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Al-Daghistani HI, Zein S, Abbas MA. Microbial communities in the Dead Sea and their potential biotechnological applications. Commun Integr Biol 2024; 17:2369782. [PMID: 38919836 PMCID: PMC11197920 DOI: 10.1080/19420889.2024.2369782] [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: 04/02/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
The Dead Sea is unique compared to other extreme halophilic habitats. Its salinity exceeds 34%, and it is getting saltier. The Dead Sea environment is characterized by a dominance of divalent cations, with magnesium chloride (MgCl2) levels approaching the predicted 2.3 M upper limit for life, an acidic pH of 6.0, and high levels of absorbed ultraviolet radiation. Consequently, only organisms adapted to such a polyextreme environment can survive in the surface, sinkholes, sediments, muds, and underwater springs of the Dead Sea. Metagenomic sequence analysis and amino acid profiling indicated that the Dead Sea is predominantly composed of halophiles that have various adaptation mechanisms and produce metabolites that can be utilized for biotechnological purposes. A variety of products have been obtained from halophilic microorganisms isolated from the Dead Sea, such as antimicrobials, bioplastics, biofuels, extremozymes, retinal proteins, colored pigments, exopolysaccharides, and compatible solutes. These resources find applications in agriculture, food, biofuel production, industry, and bioremediation for the detoxification of wastewater and soil. Utilizing halophiles as a bioprocessing platform offers advantages such as reduced energy consumption, decreased freshwater demand, minimized capital investment, and continuous production.
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Affiliation(s)
- Hala I. Al-Daghistani
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Sima Zein
- Department of Pharmaceutical Biotechnology, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Manal A. Abbas
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
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2
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Liu Z, Huang Y, Chen H, Liu C, Wang M, Bian C, Wang L, Song L. Chromosome-level genome assembly of the deep-sea snail Phymorhynchus buccinoides provides insights into the adaptation to the cold seep habitat. BMC Genomics 2023; 24:679. [PMID: 37950158 PMCID: PMC10638732 DOI: 10.1186/s12864-023-09760-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/22/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND The deep-sea snail Phymorhynchus buccinoides belongs to the genus Phymorhynchus (Neogastropoda: Raphitomidae), and it is a dominant specie in the cold seep habitat. As the environment of the cold seep is characterized by darkness, hypoxia and high concentrations of toxic substances such as hydrogen sulfide (H2S), exploration of the diverse fauna living around cold seeps will help to uncover the adaptive mechanisms to this unique habitat. In the present study, a chromosome-level genome of P. buccinoides was constructed and a series of genomic and transcriptomic analyses were conducted to explore its molecular adaptation mechanisms to the cold seep environments. RESULTS The assembled genome size of the P. buccinoides was approximately 2.1 Gb, which is larger than most of the reported snail genomes, possibly due to the high proportion of repetitive elements. About 92.0% of the assembled base pairs of contigs were anchored to 34 pseudo-chromosomes with a scaffold N50 size of 60.0 Mb. Compared with relative specie in the shallow water, the glutamate regulative and related genes were expanded in P. buccinoides, which contributes to the acclimation to hypoxia and coldness. Besides, the relatively high mRNA expression levels of the olfactory/chemosensory genes in osphradium indicate that P. buccinoides might have evolved a highly developed and sensitive olfactory organ for its orientation and predation. Moreover, the genome and transcriptome analyses demonstrate that P. buccinoides has evolved a sulfite-tolerance mechanism by performing H2S detoxification. Many genes involved in H2S detoxification were highly expressed in ctenidium and hepatopancreas, suggesting that these tissues might be critical for H2S detoxification and sulfite tolerance. CONCLUSIONS In summary, our report of this chromosome-level deep-sea snail genome provides a comprehensive genomic basis for the understanding of the adaptation strategy of P. buccinoides to the extreme environment at the deep-sea cold seeps.
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Affiliation(s)
- Zhaoqun Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Yuting Huang
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Chen
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chang Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Minxiao Wang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chao Bian
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China.
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China.
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
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3
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Webster G, Cragg BA, Rinna J, Watkins AJ, Sass H, Weightman AJ, Parkes RJ. Methanogen activity and microbial diversity in Gulf of Cádiz mud volcano sediments. Front Microbiol 2023; 14:1157337. [PMID: 37293223 PMCID: PMC10244519 DOI: 10.3389/fmicb.2023.1157337] [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: 02/02/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023] Open
Abstract
The Gulf of Cádiz is a tectonically active continental margin with over sixty mud volcanoes (MV) documented, some associated with active methane (CH4) seepage. However, the role of prokaryotes in influencing this CH4 release is largely unknown. In two expeditions (MSM1-3 and JC10) seven Gulf of Cádiz MVs (Porto, Bonjardim, Carlos Ribeiro, Captain Arutyunov, Darwin, Meknes, and Mercator) were analyzed for microbial diversity, geochemistry, and methanogenic activity, plus substrate amended slurries also measured potential methanogenesis and anaerobic oxidation of methane (AOM). Prokaryotic populations and activities were variable in these MV sediments reflecting the geochemical heterogeneity within and between them. There were also marked differences between many MV and their reference sites. Overall direct cell numbers below the SMTZ (0.2-0.5 mbsf) were much lower than the general global depth distribution and equivalent to cell numbers from below 100 mbsf. Methanogenesis from methyl compounds, especially methylamine, were much higher than the usually dominant substrates H2/CO2 or acetate. Also, CH4 production occurred in 50% of methylated substrate slurries and only methylotrophic CH4 production occurred at all seven MV sites. These slurries were dominated by Methanococcoides methanogens (resulting in pure cultures), and prokaryotes found in other MV sediments. AOM occurred in some slurries, particularly, those from Captain Arutyunov, Mercator and Carlos Ribeiro MVs. Archaeal diversity at MV sites showed the presence of both methanogens and ANME (Methanosarcinales, Methanococcoides, and ANME-1) related sequences, and bacterial diversity was higher than archaeal diversity, dominated by members of the Atribacterota, Chloroflexota, Pseudomonadota, Planctomycetota, Bacillota, and Ca. "Aminicenantes." Further work is essential to determine the full contribution of Gulf of Cádiz mud volcanoes to the global methane and carbon cycles.
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Affiliation(s)
- Gordon Webster
- Microbiomes, Microbes and Informatics Group, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Barry A. Cragg
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Joachim Rinna
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
- Aker BP ASA, Lysaker, Norway
| | - Andrew J. Watkins
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
- The Wales Research and Diagnostic Positron Emission Tomography Imaging Centre (PETIC), School of Medicine, Cardiff University, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Henrik Sass
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Andrew J. Weightman
- Microbiomes, Microbes and Informatics Group, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - R. John Parkes
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, United Kingdom
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Li C, Ding A, Guo J, Song F, Lu P. Response of denitrifying anaerobic methane oxidation enrichment to salinity stress: Process and microbiology. ENVIRONMENTAL RESEARCH 2022; 214:114069. [PMID: 35964668 DOI: 10.1016/j.envres.2022.114069] [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: 06/19/2022] [Revised: 07/27/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Denitrifying anaerobic methane oxidation (DAMO) is a novel biological process which could decrease nitrogen pollution and methane emission simultaneously in wastewater treatment. Salinity as a key environmental factor has important effects on microbial community and activity, however, it remains unclear for DAMO microorganisms. In this study, response of the enrichment of DAMO archaea and bacteria to different salinity was investigated from the aspect of process and microbiology. The results showed that the increasing salinity from 0.14% to 25% evidently deteriorated DAMO process, with the average removal rate of nitrate and methane decreased from 1.91 mg N/(L·d) to 0.07 mg N/(L·d) and 3.22 μmol/d to 0.59 μmol/d, respectively. The observed IC50 value of salinity on the DAMO culture was 1.73%. Further microbial analyses at the gene level suggested that the relative abundance of DAMO archaea in the enrichment decreased to 46%, 39%, 38% and 33% of the initial value. However, DAMO bacteria suffered less impact with the relative abundance maintaining over 75% of the initial value (except 1% salinity). In functional genes of DAMO bacteria, pmoA, decreased gradually from 100% to 86%, 43%, 15% and 2%, while mcrA (DAMO archaea) maintained at 67%-97%. This difference probably indicated DAMO bacteria appeared functional inhibition prior to community inhibition, which was opposite for the DAMO archaea. Results above-mentioned concluded that, though the process of nitrate-dependent anaerobic methane oxidation was driven by the couple of DAMO archaea and bacteria, they individually featured different response to high salinity stress. These findings could be helpful for the application of DAMO-based process in high salinity wastewater treatment, and also the understanding to DAMO microorganisms.
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Affiliation(s)
- Chaoyang Li
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China; Key Laboratory of Three Gorges Reservoir Region 's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Aqiang Ding
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China; Key Laboratory of Three Gorges Reservoir Region 's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing, 400045, China.
| | - Junliang Guo
- Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Fuzhong Song
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China; Key Laboratory of Three Gorges Reservoir Region 's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing, 400045, China
| | - Peili Lu
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China; Key Laboratory of Three Gorges Reservoir Region 's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; Department of Environmental Science, College of Environment and Ecology, Chongqing University, Chongqing, 400045, China.
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5
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Vulcano F, Hahn CJ, Roerdink D, Dahle H, Reeves EP, Wegener G, Steen IH, Stokke R. Phylogenetic and functional diverse ANME-1 thrive in Arctic hydrothermal vents. FEMS Microbiol Ecol 2022; 98:6747120. [PMID: 36190327 PMCID: PMC9576274 DOI: 10.1093/femsec/fiac117] [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: 02/12/2022] [Revised: 09/15/2022] [Accepted: 09/29/2022] [Indexed: 01/21/2023] Open
Abstract
The methane-rich areas, the Loki's Castle vent field and the Jan Mayen vent field at the Arctic Mid Ocean Ridge (AMOR), host abundant niches for anaerobic methane-oxidizers, which are predominantly filled by members of the ANME-1. In this study, we used a metagenomic-based approach that revealed the presence of phylogenetic and functional different ANME-1 subgroups at AMOR, with heterogeneous distribution. Based on a common analysis of ANME-1 genomes from AMOR and other geographic locations, we observed that AMOR subgroups clustered with a vent-specific ANME-1 group that occurs solely at vents, and with a generalist ANME-1 group, with a mixed environmental origin. Generalist ANME-1 are enriched in genes coding for stress response and defense strategies, suggesting functional diversity among AMOR subgroups. ANME-1 encode a conserved energy metabolism, indicating strong adaptation to sulfate-methane-rich sediments in marine systems, which does not however prevent global dispersion. A deep branching family named Ca. Veteromethanophagaceae was identified. The basal position of vent-related ANME-1 in phylogenomic trees suggests that ANME-1 originated at hydrothermal vents. The heterogeneous and variable physicochemical conditions present in diffuse venting areas of hydrothermal fields could have favored the diversification of ANME-1 into lineages that can tolerate geochemical and environmental variations.
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Affiliation(s)
- F Vulcano
- Corresponding author: Thormølens gate 53 A 5006 Bergen Postboks 7803 5020 Bergen. E-mail:
| | - C J Hahn
- Max-Plank Institute for Marine Microbiology, HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Bremen, 28359, Germany
| | - D Roerdink
- Department of Earth Science, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - H Dahle
- Computational Biological Unit, Department of Informatics, Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - E P Reeves
- Department of Earth Science, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - G Wegener
- Max-Plank Institute for Marine Microbiology, HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Bremen, 28359, Germany,MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, 28359, Germany,Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - I H Steen
- Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - R Stokke
- Corresponding author: Thormølens gate 53 A 5006 Bergen Postboks 7803 5020 Bergen. E-mail:
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6
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Magnuson E, Altshuler I, Fernández-Martínez MÁ, Chen YJ, Maggiori C, Goordial J, Whyte LG. Active lithoautotrophic and methane-oxidizing microbial community in an anoxic, sub-zero, and hypersaline High Arctic spring. THE ISME JOURNAL 2022; 16:1798-1808. [PMID: 35396347 PMCID: PMC9213412 DOI: 10.1038/s41396-022-01233-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 03/21/2022] [Accepted: 03/29/2022] [Indexed: 05/01/2023]
Abstract
Lost Hammer Spring, located in the High Arctic of Nunavut, Canada, is one of the coldest and saltiest terrestrial springs discovered to date. It perennially discharges anoxic (<1 ppm dissolved oxygen), sub-zero (~-5 °C), and hypersaline (~24% salinity) brines from the subsurface through up to 600 m of permafrost. The sediment is sulfate-rich (1 M) and continually emits gases composed primarily of methane (~50%), making Lost Hammer the coldest known terrestrial methane seep and an analog to extraterrestrial habits on Mars, Europa, and Enceladus. A multi-omics approach utilizing metagenome, metatranscriptome, and single-amplified genome sequencing revealed a rare surface terrestrial habitat supporting a predominantly lithoautotrophic active microbial community driven in part by sulfide-oxidizing Gammaproteobacteria scavenging trace oxygen. Genomes from active anaerobic methane-oxidizing archaea (ANME-1) showed evidence of putative metabolic flexibility and hypersaline and cold adaptations. Evidence of anaerobic heterotrophic and fermentative lifestyles were found in candidate phyla DPANN archaea and CG03 bacteria genomes. Our results demonstrate Mars-relevant metabolisms including sulfide oxidation, sulfate reduction, anaerobic oxidation of methane, and oxidation of trace gases (H2, CO2) detected under anoxic, hypersaline, and sub-zero ambient conditions, providing evidence that similar extant microbial life could potentially survive in similar habitats on Mars.
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Affiliation(s)
- Elisse Magnuson
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Ianina Altshuler
- School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Ya-Jou Chen
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Catherine Maggiori
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | | | - Lyle G Whyte
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada.
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7
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Chen Y, Xu C, Wu N, Sun Z, Liu C, Zhen Y, Xin Y, Zhang X, Geng W, Cao H, Zhai B, Li J, Qin S, Zhou Y. Diversity of Anaerobic Methane Oxidizers in the Cold Seep Sediments of the Okinawa Trough. Front Microbiol 2022; 13:819187. [PMID: 35495656 PMCID: PMC9048799 DOI: 10.3389/fmicb.2022.819187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 03/09/2022] [Indexed: 11/16/2022] Open
Abstract
Active cold seeps in the Okinawa Trough (OT) have been widely identified, but the sediment microbial communities associated with these sites are still poorly understood. Here, we investigated the distribution and biomass of the microbial communities, particularly those associated with the anaerobic oxidation of methane (AOM), in sediments from an active cold seep in the mid-Okinawa Trough. Methane-oxidizing archaea, including ANME-1a, ANME-1b, ANME-2a/b, ANME-2c, and ANME-3, were detected in the OT cold seep sediments. Vertical stratification of anaerobic methanotrophic archaea (ANME) communities was observed in the following order: ANME-3, ANME-1a, and ANME-1b. In addition, the abundance of methyl coenzyme M reductase A (mcrA) genes corresponded to high levels of dissolved iron, suggesting that methane-metabolizing archaea might participate in iron reduction coupled to methane oxidation (Fe-AOM) in the OT cold seep. Furthermore, the relative abundance of ANME-1a was strongly related to the concentration of dissolved iron, indicating that ANME-1a is a key microbial player for Fe-AOM in the OT cold seep sediments. Co-occurrence analysis revealed that methane-metabolizing microbial communities were mainly associated with heterotrophic microorganisms, such as JS1, Bathy-1, and Bathy-15.
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Affiliation(s)
- Ye Chen
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Cuiling Xu
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Nengyou Wu
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- *Correspondence: Nengyou Wu,
| | - Zhilei Sun
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Zhilei Sun,
| | - Changling Liu
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu Zhen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Youzhi Xin
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xilin Zhang
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wei Geng
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hong Cao
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Bin Zhai
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jing Li
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shuangshuang Qin
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China
| | - Yucheng Zhou
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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8
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Abou Khalil C, Prince VL, Prince RC, Greer CW, Lee K, Zhang B, Boufadel MC. Occurrence and biodegradation of hydrocarbons at high salinities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 762:143165. [PMID: 33131842 DOI: 10.1016/j.scitotenv.2020.143165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Hypersaline environments are found around the world, above and below ground, and many are exposed to hydrocarbons on a continuous or a frequent basis. Some surface hypersaline environments are exposed to hydrocarbons because they have active petroleum seeps while others are exposed because of oil exploration and production, or nearby human activities. Many oil reservoirs overlie highly saline connate water, and some national oil reserves are stored in salt caverns. Surface hypersaline ecosystems contain consortia of halophilic and halotolerant microorganisms that decompose organic compounds including hydrocarbons, and subterranean ones are likely to contain the same. However, the rates and extents of hydrocarbon biodegradation are poorly understood in such ecosystems. Here we describe hypersaline environments potentially or likely to become contaminated with hydrocarbons, including perennial and transient environments above and below ground, and discuss what is known about the microbes degrading hydrocarbons and the extent of their activities. We also discuss what limits the microbial hydrocarbon degradation in hypersaline environments and whether there are opportunities for inhibiting (oil storage) or stimulating (oil spills) such biodegradation as the situation requires.
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Affiliation(s)
- Charbel Abou Khalil
- Center for Natural Resources, Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | | | | | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montreal, QC H4P 2R2, Canada
| | - Kenneth Lee
- Fisheries and Oceans Canada, Ecosystem Science, Ottawa, ON K1A 0E6, Canada
| | - Baiyu Zhang
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
| | - Michel C Boufadel
- Center for Natural Resources, Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA.
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Zhang T, Xiao X, Chen S, Zhao J, Chen Z, Feng J, Liang Q, Phelps TJ, Zhang C. Active Anaerobic Archaeal Methanotrophs in Recently Emerged Cold Seeps of Northern South China Sea. Front Microbiol 2021; 11:612135. [PMID: 33391242 PMCID: PMC7772427 DOI: 10.3389/fmicb.2020.612135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
Cold seep ecosystems are developed from methane-rich fluids in organic rich continental slopes, which are the source of various dense microbial and faunal populations. Extensive studies have been conducted on microbial populations in this unique environment; most of them were based on DNA, which could not resolve the activity of extant organisms. In this study, RNA and DNA analyses were performed to evaluate the active archaeal and bacterial communities and their network correlations, particularly those participating in the methane cycle at three sites of newly developed cold seeps in the northern South China Sea (nSCS). The results showed that both archaeal and bacterial communities were significantly different at the RNA and DNA levels, revealing a higher abundance of methane-metabolizing archaea and sulfate-reducing bacteria in RNA sequencing libraries. Site ROV07-01, which exhibited extensive accumulation of deceased Calyptogena clam shells, was highly developed, and showed diverse and active anaerobic archaeal methanotrophs (ANME)-2a/b and sulfate-reducing bacteria from RNA libraries. Site ROV07-02, located near carbonate crusts with few clam shell debris, appeared to be poorly developed, less anaerobic and less active. Site ROV05-02, colonized by living Calyptogena clams, could likely be intermediary between ROV07-01 and ROV07-02, showing abundant ANME-2dI and sulfate-reducing bacteria in RNA libraries. The high-proportions of ANME-2dI, with respect to ANME-2dII in the site ROV07-01 was the first report from nSCS, which could be associated with recently developed cold seeps. Both ANME-2dI and ANME-2a/b showed close networked relationships with sulfate-reducing bacteria; however, they were not associated with the same microbial operational taxonomic units (OTUs). Based on the geochemical gradients and the megafaunal settlements as well as the niche specificities and syntrophic relationships, ANMEs appeared to change in community structure with the evolution of cold seeps, which may be associated with the heterogeneity of their geochemical processes. This study enriched our understanding of more active sulfate-dependent anaerobic oxidation of methane (AOM) in poorly developed and active cold seep sediments by contrasting DNA- and RNA-derived community structure and activity indicators.
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Affiliation(s)
- Tingting Zhang
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China.,Gas Hydrate Engineering Technology Center, China Geological Survey, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xi Xiao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China.,Gas Hydrate Engineering Technology Center, China Geological Survey, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Songze Chen
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Jing Zhao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Zongheng Chen
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Junxi Feng
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China.,Gas Hydrate Engineering Technology Center, China Geological Survey, Guangzhou, China
| | - Qianyong Liang
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China.,Gas Hydrate Engineering Technology Center, China Geological Survey, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Tommy J Phelps
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Earth and Planetary Sciences, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Chuanlun Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
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10
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Dong X, Rattray JE, Campbell DC, Webb J, Chakraborty A, Adebayo O, Matthews S, Li C, Fowler M, Morrison NM, MacDonald A, Groves RA, Lewis IA, Wang SH, Mayumi D, Greening C, Hubert CRJ. Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep. Nat Commun 2020; 11:5825. [PMID: 33203858 PMCID: PMC7673041 DOI: 10.1038/s41467-020-19648-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 10/06/2020] [Indexed: 11/08/2022] Open
Abstract
At marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically diverse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. Here we combined geophysical, geochemical, metagenomic and metabolomic measurements to profile microbial activities at a newly discovered cold seep in the deep sea. Metagenomic profiling revealed compositional and functional differentiation between near-surface sediments and deeper subsurface layers. In both sulfate-rich and sulfate-depleted depths, various archaeal and bacterial community members are actively oxidizing thermogenic hydrocarbons anaerobically. Depth distributions of hydrocarbon-oxidizing archaea revealed that they are not necessarily associated with sulfate reduction, which is especially surprising for anaerobic ethane and butane oxidizers. Overall, these findings link subseafloor microbiomes to various biochemical mechanisms for the anaerobic degradation of deeply-sourced thermogenic hydrocarbons.
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Affiliation(s)
- Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | - Jayne E Rattray
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - D Calvin Campbell
- Geological Survey of Canada-Atlantic, Dartmouth, NS, B3B 1A6, Canada
| | - Jamie Webb
- Applied Petroleum Technology (Canada), Calgary, AB, T2N 1Z6, Canada
| | - Anirban Chakraborty
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Oyeboade Adebayo
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Stuart Matthews
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Carmen Li
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Martin Fowler
- Applied Petroleum Technology (Canada), Calgary, AB, T2N 1Z6, Canada
| | - Natasha M Morrison
- Nova Scotia Department of Energy and Mines, Halifax, NS, B2Y 4A2, Canada
| | - Adam MacDonald
- Nova Scotia Department of Energy and Mines, Halifax, NS, B2Y 4A2, Canada
| | - Ryan A Groves
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Ian A Lewis
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Scott H Wang
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Daisuke Mayumi
- Institute for Geo-Resources and Environment, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, 305-8567, Japan
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
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11
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Carrier V, Svenning MM, Gründger F, Niemann H, Dessandier PA, Panieri G, Kalenitchenko D. The Impact of Methane on Microbial Communities at Marine Arctic Gas Hydrate Bearing Sediment. Front Microbiol 2020; 11:1932. [PMID: 33071992 PMCID: PMC7541813 DOI: 10.3389/fmicb.2020.01932] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 07/22/2020] [Indexed: 01/26/2023] Open
Abstract
Cold seeps are characterized by high biomass, which is supported by the microbial oxidation of the available methane by capable microorganisms. The carbon is subsequently transferred to higher trophic levels. South of Svalbard, five geological mounds shaped by the formation of methane gas hydrates, have been recently located. Methane gas seeping activity has been observed on four of them, and flares were primarily concentrated at their summits. At three of these mounds, and along a distance gradient from their summit to their outskirt, we investigated the eukaryotic and prokaryotic biodiversity linked to 16S and 18S rDNA. Here we show that local methane seepage and other environmental conditions did affect the microbial community structure and composition. We could not demonstrate a community gradient from the summit to the edge of the mounds. Instead, a similar community structure in any methane-rich sediments could be retrieved at any location on these mounds. The oxidation of methane was largely driven by anaerobic methanotrophic Archaea-1 (ANME-1) and the communities also hosted high relative abundances of sulfate reducing bacterial groups although none demonstrated a clear co-occurrence with the predominance of ANME-1. Additional common taxa were observed and their abundances were likely benefiting from the end products of methane oxidation. Among these were sulfide-oxidizing Campilobacterota, organic matter degraders, such as Bathyarchaeota, Woesearchaeota, or thermoplasmatales marine benthic group D, and heterotrophic ciliates and Cercozoa.
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Affiliation(s)
- Vincent Carrier
- Department of Arctic and Marine Biology, The Arctic University of Norway, Tromsø, Norway.,Centre for Arctic Gas Hydrate, Environment and Climate, The Arctic University of Norway, Tromsø, Norway
| | - Mette M Svenning
- Department of Arctic and Marine Biology, The Arctic University of Norway, Tromsø, Norway.,Centre for Arctic Gas Hydrate, Environment and Climate, The Arctic University of Norway, Tromsø, Norway
| | - Friederike Gründger
- Department of Bioscience, Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Helge Niemann
- Centre for Arctic Gas Hydrate, Environment and Climate, The Arctic University of Norway, Tromsø, Norway.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Pierre-Antoine Dessandier
- Centre for Arctic Gas Hydrate, Environment and Climate, The Arctic University of Norway, Tromsø, Norway
| | - Giuliana Panieri
- Centre for Arctic Gas Hydrate, Environment and Climate, The Arctic University of Norway, Tromsø, Norway
| | - Dimitri Kalenitchenko
- Centre for Arctic Gas Hydrate, Environment and Climate, The Arctic University of Norway, Tromsø, Norway
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12
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Diversity, ecology and evolution of Archaea. Nat Microbiol 2020; 5:887-900. [PMID: 32367054 DOI: 10.1038/s41564-020-0715-z] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/30/2020] [Indexed: 12/23/2022]
Abstract
Compared to bacteria, our knowledge of archaeal biology is limited. Historically, microbiologists have mostly relied on culturing and single-gene diversity surveys to understand Archaea in nature. However, only six of the 27 currently proposed archaeal phyla have cultured representatives. Advances in genomic sequencing and computational approaches are revolutionizing our understanding of Archaea. The recovery of genomes belonging to uncultured groups from the environment has resulted in the description of several new phyla, many of which are globally distributed and are among the predominant organisms on the planet. In this Review, we discuss how these genomes, together with long-term enrichment studies and elegant in situ measurements, are providing insights into the metabolic capabilities of the Archaea. We also debate how such studies reveal how important Archaea are in mediating an array of ecological processes, including global carbon and nutrient cycles, and how this increase in archaeal diversity has expanded our view of the tree of life and early archaeal evolution, and has provided new insights into the origin of eukaryotes.
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13
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Bhattarai S, Cassarini C, Lens PNL. Physiology and Distribution of Archaeal Methanotrophs That Couple Anaerobic Oxidation of Methane with Sulfate Reduction. Microbiol Mol Biol Rev 2019; 83:e00074-18. [PMID: 31366606 PMCID: PMC6710461 DOI: 10.1128/mmbr.00074-18] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In marine anaerobic environments, methane is oxidized where sulfate-rich seawater meets biogenic or thermogenic methane. In those niches, a few phylogenetically distinct microbial types, i.e., anaerobic methanotrophs (ANME), are able to grow through anaerobic oxidation of methane (AOM). Due to the relevance of methane in the global carbon cycle, ANME have drawn the attention of a broad scientific community for 4 decades. This review presents and discusses the microbiology and physiology of ANME up to the recent discoveries, revealing novel physiological types of anaerobic methane oxidizers which challenge the view of obligate syntrophy for AOM. An overview of the drivers shaping the distribution of ANME in different marine habitats, from cold seep sediments to hydrothermal vents, is given. Multivariate analyses of the abundance of ANME in various habitats identify a distribution of distinct ANME types driven by the mode of methane transport. Intriguingly, ANME have not yet been cultivated in pure culture, despite intense attempts. Further advances in understanding this microbial process are hampered by insufficient amounts of enriched cultures. This review discusses the advantages, limitations, and potential improvements for ANME laboratory-based cultivation systems.
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Affiliation(s)
- S Bhattarai
- UNESCO-IHE, Institute for Water Education, Delft, The Netherlands
| | - C Cassarini
- UNESCO-IHE, Institute for Water Education, Delft, The Netherlands
- National University of Ireland Galway, Galway, Ireland
| | - P N L Lens
- UNESCO-IHE, Institute for Water Education, Delft, The Netherlands
- National University of Ireland Galway, Galway, Ireland
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14
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Gründger F, Carrier V, Svenning MM, Panieri G, Vonnahme TR, Klasek S, Niemann H. Methane-fuelled biofilms predominantly composed of methanotrophic ANME-1 in Arctic gas hydrate-related sediments. Sci Rep 2019; 9:9725. [PMID: 31278352 PMCID: PMC6611871 DOI: 10.1038/s41598-019-46209-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/25/2019] [Indexed: 11/21/2022] Open
Abstract
Sedimentary biofilms comprising microbial communities mediating the anaerobic oxidation of methane are rare. Here, we describe two biofilm communities discovered in sediment cores recovered from Arctic cold seep sites (gas hydrate pingos) in the north-western Barents Sea, characterized by steady methane fluxes. We found macroscopically visible biofilms in pockets in the sediment matrix at the depth of the sulphate-methane-transition zone. 16S rRNA gene surveys revealed that the microbial community in one of the two biofilms comprised exclusively of putative anaerobic methanotrophic archaea of which ANME-1 was the sole archaeal taxon. The bacterial community consisted of relatives of sulphate-reducing bacteria (SRB) belonging to uncultured Desulfobacteraceae clustering into SEEP-SRB1 (i.e. the typical SRB associated to ANME-1), and members of the atribacterial JS1 clade. Confocal laser scanning microscopy demonstrates that this biofilm is composed of multicellular strands and patches of ANME-1 that are loosely associated with SRB cells, but not tightly connected in aggregates. Our discovery of methanotrophic biofilms in sediment pockets closely associated with methane seeps constitutes a hitherto overlooked and potentially widespread sink for methane and sulphate in marine sediments.
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Affiliation(s)
- Friederike Gründger
- CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT The Arctic University of Norway, Tromsø, Norway.
| | - Vincent Carrier
- CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Mette M Svenning
- CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT The Arctic University of Norway, Tromsø, Norway.,Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Giuliana Panieri
- CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Tobias R Vonnahme
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Scott Klasek
- Department of Microbiology, College of Sciences, Oregon State University, Corvallis, OR, USA
| | - Helge Niemann
- CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT The Arctic University of Norway, Tromsø, Norway.,Department of Marine Microbiology & Biogeochemistry, and Utrecht University, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, The Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
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15
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Chen SC, Musat N, Lechtenfeld OJ, Paschke H, Schmidt M, Said N, Popp D, Calabrese F, Stryhanyuk H, Jaekel U, Zhu YG, Joye SB, Richnow HH, Widdel F, Musat F. Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep. Nature 2019; 568:108-111. [PMID: 30918404 DOI: 10.1038/s41586-019-1063-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/27/2019] [Indexed: 11/09/2022]
Abstract
Ethane is the second most abundant component of natural gas in addition to methane, and-similar to methane-is chemically unreactive. The biological consumption of ethane under anoxic conditions was suggested by geochemical profiles at marine hydrocarbon seeps1-3, and through ethane-dependent sulfate reduction in slurries4-7. Nevertheless, the microorganisms and reactions that catalyse this process have to date remained unknown8. Here we describe ethane-oxidizing archaea that were obtained by specific enrichment over ten years, and analyse these archaea using phylogeny-based fluorescence analyses, proteogenomics and metabolite studies. The co-culture, which oxidized ethane completely while reducing sulfate to sulfide, was dominated by an archaeon that we name 'Candidatus Argoarchaeum ethanivorans'; other members were sulfate-reducing Deltaproteobacteria. The genome of Ca. Argoarchaeum contains all of the genes that are necessary for a functional methyl-coenzyme M reductase, and all subunits were detected in protein extracts. Accordingly, ethyl-coenzyme M (ethyl-CoM) was identified as an intermediate by liquid chromatography-tandem mass spectrometry. This indicated that Ca. Argoarchaeum initiates ethane oxidation by ethyl-CoM formation, analogous to the recently described butane activation by 'Candidatus Syntrophoarchaeum'9. Proteogenomics further suggests that oxidation of intermediary acetyl-CoA to CO2 occurs through the oxidative Wood-Ljungdahl pathway. The identification of an archaeon that uses ethane (C2H6) fills a gap in our knowledge of microorganisms that specifically oxidize members of the homologous alkane series (CnH2n+2) without oxygen. Detection of phylogenetic and functional gene markers related to those of Ca. Argoarchaeum at deep-sea gas seeps10-12 suggests that archaea that are able to oxidize ethane through ethyl-CoM are widespread members of the local communities fostered by venting gaseous alkanes around these seeps.
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Affiliation(s)
- Song-Can Chen
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Oliver J Lechtenfeld
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Heidrun Paschke
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Matthias Schmidt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Nedal Said
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Denny Popp
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Federica Calabrese
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ulrike Jaekel
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department for Research Infrastructures, The Research Council of Norway, Oslo, Norway
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | | | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany. .,Max Planck Institute for Marine Microbiology, Bremen, Germany.
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16
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Cui H, Su X, Chen F, Holland M, Yang S, Liang J, Su P, Dong H, Hou W. Microbial diversity of two cold seep systems in gas hydrate-bearing sediments in the South China Sea. MARINE ENVIRONMENTAL RESEARCH 2019; 144:230-239. [PMID: 30732863 DOI: 10.1016/j.marenvres.2019.01.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/29/2018] [Accepted: 01/14/2019] [Indexed: 05/05/2023]
Abstract
Cold seep is a unique habitat for microorganisms in deep marine sediments, and microbial communities and biogeochemical processes are still poorly understood, especially in relation to hydrate-bearing geo-systems. In this study, two cold seep systems were sampled and microbial diversity was studied at Site GMGS2-08 in the northern part of the South China Sea (SCS) during the GMGS2 gas hydrate expedition. The current cold seep system was composed of a sulfate methane transition zone (SMTZ) and an upper gas hydrate zone (UGHZ). The buried cold seep system was composed of an authigenic carbonate zone (ACZ) and a lower gas hydrate zone (LGHZ). These drill core samples provided an excellent opportunity for analyzing the microbial abundance and diversity based on quantitative polymerase chain reaction (qPCR) and high-throughput 16S rRNA gene sequencing. Compared to previous studies, the high relative abundance of ANME-1b, a clade of anaerobic methanotrophic archaea (ANME), may perform anaerobic oxidation of methane (AOM) in collaboration with ANME-2c and Desulfobacteraceae in the SMTZ, and the high relative abundances of Hadesarchaea, ANME-1b archaea and Aerophobetes bacteria were found in the gas hydrate zone (GHZ) at Site GMGS2-08. ANME-1b, detected in the GHZ, might mainly mediate the AOM process, and the process might occur in a wide depth range within the LGHZ. Moreover, bacterial communities were significantly different between the GHZ and non-GHZ sediments. In the ACZ, archaeal communities were different between the two samples from the upper and the lower layers, while bacterial communities shared similarities. Overall, this new record of cold seep microbial diversity at Site GMGS2-08 showed the complexity of the interaction between biogeochemical reactions and environmental conditions.
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Affiliation(s)
- Hongpeng Cui
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Xin Su
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China.
| | - Fang Chen
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China
| | | | - Shengxiong Yang
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China
| | - Jinqiang Liang
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China.
| | - Pibo Su
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China; Department of Geology and Environmental Earth Science, Miami University, OH, 45056, USA
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
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17
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Labrado AL, Brunner B, Bernasconi SM, Peckmann J. Formation of Large Native Sulfur Deposits Does Not Require Molecular Oxygen. Front Microbiol 2019; 10:24. [PMID: 30740094 PMCID: PMC6355691 DOI: 10.3389/fmicb.2019.00024] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/09/2019] [Indexed: 01/05/2023] Open
Abstract
Large native (i.e., elemental) sulfur deposits can be part of caprock assemblages found on top of or in lateral position to salt diapirs and as stratabound mineralization in gypsum and anhydrite lithologies. Native sulfur is formed when hydrocarbons come in contact with sulfate minerals in presence of liquid water. The prevailing model for native sulfur formation in such settings is that sulfide produced by sulfate-reducing bacteria is oxidized to zero-valent sulfur in presence of molecular oxygen (O2). Although possible, such a scenario is problematic because: (1) exposure to oxygen would drastically decrease growth of microbial sulfate-reducing organisms, thereby slowing down sulfide production; (2) on geologic timescales, excess supply with oxygen would convert sulfide into sulfate rather than native sulfur; and (3) to produce large native sulfur deposits, enormous amounts of oxygenated water would need to be brought in close proximity to environments in which ample hydrocarbon supply sustains sulfate reduction. However, sulfur stable isotope data from native sulfur deposits emplaced at a stage after the formation of the host rocks indicate that the sulfur was formed in a setting with little solute exchange with the ambient environment and little supply of dissolved oxygen. We deduce that there must be a process for the formation of native sulfur in absence of an external oxidant for sulfide. We hypothesize that in systems with little solute exchange, sulfate-reducing organisms, possibly in cooperation with other anaerobic microbial partners, drive the formation of native sulfur deposits. In order to cope with sulfide stress, microbes may shift from harmful sulfide production to non-hazardous native sulfur production. We propose four possible mechanisms as a means to form native sulfur: (1) a modified sulfate reduction process that produces sulfur compounds with an intermediate oxidation state, (2) coupling of sulfide oxidation to methanogenesis that utilizes methylated compounds, acetate or carbon dioxide, (3) ammonium oxidation coupled to sulfate reduction, and (4) sulfur comproportionation of sulfate and sulfide. We show these reactions are thermodynamically favorable and especially useful in environments with multiple stressors, such as salt and dissolved sulfide, and provide evidence that microbial species functioning in such environments produce native sulfur. Integrating these insights, we argue that microbes may form large native sulfur deposits in absence of light and external oxidants such as O2, nitrate, and metal oxides. The existence of such a process would not only explain enigmatic occurrences of native sulfur in the geologic record, but also provide an explanation for cryptic sulfur and carbon cycling beneath the seabed.
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Affiliation(s)
- Amanda L. Labrado
- Department of Geological Sciences, The University of Texas at El Paso, El Paso, TX, United States
| | - Benjamin Brunner
- Department of Geological Sciences, The University of Texas at El Paso, El Paso, TX, United States
| | | | - Jörn Peckmann
- Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany
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18
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Bhattarai S, Cassarini C, Rene ER, Zhang Y, Esposito G, Lens PNL. Enrichment of sulfate reducing anaerobic methane oxidizing community dominated by ANME-1 from Ginsburg Mud Volcano (Gulf of Cadiz) sediment in a biotrickling filter. BIORESOURCE TECHNOLOGY 2018; 259:433-441. [PMID: 29602106 DOI: 10.1016/j.biortech.2018.03.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 06/08/2023]
Abstract
This study was performed to enrich anaerobic methane-oxidizing archaea (ANME) present in sediment from the Ginsburg Mud Volcano (Gulf of Cadiz) in a polyurethane foam packed biotrickling filter (BTF). The BTF was operated at 20 (±2) °C, ambient pressure with continuous supply of methane for 248 days. Sulfate reduction with simultaneous sulfide production (accumulating ∼7 mM) after 200 days of BTF operation evidenced anaerobic oxidation of methane (AOM) coupled to sulfate reduction. High-throughput sequence analysis of 16S rRNA genes showed that after 248 days of BTF operation, the ANME clades enriched to more than 50% of the archaeal sequences, including ANME-1b (40.3%) and ANME-2 (10.0%). Enrichment of the AOM community was beneficial to Desulfobacteraceae, which increased from 0.2% to 1.8%. Both the inoculum and the BTF enrichment contained large populations of anaerobic sulfur oxidizing bacteria, suggesting extensive sulfur cycling in the BTF.
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Affiliation(s)
- Susma Bhattarai
- UNESCO-IHE, Institute for Water Education, Westvest 7, P.O. Box 3015, 2601 DA Delft, The Netherlands.
| | - Chiara Cassarini
- UNESCO-IHE, Institute for Water Education, Westvest 7, P.O. Box 3015, 2601 DA Delft, The Netherlands; National University of Ireland Galway, University Road, Galway H91 TK33, Ireland
| | - Eldon R Rene
- UNESCO-IHE, Institute for Water Education, Westvest 7, P.O. Box 3015, 2601 DA Delft, The Netherlands
| | - Yu Zhang
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Dongchuan Road 800, 200240 Shanghai, China; Institute of Oceanography, Shanghai Jiao Tong University, Dongchuan Road 800, 200240 Shanghai, China
| | - Giovanni Esposito
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, via Di Biasio 43, 03043 Cassino, FR, Italy
| | - Piet N L Lens
- UNESCO-IHE, Institute for Water Education, Westvest 7, P.O. Box 3015, 2601 DA Delft, The Netherlands; National University of Ireland Galway, University Road, Galway H91 TK33, Ireland
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19
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Steinle L, Knittel K, Felber N, Casalino C, de Lange G, Tessarolo C, Stadnitskaia A, Sinninghe Damsté JS, Zopfi J, Lehmann MF, Treude T, Niemann H. Life on the edge: active microbial communities in the Kryos MgCl 2-brine basin at very low water activity. ISME JOURNAL 2018; 12:1414-1426. [PMID: 29666446 DOI: 10.1038/s41396-018-0107-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/19/2018] [Accepted: 03/12/2018] [Indexed: 11/09/2022]
Abstract
The Kryos Basin is a deep-sea hypersaline anoxic basin (DHAB) located in the Eastern Mediterranean Sea (34.98°N 22.04°E). It is filled with brine of re-dissolved Messinian evaporites and is nearly saturated with MgCl2-equivalents, which makes this habitat extremely challenging for life. The strong density difference between the anoxic brine and the overlying oxic Mediterranean seawater impedes mixing, giving rise to a narrow chemocline. Here, we investigate the microbial community structure and activities across the seawater-brine interface using a combined biogeochemical, next-generation sequencing, and lipid biomarker approach. Within the interface, we detected fatty acids that were distinctly 13C-enriched when compared to other fatty acids. These likely originated from sulfide-oxidizing bacteria that fix carbon via the reverse tricarboxylic acid cycle. In the lower part of the interface, we also measured elevated rates of methane oxidation, probably mediated by aerobic methanotrophs under micro-oxic conditions. Sulfate reduction rates increased across the interface and were highest within the brine, providing first evidence that sulfate reducers (likely Desulfovermiculus and Desulfobacula) thrive in the Kryos Basin at a water activity of only ~0.4 Aw. Our results demonstrate that a highly specialized microbial community in the Kryos Basin has adapted to the poly-extreme conditions of a DHAB with nearly saturated MgCl2 brine, extending the known environmental range where microbial life can persist.
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Affiliation(s)
- Lea Steinle
- Department of Environmental Sciences, University of Basel, Basel, Switzerland. .,GEOMAR, Helmholtz Centre for Ocean Research, Kiel, Germany.
| | - Katrin Knittel
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Nicole Felber
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Claudia Casalino
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Gert de Lange
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Chiara Tessarolo
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Alina Stadnitskaia
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands.,Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Texel, The Netherlands
| | - Jakob Zopfi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Moritz F Lehmann
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Tina Treude
- Department of Earth, Planetary and Space Sciences, University of Los Angeles, Los Angeles, CA, USA.,Department of Atmospheric and Oceanic Sciences, University of Los Angeles, Los Angeles, CA, USA
| | - Helge Niemann
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.,Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Texel, The Netherlands.,Department of Geology, Centre for Arctic Gas Hydrate, Environment and Climate, UiT the Arctic University of Norway, 9037, Tromsø, Norway
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20
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He Z, Zhang Q, Feng Y, Luo H, Pan X, Gadd GM. Microbiological and environmental significance of metal-dependent anaerobic oxidation of methane. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 610-611:759-768. [PMID: 28830047 DOI: 10.1016/j.scitotenv.2017.08.140] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/22/2017] [Accepted: 08/14/2017] [Indexed: 06/07/2023]
Abstract
Anaerobic oxidation of methane (AOM) can be coupled to the reduction of sulfate, nitrate and nitrite, which effectively reduces methane emission into the atmosphere. Recently, metal-dependent AOM (metal-AOM, AOM coupled to metal reduction) was demonstrated to occur in both environmental samples and enrichment cultures. Anaerobic methanotrophs are capable of respiration using Fe(III) or Mn(IV), whether they are in the form of soluble metal species or insoluble minerals. Given the wide distribution of Fe(III)/Mn(IV)-bearing minerals in aquatic methane-rich environments, metal-AOM is considered to be globally important, although it has generally been overlooked in previous studies. In this article, we discuss the discovery of this process, the microorganisms and mechanisms involved, environmental significance and factors influencing metal-AOM. Since metal-AOM is poorly studied to date, some discussion is included on the present understanding of sulfate- and nitrate-AOM and traditional metal reduction processes using organic substrates or hydrogen as electron donors. Metal-AOM is a relatively new research field, and therefore more studies are needed to fully characterize the process. This review summarizes current studies and discusses the many unanswered questions, which should be useful for future research in this field.
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Affiliation(s)
- Zhanfei He
- College of Environment, Zhejiang University of Technology, Hangzhou, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Qingying Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Yudong Feng
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Hongwei Luo
- College of Environment, Zhejiang University of Technology, Hangzhou, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Xiangliang Pan
- College of Environment, Zhejiang University of Technology, Hangzhou, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China.
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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21
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Reverse Methanogenesis and Respiration in Methanotrophic Archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2017; 2017:1654237. [PMID: 28154498 PMCID: PMC5244752 DOI: 10.1155/2017/1654237] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/11/2016] [Accepted: 10/31/2016] [Indexed: 12/21/2022]
Abstract
Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., “trace methane oxidation”). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux). Net AOM is exergonic when coupled to an external electron acceptor such as sulfate (ANME-1, ANME-2abc, and ANME-3), nitrate (ANME-2d), or metal (oxides). In this review, the reversibility of the methanogenesis pathway and essential differences between ANME and methanogens are described by combining published information with domain based (meta)genome comparison of archaeal methanotrophs and selected archaea. These differences include abundances and special structure of methyl coenzyme M reductase and of multiheme cytochromes and the presence of menaquinones or methanophenazines. ANME-2a and ANME-2d can use electron acceptors other than sulfate or nitrate for AOM, respectively. Environmental studies suggest that ANME-2d are also involved in sulfate-dependent AOM. ANME-1 seem to use a different mechanism for disposal of electrons and possibly are less versatile in electron acceptors use than ANME-2. Future research will shed light on the molecular basis of reversal of the methanogenic pathway and electron transfer in different ANME types.
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22
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Growth of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a high-pressure membrane capsule bioreactor. Appl Environ Microbiol 2016; 81:1286-96. [PMID: 25501484 DOI: 10.1128/aem.03255-14] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Communities of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB) grow slowly, which limits the ability to perform physiological studies. High methane partial pressure was previously successfully applied to stimulate growth, but it is not clear how different ANME subtypes and associated SRB are affected by it. Here, we report on the growth of ANME-SRB in a membrane capsule bioreactor inoculated with Eckernförde Bay sediment that combines high-pressure incubation (10.1 MPa methane) and thorough mixing (100 rpm) with complete cell retention by a 0.2-m-pore-size membrane. The results were compared to previously obtained data from an ambient-pressure (0.101 MPa methane) bioreactor inoculated with the same sediment. The rates of oxidation of labeled methane were not higher at 10.1 MPa, likely because measurements were done at ambient pressure. The subtype ANME-2a/b was abundant in both reactors, but subtype ANME-2c was enriched only at 10.1 MPa. SRB at 10.1 MPa mainly belonged to the SEEP-SRB2 and Eel-1 groups and the Desulfuromonadales and not to the typically found SEEP-SRB1 group. The increase of ANME-2a/b occurred in parallel with the increase of SEEP-SRB2, which was previously found to be associated only with ANME-2c. Our results imply that the syntrophic association is flexible and that methane pressure and sulfide concentration influence the growth of different ANME-SRB consortia. We also studied the effect of elevated methane pressure on methane production and oxidation by a mixture of methanogenic and sulfate-reducing sludge. Here, methane oxidation rates decreased and were not coupled to sulfide production, indicating trace methane oxidation during net methanogenesis and not anaerobic methane oxidation, even at a high methane partial pressure.
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23
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Timmers PHA, Widjaja-Greefkes HCA, Ramiro-Garcia J, Plugge CM, Stams AJM. Growth and activity of ANME clades with different sulfate and sulfide concentrations in the presence of methane. Front Microbiol 2015; 6:988. [PMID: 26441917 PMCID: PMC4585129 DOI: 10.3389/fmicb.2015.00988] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/04/2015] [Indexed: 01/19/2023] Open
Abstract
Extensive geochemical data showed that significant methane oxidation activity exists in marine sediments. The organisms responsible for this activity are anaerobic methane-oxidizing archaea (ANME) that occur in consortia with sulfate-reducing bacteria. A distinct zonation of different clades of ANME (ANME-1, ANME-2a/b, and ANME-2c) exists in marine sediments, which could be related to the localized concentrations of methane, sulfate, and sulfide. In order to test this hypothesis we performed long-term incubation of marine sediments under defined conditions with methane as a headspace gas: low or high sulfate (±4 and ±21 mM, respectively) in combination with low or high sulfide (±0.1 and ±4 mM, respectively) concentrations. Control incubations were also performed, with only methane, high sulfate, or high sulfide. Methane oxidation was monitored and growth of subtypes ANME-1, ANME-2a/b, and ANME-2c assessed using qPCR analysis. A preliminary archaeal community analysis was performed to gain insight into the ecological and taxonomic diversity. Almost all of the incubations with methane had methane oxidation activity, with the exception of the incubations with combined low sulfate and high sulfide concentrations. Sulfide inhibition occurred only with low sulfate concentrations, which could be due to the lower Gibbs free energy available as well as sulfide toxicity. ANME-2a/b appears to mainly grow in incubations which had high sulfate levels and methane oxidation activity, whereas ANME-1 did not show this distinction. ANME-2c only grew in incubations with only sulfate addition. These findings are consistent with previously published in situ profiling analysis of ANME subclusters in different marine sediments. Interestingly, since all ANME subtypes also grew in incubations with only methane or sulfate addition, ANME may also be able to perform anaerobic methane oxidation under substrate limited conditions or alternatively perform additional metabolic processes.
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Affiliation(s)
- Peer H A Timmers
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | | | - Javier Ramiro-Garcia
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands ; Laboratory of Systems and Synthetic Biology, Wageningen University Wageningen, Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands ; European Centre of Excellence for Sustainable Water Technology Wetsus, Leeuwarden, Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands ; Centre of Biological Engineering, University of Minho Braga, Portugal
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24
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Cao H, Zhang W, Wang Y, Qian PY. Microbial community changes along the active seepage site of one cold seep in the Red Sea. Front Microbiol 2015; 6:739. [PMID: 26284035 PMCID: PMC4523032 DOI: 10.3389/fmicb.2015.00739] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/06/2015] [Indexed: 01/11/2023] Open
Abstract
The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.
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Affiliation(s)
- Huiluo Cao
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong
| | - Weipeng Zhang
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong
| | - Yong Wang
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong ; Sanya Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences Sanya, China
| | - Pei-Yuan Qian
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong
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25
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Kormas KA, Pachiadaki MG, Karayanni H, Leadbetter ER, Bernhard JM, Edgcomb VP. Inter-comparison of the potentially active prokaryotic communities in the halocline sediments of Mediterranean deep-sea hypersaline basins. Extremophiles 2015; 19:949-60. [DOI: 10.1007/s00792-015-0770-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/28/2015] [Indexed: 11/29/2022]
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26
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 rlike (select (case when (5853=5853) then 0x31302e313132382f61656d2e30303134372d3135 else 0x28 end))-- yhjw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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27
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 and (select (case when (4843=4843) then null else ctxsys.drithsx.sn(1,4843) end) from dual) is null] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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28
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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29
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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30
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 and (select (case when (4809=6114) then null else ctxsys.drithsx.sn(1,4809) end) from dual) is null-- zlmh] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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31
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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32
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 and extractvalue(5836,concat(0x5c,0x7162707671,(select (elt(5836=5836,1))),0x717a6b7171))-- jijh] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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33
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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34
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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35
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 order by 1-- wjpz] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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36
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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37
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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38
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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39
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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40
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 or extractvalue(9645,concat(0x5c,0x7162707671,(select (elt(9645=9645,1))),0x717a6b7171))-- tzdx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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41
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 order by 1#] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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42
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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43
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 and 9969=9969-- bqjm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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44
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 and 5417=7636-- tabb] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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45
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 order by 1-- ntbd] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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46
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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47
|
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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48
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 rlike (select (case when (7991=6814) then 0x31302e313132382f61656d2e30303134372d3135 else 0x28 end))-- awkz] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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49
|
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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50
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 and (select (case when (8714=1632) then null else ctxsys.drithsx.sn(1,8714) end) from dual) is null] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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|