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Venetz J, Żygadłowska OM, Dotsios N, Wallenius AJ, van Helmond NAGM, Lenstra WK, Klomp R, Slomp CP, Jetten MSM, Veraart AJ. Seasonal dynamics of the microbial methane filter in the water column of a eutrophic coastal basin. FEMS Microbiol Ecol 2024; 100:fiae007. [PMID: 38281061 PMCID: PMC10939384 DOI: 10.1093/femsec/fiae007] [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: 10/30/2023] [Revised: 12/08/2023] [Accepted: 01/25/2024] [Indexed: 01/29/2024] Open
Abstract
In coastal waters, methane-oxidizing bacteria (MOB) can form a methane biofilter and mitigate methane emissions. The metabolism of these MOBs is versatile, and the resilience to changing oxygen concentrations is potentially high. It is still unclear how seasonal changes in oxygen availability and water column chemistry affect the functioning of the methane biofilter and MOB community composition. Here, we determined water column methane and oxygen depth profiles, the methanotrophic community structure, methane oxidation potential, and water-air methane fluxes of a eutrophic marine basin during summer stratification and in the mixed water in spring and autumn. In spring, the MOB diversity and relative abundance were low. Yet, MOB formed a methane biofilter with up to 9% relative abundance and vertical niche partitioning during summer stratification. The vertical distribution and potential methane oxidation of MOB did not follow the upward shift of the oxycline during summer, and water-air fluxes remained below 0.6 mmol m-2 d-1. Together, this suggests active methane removal by MOB in the anoxic water. Surprisingly, with a weaker stratification, and therefore potentially increased oxygen supply, methane oxidation rates decreased, and water-air methane fluxes increased. Thus, despite the potential resilience of the MOB community, seasonal water column dynamics significantly influence methane removal.
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Affiliation(s)
- Jessica Venetz
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Olga M Żygadłowska
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Nicky Dotsios
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Anna J Wallenius
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Niels A G M van Helmond
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Wytze K Lenstra
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Robin Klomp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Caroline P Slomp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
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Venetz J, Żygadłowska OM, Lenstra WK, van Helmond NAGM, Nuijten GHL, Wallenius AJ, Dalcin Martins P, Slomp CP, Jetten MSM, Veraart AJ. Versatile methanotrophs form an active methane biofilter in the oxycline of a seasonally stratified coastal basin. Environ Microbiol 2023; 25:2277-2288. [PMID: 37381163 DOI: 10.1111/1462-2920.16448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 05/31/2023] [Indexed: 06/30/2023]
Abstract
The potential and drivers of microbial methane removal in the water column of seasonally stratified coastal ecosystems and the importance of the methanotrophic community composition for ecosystem functioning are not well explored. Here, we combined depth profiles of oxygen and methane with 16S rRNA gene amplicon sequencing, metagenomics and methane oxidation rates at discrete depths in a stratified coastal marine system (Lake Grevelingen, The Netherlands). Three amplicon sequence variants (ASVs) belonging to different genera of aerobic Methylomonadaceae and the corresponding three methanotrophic metagenome-assembled genomes (MOB-MAGs) were retrieved by 16S rRNA sequencing and metagenomic analysis, respectively. The abundances of the different methanotrophic ASVs and MOB-MAGs peaked at different depths along the methane oxygen counter-gradient and the MOB-MAGs show a quite diverse genomic potential regarding oxygen metabolism, partial denitrification and sulphur metabolism. Moreover, potential aerobic methane oxidation rates indicated high methanotrophic activity throughout the methane oxygen counter-gradient, even at depths with low in situ methane or oxygen concentration. This suggests that niche-partitioning with high genomic versatility of the present Methylomonadaceae might contribute to the functional resilience of the methanotrophic community and ultimately the efficiency of methane removal in the stratified water column of a marine basin.
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Affiliation(s)
- Jessica Venetz
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Olga M Żygadłowska
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Wytze K Lenstra
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Niels A G M van Helmond
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Guylaine H L Nuijten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Anna J Wallenius
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Paula Dalcin Martins
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Caroline P Slomp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
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Lenstra WK, van Helmond NAGM, Martins PD, Wallenius AJ, Jetten MSM, Slomp CP. Gene-Based Modeling of Methane Oxidation in Coastal Sediments: Constraints on the Efficiency of the Microbial Methane Filter. Environ Sci Technol 2023; 57:12722-12731. [PMID: 37585543 PMCID: PMC10469488 DOI: 10.1021/acs.est.3c02023] [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: 03/16/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/18/2023]
Abstract
Methane is a powerful greenhouse gas that is produced in large quantities in marine sediments. Microbially mediated oxidation of methane in sediments, when in balance with methane production, prevents the release of methane to the overlying water. Here, we present a gene-based reactive transport model that includes both microbial and geochemical dynamics and use it to investigate whether the rate of growth of methane oxidizers in sediments impacts the efficiency of the microbial methane filter. We focus on iron- and methane-rich coastal sediments and, with the model, show that at our site, up to 10% of all methane removed is oxidized by iron and manganese oxides, with the remainder accounted for by oxygen and sulfate. We demonstrate that the slow growth rate of anaerobic methane-oxidizing microbes limits their ability to respond to transient perturbations, resulting in periodic benthic release of methane. Eutrophication and deoxygenation decrease the efficiency of the microbial methane filter further, thereby enhancing the role of coastal environments as a source of methane to the atmosphere.
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Affiliation(s)
- Wytze K. Lenstra
- Department
of Earth Sciences—Geochemistry, Utrecht
University, Princetonlaan 8a, 3584 CB Utrecht, The Netherlands
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Niels A. G. M. van Helmond
- Department
of Earth Sciences—Geochemistry, Utrecht
University, Princetonlaan 8a, 3584 CB Utrecht, The Netherlands
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Paula Dalcin Martins
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Anna J. Wallenius
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Mike S. M. Jetten
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Caroline P. Slomp
- Department
of Earth Sciences—Geochemistry, Utrecht
University, Princetonlaan 8a, 3584 CB Utrecht, The Netherlands
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Wallenius AJ, Dalcin Martins P, Slomp CP, Jetten MSM. Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments. Front Microbiol 2021; 12:631621. [PMID: 33679659 PMCID: PMC7935538 DOI: 10.3389/fmicb.2021.631621] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 11/20/2020] [Accepted: 01/29/2021] [Indexed: 12/05/2022] Open
Abstract
Large amounts of methane, a potent greenhouse gas, are produced in anoxic sediments by methanogenic archaea. Nonetheless, over 90% of the produced methane is oxidized via sulfate-dependent anaerobic oxidation of methane (S-AOM) in the sulfate-methane transition zone (SMTZ) by consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Coastal systems account for the majority of total marine methane emissions and typically have lower sulfate concentrations, hence S-AOM is less significant. However, alternative electron acceptors such as metal oxides or nitrate could be used for AOM instead of sulfate. The availability of electron acceptors is determined by the redox zonation in the sediment, which may vary due to changes in oxygen availability and the type and rate of organic matter inputs. Additionally, eutrophication and climate change can affect the microbiome, biogeochemical zonation, and methane cycling in coastal sediments. This review summarizes the current knowledge on the processes and microorganisms involved in methane cycling in coastal sediments and the factors influencing methane emissions from these systems. In eutrophic coastal areas, organic matter inputs are a key driver of bottom water hypoxia. Global warming can reduce the solubility of oxygen in surface waters, enhancing water column stratification, increasing primary production, and favoring methanogenesis. ANME are notoriously slow growers and may not be able to effectively oxidize methane upon rapid sedimentation and shoaling of the SMTZ. In such settings, ANME-2d (Methanoperedenaceae) and ANME-2a may couple iron- and/or manganese reduction to AOM, while ANME-2d and NC10 bacteria (Methylomirabilota) could couple AOM to nitrate or nitrite reduction. Ultimately, methane may be oxidized by aerobic methanotrophs in the upper millimeters of the sediment or in the water column. The role of these processes in mitigating methane emissions from eutrophic coastal sediments, including the exact pathways and microorganisms involved, are still underexplored, and factors controlling these processes are unclear. Further studies are needed in order to understand the factors driving methane-cycling pathways and to identify the responsible microorganisms. Integration of the knowledge on microbial pathways and geochemical processes is expected to lead to more accurate predictions of methane emissions from coastal zones in the future.
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Affiliation(s)
- Anna J. Wallenius
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Paula Dalcin Martins
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Caroline P. Slomp
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
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Picone N, Blom P, Wallenius AJ, Hogendoorn C, Mesman R, Cremers G, Gagliano AL, D'Alessandro W, Quatrini P, Jetten MSM, Pol A, Op den Camp HJM. Methylacidimicrobium thermophilum AP8, a Novel Methane- and Hydrogen-Oxidizing Bacterium Isolated From Volcanic Soil on Pantelleria Island, Italy. Front Microbiol 2021; 12:637762. [PMID: 33643272 PMCID: PMC7907005 DOI: 10.3389/fmicb.2021.637762] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 12/04/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
The Favara Grande is a geothermal area located on Pantelleria Island, Italy. The area is characterized high temperatures in the top layer of the soil (60°C), low pH (3–5) and hydrothermal gas emissions mainly composed of carbon dioxide (CO2), methane (CH4), and hydrogen (H2). These geothermal features may provide a suitable niche for the growth of chemolithotrophic thermoacidophiles, including the lanthanide-dependent methanotrophs of the phylum Verrucomicrobia. In this study, we started enrichment cultures inoculated with soil of the Favara Grande at 50 and 60°C with CH4 as energy source and medium containing sufficient lanthanides at pH 3 and 5. From these cultures, a verrucomicrobial methanotroph could be isolated via serial dilution and floating filters techniques. The genome of strain AP8 was sequenced and based on phylogenetic analysis we propose to name this new species Methylacidimicrobium thermophilum AP8. The transcriptome data at μmax (0.051 ± 0.001 h−1, doubling time ~14 h) of the new strain showed a high expression of the pmoCAB2 operon encoding the membrane-bound methane monooxygenase and of the gene xoxF1, encoding the lanthanide-dependent methanol dehydrogenase. A second pmoCAB operon and xoxF2 gene were not expressed. The physiology of strain AP8 was further investigated and revealed an optimal growth in a pH range of 3–5 at 50°C, representing the first thermophilic strain of the genus Methylacidimicrobium. Moreover, strain AP8 had a KS(app) for methane of 8 ± 1 μM. Beside methane, a type 1b [NiFe] hydrogenase enabled hydrogen oxidation at oxygen concentrations up to 1%. Taken together, our results expand the knowledge on the characteristics and adaptations of verrucomicrobial methanotrophs in hydrothermal environments and add a new thermophilic strain to the genus Methylacidimicrobium.
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Affiliation(s)
- Nunzia Picone
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Pieter Blom
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Anna J Wallenius
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Carmen Hogendoorn
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Rob Mesman
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Geert Cremers
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | | | | | - Paola Quatrini
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Arjan Pol
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
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