.1016/0025-3227(93)90146-M	journal	July 1993
A Detailed Phylogeny for the Methanomicrobiales Rouvière, P.; Mandelco, L.; Winker, S. Systematic and Applied Microbiology, Vol. 15, Issue 3 https://doi.org/10.1016/S0723-2020(11)80209-2	journal	August 1992
Diel fluctuations in solute distributions and biogeochemical cycling in a hypersaline microbial mat from Shark Bay, WA Pages, Anais; Welsh, David T.; Teasdale, Peter R. Marine Chemistry, Vol. 167 https://doi.org/10.1016/j.marchem.2014.05.003	journal	December 2014
Modern analogues and the early history of microbial life Burns, Brendan P.; Anitori, Roberto; Butterworth, Philip Precambrian Research, Vol. 173, Issue 1-4 https://doi.org/10.1016/j.precamres.2009.05.006	journal	September 2009
Microbial lithification in marine stromatolites and hypersaline mats Dupraz, Christophe; Visscher, Pieter T. Trends in Microbiology, Vol. 13, Issue 9 https://doi.org/10.1016/j.tim.2005.07.008	journal	September 2005
Quorum sensing in natural environments: emerging views from microbial mats Decho, Alan W.; Norman, R. Sean; Visscher, Pieter T. Trends in Microbiology, Vol. 18, Issue 2 https://doi.org/10.1016/j.tim.2009.12.008	journal	February 2010
Salinity history of the Earth's early ocean Knauth, L. Paul Nature, Vol. 395, Issue 6702 https://doi.org/10.1038/26879	journal	October 1998
The role of microbial mats in the production of reduced gases on the early Earth Hoehler, Tori M.; Bebout, Brad M.; Des Marais, David J. Nature, Vol. 412, Issue 6844 https://doi.org/10.1038/35085554	journal	July 2001
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
Diversity of halophilic microorganisms: Environments, phylogeny, physiology, and applications Oren, A. Journal of Industrial Microbiology & Biotechnology, Vol. 28, Issue 1 https://doi.org/10.1038/sj/jim/7000176	journal	January 2002
Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats Wong, Hon Lun; Smith, Daniela-Lee; Visscher, Pieter T. Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep15607	journal	October 2015
A comparison of methods for the quantification of bacterial sulfate reduction in coastal marine sediments: I. Measurement with radiotracer techniques J⊘rgensen, Bo Barker Geomicrobiology Journal, Vol. 1, Issue 1 https://doi.org/10.1080/01490457809377721	journal	January 1978
Calcification in cyanobacterial biofilms of alkaline salt lakes Arp, Gernot; Reimer, Andreas; Reitner, Joachim European Journal of Phycology, Vol. 34, Issue 4 https://doi.org/10.1080/09670269910001736452	journal	October 1999
Osmoadaptive Strategies of the Archaeon Halococcus hamelinensis Isolated from a Hypersaline Stromatolite Environment Goh, Falicia; Jeon, Young Jae; Barrow, Kevin Astrobiology, Vol. 11, Issue 6 https://doi.org/10.1089/ast.2010.0591	journal	July 2011
The unequal variance t-test is an underused alternative to Student's t-test and the Mann–Whitney U test Ruxton, Graeme D. Behavioral Ecology, Vol. 17, Issue 4 https://doi.org/10.1093/beheco/ark016	journal	May 2006
STAMP: statistical analysis of taxonomic and functional profiles Parks, Donovan H.; Tyson, Gene W.; Hugenholtz, Philip Bioinformatics, Vol. 30, Issue 21 https://doi.org/10.1093/bioinformatics/btu494	journal	July 2014
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1219	journal	November 2012
Lipophilic Pigments from Cyanobacterial (Blue-Green Algal) and Diatom mats in Hamelin Pool, Shark bay, Western Australia1 Palmisano, Anna C.; Summons, Roger E.; Cronin, Sonja E. Journal of Phycology, Vol. 25, Issue 4 https://doi.org/10.1111/j.0022-3646.1989.00655.x	journal	December 1989
Microbe-mineral interactions: early carbonate precipitation in a hypersaline lake (Eleuthera Island, Bahamas): Microbe-mineral interactions, Eleuthera Island, Bahamas Dupraz, C.; Visscher, P. T.; Baumgartner, L. K. Sedimentology, Vol. 51, Issue 4 https://doi.org/10.1111/j.1365-3091.2004.00649.x	journal	June 2004
Microbially mediated carbonate precipitation in a hypersaline lake, Big Pond (Eleuthera, Bahamas): Microbially mediated carbonate precipitation Glunk, Christina; Dupraz, Christophe; Braissant, Olivier Sedimentology, Vol. 58, Issue 3 https://doi.org/10.1111/j.1365-3091.2010.01180.x	journal	August 2010
Shifts in methanogen community structure and function associated with long-term manipulation of sulfate and salinity in a hypersaline microbial mat Smith, Jason M.; Green, Stefan J.; Kelley, Cheryl A. Environmental Microbiology, Vol. 10, Issue 2 https://doi.org/10.1111/j.1462-2920.2007.01459.x	journal	February 2008
Methanogenic diversity and activity in hypersaline sediments of the centre of the Napoli mud volcano, Eastern Mediterranean Sea: Methanogenesis in hypersaline sediments of Napoli Lazar, Cassandre Sara; Parkes, R. John; Cragg, Barry A. Environmental Microbiology, Vol. 13, Issue 8 https://doi.org/10.1111/j.1462-2920.2011.02425.x	journal	March 2011
A late methanogen origin for molybdenum-dependent nitrogenase: A late methanogen origin for Mo-nitrogenase Boyd, E. S.; Anbar, A. D.; Miller, S. Geobiology, Vol. 9, Issue 3 https://doi.org/10.1111/j.1472-4669.2011.00278.x	journal	April 2011
Metabolism of dimethylsulfoniopropionate and glycine betaine by a marine bacterium Diaz, Mara R.; Visscher, Pieter T.; Taylor, Barrie F. FEMS Microbiology Letters, Vol. 96, Issue 1 https://doi.org/10.1111/j.1574-6968.1992.tb05394.x	journal	September 1992
Photosynthesis-Induced Biofilm Calcification and Calcium Concentrations in Phanerozoic Oceans Arp, G. Science, Vol. 292, Issue 5522 https://doi.org/10.1126/science.1057204	journal	June 2001
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform Kozich, James J.; Westcott, Sarah L.; Baxter, Nielson T. Applied and Environmental Microbiology, Vol. 79, Issue 17 https://doi.org/10.1128/AEM.01043-13	journal	June 2013
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities Schloss, P. D.; Westcott, S. L.; Ryabin, T. Applied and Environmental Microbiology, Vol. 75, Issue 23, p. 7537-7541 https://doi.org/10.1128/AEM.01541-09	journal	October 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
Glycine Betaine as a Direct Substrate for Methanogens (Methanococcoides spp.) Watkins, Andrew J.; Roussel, Erwan G.; Parkes, R. John Applied and Environmental Microbiology, Vol. 80, Issue 1 https://doi.org/10.1128/AEM.03076-13	journal	October 2013
Methanogenesis and Sulfate Reduction: Competitive and Noncompetitive Substrates in Estuarine Sediments Oremland, Ronald S.; Polcin, Sandra Applied and Environmental Microbiology, Vol. 44, Issue 6 https://doi.org/10.1128/AEM.44.6.1270-1276.1982	journal	January 1982
Metabolism of Acetate, Methanol, and Methylated Amines in Intertidal Sediments of Lowes Cove, Maine † King, Gary M.; Klug, M. J.; Lovley, D. R. Applied and Environmental Microbiology, Vol. 45, Issue 6 https://doi.org/10.1128/AEM.45.6.1848-1853.1983	journal	January 1983
Metabolism of Trimethylamine, Choline, and Glycine Betaine by Sulfate-Reducing and Methanogenic Bacteria in Marine Sediments † King, Gary M. Applied and Environmental Microbiology, Vol. 48, Issue 4 https://doi.org/10.1128/AEM.48.4.719-725.1984	journal	January 1984
Metabolism of Reduced Methylated Sulfur Compounds in Anaerobic Sediments and by a Pure Culture of an Estuarine Methanogen † Kiene, Ronald P.; Oremland, Ronald S.; Catena, Anthony Applied and Environmental Microbiology, Vol. 52, Issue 5 https://doi.org/10.1128/AEM.52.5.1037-1045.1986	journal	January 1986
Methanogenesis from Methylated Amines in a Hypersaline Algal Mat † King, Gary M. Applied and Environmental Microbiology, Vol. 54, Issue 1 https://doi.org/10.1128/AEM.54.1.130-136.1988	journal	January 1988
Production and Consumption of Dimethylsulfoniopropionate in Marine Microbial Mats Visscher, Pieter T.; van Gemerden, Hans Applied and Environmental Microbiology, Vol. 57, Issue 11 https://doi.org/10.1128/AEM.57.11.3237-3242.1991	journal	January 1991
Composition and Structure of Microbial Communities from Stromatolites of Hamelin Pool in Shark Bay, Western Australia Papineau, D.; Walker, J. J.; Mojzsis, S. J. Applied and Environmental Microbiology, Vol. 71, Issue 8 https://doi.org/10.1128/AEM.71.8.4822-4832.2005	journal	August 2005
Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat Ley, R. E.; Harris, J. K.; Wilcox, J. Applied and Environmental Microbiology, Vol. 72, Issue 5 https://doi.org/10.1128/AEM.72.5.3685-3695.2006	journal	May 2006
Microscale observations of sulfate reduction: Correlation of microbial activity with lithified micritic laminae in modern marine stromatolites Visscher, Pieter T.; Pamela Reid, R.; Bebout, Brad M. Geology, Vol. 28, Issue 10 https://doi.org/10.1130/0091-7613(2000)28<919:MOOSRC>2.0.CO;2	journal	January 2000
STROMATOLITES IN PRECAMBRIAN CARBONATES: Evolutionary Mileposts or Environmental Dipsticks? Grotzinger, John P.; Knoll, Andrew H. Annual Review of Earth and Planetary Sciences, Vol. 27, Issue 1 https://doi.org/10.1146/annurev.earth.27.1.313	journal	May 1999
A method of linking multivariate community structure to environmental variables Clarke, Kr; Ainsworth, M. Marine Ecology Progress Series, Vol. 92 https://doi.org/10.3354/meps092205	journal	January 1993
Changing Microspatial Patterns of Sulfate-Reducing Microorganisms (SRM) during Cycling of Marine Stromatolite Mats Petrisor, Alexandru; Szyjka, Sandra; Kawaguchi, Tomohiro International Journal of Molecular Sciences, Vol. 15, Issue 1 https://doi.org/10.3390/ijms15010850	journal	January 2014
Primary production of microalgae in sediments measured by oxygen microprofile, H ₁₄ CO ₃ - fixation, and oxygen exchange methods1 : Primary production of sediments Revsbech, Niels Peter; JØrgensen, Bo Barker; Brix, Ole Limnology and Oceanography, Vol. 26, Issue 4 https://doi.org/10.4319/lo.1981.26.4.0717	journal	July 1981
Increases in the abundance of microbial genes encoding halotolerance and photosynthesis along a sediment salinity gradient Jeffries, T. C.; Seymour, J. R.; Newton, K. Biogeosciences, Vol. 9, Issue 2 https://doi.org/10.5194/bg-9-815-2012	journal	January 2012

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Biodegradability of legacy crude oil contamination in Gulf War damaged groundwater wells in Northern Kuwait Bruckberger, Melanie C.; Morgan, Matthew J.; Walsh, Tom Biodegradation, Vol. 30, Issue 1 https://doi.org/10.1007/s10532-019-09867-w	journal	February 2019
Methylotrophic methanogens everywhere — physiology and ecology of novel players in global methane cycling Söllinger, Andrea; Urich, Tim Biochemical Society Transactions, Vol. 47, Issue 6 https://doi.org/10.1042/bst20180565	journal	December 2019
Anti-biofilm effect of a butenolide/polymer coating and metatranscriptomic analyses Ding, Wei; Ma, Chunfeng; Zhang, Weipeng Biofouling, Vol. 34, Issue 1 https://doi.org/10.1080/08927014.2017.1409891	journal	January 2018
Isolation of novel quorum-sensing active bacteria from microbial mats in Shark Bay Australia Charlesworth, James C.; Watters, Cara; Wong, Hon Lun FEMS Microbiology Ecology, Vol. 95, Issue 4 https://doi.org/10.1093/femsec/fiz035	journal	March 2019
A year in the life of a thrombolite: comparative metatranscriptomics reveals dynamic metabolic changes over diel and seasonal cycles: A year in the life of a thrombolite Louyakis, Artemis S.; Gourlé, Hadrien; Casaburi, Giorgio Environmental Microbiology, Vol. 20, Issue 2 https://doi.org/10.1111/1462-2920.14029	journal	December 2017
A year in the life of a thrombolite: comparative metatranscriptomics reveals dynamic metabolic changes over diel and seasonal cycles Louyakis, Artemis S.; Gourle, Hadrien; Casaburi, Giorgio Environmental Microbiology, Vol. 20, Issue 7, p. 2670-2670 https://doi.org/10.1111/1462-2920.14277	journal	July 2018
Bioinformatic, phylogenetic and chemical analysis of the UV-absorbing compounds scytonemin and mycosporine-like amino acids from the microbial mat communities of Shark Bay, Australia: Sunscreens from Shark Bay microbial mats D'Agostino, Paul M.; Woodhouse, Jason N.; Liew, Heng Tai Environmental Microbiology, Vol. 21, Issue 2 https://doi.org/10.1111/1462-2920.14517	journal	January 2019
Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar, Mexico Johnson, D. B.; Beddows, P. A.; Flynn, T. M. Geobiology, Vol. 16, Issue 3 https://doi.org/10.1111/gbi.12283	journal	April 2018
Archaeal Communities in Deep Terrestrial Subsurface Underneath the Deccan Traps, India Dutta, Avishek; Sar, Pinaki; Sarkar, Jayeeta Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01362	journal	July 2019

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