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Rubin-Blum M, Makovsky Y, Rahav E, Belkin N, Antler G, Sisma-Ventura G, Herut B. Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106497. [PMID: 38631226 DOI: 10.1016/j.marenvres.2024.106497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/05/2024] [Accepted: 04/07/2024] [Indexed: 04/19/2024]
Abstract
Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼106 cell ml-1) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22 °C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 μg C L-1 d-1 ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.
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Affiliation(s)
- Maxim Rubin-Blum
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel; The Department of Marine Biology, Charney School of Marine Sciences, University of Haifa, Haifa, Israel.
| | - Yizhaq Makovsky
- The Dr. Moses Strauss Department of Marine Geosciences, Charney School of Marine Sciences , University of Haifa, Haifa, Israel; The Hatter Department of Marine Technologies, Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Eyal Rahav
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Natalia Belkin
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Gilad Antler
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel; The Interuniversity Institute for Marine Sciences, Eilat, Israel
| | - Guy Sisma-Ventura
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Barak Herut
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel; The Dr. Moses Strauss Department of Marine Geosciences, Charney School of Marine Sciences , University of Haifa, Haifa, Israel
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Watson SJ, Arisdakessian C, Petelo M, Keliipuleole K, Tachera DK, Okuhata BK, Frank KL. Groundwater microbial communities reflect geothermal activity on volcanic island. GEOBIOLOGY 2024; 22:e12591. [PMID: 38458993 PMCID: PMC11027952 DOI: 10.1111/gbi.12591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/23/2024] [Accepted: 02/19/2024] [Indexed: 03/10/2024]
Abstract
Studies of the effects of volcanic activity on the Hawaiian Islands are extremely relevant due to the past and current co-eruptions at both Mauna Loa and Kīlauea. The Big Island of Hawai'i is one of the most seismically monitored volcanic systems in the world, and recent investigations of the Big Island suggest a widespread subsurface connectivity between volcanoes. Volcanic activity has the potential to add mineral contaminants into groundwater ecosystems, thus affecting water quality, and making inhabitants of volcanic islands particularly vulnerable due to dependence on groundwater aquifers. As part of an interdisciplinary study on groundwater aquifers in Kona, Hawai'i, over 40 groundwater wells were sampled quarterly from August 2017 through March 2019, before and after the destructive eruption of the Kīlauea East Rift Zone in May 2018. Sample sites occurred at great distance (~80 km) from Kīlauea, allowing us to pose questions of how volcanic groundwater aquifers might be influenced by volcanic subsurface activity. Approximately 400 water samples were analyzed and temporally split by pre-eruption and post-eruption for biogeochemical analysis. While most geochemical constituents did not differ across quarterly sampling, microbial communities varied temporally (pre- and post-eruption). When a salinity threshold amongst samples was set, the greatest microbial community differences were observed in the freshest groundwater samples. Differential analysis indicated bacterial families with sulfur (S) metabolisms (sulfate reducers, sulfide oxidation, and disproportionation of S-intermediates) were enriched post-eruption. The diversity in S-cyclers without a corresponding change in sulfate geochemistry suggests cryptic cycling may occur in groundwater aquifers as a result of distant volcanic subsurface activity. Microbial communities, including taxa that cycle S, may be superior tracers to changes in groundwater quality, especially from direct inputs of subsurface volcanic activity.
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Affiliation(s)
- Sheree J Watson
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Cédric Arisdakessian
- Department of Information and Computer Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Maria Petelo
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Kekuʻiapōiula Keliipuleole
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Diamond K Tachera
- Department of Earth Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Brytne K Okuhata
- Department of Earth Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Kiana L Frank
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
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Hinkle JE, Mara P, Beaudoin DJ, Edgcomb VP, Teske AP. A PCR-Based Survey of Methane-Cycling Archaea in Methane-Soaked Subsurface Sediments of Guaymas Basin, Gulf of California. Microorganisms 2023; 11:2956. [PMID: 38138100 PMCID: PMC10745291 DOI: 10.3390/microorganisms11122956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, the rapid deposition of organic-rich sediments, steep geothermal gradients, and abundant methane of mixed thermogenic and microbial origin. Subsurface sediment samples from eight drilling sites with distinct geochemical and thermal profiles were selected for DNA extraction and PCR amplification to explore the diversity of methane-cycling archaea in the Guaymas Basin subsurface. We performed PCR amplifications with general (mcrIRD), and ANME-1 specific primers that target the alpha (α) subunit of methyl coenzyme M reductase (mcrA). Diverse ANME-1 lineages associated with anaerobic methane oxidation were detected in seven out of the eight drilling sites, preferentially around the methane-sulfate interface, and in several cases, showed preferences for specific sampling sites. Phylogenetically, most ANME-1 sequences from the Guaymas Basin subsurface were related to marine mud volcanoes, seep sites, and the shallow marine subsurface. The most frequently recovered methanogenic phylotypes were closely affiliated with the hyperthermophilic Methanocaldococcaceae, and found at the hydrothermally influenced Ringvent site. The coolest drilling site, in the northern axial trough of Guaymas Basin, yielded the greatest diversity in methanogen lineages. Our survey indicates the potential for extensive microbial methane cycling within subsurface sediments of Guaymas Basin.
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Affiliation(s)
- John E. Hinkle
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Paraskevi Mara
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Falmouth, MA 02543, USA; (P.M.); (D.J.B.); (V.P.E.)
| | - David J. Beaudoin
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Falmouth, MA 02543, USA; (P.M.); (D.J.B.); (V.P.E.)
| | - Virginia P. Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Falmouth, MA 02543, USA; (P.M.); (D.J.B.); (V.P.E.)
| | - Andreas P. Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Veloso M, Waldisperg A, Arros P, Berríos-Pastén C, Acosta J, Colque H, Varas MA, Allende ML, Orellana LH, Marcoleta AE. Diversity, Taxonomic Novelty, and Encoded Functions of Salar de Ascotán Microbiota, as Revealed by Metagenome-Assembled Genomes. Microorganisms 2023; 11:2819. [PMID: 38004830 PMCID: PMC10673233 DOI: 10.3390/microorganisms11112819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Salar de Ascotán is a high-altitude arsenic-rich salt flat exposed to high ultraviolet radiation in the Atacama Desert, Chile. It hosts unique endemic flora and fauna and is an essential habitat for migratory birds, making it an important site for conservation and protection. However, there is limited information on the resident microbiota's diversity, genomic features, metabolic potential, and molecular mechanisms that enable it to thrive in this extreme environment. We used long- and short-read metagenomics to investigate the microbial communities in Ascotán's water, sediment, and soil. Bacteria predominated, mainly Pseudomonadota, Acidobacteriota, and Bacteroidota, with a remarkable diversity of archaea in the soil. Following hybrid assembly, we recovered high-quality bacterial (101) and archaeal (6) metagenome-assembled genomes (MAGs), including representatives of two putative novel families of Patescibacteria and Pseudomonadota and two novel orders from the archaeal classes Halobacteriota and Thermoplasmata. We found different metabolic capabilities across distinct lineages and a widespread presence of genes related to stress response, DNA repair, and resistance to arsenic and other metals. These results highlight the remarkable diversity and taxonomic novelty of the Salar de Ascotán microbiota and its rich functional repertoire, making it able to resist different harsh conditions. The highly complete MAGs described here could serve future studies and bioprospection efforts focused on salt flat extremophiles, and contribute to enriching databases with microbial genome data from underrepresented regions of our planet.
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Affiliation(s)
- Marcelo Veloso
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Angie Waldisperg
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Patricio Arros
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Joaquín Acosta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Hazajem Colque
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
| | - Macarena A. Varas
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
- Millenium Institute Center for Genome Regulation, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
| | - Miguel L. Allende
- Millenium Institute Center for Genome Regulation, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
| | - Luis H. Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany;
| | - Andrés E. Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Faculty of Science, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile; (M.V.); (A.W.); (P.A.); (C.B.-P.); (J.A.); (H.C.); (M.A.V.)
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Sun K, Yu M, Zhu XY, Xue CX, Zhang Y, Chen X, Yao P, Chen L, Fu L, Yang Z, Zhang XH. Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole. Microbiol Spectr 2023; 11:e0114923. [PMID: 37623326 PMCID: PMC10580873 DOI: 10.1128/spectrum.01149-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/13/2023] [Indexed: 08/26/2023] Open
Abstract
The Sansha Yongle Blue Hole (SYBH), the deepest blue hole in the world, is an excellent habitat for revealing biogeochemical cycles in the anaerobic environment. However, how sulfur cycling is mediated by microorganisms in the SYBH hasn't been fully understood. In this study, the water layers of the SYBH were divided into oxic zone, hypoxic zone, anoxic zone I and II, and microbial-mediated sulfur cycling in the SYBH was comprehensively interpreted. The 16S rRNA genes/transcripts analyses showed that the microbial community structures associated with the sulfur cycling in each zone had distinctive features. Sulfur-oxidizing bacteria were mostly constituted by Gammaproteobacteria, Alphaproteobacteria, Campylobacterota, and Chlorobia above the anoxic zone I and sulfate-reducing bacteria were dominated by Desulfobacterota in anoxic zones. Metagenomic analyses showed that the sulfide-oxidation-related gene sqr and genes encoding the Sox system were mainly distributed in the anoxic zone I, while genes related to dissimilatory sulfate reduction and sulfur intermediate metabolite reduction were mainly distributed in the anoxic zone II, indicating different sulfur metabolic processes between these two zones. Moreover, sulfur-metabolism-related genes were identified in 81 metagenome-assembled genomes (MAGs), indicating a high diversity of microbial communities involved in sulfur cycling. Among them, three MAGs from the candidate phyla JdFR-76 and AABM5-125-24 with genes related to dissimilatory sulfate reduction exhibited distinctive metabolic features. Our results showed unique and novel microbial populations in the SYBH sulfur cycle correlated to the sharp redox gradients, revealing complex biogeochemical processes in this extreme environment. IMPORTANCE Oxygen-deficient regions in the global ocean are expanding rapidly and affect the growth, reproduction and ecological processes of marine organisms. The anaerobic water body of about 150 m in the Sansha Yongle Blue Hole (SYBH) provided a suitable environment to study the specific microbial metabolism in anaerobic seawater. Here, we found that the vertical distributions of the total and active communities of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) were different in each water layer of the SYBH according to the dissolved oxygen content. Genes related to sulfur metabolism also showed distinct stratification characteristics. Furthermore, we have obtained diverse metagenome-assembled genomes, some of which exhibit special sulfur metabolic characteristics, especially candidate phyla JdFR-76 and AABM5-125-24 were identified as potential novel SRB. The results of this study will promote further understanding of the sulfur cycle in extreme environments, as well as the environmental adaptability of microorganisms in blue holes.
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Affiliation(s)
- Kai Sun
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Min Yu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao-Yu Zhu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chun-Xu Xue
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunhui Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xing Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Lin Chen
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Liang Fu
- Sansha Track Ocean Coral Reef Conservation Research Institute, Sansha, China
| | - Zuosheng Yang
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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Yu T, Wu W, Liang W, Wang Y, Hou J, Chen Y, Elvert M, Hinrichs KU, Wang F. Anaerobic degradation of organic carbon supports uncultured microbial populations in estuarine sediments. MICROBIOME 2023; 11:81. [PMID: 37081504 PMCID: PMC10116835 DOI: 10.1186/s40168-023-01531-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND A large proportion of prokaryotic microbes in marine sediments remains uncultured, hindering our understanding of their ecological functions and metabolic features. Recent environmental metagenomic studies suggested that many of these uncultured microbes contribute to the degradation of organic matter, accompanied by acetogenesis, but the supporting experimental evidence is limited. RESULTS Estuarine sediments were incubated with different types of organic matters under anaerobic conditions, and the increase of uncultured bacterial populations was monitored. We found that (1) lignin stimulated the increase of uncultured bacteria within the class Dehalococcoidia. Their ability to metabolize lignin was further supported by the presence of genes associated with a nearly complete degradation pathway of phenolic monomers in the Dehalococcoidia metagenome-assembled genomes (MAGs). (2) The addition of cellulose stimulated the increase of bacteria in the phylum Ca. Fermentibacterota and family Fibrobacterales, a high copy number of genes encoding extracellular endoglucanase or/and 1,4-beta-cellobiosidase for cellulose decomposition and multiple sugar transporters were present in their MAGs. (3) Uncultured lineages in the order Bacteroidales and the family Leptospiraceae were enriched by the addition of casein and oleic acid, respectively, a high copy number of genes encoding extracellular peptidases, and the complete β-oxidation pathway were found in those MAGs of Bacteroidales and Leptospiraceae, respectively. (4) The growth of unclassified bacteria of the order Clostridiales was found after the addition of both casein and cellulose. Their MAGs contained multiple copies of genes for extracellular peptidases and endoglucanase. Additionally, 13C-labeled acetate was produced in the incubations when 13C-labeled dissolved inorganic carbon was provided. CONCLUSIONS Our results provide new insights into the roles of microorganisms during organic carbon degradation in anaerobic estuarine sediments and suggest that these macro and single molecular organic carbons support the persistence and increase of uncultivated bacteria. Acetogenesis is an additional important microbial process alongside organic carbon degradation. Video Abstract.
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Affiliation(s)
- Tiantian Yu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, China
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weichao Wu
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
- Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Wenyue Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yunru Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Marcus Elvert
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
- Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
- Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Fengping Wang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, China.
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Zhang C, Fang YX, Yin X, Lai H, Kuang Z, Zhang T, Xu XP, Wegener G, Wang JH, Dong X. The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules. MICROBIOME 2023; 11:37. [PMID: 36864529 PMCID: PMC9979476 DOI: 10.1186/s40168-023-01482-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/30/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Gas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Within these sediments, organic matter and upward-migrating methane are important carbon and energy sources fueling a light-independent biosphere. However, the type of metabolism that dominates the deep subseafloor of the gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas hydrate-rich sediments up to 49 m below the seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions and performed metagenomic and metatranscriptomic analyses to characterize microbial communities and their role in carbon mineralization. RESULTS Comparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones were clearly distinguished from those below the SMI. Chloroflexota were most abundant above the SMI, whereas Caldatribacteriota dominated below the SMI. Verrucomicrobiota, Bathyarchaeia, and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest an important role in the fermentation of macromolecules. In contrast, sulfate reducers and methanogens that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs and alkanotrophs that anaerobically grow on alkanes were also identified to be at low abundances. The ANME-1 group actively thrived in or slightly below the current SMI. Members from Heimdallarchaeia were found to encode the potential for anaerobic oxidation of short-chain hydrocarbons. CONCLUSIONS These findings indicate that the fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes. Video Abstract.
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Affiliation(s)
- Chuwen Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yun-Xin Fang
- Guangzhou Marine Geological Survey, China Geological Survey, Ministry of Natural Resources, Guangzhou, China
| | - Xiuran Yin
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hongfei Lai
- Guangzhou Marine Geological Survey, China Geological Survey, Ministry of Natural Resources, Guangzhou, China
| | - Zenggui Kuang
- Guangzhou Marine Geological Survey, China Geological Survey, Ministry of Natural Resources, Guangzhou, China
| | - Tianxueyu Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Xiang-Po Xu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Gunter Wegener
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jiang-Hai Wang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China.
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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Zhou Z, St John E, Anantharaman K, Reysenbach AL. Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits. MICROBIOME 2022; 10:241. [PMID: 36572924 PMCID: PMC9793634 DOI: 10.1186/s40168-022-01424-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/11/2022] [Indexed: 05/16/2023]
Abstract
BACKGROUND When deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal deposits support a rich diversity of thermophilic microorganisms which are involved in a range of carbon, sulfur, nitrogen, and hydrogen metabolisms. Global patterns of thermophilic microbial diversity in deep-sea hydrothermal ecosystems have illustrated the strong connectivity between geological processes and microbial colonization, but little is known about the genomic diversity and physiological potential of these novel taxa. Here we explore this genomic diversity in 42 metagenomes from four deep-sea hydrothermal vent fields and a deep-sea volcano collected from 2004 to 2018 and document their potential implications in biogeochemical cycles. RESULTS Our dataset represents 3635 metagenome-assembled genomes encompassing 511 novel and recently identified genera from deep-sea hydrothermal settings. Some of the novel bacterial (107) and archaeal genera (30) that were recently reported from the deep-sea Brothers volcano were also detected at the deep-sea hydrothermal vent fields, while 99 bacterial and 54 archaeal genera were endemic to the deep-sea Brothers volcano deposits. We report some of the first examples of medium- (≥ 50% complete, ≤ 10% contaminated) to high-quality (> 90% complete, < 5% contaminated) MAGs from phyla and families never previously identified, or poorly sampled, from deep-sea hydrothermal environments. We greatly expand the novel diversity of Thermoproteia, Patescibacteria (Candidate Phyla Radiation, CPR), and Chloroflexota found at deep-sea hydrothermal vents and identify a small sampling of two potentially novel phyla, designated JALSQH01 and JALWCF01. Metabolic pathway analysis of metagenomes provides insights into the prevalent carbon, nitrogen, sulfur, and hydrogen metabolic processes across all sites and illustrates sulfur and nitrogen metabolic "handoffs" in community interactions. We confirm that Campylobacteria and Gammaproteobacteria occupy similar ecological guilds but their prevalence in a particular site is driven by shifts in the geochemical environment. CONCLUSION Our study of globally distributed hydrothermal vent deposits provides a significant expansion of microbial genomic diversity associated with hydrothermal vent deposits and highlights the metabolic adaptation of taxonomic guilds. Collectively, our results illustrate the importance of comparative biodiversity studies in establishing patterns of shared phylogenetic diversity and physiological ecology, while providing many targets for enrichment and cultivation of novel and endemic taxa. Video Abstract.
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Affiliation(s)
- Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Emily St John
- Center for Life in Extreme Environments, Biology Department, Portland State University, Portland, OR, 97201, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Anna-Louise Reysenbach
- Center for Life in Extreme Environments, Biology Department, Portland State University, Portland, OR, 97201, USA.
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9
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Lazar CS, Schmidt F, Elvert M, Heuer VB, Hinrichs KU, Teske AP. Microbial diversity gradients in the geothermal mud volcano underlying the hypersaline Urania Basin. Front Microbiol 2022; 13:1043414. [PMID: 36620052 PMCID: PMC9812581 DOI: 10.3389/fmicb.2022.1043414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
Mud volcanoes transport deep fluidized sediment and their microbial communities and thus provide a window into the deep biosphere. However, mud volcanoes are commonly sampled at the surface and not probed at greater depths, with the consequence that their internal geochemistry and microbiology remain hidden from view. Urania Basin, a hypersaline seafloor basin in the Mediterranean, harbors a mud volcano that erupts fluidized mud into the brine. The vertical mud pipe was amenable to shipboard Niskin bottle and multicorer sampling and provided an opportunity to investigate the downward sequence of bacterial and archaeal communities of the Urania Basin brine, fluid mud layers and consolidated subsurface sediments using 16S rRNA gene sequencing. These microbial communities show characteristic, habitat-related trends as they change throughout the sample series, from extremely halophilic bacteria (KB1) and archaea (Halodesulfoarchaeum spp.) in the brine, toward moderately halophilic and thermophilic endospore-forming bacteria and uncultured archaeal lineages in the mud fluid, and finally ending in aromatics-oxidizing bacteria, uncultured spore formers, and heterotrophic subsurface archaea (Thermoplasmatales, Bathyarchaeota, and Lokiarcheota) in the deep subsurface sediment at the bottom of the mud volcano. Since these bacterial and archaeal lineages are mostly anaerobic heterotrophic fermenters, the microbial ecosystem in the brine and fluidized mud functions as a layered fermenter for the degradation of sedimentary biomass and hydrocarbons. By spreading spore-forming, thermophilic Firmicutes during eruptions, the Urania Basin mud volcano likely functions as a source of endospores that occur widely in cold seafloor sediments.
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Affiliation(s)
- Cassandre Sara Lazar
- Department of Biological Sciences, Université du Québec à Montréal, Montréal, QC, Canada
| | - Frauke Schmidt
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Verena B. Heuer
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Andreas P. Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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10
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Bell E, Rattray JE, Sloan K, Sherry A, Pilloni G, Hubert CRJ. Hyperthermophilic endospores germinate and metabolize organic carbon in sediments heated to 80°C. Environ Microbiol 2022; 24:5534-5545. [PMID: 36100999 PMCID: PMC9826295 DOI: 10.1111/1462-2920.16167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 08/10/2022] [Indexed: 01/11/2023]
Abstract
Cold surface sediments host a seedbank of functionally diverse thermophilic bacteria. These thermophiles are present as endospores, which are widely dispersed in aquatic environments. Here, we investigated the functional potential of endospore populations in cold surface sediments heated to 80°C. Microbial production of acetate was observed at 80°C and could be enhanced by supplying additional organic carbon substrates. Comparison of 16S rRNA gene amplicon libraries from 80°C enrichments to sediments heated to lower temperatures (50-70°C) showed that temperature selects for distinct populations of endospore-forming bacteria. Whereas sulfate-reducing thermophiles were enriched in 50-70°C incubations, 80°C exceeds their thermal tolerance and selects for hyperthermophilic organotrophic bacteria that are similarly detected in amplicon libraries from sediments heated to 90°C. Genome-resolved metagenomics revealed novel carbon cycling members of Symbiobacteriales, Thermosediminibacteraceae, Thermanaeromonas and Calditerricola with the genomic potential for the degradation of carbohydrates, sugars, amino acids and nucleotides. Endospores of thermophilic bacteria are deposited on seabed sediments worldwide where they remain dormant as they are buried in the accumulating sediments. Our results suggest that endospore populations could be activated by temperature increases encountered during burial and show the potential for organotrophic metabolic activity contributing to acetate generation in deep hot sediments.
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Affiliation(s)
- Emma Bell
- Geomicrobiology Group, Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada,School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Jayne E. Rattray
- Geomicrobiology Group, Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Kathryn Sloan
- Geomicrobiology Group, Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Angela Sherry
- Hub for Biotechnology in the Built Environment, Department of Applied SciencesNorthumbria UniversityNewcastle upon TyneUK
| | - Giovanni Pilloni
- ExxonMobil Technology and Engineering CompanyAnnandaleNew JerseyUSA
| | - Casey R. J. Hubert
- Geomicrobiology Group, Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada,School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUK
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11
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Benito Merino D, Zehnle H, Teske A, Wegener G. Deep-branching ANME-1c archaea grow at the upper temperature limit of anaerobic oxidation of methane. Front Microbiol 2022; 13:988871. [PMID: 36212815 PMCID: PMC9539880 DOI: 10.3389/fmicb.2022.988871] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/15/2022] [Indexed: 01/03/2023] Open
Abstract
In seafloor sediments, the anaerobic oxidation of methane (AOM) consumes most of the methane formed in anoxic layers, preventing this greenhouse gas from reaching the water column and finally the atmosphere. AOM is performed by syntrophic consortia of specific anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Cultures with diverse AOM partners exist at temperatures between 12°C and 60°C. Here, from hydrothermally heated sediments of the Guaymas Basin, we cultured deep-branching ANME-1c that grow in syntrophic consortia with Thermodesulfobacteria at 70°C. Like all ANME, ANME-1c oxidize methane using the methanogenesis pathway in reverse. As an uncommon feature, ANME-1c encode a nickel-iron hydrogenase. This hydrogenase has low expression during AOM and the partner Thermodesulfobacteria lack hydrogen-consuming hydrogenases. Therefore, it is unlikely that the partners exchange hydrogen during AOM. ANME-1c also does not consume hydrogen for methane formation, disputing a recent hypothesis on facultative methanogenesis. We hypothesize that the ANME-1c hydrogenase might have been present in the common ancestor of ANME-1 but lost its central metabolic function in ANME-1c archaea. For potential direct interspecies electron transfer (DIET), both partners encode and express genes coding for extracellular appendages and multiheme cytochromes. Thermodesulfobacteria encode and express an extracellular pentaheme cytochrome with high similarity to cytochromes of other syntrophic sulfate-reducing partner bacteria. ANME-1c might associate specifically to Thermodesulfobacteria, but their co-occurrence is so far only documented for heated sediments of the Gulf of California. However, in the deep seafloor, sulfate-methane interphases appear at temperatures up to 80°C, suggesting these as potential habitats for the partnership of ANME-1c and Thermodesulfobacteria.
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Affiliation(s)
- David Benito Merino
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Hanna Zehnle
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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12
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Zhu QZ, Wegener G, Hinrichs KU, Elvert M. Activity of Ancillary Heterotrophic Community Members in Anaerobic Methane-Oxidizing Cultures. Front Microbiol 2022; 13:912299. [PMID: 35722308 PMCID: PMC9201399 DOI: 10.3389/fmicb.2022.912299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria mediate the anaerobic oxidation of methane (AOM) in marine sediments. However, even sediment-free cultures contain a substantial number of additional microorganisms not directly related to AOM. To track the heterotrophic activity of these community members and their possible relationship with AOM, we amended meso- (37°C) and thermophilic (50°C) AOM cultures (dominated by ANME-1 archaea and their partner bacteria of the Seep-SRB2 clade or Candidatus Desulfofervidus auxilii) with L-leucine-3-13C (13C-leu). Various microbial lipids incorporated the labeled carbon from this amino acid, independent of the presence of methane as an energy source, specifically bacterial fatty acids, such as iso and anteiso-branched C15:0 and C17:0, as well as unsaturated C18:1ω9 and C18:1ω7. In natural methane-rich environments, these bacterial fatty acids are strongly 13C-depleted. We, therefore, suggest that those fatty acids are produced by ancillary bacteria that grow on 13C-depleted necromass or cell exudates/lysates of the AOM core communities. Candidates that likely benefit from AOM biomass are heterotrophic bacterial members of the Spirochetes and Anaerolineae—known to produce abundant branched fatty acids and present in all the AOM enrichment cultures. For archaeal lipids, we observed minor 13C-incorporation, but still suggesting some 13C-leu anabolism. Based on their relatively high abundance in the culture, the most probable archaeal candidates are Bathyarchaeota, Thermoplasmatales, and Lokiarchaeota. The identified heterotrophic bacterial and archaeal ancillary members are likely key players in organic carbon recycling in anoxic marine sediments.
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Affiliation(s)
- Qing-Zeng Zhu
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Gunter Wegener
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany
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13
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Microbiomes in the Challenger Deep slope and bottom-axis sediments. Nat Commun 2022; 13:1515. [PMID: 35314706 PMCID: PMC8938466 DOI: 10.1038/s41467-022-29144-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/01/2022] [Indexed: 12/24/2022] Open
Abstract
Hadal trenches are the deepest and most remote regions of the ocean. The 11-kilometer deep Challenger Deep is the least explored due to the technical challenges of sampling hadal depths. It receives organic matter and heavy metals from the overlying water column that accumulate differently across its V-shaped topography. Here, we collected sediments across the slope and bottom-axis of the Challenger Deep that enable insights into its in situ microbial communities. Analyses of 586 metagenome-assembled genomes retrieved from 37 metagenomes show distinct diversity and metabolic capacities between bottom-axis and slope sites. 26% of prokaryotic 16S rDNA reads in metagenomes were novel, with novelty increasing with water and sediment depths. These predominantly heterotrophic microbes can recycle macromolecules and utilize simple and complex hydrocarbons as carbon sources. Metagenome and metatranscriptome data support reduction and biotransformation of arsenate for energy gain in sediments that present a two-fold greater accumulation of arsenic compared to non-hadal sites. Complete pathways for anaerobic ammonia oxidation are predominantly identified in genomes recovered from bottom-axis sediments compared to slope sites. Our results expand knowledge of microbially-mediated elemental cycling in hadal sediments, and reveal differences in distribution of processes involved in nitrogen loss across the trench. The V-shaped Challenger Deep in the Mariana Trench is the deepest part of the world’s oceans. Using 586 prokaryotic metagenome-assembled genomes and metatranscriptomic data, this study explores metabolic capabilities and activities of microorganisms involved in elemental cycling in hadal sediments, and reveals the different distribution of processes between its bottom-axis and slope.
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14
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Ruff SE. Editorial: Microbial Communities and Metabolisms Involved in the Degradation of Cellular and Extracellular Organic Biopolymers. Front Microbiol 2022; 12:802619. [PMID: 35058915 PMCID: PMC8764131 DOI: 10.3389/fmicb.2021.802619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/29/2021] [Indexed: 11/22/2022] Open
Affiliation(s)
- S Emil Ruff
- Marine Biological Laboratory, Woods Hole, MA, United States
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15
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Krukenberg V, Reichart NJ, Spietz RL, Hatzenpichler R. Microbial Community Response to Polysaccharide Amendment in Anoxic Hydrothermal Sediments of the Guaymas Basin. Front Microbiol 2021; 12:763971. [PMID: 34956126 PMCID: PMC8703129 DOI: 10.3389/fmicb.2021.763971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/09/2021] [Indexed: 11/25/2022] Open
Abstract
Organic-rich, hydrothermal sediments of the Guaymas Basin are inhabited by diverse microbial communities including many uncultured lineages with unknown metabolic potential. Here we investigated the short-term effect of polysaccharide amendment on a sediment microbial community to identify taxa involved in the initial stage of macromolecule degradation. We incubated anoxic sediment with cellulose, chitin, laminarin, and starch and analyzed the total and active microbial communities using bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Our results show a response of an initially minor but diverse population of Clostridia particularly after amendment with the lower molecular weight polymers starch and laminarin. Thus, Clostridia may readily become key contributors to the heterotrophic community in Guaymas Basin sediments when substrate availability and temperature range permit their metabolic activity and growth, which expands our appreciation of the potential diversity and niche differentiation of heterotrophs in hydrothermally influenced sediments. BONCAT-FACS, although challenging in its application to complex samples, detected metabolic responses prior to growth and thus can provide complementary insight into a microbial community's metabolic potential and succession pattern. As a primary application of BONCAT-FACS on a diverse deep-sea sediment community, our study highlights important considerations and demonstrates inherent limitations associated with this experimental approach.
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Affiliation(s)
- Viola Krukenberg
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
- Thermal Biology Institute, Montana State University, Bozeman, MT, United States
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Nicholas J. Reichart
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
- Thermal Biology Institute, Montana State University, Bozeman, MT, United States
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Rachel L. Spietz
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
- Thermal Biology Institute, Montana State University, Bozeman, MT, United States
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
- Thermal Biology Institute, Montana State University, Bozeman, MT, United States
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
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