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Dalcin Martins P, de Jong A, Lenstra WK, van Helmond NAGM, Slomp CP, Jetten MSM, Welte CU, Rasigraf O. Enrichment of novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria in an oxygen-limited methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments. Microbiologyopen 2021; 10:e1175. [PMID: 33650794 PMCID: PMC7914226 DOI: 10.1002/mbo3.1175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 11/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/16/2022] Open
Abstract
Microbial methane oxidation is a major biofilter preventing larger emissions of this powerful greenhouse gas from marine coastal areas into the atmosphere. In these zones, various electron acceptors such as sulfate, metal oxides, nitrate, or oxygen can be used. However, the key microbial players and mechanisms of methane oxidation are poorly understood. In this study, we inoculated a bioreactor with methane‐ and iron‐rich sediments from the Bothnian Sea to investigate microbial methane and iron cycling under low oxygen concentrations. Using metagenomics, we investigated shifts in microbial community composition after approximately 2.5 years of bioreactor operation. Marker genes for methane and iron cycling, as well as respiratory and fermentative metabolism, were identified and used to infer putative microbial metabolism. Metagenome‐assembled genomes representing novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria were recovered and revealed a potential for methane oxidation, organic matter degradation, and iron cycling, respectively. This work brings new hypotheses on the identity and metabolic versatility of microorganisms that may be members of such functional guilds in coastal marine sediments and highlights that microorganisms potentially composing the methane biofilter in these sediments may be more diverse than previously appreciated.
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Affiliation(s)
- Paula Dalcin Martins
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology (SIAM), Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Anniek de Jong
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.,Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands
| | - Wytze K Lenstra
- Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands.,Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Niels A G M van Helmond
- Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands.,Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Caroline P Slomp
- Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands.,Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology (SIAM), Radboud University Nijmegen, Nijmegen, The Netherlands.,Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology (SIAM), Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.,Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands.,Geomicrobiology, German Research Centre for Geosciences (GFZ), Potsdam, Germany
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Guerrero-Cruz S, Cremers G, van Alen TA, Op den Camp HJM, Jetten MSM, Rasigraf O, Vaksmaa A. Response of the Anaerobic Methanotroph " Candidatus Methanoperedens nitroreducens" to Oxygen Stress. Appl Environ Microbiol 2018; 84:e01832-18. [PMID: 30291120 PMCID: PMC6275348 DOI: 10.1128/aem.01832-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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: 07/26/2018] [Accepted: 10/01/2018] [Indexed: 11/20/2022] Open
Abstract
"Candidatus Methanoperedens nitroreducens" is an archaeon that couples the anaerobic oxidation of methane to nitrate reduction. In natural and man-made ecosystems, this archaeon is often found at oxic-anoxic interfaces where nitrate, the product of aerobic nitrification, cooccurs with methane produced by methanogens. As such, populations of "Ca Methanoperedens nitroreducens" could be prone to regular oxygen exposure. Here, we investigated the effect of 5% (vol/vol) oxygen exposure in batch activity assays on a "Ca Methanoperedens nitroreducens" culture, enriched from an Italian paddy field. Metagenome sequencing of the DNA extracted from the enrichment culture revealed that 83% of 16S rRNA gene reads were assigned to a novel strain, "Candidatus Methanoperedens nitroreducens Verserenetto." RNA was extracted, and metatranscriptome sequencing upon oxygen exposure revealed that the active community changed, most notably in the appearance of aerobic methanotrophs. The gene expression of "Ca Methanoperedens nitroreducens" revealed that the key genes encoding enzymes of the methane oxidation and nitrate reduction pathways were downregulated. In contrast to this, we identified upregulation of glutaredoxin, thioredoxin family/like proteins, rubrerythrins, peroxiredoxins, peroxidase, alkyl hydroperoxidase, type A flavoproteins, FeS cluster assembly protein, and cysteine desulfurases, indicating the genomic potential of "Ca Methanoperedens nitroreducens Verserenetto" to counteract the oxidative damage and adapt in environments where they might be exposed to regular oxygen intrusion.IMPORTANCE "Candidatus Methanoperedens nitroreducens" is an anaerobic archaeon which couples the reduction of nitrate to the oxidation of methane. This microorganism is present in a wide range of aquatic environments and man-made ecosystems, such as paddy fields and wastewater treatment systems. In such environments, these archaea may experience regular oxygen exposure. However, "Ca Methanoperedens nitroreducens" is able to thrive under such conditions and could be applied for the simultaneous removal of dissolved methane and nitrogenous pollutants in oxygen-limited systems. To understand what machinery "Ca Methanoperedens nitroreducens" possesses to counteract the oxidative stress and survive, we characterized the response to oxygen exposure using a multi-omics approach.
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Affiliation(s)
- Simon Guerrero-Cruz
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Geert Cremers
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Theo A van Alen
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
- Royal Netherlands Institute for Sea Research, Texel, the Netherlands
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de Jong AEE, In 't Zandt MH, Meisel OH, Jetten MSM, Dean JF, Rasigraf O, Welte CU. Increases in temperature and nutrient availability positively affect methane-cycling microorganisms in Arctic thermokarst lake sediments. Environ Microbiol 2018; 20:4314-4327. [PMID: 29968310 PMCID: PMC6334529 DOI: 10.1111/1462-2920.14345] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/27/2018] [Accepted: 06/27/2018] [Indexed: 11/30/2022]
Abstract
Arctic permafrost soils store large amounts of organic matter that is sensitive to temperature increases and subsequent microbial degradation to methane (CH4) and carbon dioxide (CO2). Here, we studied methanogenic and methanotrophic activity and community composition in thermokarst lake sediments from Utqiag˙vik (formerly Barrow), Alaska. This experiment was carried out under in situ temperature conditions (4°C) and the IPCC 2013 Arctic climate change scenario (10°C) after addition of methanogenic and methanotrophic substrates for nearly a year. Trimethylamine (TMA) amendment with warming showed highest maximum CH4production rates, being 30% higher at 10°C than at 4°C. Maximum methanotrophic rates increased by up to 57% at 10°C compared to 4°C. 16S rRNA gene sequencing indicated high relative abundance of Methanosarcinaceae in TMA amended incubations, and for methanotrophic incubations Methylococcaeae were highly enriched. Anaerobic methanotrophic activity with nitrite or nitrate as electron acceptor was not detected. This study indicates that the methane cycling microbial community can adapt to temperature increases and that their activity is highly dependent on substrate availability.
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Affiliation(s)
- Anniek E E de Jong
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Michiel H In 't Zandt
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Ove H Meisel
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands.,Department of Earth Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Joshua F Dean
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands.,Department of Earth Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Rasigraf O, Schmitt J, Jetten MSM, Lüke C. Metagenomic potential for and diversity of N-cycle driving microorganisms in the Bothnian Sea sediment. Microbiologyopen 2017; 6. [PMID: 28544522 PMCID: PMC5552932 DOI: 10.1002/mbo3.475] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [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: 10/22/2016] [Revised: 02/13/2017] [Accepted: 02/22/2017] [Indexed: 11/10/2022] Open
Abstract
The biological nitrogen cycle is driven by a plethora of reactions transforming nitrogen compounds between various redox states. Here, we investigated the metagenomic potential for nitrogen cycle of the in situ microbial community in an oligotrophic, brackish environment of the Bothnian Sea sediment. Total DNA from three sediment depths was isolated and sequenced. The characterization of the total community was performed based on 16S rRNA gene inventory using SILVA database as reference. The diversity of diagnostic functional genes coding for nitrate reductases (napA;narG), nitrite:nitrate oxidoreductase (nxrA), nitrite reductases (nirK;nirS;nrfA), nitric oxide reductase (nor), nitrous oxide reductase (nosZ), hydrazine synthase (hzsA), ammonia monooxygenase (amoA), hydroxylamine oxidoreductase (hao), and nitrogenase (nifH) was analyzed by blastx against curated reference databases. In addition, Polymerase chain reaction (PCR)‐based amplification was performed on the hzsA gene of anammox bacteria. Our results reveal high genomic potential for full denitrification to N2, but minor importance of anaerobic ammonium oxidation and dissimilatory nitrite reduction to ammonium. Genomic potential for aerobic ammonia oxidation was dominated by Thaumarchaeota. A higher diversity of anammox bacteria was detected in metagenomes than with PCR‐based technique. The results reveal the importance of various N‐cycle driving processes and highlight the advantage of metagenomics in detection of novel microbial key players.
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Affiliation(s)
- Olivia Rasigraf
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Julia Schmitt
- DVGW-Forschungsstelle TUHH, Hamburg University of Technology, Hamburg, Germany
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
| | - Claudia Lüke
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
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Welte CU, Rasigraf O, Vaksmaa A, Versantvoort W, Arshad A, Op den Camp HJM, Jetten MSM, Lüke C, Reimann J. Nitrate- and nitrite-dependent anaerobic oxidation of methane. Environ Microbiol Rep 2016; 8:941-955. [PMID: 27753265 DOI: 10.1111/1758-2229.12487] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Microbial methane oxidation is an important process to reduce the emission of the greenhouse gas methane. Anaerobic microorganisms couple the oxidation of methane to the reduction of sulfate, nitrate and nitrite, and possibly oxidized iron and manganese minerals. In this article, we review the recent finding of the intriguing nitrate- and nitrite-dependent anaerobic oxidation of methane (AOM). Nitrate-dependent AOM is catalyzed by anaerobic archaea belonging to the ANME-2d clade closely related to Methanosarcina methanogens. They were named 'Candidatus Methanoperedens nitroreducens' and use reverse methanogenesis with the key enzyme methyl-coenzyme M (methyl-CoM) reductase for methane activation. Their major end product is nitrite which can be taken up by nitrite-dependent methanotrophs. Nitrite-dependent AOM is performed by the NC10 bacterium 'Candidatus Methylomirabilis oxyfera' that probably utilizes an intra-aerobic pathway through the dismutation of NO to N2 and O2 for aerobic methane activation by methane monooxygenase, yet being a strictly anaerobic microbe. Environmental distribution, physiological and biochemical aspects are discussed in this article as well as the cooperation of the microorganisms involved.
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Affiliation(s)
- Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Netherlands Earth Systems Science Center, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Arslan Arshad
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Netherlands Earth Systems Science Center, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Claudia Lüke
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
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Egger M, Rasigraf O, Sapart CJ, Jilbert T, Jetten MSM, Röckmann T, van der Veen C, Bândă N, Kartal B, Ettwig KF, Slomp CP. Iron-mediated anaerobic oxidation of methane in brackish coastal sediments. Environ Sci Technol 2015; 49:277-283. [PMID: 25412274 DOI: 10.1021/es503663z] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Methane is a powerful greenhouse gas and its biological conversion in marine sediments, largely controlled by anaerobic oxidation of methane (AOM), is a crucial part of the global carbon cycle. However, little is known about the role of iron oxides as an oxidant for AOM. Here we provide the first field evidence for iron-dependent AOM in brackish coastal surface sediments and show that methane produced in Bothnian Sea sediments is oxidized in distinct zones of iron- and sulfate-dependent AOM. At our study site, anthropogenic eutrophication over recent decades has led to an upward migration of the sulfate/methane transition zone in the sediment. Abundant iron oxides and high dissolved ferrous iron indicate iron reduction in the methanogenic sediments below the newly established sulfate/methane transition. Laboratory incubation studies of these sediments strongly suggest that the in situ microbial community is capable of linking methane oxidation to iron oxide reduction. Eutrophication of coastal environments may therefore create geochemical conditions favorable for iron-mediated AOM and thus increase the relevance of iron-dependent methane oxidation in the future. Besides its role in mitigating methane emissions, iron-dependent AOM strongly impacts sedimentary iron cycling and related biogeochemical processes through the reduction of large quantities of iron oxides.
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Affiliation(s)
- Matthias Egger
- Department of Earth Sciences - Geochemistry, Faculty of Geosciences, Utrecht University , Budapestlaan 4, 3584 CD Utrecht, The Netherlands
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