1
|
Du Y, Xiong Y, Deng Y, Tao Y, Tian H, Zhang Y, Li Q, Gan Y, Wang Y. Geogenic Phosphorus Enrichment in Groundwater due to Anaerobic Methane Oxidation-Coupled Fe(III) Oxide Reduction. Environ Sci Technol 2024; 58:8032-8042. [PMID: 38670935 DOI: 10.1021/acs.est.4c00267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Accumulation of geogenic phosphorus (P) in groundwater is an emerging environmental concern, which is closely linked to coupled processes involving FeOOH and organic matter under methanogenic conditions. However, it remains unclear how P enrichment is associated with methane cycling, particularly the anaerobic methane oxidation (AMO). This study conducted a comprehensive investigation of carbon isotopes in dissolved inorganic carbon (DIC), CO2, and CH4, alongside Fe isotopes, microbial communities, and functions in quaternary aquifers of the central Yangtze River plain. The study found that P concentrations tended to increase with Fe(II) concentrations, δ56Fe, and δ13C-DIC, suggesting P accumulation due to the reductive dissolution of FeOOH under methanogenic conditions. The positive correlations of pmoA gene abundance versus δ13C-CH4 and Fe concentrations versus δ13C-CH4, and the prevalent presence of Candidatus_Methanoperedens, jointly demonstrated the potential significance of Fe(III)-mediated AMO process (Fe-AMO) alongside traditional methanogenesis. The increase of P concentration with δ13C-CH4 value, pmoA gene abundance, and Fe concentration suggested that the Fe-AMO process facilitated P enrichment in groundwater. Redundancy analysis confirmed this assertion, identifying P concentration as the primary determinant and the cooperative influence of Fe-AMO microorganisms such as Candidatus_Methanoperedens and Geobacter on P enrichment. Our work provided new insights into P dynamics in subsurface environments.
Collapse
Affiliation(s)
- Yao Du
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, Wuhan 430078, China
| | - Yaojin Xiong
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, Wuhan 430078, China
| | - Yamin Deng
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, Wuhan 430078, China
| | - Yanqiu Tao
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, Wuhan 430078, China
| | - Hao Tian
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, Wuhan 430078, China
| | - Yanpeng Zhang
- Wuhan Center of China Geological Survey, Wuhan 430205, China
| | - Qinghua Li
- Wuhan Center of China Geological Survey, Wuhan 430205, China
| | - Yiqun Gan
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, Wuhan 430078, China
| | - Yanxin Wang
- Key Laboratory of Groundwater Quality and Health (China University of Geosciences), Ministry of Education, Wuhan 430078, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, Wuhan 430078, China
| |
Collapse
|
2
|
Jiang Q, Jing H, Li X, Wan Y, Chou IM, Hou L, Dong H, Niu Y, Gao D. Active pathways of anaerobic methane oxidization in deep-sea cold seeps of the South China Sea. Microbiol Spectr 2023; 11:e0250523. [PMID: 37916811 PMCID: PMC10715046 DOI: 10.1128/spectrum.02505-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/08/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Cold seeps occur in continental margins worldwide and are deep-sea oases. Anaerobic oxidation of methane is an important microbial process in the cold seeps and plays an important role in regulating methane content. This study elucidates the diversity and potential activities of major microbial groups in dependent anaerobic methane oxidation and sulfate-dependent anaerobic methane oxidation processes and provides direct evidence for the occurrence of nitrate-/nitrite-dependent anaerobic methane oxidation (Nr-/N-DAMO) as a previously overlooked microbial methane sink in the hydrate-bearing sediments of the South China Sea. This study provides direct evidence for occurrence of Nr-/N-DAMO as an important methane sink in the deep-sea cold seeps.
Collapse
Affiliation(s)
- Qiuyun Jiang
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, Guangdong, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Xuegong Li
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ye Wan
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - I-Ming Chou
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Costal Research, East China Normal University, Shanghai, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Costal Research, East China Normal University, Shanghai, China
| | - Yuhui Niu
- State Key Laboratory of Estuarine and Costal Research, East China Normal University, Shanghai, China
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Costal Research, East China Normal University, Shanghai, China
| |
Collapse
|
3
|
Chen L, Guo Y, Zhang S, Ma W. Simultaneous denitrification and electricity generation in a methane-powered bioelectrochemical system. Water Environ Res 2023; 95:e10910. [PMID: 37461353 DOI: 10.1002/wer.10910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/29/2023] [Accepted: 07/13/2023] [Indexed: 08/04/2023]
Abstract
Bioelectrochemical system is a novel method for controlling down nitrate pollution, yet the feasibility of using methane as the electron donors for denitrification in this system remains unknown. In this study, using the effluent from mother BESs as inocula, a denitrifying anaerobic methane oxidation bioelectrochemical system was successfully started up in 92 days. When operated with 50 mmol/L phosphate buffer solution at pH 7 and 30°C, the maximum methane consumption, nitrate, and total nitrogen removal load reached 0.23 ± 0.01 mmol/d, 551.0 ± 22.1 mg N/m3 /d, and 64.0 ± 18.8 mg N/m3 /d, respectively. Meanwhile, the peak voltage of 93 ± 4 mV, the anodic coulombic efficiency of 6.99 ± 0.20%, and the maximum power density of 219.86 mW/m3 were obtained. The metagenomics profiles revealed that the dominant denitrifying bacteria in the cathodic chamber reduced most nitrate to nitrite through denitrification and assimilatory reduction. In the anodic chamber, various archaea including methanotrophs and methanogens converted methane via reverse methanogenesis to form formate (or H2 ), acetate, and methyl compounds, which were than utilized by electroactive bacteria to generate electricity. PRACTITIONER POINTS: A denitrifying anaerobic methane oxidation BES was successfully started up in 92 d. Simultaneous removal of methane and nitrate was achieved in the DAMO-BES. Functional genes related to AMO and denitrification were detected in the DAMO-BES. Methylocystis can mediate AMO in the anode and denitrification in the cathode.
Collapse
Affiliation(s)
- Long Chen
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, China
| | - Yanli Guo
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, China
| | - Shaohui Zhang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, China
- Hubei Key Laboratory of Fuel Cell, Wuhan University of Technology, Wuhan, China
| | - Wenqing Ma
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, China
| |
Collapse
|
4
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
5
|
Jiang Q, Jing H, Liu H, Du M. Biogeographic distributions of microbial communities associated with anaerobic methane oxidation in the surface sediments of deep-sea cold seeps in the South China Sea. Front Microbiol 2022; 13:1060206. [PMID: 36620029 PMCID: PMC9822730 DOI: 10.3389/fmicb.2022.1060206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Cold seeps are oasis for the microbes in the deep-sea ecosystems, and various cold seeps are located along the northern slope of the South China Sea (SCS). However, by far most microbial ecological studies were limited to specific cold seep in the SCS, and lack of comparison between different regions. Here, the surface sediments (0-4 cm) from the Site F/Haima cold seeps and the Xisha trough in the SCS were used to elucidate the biogeography of microbial communities, with particular interest in the typical functional groups involved in the anaerobic oxidation of methane (AOM) process. Distinct microbial clusters corresponding to the three sampling regions were formed, and significantly higher gene abundance of functional groups were present in the cold seeps than the trough. This biogeographical distribution could be explained by the geochemical characteristics of sediments, such as total nitrogen (TN), total phosphorus (TP), nitrate (NO3 -), total sulfur (TS) and carbon to nitrogen ratios (C/N). Phylogenetic analysis demonstrated that mcrA and pmoA genotypes were closely affiliated with those from wetland and mangroves, where denitrifying anaerobic methane oxidation (DAMO) process frequently occurred; and highly diversified dsrB genotypes were revealed as well. In addition, significantly higher relative abundance of NC10 group was found in the Xisha trough, suggesting that nitrite-dependent DAMO (N-DAMO) process was more important in the hydrate-bearing trough, although its potential ecological contribution to AOM deserves further investigation. Our study also further demonstrated the necessity of combining functional genes and 16S rRNA gene to obtain a comprehensive picture of the population shifts of natural microbial communities among different oceanic regions.
Collapse
Affiliation(s)
- Qiuyun Jiang
- CAS Key Laboratory for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China,University of Chinese Academy of Sciences, Beijing, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China,HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China,*Correspondence: Hongmei Jing,
| | - Hao Liu
- CAS Key Laboratory for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Mengran Du
- CAS Key Laboratory for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| |
Collapse
|
6
|
Heryakusuma C, Susanti D, Yu H, Li Z, Purwantini E, Hettich RL, Orphan VJ, Mukhopadhyay B. A Reduced F 420-Dependent Nitrite Reductase in an Anaerobic Methanotrophic Archaeon. J Bacteriol 2022;:e0007822. [PMID: 35695516 DOI: 10.1128/jb.00078-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic methanotrophic archaea (ANME), which oxidize methane in marine sediments through syntrophic associations with sulfate-reducing bacteria, carry homologs of coenzyme F420-dependent sulfite reductase (Fsr) of Methanocaldococcus jannaschii, a hyperthermophilic methanogen from deep-sea hydrothermal vents. M. jannaschii Fsr (MjFsr) and ANME-Fsr belong to two phylogenetically distinct groups, FsrI and FsrII, respectively. MjFsrI reduces sulfite to sulfide with reduced F420 (F420H2), protecting methyl coenzyme M reductase (Mcr), an essential enzyme for methanogens, from sulfite inhibition. However, the function of FsrIIs in ANME, which also rely on Mcr and live in sulfidic environments, is unknown. We have determined the catalytic properties of FsrII from a member of ANME-2c. Since ANME remain to be isolated, we expressed ANME2c-FsrII in a closely related methanogen, Methanosarcina acetivorans. Purified recombinant FsrII contained siroheme, indicating that the methanogen, which lacks a native sulfite reductase, produced this coenzyme. Unexpectedly, FsrII could not reduce sulfite or thiosulfate with F420H2. Instead, it acted as an F420H2-dependent nitrite reductase (FNiR) with physiologically relevant Km values (nitrite, 5 μM; F420H2, 14 μM). From kinetic, thermodynamic, and structural analyses, we hypothesize that in FNiR, F420H2-derived electrons are delivered at the oxyanion reduction site at a redox potential that is suitable for reducing nitrite (E0' [standard potential], +440 mV) but not sulfite (E0', -116 mV). These findings and the known nitrite sensitivity of Mcr suggest that FNiR may protect nondenitrifying ANME from nitrite toxicity. Remarkably, by reorganizing the reductant processing system, Fsr transforms two analogous oxyanions in two distinct archaeal lineages with different physiologies and ecologies. IMPORTANCE Coenzyme F420-dependent sulfite reductase (Fsr) protects methanogenic archaea inhabiting deep-sea hydrothermal vents from the inactivation of methyl coenzyme M reductase (Mcr), one of their essential energy production enzymes. Anaerobic methanotrophic archaea (ANME) that oxidize methane and rely on Mcr, carry Fsr homologs that form a distinct clade. We show that a member of this clade from ANME-2c functions as F420-dependent nitrite reductase (FNiR) and lacks Fsr activity. This specialization arose from a distinct feature of the reductant processing system and not the substrate recognition element. We hypothesize FNiR may protect ANME Mcr from inactivation by nitrite. This is an example of functional specialization within a protein family that is induced by changes in electron transfer modules to fit an ecological need.
Collapse
|
7
|
Ouboter HT, Berben T, Berger S, Jetten MSM, Sleutels T, Ter Heijne A, Welte CU. Methane-Dependent Extracellular Electron Transfer at the Bioanode by the Anaerobic Archaeal Methanotroph " Candidatus Methanoperedens". Front Microbiol 2022; 13:820989. [PMID: 35495668 PMCID: PMC9039326 DOI: 10.3389/fmicb.2022.820989] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/10/2022] [Indexed: 12/11/2022] Open
Abstract
Anaerobic methanotrophic (ANME) archaea have recently been reported to be capable of using insoluble extracellular electron acceptors via extracellular electron transfer (EET). In this study, we investigated EET by a microbial community dominated by "Candidatus Methanoperedens" archaea at the anode of a bioelectrochemical system (BES) poised at 0 V vs. standard hydrogen electrode (SHE), in this way measuring current as a direct proxy of EET by this community. After inoculation of the BES, the maximum current density was 274 mA m-2 (stable current up to 39 mA m-2). Concomitant conversion of 13CH4 into 13CO2 demonstrated that current production was methane-dependent, with 38% of the current attributed directly to methane supply. Based on the current production and methane uptake in a closed system, the Coulombic efficiency was about 17%. Polarization curves demonstrated that the current was limited by microbial activity at potentials above 0 V. The metatranscriptome of the inoculum was mined for the expression of c-type cytochromes potentially used for EET, which led to the identification of several multiheme c-type cytochrome-encoding genes among the most abundant transcripts in "Ca. Methanoperedens." Our study provides strong indications of EET in ANME archaea and describes a system in which ANME-mediated EET can be investigated under laboratory conditions, which provides new research opportunities for mechanistic studies and possibly the generation of axenic ANME cultures.
Collapse
Affiliation(s)
- Heleen T Ouboter
- Institute for Water and Wetland Research, Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - Tom Berben
- Institute for Water and Wetland Research, Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - Stefanie Berger
- Institute for Water and Wetland Research, Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - Mike S M Jetten
- Institute for Water and Wetland Research, Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - Tom Sleutels
- Wetsus, European Center of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands.,Faculty of Science and Engineering, University of Groningen, Groningen, Netherlands
| | | | - Cornelia U Welte
- Institute for Water and Wetland Research, Department of Microbiology, Radboud University, Nijmegen, Netherlands
| |
Collapse
|
8
|
Dalcin Martins P, Echeveste Medrano MJ, Arshad A, Kurth JM, Ouboter HT, Op den Camp HJM, Jetten MSM, Welte CU. Unraveling Nitrogen, Sulfur, and Carbon Metabolic Pathways and Microbial Community Transcriptional Responses to Substrate Deprivation and Toxicity Stresses in a Bioreactor Mimicking Anoxic Brackish Coastal Sediment Conditions. Front Microbiol 2022; 13:798906. [PMID: 35283857 PMCID: PMC8906906 DOI: 10.3389/fmicb.2022.798906] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/12/2022] [Indexed: 12/25/2022] Open
Abstract
Microbial communities are key drivers of carbon, sulfur, and nitrogen cycling in coastal ecosystems, where they are subjected to dynamic shifts in substrate availability and exposure to toxic compounds. However, how these shifts affect microbial interactions and function is poorly understood. Unraveling such microbial community responses is key to understand their environmental distribution and resilience under current and future disturbances. Here, we used metagenomics and metatranscriptomics to investigate microbial community structure and transcriptional responses to prolonged ammonium deprivation, and sulfide and nitric oxide toxicity stresses in a controlled bioreactor system mimicking coastal sediment conditions. Ca. Nitrobium versatile, identified in this study as a sulfide-oxidizing denitrifier, became a rare community member upon ammonium removal. The ANaerobic Methanotroph (ANME) Ca. Methanoperedens nitroreducens showed remarkable resilience to both experimental conditions, dominating transcriptional activity of dissimilatory nitrate reduction to ammonium (DNRA). During the ammonium removal experiment, increased DNRA was unable to sustain anaerobic ammonium oxidation (anammox) activity. After ammonium was reintroduced, a novel anaerobic bacterial methanotroph species that we have named Ca. Methylomirabilis tolerans outcompeted Ca. Methylomirabilis lanthanidiphila, while the anammox Ca. Kuenenia stuttgartiensis outcompeted Ca. Scalindua rubra. At the end of the sulfide and nitric oxide experiment, a gammaproteobacterium affiliated to the family Thiohalobacteraceae was enriched and dominated transcriptional activity of sulfide:quinone oxidoreductases. Our results indicate that some community members could be more resilient to the tested experimental conditions than others, and that some community functions such as methane and sulfur oxidation coupled to denitrification can remain stable despite large shifts in microbial community structure. Further studies on complex bioreactor enrichments are required to elucidate coastal ecosystem responses to future disturbances.
Collapse
Affiliation(s)
| | | | - Arslan Arshad
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Julia M Kurth
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Heleen T Ouboter
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | | | - Mike S M Jetten
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Cornelia U Welte
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| |
Collapse
|
9
|
Gambelli L, Mesman R, Versantvoort W, Diebolder CA, Engel A, Evers W, Jetten MSM, Pabst M, Daum B, van Niftrik L. The Polygonal Cell Shape and Surface Protein Layer of Anaerobic Methane-Oxidizing Methylomirabilis lanthanidiphila Bacteria. Front Microbiol 2021; 12:766527. [PMID: 34925275 PMCID: PMC8671808 DOI: 10.3389/fmicb.2021.766527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/08/2021] [Indexed: 11/25/2022] Open
Abstract
Methylomirabilis bacteria perform anaerobic methane oxidation coupled to nitrite reduction via an intra-aerobic pathway, producing carbon dioxide and dinitrogen gas. These diderm bacteria possess an unusual polygonal cell shape with sharp ridges that run along the cell body. Previously, a putative surface protein layer (S-layer) was observed as the outermost cell layer of these bacteria. We hypothesized that this S-layer is the determining factor for their polygonal cell shape. Therefore, we enriched the S-layer from M. lanthanidiphila cells and through LC-MS/MS identified a 31 kDa candidate S-layer protein, mela_00855, which had no homology to any other known protein. Antibodies were generated against a synthesized peptide derived from the mela_00855 protein sequence and used in immunogold localization to verify its identity and location. Both on thin sections of M. lanthanidiphila cells and in negative-stained enriched S-layer patches, the immunogold localization identified mela_00855 as the S-layer protein. Using electron cryo-tomography and sub-tomogram averaging of S-layer patches, we observed that the S-layer has a hexagonal symmetry. Cryo-tomography of whole cells showed that the S-layer and the outer membrane, but not the peptidoglycan layer and the cytoplasmic membrane, exhibited the polygonal shape. Moreover, the S-layer consisted of multiple rigid sheets that partially overlapped, most likely giving rise to the unique polygonal cell shape. These characteristics make the S-layer of M. lanthanidiphila a distinctive and intriguing case to study.
Collapse
Affiliation(s)
- Lavinia Gambelli
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands.,Living Systems Institute, University of Exeter, Exeter, United Kingdom.,College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom
| | - Rob Mesman
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Christoph A Diebolder
- Netherlands Centre for Electron Nanoscopy (NeCEN), Leiden University, Leiden, Netherlands
| | - Andreas Engel
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands
| | - Wiel Evers
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Department of Chemical Engineering, Delft University of Technology, Delft, Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Laura van Niftrik
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| |
Collapse
|
10
|
Roland FAE, Borges AV, Bouillon S, Morana C. Nitrate-dependent anaerobic methane oxidation and chemolithotrophic denitrification in a temperate eutrophic lake. FEMS Microbiol Ecol 2021; 97:6360975. [PMID: 34468740 DOI: 10.1093/femsec/fiab124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/30/2021] [Indexed: 11/12/2022] Open
Abstract
While the emissions of methane (CH4) by natural systems have been widely investigated, CH4 aquatic sinks are still poorly constrained. Here, we investigated the CH4 cycle and its interactions with nitrogen (N), iron (Fe) and manganese (Mn) cycles in the oxic-anoxic interface and deep anoxic waters of a small, meromictic and eutrophic lake, during two summertime sampling campaigns. Anaerobic CH4 oxidation (AOM) was measured from the temporal decrease of CH4 concentrations, with the addition of three potential electron acceptors (NO3-, iron oxides (Fe(OH)3) and manganese oxides (MnO2)). Experiments with the addition of either 15N-labeled nitrate (15N-NO3-) or 15N-NO3- combined with sulfide (H2S), to measure denitrification, chemolithotrophic denitrification and anaerobic ammonium oxidation (anammox) rates, were also performed. Measurements showed AOM rates up to 3.8 µmol CH4 L-1 d-1 that strongly increased with the addition of NO3- and moderately increased with the addition of Fe(OH)3. No stimulation was observed with MnO2 added. Potential denitrification and anammox rates up to 63 and 0.27 µmol N2 L-1 d-1, respectively, were measured when only 15N-NO3- was added. When H2S was added, both denitrification and anammox rates increased. Altogether, these results suggest that prokaryote communities in the redoxcline are able to efficiently use the most available substrates.
Collapse
Affiliation(s)
- Fleur A E Roland
- Chemical Oceanography Unit, Université de Liège, 4000 Liège, Belgium
| | - Alberto V Borges
- Chemical Oceanography Unit, Université de Liège, 4000 Liège, Belgium
| | - Steven Bouillon
- Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven (KU Leuven), 3001 Leuven, Belgium
| | - Cédric Morana
- Chemical Oceanography Unit, Université de Liège, 4000 Liège, Belgium
| |
Collapse
|
11
|
van Kessel MAHJ, Stultiens K, Pol A, Jetten MSM, Kartal B, Op den Camp HJM. Simultaneous Anaerobic and Aerobic Ammonia and Methane Oxidation under Oxygen Limitation Conditions. Appl Environ Microbiol 2021; 87:e0004321. [PMID: 33893122 DOI: 10.1128/AEM.00043-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methane and ammonia have to be removed from wastewater treatment effluent in order to discharge it to receiving water bodies. A potential solution for this is a combination of simultaneous ammonia and methane oxidation by anaerobic ammonia oxidation (anammox) bacteria and nitrite/nitrate-dependent anaerobic methane oxidation (N-damo) microorganisms. When applied, these microorganisms will be exposed to oxygen, but little is known about the effect of a low concentration of oxygen on a culture containing these microorganisms. In this study, a stable coculture containing anammox and N-damo microorganisms in a laboratory scale bioreactor was established under oxygen limitation. Membrane inlet mass spectrometry (MIMS) was used to directly measure the in situ simultaneous activity of N-damo, anammox, and aerobic ammonia-oxidizing microorganisms. In addition, batch tests revealed that the bioreactor also harbored aerobic methanotrophs and anaerobic methanogens. Together with fluorescence in situ hybridization (FISH) analysis and metagenomics, these results indicate that the combination of N-damo and anammox activity under the continuous supply of limiting oxygen concentrations is feasible and can be implemented for the removal of methane and ammonia from anaerobic digester effluents. IMPORTANCE Nitrogen in wastewater leads to eutrophication of the receiving water bodies, and methane is a potent greenhouse gas; it is therefore important that these are removed from wastewater. A potential solution for the simultaneous removal of nitrogenous compounds and methane is the application of a combination of nitrite/nitrate-dependent methane oxidation (N-damo) and anaerobic ammonia oxidation (annamox). In order to do so, it is important to investigate the effect of oxygen on these two anaerobic processes. In this study, we investigate the effect of a continuous oxygen supply on the activity of an anaerobic methane- and ammonia-oxidizing coculture. The findings presented in this study are important for the potential application of these two microbial processes in wastewater treatment.
Collapse
|
12
|
van Grinsven S, Sinninghe Damsté JS, Villanueva L. Assessing the Effect of Humic Substances and Fe(III) as Potential Electron Acceptors for Anaerobic Methane Oxidation in a Marine Anoxic System. Microorganisms 2020; 8:E1288. [PMID: 32846903 PMCID: PMC7564286 DOI: 10.3390/microorganisms8091288] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/06/2020] [Accepted: 08/17/2020] [Indexed: 12/13/2022] Open
Abstract
Marine anaerobic methane oxidation (AOM) is generally assumed to be coupled to sulfate reduction, via a consortium of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). ANME-1 are, however, often found as single cells, or only loosely aggregated with SRB, suggesting they perform a form of AOM independent of sulfate reduction. Oxidized metals and humic substances have been suggested as potential electron acceptors for ANME, but up to now, AOM linked to reduction of these compounds has only been shown for the ANME-2 and ANME-3 clades. Here, the effect of the electron acceptors anthraquinone-disulfonate (AQDS), a humic acids analog, and Fe3+ on anaerobic methane oxidation were assessed by incubation experiments with anoxic Black Sea water containing ANME-1b. Incubation experiments with 13C-methane and AQDS showed a stimulating effect of AQDS on methane oxidation. Fe3+ enhanced the ANME-1b abundance but did not substantially increase methane oxidation. Sodium molybdate, which was added as an inhibitor of sulfate reduction, surprisingly enhanced methane oxidation, possibly related to the dominant abundance of Sulfurospirillum in those incubations. The presented data suggest the potential involvement of ANME-1b in AQDS-enhanced anaerobic methane oxidation, possibly via electron shuttling to AQDS or via interaction with other members of the microbial community.
Collapse
Affiliation(s)
- Sigrid van Grinsven
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, 1797 SZ ’t Horntje, Texel, The Netherlands; (J.S.S.D.); (L.V.)
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, 1797 SZ ’t Horntje, Texel, The Netherlands; (J.S.S.D.); (L.V.)
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CB Utrecht, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, 1797 SZ ’t Horntje, Texel, The Netherlands; (J.S.S.D.); (L.V.)
| |
Collapse
|
13
|
Oremland RS. Why I never worked on anaerobic oxidation of methane (AOM) beyond the unsuccessful attempts of my NRC postdoc at NASA Ames Research Center (Sept. 1976-Sept. 1977). FEMS Microbiol Lett 2019; 366:5556530. [PMID: 31504454 DOI: 10.1093/femsle/fnz186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 08/28/2019] [Indexed: 11/14/2022] Open
Abstract
Anaeobes that consumed methane (and me).
Collapse
|
14
|
Liang L, Wang Y, Sivan O, Wang F. Metal-dependent anaerobic methane oxidation in marine sediment: Insights from marine settings and other systems. Sci China Life Sci 2019; 62:1287-1295. [PMID: 31209798 DOI: 10.1007/s11427-018-9554-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/22/2019] [Indexed: 11/26/2022]
Abstract
Anaerobic oxidation of methane (AOM) plays a crucial role in controlling global methane emission. This is a microbial process that relies on the reduction of external electron acceptors such as sulfate, nitrate/nitrite, and transient metal ions. In marine settings, the dominant electron acceptor for AOM is sulfate, while other known electron acceptors are transient metal ions such as iron and manganese oxides. Despite the AOM process coupled with sulfate reduction being relatively well characterized, researches on metal-dependent AOM process are few, and no microorganism has to date been identified as being responsible for this reaction in natural marine environments. In this review, geochemical evidences of metal-dependent AOM from sediment cores in various marine environments are summarized. Studies have showed that iron and manganese are reduced in accordance with methane oxidation in seeps or diffusive profiles below the methanogenesis zone. The potential biochemical basis and mechanisms for metal-dependent AOM processes are here presented and discussed. Future research will shed light on the microbes involved in this process and also on the molecular basis of the electron transfer between these microbes and metals in natural marine environments.
Collapse
Affiliation(s)
- Lewen Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Orit Sivan
- Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China.
| |
Collapse
|
15
|
Sturm A, Fowle DA, Jones C, Leslie K, Nomosatryo S, Henny C, Canfield DE, Crowe SA. Rates and pathways of CH 4 oxidation in ferruginous Lake Matano, Indonesia. Geobiology 2019; 17:294-307. [PMID: 30593722 DOI: 10.1111/gbi.12325] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/16/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
This study evaluates rates and pathways of methane (CH4 ) oxidation and uptake using 14 C-based tracer experiments throughout the oxic and anoxic waters of ferruginous Lake Matano. Methane oxidation rates in Lake Matano are moderate (0.36 nmol L-1 day-1 to 117 μmol L-1 day-1 ) compared to other lakes, but are sufficiently high to preclude strong CH4 fluxes to the atmosphere. In addition to aerobic CH4 oxidation, which takes place in Lake Matano's oxic mixolimnion, we also detected CH4 oxidation in Lake Matano's anoxic ferruginous waters. Here, CH4 oxidation proceeds in the apparent absence of oxygen (O2 ) and instead appears to be coupled to some as yet uncertain combination of nitrate ( NO 3 - ), nitrite ( NO 2 - ), iron (Fe) or manganese (Mn), or sulfate ( SO 4 2 - ) reduction. Throughout the lake, the fraction of CH4 carbon that is assimilated vs. oxidized to carbon dioxide (CO2 ) is high (up to 93%), indicating extensive CH4 conversion to biomass and underscoring the importance of CH4 as a carbon and energy source in Lake Matano and potentially other ferruginous or low productivity environments.
Collapse
Affiliation(s)
- Arne Sturm
- Department of Geology, University of Kansas, Lawrence, Kansas
| | - David A Fowle
- Department of Geology, University of Kansas, Lawrence, Kansas
| | - CarriAyne Jones
- Department of Microbiology and Immunology and Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Nordic Center for Earth Evolution, Institute of Biology, University of Southern Denmark, Odensee, Denmark
| | - Karla Leslie
- Department of Geology, University of Kansas, Lawrence, Kansas
| | - Sulung Nomosatryo
- Research Center for Limnology, Indonesian Institute of Sciences (LIPI), Cibinong-Bogor, Indonesia
| | - Cynthia Henny
- Research Center for Limnology, Indonesian Institute of Sciences (LIPI), Cibinong-Bogor, Indonesia
| | - Donald E Canfield
- Nordic Center for Earth Evolution, Institute of Biology, University of Southern Denmark, Odensee, Denmark
| | - Sean A Crowe
- Department of Microbiology and Immunology and Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Nordic Center for Earth Evolution, Institute of Biology, University of Southern Denmark, Odensee, Denmark
| |
Collapse
|
16
|
Guerrero-Cruz S, Stultiens K, van Kessel MAHJ, Versantvoort W, Jetten MSM, Op den Camp HJM, Kartal B. Key Physiology of a Nitrite-Dependent Methane-Oxidizing Enrichment Culture. Appl Environ Microbiol 2019; 85:e00124-19. [PMID: 30770408 PMCID: PMC6450021 DOI: 10.1128/aem.00124-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/11/2019] [Indexed: 11/20/2022] Open
Abstract
Nitrite-dependent methane-oxidizing bacteria couple the reduction of nitrite to the oxidation of methane via a unique oxygen-producing pathway. This process is carried out by members of the genus Methylomirabilis that belong to the NC10 phylum. Contrary to other known anaerobic methane oxidizers, they do not employ the reverse methanogenesis pathway for methane activation but instead a canonical particulate methane monooxygenase similar to those used by aerobic methanotrophs. Methylomirabilis-like bacteria are detected in many natural and manmade ecosystems, but their physiology is not well understood. Here, using continuous cultivation techniques, batch activity assays, and state-of-the-art membrane-inlet mass spectrometry, we determined growth rate, doubling time, and methane and nitrite affinities of the nitrite-dependent methane-oxidizing bacterium "Candidatus Methylomirabilis lanthanidiphila." Our results provide insight into understanding the interactions of these microorganisms with methanotrophs and other nitrite-reducing microorganisms, such as anaerobic ammonium-oxidizing bacteria. Furthermore, our data can be used in modeling studies as well as wastewater treatment plant design.IMPORTANCE Methane is an important greenhouse gas with a radiative forcing 28 times that of carbon dioxide over a 100-year time scale. The emission of methane to the atmosphere is controlled by aerobic and anaerobic methanotrophs, which are microorganisms that are able to oxidize methane to conserve energy. While aerobic methanotrophs have been studied for over a century, knowledge on the physiological characteristics of anaerobic methanotrophs is scarce. Here, we describe kinetic properties of "Candidatus Methylomirabilis lanthanidiphila," a nitrite-dependent methane-oxidizing microorganism, which is ecologically important and can be applied in wastewater treatment.
Collapse
Affiliation(s)
- Simon Guerrero-Cruz
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Karin Stultiens
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | | | - Wouter Versantvoort
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | | | - Boran Kartal
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| |
Collapse
|
17
|
Versantvoort W, Guerrero-Cruz S, Speth DR, Frank J, Gambelli L, Cremers G, van Alen T, Jetten MSM, Kartal B, Op den Camp HJM, Reimann J. Comparative Genomics of Candidatus Methylomirabilis Species and Description of Ca. Methylomirabilis Lanthanidiphila. Front Microbiol 2018; 9:1672. [PMID: 30140258 PMCID: PMC6094997 DOI: 10.3389/fmicb.2018.01672] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/04/2018] [Indexed: 11/18/2022] Open
Abstract
Methane is a potent greenhouse gas, which can be converted by microorganism at the expense of oxygen, nitrate, nitrite, metal-oxides or sulfate. The bacterium ‘Candidatus Methylomirabilis oxyfera,’ a member of the NC10 phylum, is capable of nitrite-dependent anaerobic methane oxidation. Prolonged enrichment of ‘Ca. M. oxyfera’ with cerium added as trace element and without nitrate resulted in the shift of the dominant species. Here, we present a high quality draft genome of the new species ‘Candidatus Methylomirabilis lanthanidiphila’ and use comparative genomics to analyze its metabolic potential in both nitrogen and carbon cycling. To distinguish between gene content specific for the ‘Ca. Methylomirabilis’ genus and the NC10 phylum, the genome of a distantly related NC10 phylum member, CSP1-5, an aerobic methylotroph, is included in the analysis. All genes for the conversion of nitrite to N2 identified in ‘Ca. M. oxyfera’ are conserved in ‘Ca. M. lanthanidiphila,’ including the two putative genes for NO dismutase. In addition both species have several heme-copper oxidases potentially involved in NO and O2 respiration. For the oxidation of methane ‘Ca. Methylomirabilis’ species encode a membrane bound methane monooxygenase. CSP1-5 can act as a methylotroph, but lacks the ability to activate methane. In contrast to ‘Ca. M. oxyfera,’ which harbors three methanol dehydrogenases (MDH), both CSP1-5 and ‘Ca. M. lanthanidiphila’ only encode a lanthanide-dependent XoxF-type MDH, once more underlining the importance of rare earth elements for methylotrophic bacteria. The pathways for the subsequent oxidation of formaldehyde to carbon dioxide and for the Calvin–Benson–Bassham cycle are conserved in all species. Furthermore, CSP1-5 can only interconvert nitrate and nitrite, but lacks subsequent nitrite or NO reductases. Thus, it appears that although the conversion of methanol to carbon dioxide is present in several NC10 phylum bacteria, the coupling of nitrite reduction to the oxidation of methane is a trait so far unique to the genus ‘Ca. Methylomirabilis.’
Collapse
Affiliation(s)
- Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Simon Guerrero-Cruz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Daan R Speth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Jeroen Frank
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Lavinia Gambelli
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Geert Cremers
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Theo van Alen
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| |
Collapse
|
18
|
McGlynn SE, Chadwick GL, O'Neill A, Mackey M, Thor A, Deerinck TJ, Ellisman MH, Orphan VJ. Subgroup Characteristics of Marine Methane-Oxidizing ANME-2 Archaea and Their Syntrophic Partners as Revealed by Integrated Multimodal Analytical Microscopy. Appl Environ Microbiol 2018; 84:e00399-18. [PMID: 29625978 DOI: 10.1128/AEM.00399-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 03/31/2018] [Indexed: 02/06/2023] Open
Abstract
Phylogenetically diverse environmental ANME archaea and sulfate-reducing bacteria cooperatively catalyze the anaerobic oxidation of methane oxidation (AOM) in multicelled consortia within methane seep environments. To better understand these cells and their symbiotic associations, we applied a suite of electron microscopy approaches, including correlative fluorescence in situ hybridization-electron microscopy (FISH-EM), transmission electron microscopy (TEM), and serial block face scanning electron microscopy (SBEM) three-dimensional (3D) reconstructions. FISH-EM of methane seep-derived consortia revealed phylogenetic variability in terms of cell morphology, ultrastructure, and storage granules. Representatives of the ANME-2b clade, but not other ANME-2 groups, contained polyphosphate-like granules, while some bacteria associated with ANME-2a/2c contained two distinct phases of iron mineral chains resembling magnetosomes. 3D segmentation of two ANME-2 consortium types revealed cellular volumes of ANME and their symbiotic partners that were larger than previous estimates based on light microscopy. Polyphosphate-like granule-containing ANME (tentatively termed ANME-2b) were larger than both ANME with no granules and partner bacteria. This cell type was observed with up to 4 granules per cell, and the volume of the cell was larger in proportion to the number of granules inside it, but the percentage of the cell occupied by these granules did not vary with granule number. These results illuminate distinctions between ANME-2 archaeal lineages and partnering bacterial populations that are apparently unified in their ability to perform anaerobic methane oxidation.IMPORTANCE Methane oxidation in anaerobic environments can be accomplished by a number of archaeal groups, some of which live in syntrophic relationships with bacteria in structured consortia. Little is known of the distinguishing characteristics of these groups. Here, we applied imaging approaches to better understand the properties of these cells. We found unexpected morphological, structural, and volume variability of these uncultured groups by correlating fluorescence labeling of cells with electron microscopy observables.
Collapse
|
19
|
Schout G, Hartog N, Hassanizadeh SM, Griffioen J. Impact of an historic underground gas well blowout on the current methane chemistry in a shallow groundwater system. Proc Natl Acad Sci U S A 2018; 115:296-301. [PMID: 29279383 DOI: 10.1073/pnas.1711472115] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rapid increase in shale gas production in recent years has led to increased attention to its potential negative environmental effects, including the risks of contaminating groundwater with methane and other substances. In this context, the uncontrolled gas migration that is triggered during well blowouts is an understudied environmental hazard. We show that the methane chemistry in shallow groundwater overlying the site of a catastrophic underground blowout continues to be impacted 50 y later. The occurrence of anaerobic methane oxidation limits the spatial extent to which the dissolved thermogenic methane plume could be observed and discerned from local biogenic methane sources. However, it also highlights the requirement to carry out monitoring in close proximity to potential gas leakage sources. Blowouts present a small but genuine risk when drilling into the deep subsurface and can have an immediate and significant impact on the surrounding environment. Nevertheless, studies that document their long-term impact are scarce. In 1965, a catastrophic underground blowout occurred during the drilling of a gas well in The Netherlands, which led to the uncontrolled release of large amounts of natural gas from the reservoir to the surface. In this study, the remaining impact on methane chemistry in the overlying aquifers was investigated. Methane concentrations higher than 10 mg/L (n = 12) were all found to have δ13C-CH4 values larger than −30‰, typical of a thermogenic origin. Both δ13C-CH4 and δD-CH4 correspond to the isotopic composition of the gas reservoir. Based on analysis of local groundwater flow conditions, this methane is not a remnant but most likely the result of ongoing leakage from the reservoir as a result of the blowout. Progressive enrichment of both δ13C-CH4 and δD-CH4 is observed with increasing distance and decreasing methane concentrations. The calculated isotopic fractionation factors of εC = 3 and εD = 54 suggest anaerobic methane oxidation is partly responsible for the observed decrease in concentrations. Elevated dissolved iron and manganese concentrations at the fringe of the methane plume show that oxidation is primarily mediated by the reduction of iron and manganese oxides. Combined, the data reveal the long-term impact that underground gas well blowouts may have on groundwater chemistry, as well as the important role of anaerobic oxidation in controlling the fate of dissolved methane.
Collapse
|
20
|
Dong M, Gonzalez TD, Klems MM, Steinberg LM, Chen W, Papoutsakis ET, Bahnson BJ. In vitro methanol production from methyl coenzyme M using the Methanosarcina barkeri MtaABC protein complex. Biotechnol Prog 2017; 33:1243-1249. [PMID: 28556629 DOI: 10.1002/btpr.2503] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/09/2017] [Indexed: 01/24/2023]
Abstract
Methanol:coenzyme M methyltransferase is an enzyme complex composed of three subunits, MtaA, MtaB, and MtaC, found in methanogenic archaea and is needed for their growth on methanol ultimately producing methane. MtaABC catalyzes the energetically favorable methyl transfer from methanol to coenzyme M to form methyl coenzyme M. Here we demonstrate that this important reaction for possible production of methanol from the anaerobic oxidation of methane can be reversed in vitro. To this effect, we have expressed and purified the Methanosarcina barkeri MtaABC enzyme, and developed an in vitro functional assay that demonstrates MtaABC can catalyze the energetically unfavorable (ΔG° = 27 kJ/mol) reverse reaction starting from methyl coenzyme M and generating methanol as a product. Demonstration of an in vitro ability of MtaABC to produce methanol may ultimately enable the anaerobic oxidation of methane to produce methanol and from methanol alternative fuel or fuel-precursor molecules. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1243-1249, 2017.
Collapse
Affiliation(s)
- Ming Dong
- Dept. of Chemistry & Biochemistry, University of Delaware, Newark, DE, 19716
| | - Tara D Gonzalez
- Dept. of Chemistry & Biochemistry, University of Delaware, Newark, DE, 19716
| | - Meghan M Klems
- Dept. of Chemistry & Biochemistry, University of Delaware, Newark, DE, 19716
| | - Lisa M Steinberg
- Dept. of Chemical & Biomolecular Engineering, Delaware Biotechnology Inst., University of Delaware, Newark, DE, 19711
| | - Wilfred Chen
- Dept. of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE, 19716
| | - Eleftherios T Papoutsakis
- Dept. of Chemical & Biomolecular Engineering, Delaware Biotechnology Inst., University of Delaware, Newark, DE, 19711
| | - Brian J Bahnson
- Dept. of Chemistry & Biochemistry, University of Delaware, Newark, DE, 19716
| |
Collapse
|
21
|
Valenzuela EI, Prieto-Davó A, López-Lozano NE, Hernández-Eligio A, Vega-Alvarado L, Juárez K, García-González AS, López MG, Cervantes FJ. Anaerobic Methane Oxidation Driven by Microbial Reduction of Natural Organic Matter in a Tropical Wetland. Appl Environ Microbiol 2017; 83:e00645-17. [PMID: 28341676 DOI: 10.1128/AEM.00645-17] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 03/18/2017] [Indexed: 11/20/2022] Open
Abstract
Wetlands constitute the main natural source of methane on Earth due to their high content of natural organic matter (NOM), but key drivers, such as electron acceptors, supporting methanotrophic activities in these habitats are poorly understood. We performed anoxic incubations using freshly collected sediment, along with water samples harvested from a tropical wetland, amended with 13C-methane (0.67 atm) to test the capacity of its microbial community to perform anaerobic oxidation of methane (AOM) linked to the reduction of the humic fraction of its NOM. Collected evidence demonstrates that electron-accepting functional groups (e.g., quinones) present in NOM fueled AOM by serving as a terminal electron acceptor. Indeed, while sulfate reduction was the predominant process, accounting for up to 42.5% of the AOM activities, the microbial reduction of NOM concomitantly occurred. Furthermore, enrichment of wetland sediment with external NOM provided a complementary electron-accepting capacity, of which reduction accounted for ∼100 nmol 13CH4 oxidized · cm-3 · day-1 Spectroscopic evidence showed that quinone moieties were heterogeneously distributed in the wetland sediment, and their reduction occurred during the course of AOM. Moreover, an enrichment derived from wetland sediments performing AOM linked to NOM reduction stoichiometrically oxidized methane coupled to the reduction of the humic analogue anthraquinone-2,6-disulfonate. Microbial populations potentially involved in AOM coupled to microbial reduction of NOM were dominated by divergent biota from putative AOM-associated archaea. We estimate that this microbial process potentially contributes to the suppression of up to 114 teragrams (Tg) of CH4 · year-1 in coastal wetlands and more than 1,300 Tg · year-1, considering the global wetland area.IMPORTANCE The identification of key processes governing methane emissions from natural systems is of major importance considering the global warming effects triggered by this greenhouse gas. Anaerobic oxidation of methane (AOM) coupled to the microbial reduction of distinct electron acceptors plays a pivotal role in mitigating methane emissions from ecosystems. Given their high organic content, wetlands constitute the largest natural source of atmospheric methane. Nevertheless, processes controlling methane emissions in these environments are poorly understood. Here, we provide tracer analysis with 13CH4 and spectroscopic evidence revealing that AOM linked to the microbial reduction of redox functional groups in natural organic matter (NOM) prevails in a tropical wetland. We suggest that microbial reduction of NOM may largely contribute to the suppression of methane emissions from tropical wetlands. This is a novel avenue within the carbon cycle in which slowly decaying NOM (e.g., humic fraction) in organotrophic environments fuels AOM by serving as a terminal electron acceptor.
Collapse
|
22
|
Ruff SE, Biddle JF, Teske AP, Knittel K, Boetius A, Ramette A. Global dispersion and local diversification of the methane seep microbiome. Proc Natl Acad Sci U S A 2015; 112:4015-20. [PMID: 25775520 DOI: 10.1073/pnas.1421865112] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Methane seeps are widespread seafloor ecosystems shaped by the emission of gas from seabed reservoirs. The microorganisms inhabiting methane seeps transform the chemical energy in methane to products that sustain rich benthic communities around the gas leaks. Despite the biogeochemical relevance of microbial methane removal at seeps, the global diversity and dispersion of seep microbiota remain unknown. Here we determined the microbial diversity and community structure of 23 globally distributed methane seeps and compared these to the microbial communities of 54 other seafloor ecosystems, including sulfate-methane transition zones, hydrothermal vents, coastal sediments, and deep-sea surface and subsurface sediments. We found that methane seep communities show moderate levels of microbial richness compared with other seafloor ecosystems and harbor distinct bacterial and archaeal taxa with cosmopolitan distribution and key biogeochemical functions. The high relative sequence abundance of ANME (anaerobic methanotrophic archaea), as well as aerobic Methylococcales, sulfate-reducing Desulfobacterales, and sulfide-oxidizing Thiotrichales, matches the most favorable microbial metabolisms at methane seeps in terms of substrate supply and distinguishes the seep microbiome from other seafloor microbiomes. The key functional taxa varied in relative sequence abundance between different seeps due to the environmental factors, sediment depth and seafloor temperature. The degree of endemism of the methane seep microbiome suggests a high local diversification in these heterogeneous but long-lived ecosystems. Our results indicate that the seep microbiome is structured according to metacommunity processes and that few cosmopolitan microbial taxa mediate the bulk of methane oxidation, with global relevance to methane emission in the ocean.
Collapse
|
23
|
Zhou Z, Chen J, Cao H, Han P, Gu JD. Analysis of methane-producing and metabolizing archaeal and bacterial communities in sediments of the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes. Front Microbiol 2015; 5:789. [PMID: 25774150 PMCID: PMC4343527 DOI: 10.3389/fmicb.2014.00789] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/22/2014] [Indexed: 11/17/2022] Open
Abstract
Communities of methanogens, anaerobic methanotrophic archaea and aerobic methanotrophic bacteria (MOB) were compared by profiling polymerase chain reaction (PCR)-amplified products of mcrA and pmoA genes encoded by methyl-coenzyme M reductase alpha subunit and particulate methane monooxygenase alpha subunit, respectively, in sediments of northern South China Sea (nSCS) and Mai Po mangrove wetland. Community structures representing by mcrA gene based on 12 clone libraries from nSCS showed separate clusters indicating niche specificity, while, Methanomicrobiales, Methanosarcinales clades 1,2, and Methanomassiliicoccus-like groups of methanogens were the most abundant groups in nSCS sediment samples. Novel clusters specific to the SCS were identified and the phylogeny of mcrA gene-harboring archaea was updated. Quantitative polymerase chain reaction was used to detect mcrA gene abundance in all samples: similar abundance of mcrA gene in the surface layers of mangrove (3.4∼3.9 × 106 copies per gram dry weight) and of intertidal mudflat (5.5∼5.8 × 106 copies per gram dry weight) was observed, but higher abundance (6.9 × 106 to 1.02 × 108 copies per gram dry weight) was found in subsurface samples of both sediment types. Aerobic MOB were more abundant in surface layers (6.7∼11.1 × 105 copies per gram dry weight) than the subsurface layers (1.2∼5.9 × 105 copies per gram dry weight) based on pmoA gene. Mangrove surface layers harbored more abundant pmoA gene than intertidal mudflat, but less pmoA genes in the subsurface layers. Meanwhile, it is also noted that in surface layers of all samples, more pmoA gene copies were detected than the subsurface layers. Reedbed rhizosphere exhibited the highest gene abundance of mcrA gene (8.51 × 108 copies per gram dry weight) and pmoA gene (1.56 × 107 copies per gram dry weight). This study investigated the prokaryotic communities responsible for methane cycling in both marine and coastal wetland ecosystems, showing the distribution characteristics of mcrA gene-harboring communities in nSCS and stratification of mcrA and pmoA gene diversity and abundance in the Mai Po Nature Reserve.
Collapse
Affiliation(s)
- Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
| | - Jing Chen
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
| | - Huiluo Cao
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong China
| | - Ping Han
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
| |
Collapse
|
24
|
Hawley ER, Piao H, Scott NM, Malfatti S, Pagani I, Huntemann M, Chen A, Glavina Del Rio T, Foster B, Copeland A, Jansson J, Pati A, Tringe S, Gilbert JA, Lorenson TD, Hess M. Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California. Stand Genomic Sci 2014; 9:1259-74. [PMID: 25197496 PMCID: PMC4149020 DOI: 10.4056/sigs.5029016] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Crude oils can be major contaminants of the marine ecosystem and microorganisms play a significant role in the degradation of its main constituents. To increase our understanding of the microbial hydrocarbon degradation process in the marine ecosystem, we collected crude oil from an active seep area located in the Santa Barbara Channel (SBC) and generated a total of about 52 Gb of raw metagenomic sequence data. The assembled data comprised ~500 Mb, representing ~1.1 million genes derived primarily from chemolithoautotrophic bacteria. Members of Oceanospirillales, a bacterial order belonging to the Deltaproteobacteria, recruited less than 2% of the assembled genes within the SBC metagenome. In contrast, the microbial community associated with the oil plume that developed in the aftermath of the Deepwater Horizon (DWH) blowout in 2010, was dominated by Oceanospirillales, which comprised more than 60% of the metagenomic data generated from the DWH oil plume. This suggests that Oceanospirillales might play a less significant role in the microbially mediated hydrocarbon conversion within the SBC seep oil compared to the DWH plume oil. We hypothesize that this difference results from the SBC oil seep being mostly anaerobic, while the DWH oil plume is aerobic. Within the Archaea, the phylum Euryarchaeota, recruited more than 95% of the assembled archaeal sequences from the SBC oil seep metagenome, with more than 50% of the sequences assigned to members of the orders Methanomicrobiales and Methanosarcinales. These orders contain organisms capable of anaerobic methanogenesis and methane oxidation (AOM) and we hypothesize that these orders – and their metabolic capabilities – may be fundamental to the ecology of the SBC oil seep.
Collapse
Affiliation(s)
- Erik R Hawley
- Washington State University Tri-Cities, Richland, WA, USA
| | - Hailan Piao
- Washington State University Tri-Cities, Richland, WA, USA
| | | | - Stephanie Malfatti
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, CA, USA
| | | | | | - Amy Chen
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Brian Foster
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Janet Jansson
- DOE Joint Genome Institute, Walnut Creek, CA, USA ; Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Susannah Tringe
- DOE Joint Genome Institute, Walnut Creek, CA, USA ; Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jack A Gilbert
- Argonne National Laboratory, Lemont, IL, USA ; University of Chicago, Chicago, IL, USA
| | | | - Matthias Hess
- Washington State University Tri-Cities, Richland, WA, USA ; DOE Joint Genome Institute, Walnut Creek, CA, USA ; Washington State University, Pullman, WA, USA ; Pacific Northwest National Laboratory, Chemical & Biological Process Development Group, Richland, WA, USA ; Environmental Molecular Sciences Laboratory, Richland, WA, USA
| |
Collapse
|