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Shulman HB, Aronson EL, Dierick D, Pinto‐Tomás AA, Botthoff JK, Artavia‐León A, Allen MF. Leafcutter ants enhance microbial drought resilience in tropical forest soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13251. [PMID: 38778789 PMCID: PMC11112399 DOI: 10.1111/1758-2229.13251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/15/2024] [Indexed: 05/25/2024]
Abstract
We conducted a research campaign in a neotropical rainforest in Costa Rica throughout the drought phase of an El-Nino Southern Oscillation event to determine microbial community dynamics and soil C fluxes. Our study included nests of the leafcutter ant Atta cephalotes, as soil disturbances made by these ecosystem engineers may influence microbial drought response. Drought decreased the diversity of microbes and the abundance of core microbiome taxa, including Verrucomicrobial bacteria and Sordariomycete fungi. Despite initial responses of decreasing diversity and altered composition, 6 months post-drought the microbiomes were similar to pre-drought conditions, demonstrating the resilience of soil microbial communities to drought events. A. cephalotes nests altered fungal composition in the surrounding soil, and reduced both fungal mortality and growth of Acidobacteria post-drought. Drought increased CH4 consumption in soils due to lower soil moisture, and A. cephalotes nests decrease the variability of CH4 emissions in some soil types. CH4 emissions were tracked by the abundance of methanotrophic bacteria and fungal composition. These results characterize the microbiome of tropical soils across both time and space during drought and provide evidence for the importance of leafcutter ant nests in shaping soil microbiomes and enhancing microbial resilience during climatic perturbations.
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Affiliation(s)
- Hannah B. Shulman
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Emma L. Aronson
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
- Center for Conservation BiologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - Diego Dierick
- Department of Biological SciencesFlorida International UniversityMiamiFloridaUSA
| | - Andrian A. Pinto‐Tomás
- Centro De Investigación En Estructuras MicroscópicasUniversidad de Costa RicaSan JoséCosta Rica
| | - Jon K. Botthoff
- Center for Conservation BiologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - Allan Artavia‐León
- Centro De Investigación En Estructuras MicroscópicasUniversidad de Costa RicaSan JoséCosta Rica
| | - Michael F. Allen
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
- Center for Conservation BiologyUniversity of CaliforniaRiversideCaliforniaUSA
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2
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Vesamäki JS, Laine MB, Nissinen R, Taipale SJ. Plastic and terrestrial organic matter degradation by the humic lake microbiome continues throughout the seasons. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13302. [PMID: 38852938 PMCID: PMC11162827 DOI: 10.1111/1758-2229.13302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/15/2024] [Indexed: 06/11/2024]
Abstract
Boreal freshwaters go through four seasons, however, studies about the decomposition of terrestrial and plastic compounds often focus only on summer. We compared microbial decomposition of 13C-polyethylene, 13C-polystyrene, and 13C-plant litter (Typha latifolia) by determining the biochemical fate of the substrate carbon and identified the microbial decomposer taxa in humic lake waters in four seasons. For the first time, the annual decomposition rate including separated seasonal variation was calculated for microplastics and plant litter in the freshwater system. Polyethylene decomposition was not detected, whereas polystyrene and plant litter were degraded in all seasons. In winter, decomposition rates of polystyrene and plant litter were fivefold and fourfold slower than in summer, respectively. Carbon from each substrate was mainly respired in all seasons. Plant litter was utilized efficiently by various microbial groups, whereas polystyrene decomposition was limited to Alpha- and Gammaproteobacteria. The decomposition was not restricted only to the growth season, highlighting that the decomposition of both labile organic matter and extremely recalcitrant microplastics continues throughout the seasons.
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Affiliation(s)
- Jussi S. Vesamäki
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Miikka B. Laine
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Riitta Nissinen
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
- Department of BiologyUniversity of TurkuTurkuFinland
| | - Sami J. Taipale
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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3
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Bydalek F, Webster G, Barden R, Weightman AJ, Kasprzyk-Hordern B, Wenk J. Microbial community and antimicrobial resistance niche differentiation in a multistage, surface flow constructed wetland. WATER RESEARCH 2024; 254:121408. [PMID: 38442607 DOI: 10.1016/j.watres.2024.121408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 03/07/2024]
Abstract
Free-living (FL) and particulate-associated (PA) communities are distinct bacterioplankton lifestyles with different mobility and dissemination routes. Understanding spatio-temporal dynamics of PA and FL fractions will allow improvement to wastewater treatment processes including pathogen and AMR bacteria removal. In this study, PA, FL and sediment community composition and antimicrobial resistance gene (ARG; tetW, ermB, sul1, intI1) dynamics were investigated in a full-scale municipal wastewater free-water surface polishing constructed wetland. Taxonomic composition of PA and FL microbial communities shifted towards less diverse communities (Shannon, Chao1) at the CW effluent but retained a distinct fraction-specific composition. Wastewater treatment plant derived PA communities introduced the bulk of AMR load (70 %) into the CW. However, the FL fraction was responsible for exporting over 60 % of the effluent AMR load given its high mobility and the effective immobilization (1-3 log removal) of PA communities. Strong correlations (r2>0.8, p < 0.05) were observed between the FL fraction, tetW and emrB dynamics, and amplicon sequence variants (ASVs) of potentially pathogenic taxa, including Bacteroides, Enterobacteriaceae, Aeromonadaceae, and Lachnospiraceae. This study reveals niche differentiation of microbial communities and associated AMR in CWs and shows that free-living bacteria are a primary escape route of pathogenic and ARG load from CWs under low-flow hydraulic conditions.
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Affiliation(s)
- Franciszek Bydalek
- Department of Chemical Engineering, University of Bath, Claverton Down, Bath BA2 7AY, UK; Water Innovation and Research Centre (WIRC), University of Bath, Bath BA2 7AY, UK; GW4 NERC CDT in Freshwater Biosciences and Sustainability, Cardiff University, Cardiff CF10 3AX, UK; Organisms and Environment Division, School of Biosciences, Microbiomes, Microbes and Informatics Group, Cardiff University, Cardiff CF10 3AX, UK
| | - Gordon Webster
- Organisms and Environment Division, School of Biosciences, Microbiomes, Microbes and Informatics Group, Cardiff University, Cardiff CF10 3AX, UK
| | | | - Andrew J Weightman
- Organisms and Environment Division, School of Biosciences, Microbiomes, Microbes and Informatics Group, Cardiff University, Cardiff CF10 3AX, UK
| | - Barbara Kasprzyk-Hordern
- Water Innovation and Research Centre (WIRC), University of Bath, Bath BA2 7AY, UK; Department of Chemistry, University of Bath, Bath BA2 7AY, UK
| | - Jannis Wenk
- Department of Chemical Engineering, University of Bath, Claverton Down, Bath BA2 7AY, UK; Water Innovation and Research Centre (WIRC), University of Bath, Bath BA2 7AY, UK.
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4
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Ouyang MY, Wang S, Nie WH, Wang PH, Liao WX, Liu XH, Lin SS, Lin RP, Chen GY, Zhu B, Shen J. Methylomonas defluvii sp. nov., a type I methane-oxidizing bacterium from a secondary sedimentation tank of a wastewater treatment plant. Int J Syst Evol Microbiol 2024; 74. [PMID: 38607367 DOI: 10.1099/ijsem.0.006321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024] Open
Abstract
An aerobic methanotroph was isolated from a secondary sedimentation tank of a wastewater treatment plant and designated strain OY6T. Cells of OY6T were Gram-stain-negative, pink-pigmented, motile rods and contained an intracytoplasmic membrane structure typical of type I methanotrophs. OY6T could grow at a pH range of 4.5-7.5 (optimum pH 6.5) and at temperatures ranging from 20 °C to 37 °C (optimum 30 °C). The major cellular fatty acids were C14 : 0, C16 : 1ω7c/C16 : 1ω6c and C16 : 1ω5c; the predominant respiratory quinone was MQ-8. The genome size was 5.41 Mbp with a DNA G+C content of 51.7 mol%. OY6T represents a member of the family Methylococcaceae of the class Gammaproteobacteria and displayed 95.74-99.64 % 16S rRNA gene sequence similarity to the type strains of species of the genus Methylomonas. Whole-genome comparisons based on average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) confirmed that OY6T should be classified as representing a novel species. The most closely related type strain was Methylomonas fluvii EbBT, with 16S rRNA gene sequence similarity, ANI by blast (ANIb), ANI by MUMmer (ANIm) and dDDH values of 99.64, 90.46, 91.92 and 44.5 %, respectively. OY6T possessed genes encoding both the particulate methane monooxygenase enzyme and the soluble methane monooxygenase enzyme. It grew only on methane or methanol as carbon sources. On the basis of phenotypic, genetic and phylogenetic data, strain OY6T represents a novel species within the genus Methylomonas for which the name Methylomonas defluvii sp. nov. is proposed, with strain OY6T (=GDMCC 1.4114T=KCTC 8159T=LMG 33371T) as the type strain.
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Affiliation(s)
- Ming-Yan Ouyang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Sai Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Wen-Han Nie
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Pei-Hong Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Wei-Xue Liao
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Xiao-Hui Liu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Si-Si Lin
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Rong-Peng Lin
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Gong-You Chen
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Bo Zhu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Jian Shen
- People's Hospital, Hangzhou 310014, Zhejiang, PR China
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5
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Patil SK, Islam T, Tveit A, Hodson A, Øvreås L. Targeting methanotrophs and isolation of a novel psychrophilic Methylobacter species from a terrestrial Arctic alkaline methane seep in Lagoon Pingo, Central Spitsbergen (78° N). Antonie Van Leeuwenhoek 2024; 117:60. [PMID: 38517574 PMCID: PMC10959801 DOI: 10.1007/s10482-024-01953-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/19/2024] [Indexed: 03/24/2024]
Abstract
The microbial diversity associated with terrestrial groundwater seepage through permafrost soils is tightly coupled to the geochemistry of these fluids. Terrestrial alkaline methane seeps from Lagoon Pingo, Central Spitsbergen (78°N) in Norway, with methane-saturated and oxygen-limited groundwater discharge providing a potential habitat for methanotrophy. Here, we report on the microbial community's comparative analyses and distribution patterns at two sites close to Lagoon Pingo's methane emission source. To target methane-oxidizing bacteria from this system, we analysed the microbial community pattern of replicate samples from two sections near the main methane seepage source. DNA extraction, metabarcoding and subsequent sequencing of 16S rRNA genes revealed microbial communities where the major prokaryotic phyla were Pseudomonadota (42-47%), Gemmatimonadota (4-14%) and Actinobacteriota (7-11%). Among the Pseudomonadota, members of the genus Methylobacter were present at relative abundances between 1.6 and 4.7%. Enrichment targeting the methane oxidising bacteria was set up using methane seep sediments as inoculum and methane as the sole carbon and energy source, and this resulted in the isolation of a novel psychrophilic methane oxidizer, LS7-T4AT. The optimum growth temperature for the isolate was 13 °C and the pH optimum was 8.0. The morphology of cells was short rods, and TEM analysis revealed intracytoplasmic membranes arranged in stacks, a distinctive feature for Type I methanotrophs in the family Methylomonadaceae of the class Gammaproteobacteria. The strain belongs to the genus Methylobacter based on high 16S rRNA gene similarity to the psychrophilic species of Methylobacter psychrophilus Z-0021T (98.95%), the psychrophilic strain Methylobacter sp. strain S3L5C (99.00%), and the Arctic mesophilic species of Methylobacter tundripaludum SV96T (99.06%). The genome size of LS7-T4AT was 4,338,157 bp with a G + C content of 47.93%. The average nucleotide identities (ANIb) of strain LS7-T4AT to 10 isolated strains of genus Methylobacter were between 75.54 and 85.51%, lower than the species threshold of 95%. The strain LS7-T4AT represents a novel Arctic species, distinct from other members of the genus Methylobacter, for which the name Methylobacter svalbardensis sp. nov. is proposed. The type of strain is LS7-T4AT (DSMZ:114308, JCM:39463).
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Affiliation(s)
- Shalaka K Patil
- Department of Biological Sciences, University of Bergen, Postboks 7803, 5020, Bergen, Norway.
| | - Tajul Islam
- Department of Biological Sciences, University of Bergen, Postboks 7803, 5020, Bergen, Norway
| | - Alexander Tveit
- Department of Arctic and Marine Biology, The Arctic University of Tromsø, 9037, Tromsø, Norway
| | - Andrew Hodson
- University Centre in Svalbard, 9171, Longyearbyen, Norway
| | - Lise Øvreås
- Department of Biological Sciences, University of Bergen, Postboks 7803, 5020, Bergen, Norway
- University Centre in Svalbard, 9171, Longyearbyen, Norway
- Bjerknes Centre for Climate Research, Jahnebakken 5, 5007, Bergen, Norway
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6
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Liu C, Schmitz RA, Pol A, Hogendoorn C, Verhagen D, Peeters SH, van Alen TA, Cremers G, Mesman RA, Op den Camp HJM. Active coexistence of the novel gammaproteobacterial methanotroph 'Ca. Methylocalor cossyra' CH1 and verrucomicrobial methanotrophs in acidic, hot geothermal soil. Environ Microbiol 2024; 26:e16602. [PMID: 38454738 DOI: 10.1111/1462-2920.16602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024]
Abstract
Terrestrial geothermal ecosystems are hostile habitats, characterized by large emissions of environmentally relevant gases such as CO2 , CH4 , H2 S and H2 . These conditions provide a niche for chemolithoautotrophic microorganisms. Methanotrophs of the phylum Verrucomicrobia, which inhabit these ecosystems, can utilize these gases and grow at pH levels below 1 and temperatures up to 65°C. In contrast, methanotrophs of the phylum Proteobacteria are primarily found in various moderate environments. Previously, novel verrucomicrobial methanotrophs were detected and isolated from the geothermal soil of the Favara Grande on the island of Pantelleria, Italy. The detection of pmoA genes, specific for verrucomicrobial and proteobacterial methanotrophs in this environment, and the partially overlapping pH and temperature growth ranges of these isolates suggest that these distinct phylogenetic groups could coexist in the environment. In this report, we present the isolation and characterization of a thermophilic and acid-tolerant gammaproteobacterial methanotroph (family Methylococcaceae) from the Favara Grande. This isolate grows at pH values ranging from 3.5 to 7.0 and temperatures from 35°C to 55°C, and diazotrophic growth was demonstrated. Its genome contains genes encoding particulate and soluble methane monooxygenases, XoxF- and MxaFI-type methanol dehydrogenases, and all enzymes of the Calvin cycle. For this novel genus and species, we propose the name 'Candidatus Methylocalor cossyra' CH1.
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Affiliation(s)
- Changqing Liu
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Rob A Schmitz
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Arjan Pol
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Carmen Hogendoorn
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Daniël Verhagen
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Stijn H Peeters
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Theo A van Alen
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Geert Cremers
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Rob A Mesman
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
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7
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Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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8
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Li H, Bao L, Wang T, Guan Y. Dietary change influences the composition of the fecal microbiota in two rescued wild raccoon dogs ( Nyctereutes procyonoides). Front Microbiol 2024; 15:1335017. [PMID: 38404601 PMCID: PMC10884114 DOI: 10.3389/fmicb.2024.1335017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/23/2024] [Indexed: 02/27/2024] Open
Abstract
The gut microbiota of wild animals, influenced by various factors including diet, nutrition, gender, and age, plays a critical role in their health and disease status. This study focuses on raccoon dogs (Nyctereutes procyonoides), a commonly found wild animal, and its gut microbiota composition in response to dietary shifts. The study aimed to compare the fecal bacterial communities and diversity of rescued raccoon dogs fed three different diet types (fish and amphibians, mixed protein with maize, and solely maize) using high-throughput sequencing. Results indicated that the dietary composition significantly influenced the gut microbiota, with notable differences in the abundance of several key phyla and genera. The study identified Firmicutes as the dominant phylum in all diet groups, with notable variations in the relative abundances of Bacteroidota, Proteobacteria, and Verrucomicrobiota. Notably, the group solely fed maize exhibited a significant increase in Proteobacteria, potentially linked to dietary fiber and lignin degradation. The genus-level analysis highlighted significant differences, with Lactobacillus and Bifidobacterium responding to dietary shifts. The genus Akkermansia in Verrucomicrobiota can be identified as a marker for assessing the health of the gut and deserves further investigation. Gender-specific differences in the gut microbiota were observed, highlighting the influence of individual variation. Furthermore, the analysis of bacterial functions suggested a connection between diet and host metabolism, emphasizing the need for further research to understand the complex mechanisms underlying the relationship between dietary composition and gut microbiota in wild animals. These findings provide crucial insights into conservation and rescue efforts for wild animals.
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Affiliation(s)
- Hailong Li
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing Normal University, Beijing, China
- College of Geography and Ocean Science, Yanbian University, Yanji, China
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea
| | - Lei Bao
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing Normal University, Beijing, China
| | - Tianming Wang
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing Normal University, Beijing, China
| | - Yu Guan
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing Normal University, Beijing, China
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9
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Asiedu E, Zhao K, Anwar MN, Ross M, Balaberda AL, Ulrich AC. Biodegradation in oil sands process-affected water: A comprehensive laboratory analysis of the in situ biodegradation of dissolved organic acids. CHEMOSPHERE 2024; 349:141018. [PMID: 38141671 DOI: 10.1016/j.chemosphere.2023.141018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/25/2023]
Abstract
Oil sands process-affected water (OSPW) is a by-product of the extraction of bitumen, and volumes of OSPW have accumulated across the Alberta oil sands region due to the governments zero-discharge policy. Some dissolved organics in OSPW, including toxic naphthenic acids (NAs), can be biodegraded in oxic conditions, thereby reducing the toxicity of OSPW. While there has been much focus on degradation of NAs, the biodegradation of other dissolved organic chemicals by endogenous organisms remains understudied. Here, using the HPLC-ultrahigh resolution Orbitrap mass spectrometry, we examined the microbial biodegradation of dissolved organic acids in OSPW. Non-targeted analysis enabled the estimation of biodegradation rates for unique heteroatomic chemical classes detected in negative ion mode. The microcosm experiments were conducted with and without nutrient supplementation, and the changes in the microbial community over time were investigated. Without added nutrients, internal standard-adjusted intensities of all organics, including NAs, were largely unchanged. The addition of nutrients increased the biodegradation rate of O2- and SO2- chemical classes. While anoxic biodegradation can occur in tailings ponds and end pit lakes, microbial community analyses confirmed that the presence of oxygen stimulated biodegradation of the OSPW samples studied. We detected several aerobic hydrocarbon-degrading microbes (e.g., Pseudomonas and Brevundimonas), and microbes capable of degrading sulfur-containing hydrocarbons (e.g., Microbacterium). Microbial community diversity decreased over time with nutrient addition. Overall, the results from this study indicate that toxic dissolved organics beyond NAs can be biodegraded by endogenous organisms in OSPW, but reaffirms that biological treatment strategies require careful consideration of how nutrients and dissolved oxygen may impact efficacy.
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Affiliation(s)
- Evelyn Asiedu
- Division of Analytical & Environmental Toxicology, Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Mian Nabeel Anwar
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Matthew Ross
- Department of Physical Sciences, MacEwan University, Edmonton, Alberta, T5J 2P2, Canada
| | - Amy-Lynne Balaberda
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Ania C Ulrich
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada.
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10
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Reis PCJ, Tsuji JM, Weiblen C, Schiff SL, Scott M, Stein LY, Neufeld JD. Enigmatic persistence of aerobic methanotrophs in oxygen-limiting freshwater habitats. THE ISME JOURNAL 2024; 18:wrae041. [PMID: 38470309 PMCID: PMC11008690 DOI: 10.1093/ismejo/wrae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/06/2024] [Accepted: 03/13/2024] [Indexed: 03/13/2024]
Abstract
Methanotrophic bacteria mitigate emissions of the potent greenhouse gas methane (CH4) from a variety of anthropogenic and natural sources, including freshwater lakes, which are large sources of CH4 on a global scale. Despite a dependence on dioxygen (O2) for CH4 oxidation, abundant populations of putatively aerobic methanotrophs have been detected within microoxic and anoxic waters and sediments of lakes. Experimental work has demonstrated active aerobic methanotrophs under those conditions, but how they are able to persist and oxidize CH4 under O2 deficiency remains enigmatic. In this review, we discuss possible mechanisms that underpin the persistence and activity of aerobic methanotrophs under O2-limiting conditions in freshwater habitats, particularly lakes, summarize experimental evidence for microbial oxidation of CH4 by aerobic bacteria under low or no O2, and suggest future research directions to further explore the ecology and metabolism of aerobic methanotrophs in O2-limiting environments.
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Affiliation(s)
- Paula C J Reis
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Jackson M Tsuji
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Cerrise Weiblen
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Sherry L Schiff
- Department of Earth & Environmental Sciences, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Matthew Scott
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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11
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Wang F, Zhang S, Hu X, Lv X, Liu M, Ma Y, Manirakiza B. Floating plants reduced methane fluxes from wetlands by creating a habitat conducive to methane oxidation. J Environ Sci (China) 2024; 135:149-160. [PMID: 37778791 DOI: 10.1016/j.jes.2023.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 10/03/2023]
Abstract
Wetlands are one of the important natural sources of atmospheric methane (CH4), as an important part of wetlands, floating plants can be expected to affect methane release. However, the effects of floating plants on methane release are limited. In this study, methane fluxes, physiochemical properties of the overlying water, methane oxidation potential and rhizospheric bacterial community were investigated in simulated wetlands with floating plants Eichhornia crassipes, Hydrocharis dubia, and Trapa natans. We found that E. crassipes, H. dubia, and T. natans plants could inhibit 84.31% - 97.31%, 4.98% - 88.91% and 43.62% - 92.51% of methane fluxes at interface of water-atmosphere compared to Control, respectively. Methane fluxes were negatively related to nutrients concentration in water column but positively related to the aerenchyma proportions of roots, stems, and leaves. At the same biomass, root of E. crassipes (36.44%) had the highest methane oxidation potential, followed by H. dubia (12.99%) and T. natans (11.23%). Forty-five bacterial phyla in total were identified on roots of three plants and 7 bacterial genera (2.10% - 3.33%) were known methanotrophs. Type I methanotrophs accounted for 95.07% of total methanotrophs. The pmoA gene abundances ranged from 1.90 × 1016 to 2.30 × 1018 copies/g fresh weight of root biofilms. Abundances of pmoA gene was significantly positively correlated with environmental parameters. Methylotrophy (5.40%) and methanotrophy (3.75%) function were closely related to methane oxidation. This study highlights that floating plant restoration can purify water and promote carbon neutrality partially by reducing methane fluxes through methane oxidation in wetlands.
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Affiliation(s)
- Fuwei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Songhe Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China.
| | - Xiuren Hu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Xin Lv
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Min Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China; China Machinery International Engineering Desigh and Research Institute co., Ltd. East China Regional Center, Nanjing 210008, China
| | - Yu Ma
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
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12
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Fenibo EO, Selvarajan R, Wang H, Wang Y, Abia ALK. Untapped talents: insight into the ecological significance of methanotrophs and its prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166145. [PMID: 37579801 DOI: 10.1016/j.scitotenv.2023.166145] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/06/2023] [Accepted: 08/06/2023] [Indexed: 08/16/2023]
Abstract
The deep ocean is a rich reservoir of unique organisms with great potential for bioprospecting, ecosystem services, and the discovery of novel materials. These organisms thrive in harsh environments characterized by high hydrostatic pressure, low temperature, and limited nutrients. Hydrothermal vents and cold seeps, prominent features of the deep ocean, provide a habitat for microorganisms involved in the production and filtration of methane, a potent greenhouse gas. Methanotrophs, comprising archaea and bacteria, play a crucial role in these processes. This review examines the intricate relationship between the roles, responses, and niche specialization of methanotrophs in the deep ocean ecosystem. Our findings reveal that different types of methanotrophs dominate specific zones depending on prevailing conditions. Type I methanotrophs thrive in oxygen-rich zones, while Type II methanotrophs display adaptability to diverse conditions. Verrumicrobiota and NC10 flourish in hypoxic and extreme environments. In addition to their essential role in methane regulation, methanotrophs contribute to various ecosystem functions. They participate in the degradation of foreign compounds and play a crucial role in cycling biogeochemical elements like metals, sulfur, and nitrogen. Methanotrophs also serve as a significant energy source for the oceanic food chain and drive chemosynthesis in the deep ocean. Moreover, their presence offers promising prospects for biotechnological applications, including the production of valuable compounds such as polyhydroxyalkanoates, methanobactin, exopolysaccharides, ecotines, methanol, putrescine, and biofuels. In conclusion, this review highlights the multifaceted roles of methanotrophs in the deep ocean ecosystem, underscoring their ecological significance and their potential for advancements in biotechnology. A comprehensive understanding of their niche specialization and responses will contribute to harnessing their full potential in various domains.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria
| | - Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China; Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa
| | - Huiqi Wang
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China
| | - Yue Wang
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China
| | - Akebe Luther King Abia
- Environmental Research Foundation, Westville 3630, South Africa; Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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13
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Tucci FJ, Jodts RJ, Hoffman BM, Rosenzweig AC. Product analog binding identifies the copper active site of particulate methane monooxygenase. Nat Catal 2023; 6:1194-1204. [PMID: 38187819 PMCID: PMC10766429 DOI: 10.1038/s41929-023-01051-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/22/2023] [Indexed: 01/09/2024]
Abstract
Nature's primary methane-oxidizing enzyme, the membrane-bound particulate methane monooxygenase (pMMO), catalyzes the oxidation of methane to methanol. pMMO activity requires copper, and decades of structural and spectroscopic studies have sought to identify the active site among three candidates: the CuB, CuC, and CuD sites. Challenges associated with the isolation of active pMMO have hindered progress toward locating its catalytic center. However, reconstituting pMMO into native lipid nanodiscs stabilizes its structure and recovers its activity. Here, these active samples were incubated with 2,2,2,-trifluoroethanol (TFE), a product analog that serves as a readily visualized active-site probe. Interactions of TFE with the CuD site were observed by both pulsed ENDOR spectroscopy and cryoEM, implicating CuD and the surrounding hydrophobic pocket as the likely site of methane oxidation. Use of these orthogonal techniques on parallel samples is a powerful approach that can circumvent difficulties in interpreting metalloenzyme cryoEM maps.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
- These authors contributed equally
| | - Richard J Jodts
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
- These authors contributed equally
| | - Brian M Hoffman
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
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14
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Seppey CVW, Cabrol L, Thalasso F, Gandois L, Lavergne C, Martinez-Cruz K, Sepulveda-Jauregui A, Aguilar-Muñoz P, Astorga-España MS, Chamy R, Dellagnezze BM, Etchebehere C, Fochesatto GJ, Gerardo-Nieto O, Mansilla A, Murray A, Sweetlove M, Tananaev N, Teisserenc R, Tveit AT, Van de Putte A, Svenning MM, Barret M. Biogeography of microbial communities in high-latitude ecosystems: Contrasting drivers for methanogens, methanotrophs and global prokaryotes. Environ Microbiol 2023; 25:3364-3386. [PMID: 37897125 DOI: 10.1111/1462-2920.16526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023]
Abstract
Methane-cycling is becoming more important in high-latitude ecosystems as global warming makes permafrost organic carbon increasingly available. We explored 387 samples from three high-latitudes regions (Siberia, Alaska and Patagonia) focusing on mineral/organic soils (wetlands, peatlands, forest), lake/pond sediment and water. Physicochemical, climatic and geographic variables were integrated with 16S rDNA amplicon sequences to determine the structure of the overall microbial communities and of specific methanogenic and methanotrophic guilds. Physicochemistry (especially pH) explained the largest proportion of variation in guild composition, confirming species sorting (i.e., environmental filtering) as a key mechanism in microbial assembly. Geographic distance impacted more strongly beta diversity for (i) methanogens and methanotrophs than the overall prokaryotes and, (ii) the sediment habitat, suggesting that dispersal limitation contributed to shape the communities of methane-cycling microorganisms. Bioindicator taxa characterising different ecological niches (i.e., specific combinations of geographic, climatic and physicochemical variables) were identified, highlighting the importance of Methanoregula as generalist methanogens. Methylocystis and Methylocapsa were key methanotrophs in low pH niches while Methylobacter and Methylomonadaceae in neutral environments. This work gives insight into the present and projected distribution of methane-cycling microbes at high latitudes under climate change predictions, which is crucial for constraining their impact on greenhouse gas budgets.
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Affiliation(s)
- Christophe V W Seppey
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Institute of Environmental Science and Geography, University of Potsdam, Potsdam-Golm, Germany
| | - Léa Cabrol
- Aix-Marseille University, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | - Frederic Thalasso
- Centro de Investigacíon y de Estudios Avanzados del Instituto Politecnico Nacional (Cinvestav-IPN), Departamento de Biotecnología y Bioingeniería, México, Mexico
| | - Laure Gandois
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Céline Lavergne
- HUB AMBIENTAL UPLA, Laboratory of Aquatic Environmental Research, Universidad de Playa Ancha, Valparaíso, Chile
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Karla Martinez-Cruz
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile
- Environmental Physics Group, Limnological Institute, University of Konstanz, Konstanz, Germany
| | | | - Polette Aguilar-Muñoz
- HUB AMBIENTAL UPLA, Laboratory of Aquatic Environmental Research, Universidad de Playa Ancha, Valparaíso, Chile
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | | | - Rolando Chamy
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Bruna Martins Dellagnezze
- Microbial Ecology Laboratory, Department of Microbial Biochemistry and Genomic, Biological Research Institute "Clemente Estable", Montevideo, Uruguay
| | - Claudia Etchebehere
- Microbial Ecology Laboratory, Department of Microbial Biochemistry and Genomic, Biological Research Institute "Clemente Estable", Montevideo, Uruguay
| | - Gilberto J Fochesatto
- Department of Atmospheric Sciences, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Oscar Gerardo-Nieto
- Centro de Investigacíon y de Estudios Avanzados del Instituto Politecnico Nacional (Cinvestav-IPN), Departamento de Biotecnología y Bioingeniería, México, Mexico
| | - Andrés Mansilla
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile
| | - Alison Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, Nevada, USA
| | - Maxime Sweetlove
- Royal Belgian Institute for Natural Sciences, OD-Nature, Brussels, Belgium
| | - Nikita Tananaev
- Melnikov Permafrost Institute, Russian Academy of Sciences, Yakutsk, Russia
- Institute of Natural Sciences, North-Eastern Federal University, Yakutsk, Russia
| | - Roman Teisserenc
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anton Van de Putte
- Royal Belgian Institute for Natural Sciences, OD-Nature, Brussels, Belgium
| | - Mette M Svenning
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maialen Barret
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
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15
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Pérez G, Krause SMB, Bodelier PLE, Meima-Franke M, Pitombo L, Irisarri P. Interactions between Cyanobacteria and Methane Processing Microbes Mitigate Methane Emissions from Rice Soils. Microorganisms 2023; 11:2830. [PMID: 38137974 PMCID: PMC10745823 DOI: 10.3390/microorganisms11122830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/16/2023] [Accepted: 11/18/2023] [Indexed: 12/24/2023] Open
Abstract
Cyanobacteria play a relevant role in rice soils due to their contribution to soil fertility through nitrogen (N2) fixation and as a promising strategy to mitigate methane (CH4) emissions from these systems. However, information is still limited regarding the mechanisms of cyanobacterial modulation of CH4 cycling in rice soils. Here, we focused on the response of methane cycling microbial communities to inoculation with cyanobacteria in rice soils. We performed a microcosm study comprising rice soil inoculated with either of two cyanobacterial isolates (Calothrix sp. and Nostoc sp.) obtained from a rice paddy. Our results demonstrate that cyanobacterial inoculation reduced CH4 emissions by 20 times. Yet, the effect on CH4 cycling microbes differed for the cyanobacterial strains. Type Ia methanotrophs were stimulated by Calothrix sp. in the surface layer, while Nostoc sp. had the opposite effect. The overall pmoA transcripts of Type Ib methanotrophs were stimulated by Nostoc. Methanogens were not affected in the surface layer, while their abundance was reduced in the sub surface layer by the presence of Nostoc sp. Our results indicate that mitigation of methane emission from rice soils based on cyanobacterial inoculants depends on the proper pairing of cyanobacteria-methanotrophs and their respective traits.
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Affiliation(s)
- Germán Pérez
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
- Laboratory of Microbiology, Department of Plant Biology, Agronomy Faculty, University of the Republic, Montevideo 12900, Uruguay;
| | - Sascha M. B. Krause
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
- School of Ecology and Environmental Sciences, East China Normal University, Shanghai 200062, China
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
| | - Leonardo Pitombo
- Department of Environmental Sciences, Federal University of São Carlos (UFSCar), São Paulo 18052-780, Brazil;
| | - Pilar Irisarri
- Laboratory of Microbiology, Department of Plant Biology, Agronomy Faculty, University of the Republic, Montevideo 12900, Uruguay;
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16
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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] [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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17
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Ortiz-Rivero J, Garrido-Benavent I, Heiðmarsson S, de los Ríos A. Moss and Liverwort Covers Structure Soil Bacterial and Fungal Communities Differently in the Icelandic Highlands. MICROBIAL ECOLOGY 2023; 86:1893-1908. [PMID: 36802019 PMCID: PMC10497656 DOI: 10.1007/s00248-023-02194-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Cryptogamic covers extend over vast polar tundra regions and their main components, e.g., bryophytes and lichens, are frequently the first visible colonizers of deglaciated areas. To understand their role in polar soil development, we analyzed how cryptogamic covers dominated by different bryophyte lineages (mosses and liverworts) influence the diversity and composition of edaphic bacterial and fungal communities as well as the abiotic attributes of underlying soils in the southern part of the Highlands of Iceland. For comparison, the same traits were examined in soils devoid of bryophyte covers. We measured an increase in soil C, N, and organic matter contents coupled with a lower pH in association with bryophyte cover establishment. However, liverwort covers showed noticeably higher C and N contents than moss covers. Significant changes in diversity and composition of bacterial and fungal communities were revealed between (a) bare and bryophyte-covered soils, (b) bryophyte covers and the underlying soils, and (c) moss and liverworts covers. These differences were more obvious for fungi than bacteria, and involved different lineages of saprotrophic and symbiotic fungi, which suggests a certain specificity of microbial taxa to particular bryophyte groups. In addition, differences observed in the spatial structure of the two bryophyte covers may be also responsible for the detected differences in microbial community diversity and composition. Altogether, our findings indicate that soil microbial communities and abiotic attributes are ultimately affected by the composition of the most conspicuous elements of cryptogamic covers in polar regions, which is of great value to predict the biotic responses of these ecosystems to future climate change.
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Affiliation(s)
- Javier Ortiz-Rivero
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN-CSIC), C/ Serrano 115 dpdo, E-28045 Madrid, Spain
| | - Isaac Garrido-Benavent
- Departament de Botànica i Geologia, Fac. CC. Biològiques, Universitat de València, C/ Doctor Moliner 50, E-46100 Burjassot, Valencia Spain
| | - Starri Heiðmarsson
- Icelandic Institute of Natural History, Akureyri Division, Borgir Nordurslod, 600 Akureyri, Iceland
- Present address: Northwest Iceland Nature Research Centre, Aðalgötu 2, 550 Sauðárkrókur, Iceland
| | - Asunción de los Ríos
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN-CSIC), C/ Serrano 115 dpdo, E-28045 Madrid, Spain
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18
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Awala SI, Gwak JH, Kim Y, Seo C, Strazzulli A, Kim SG, Rhee SK. Methylacidiphilum caldifontis gen. nov., sp. nov., a thermoacidophilic methane-oxidizing bacterium from an acidic geothermal environment, and descriptions of the family Methylacidiphilaceae fam. nov. and order Methylacidiphilales ord. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37791995 DOI: 10.1099/ijsem.0.006085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Abstract
Strain IT6T, a thermoacidophilic and facultative methane-oxidizing bacterium, was isolated from a mud-water mixture collected from Pisciarelli hot spring in Pozzuoli, Italy. The novel strain is white when grown in liquid or solid media and forms Gram-negative rod-shaped, non-flagellated, non-motile cells. It conserves energy by aerobically oxidizing methane and hydrogen while deriving carbon from carbon dioxide fixation. Strain IT6T had three complete pmoCAB operons encoding particulate methane monooxygenase and genes encoding group 1d and 3b [NiFe] hydrogenases. Simple carbon-carbon substrates such as ethanol, 2-propanol, acetone, acetol and propane-1,2-diol were used as alternative electron donors and carbon sources. Optimal growth occurred at 50-55°C and between pH 2.0-3.0. The major fatty acids were C18 : 0, C15 : 0 anteiso, C14 : 0 iso, C16 : 0 and C14 : 0, and the main polar lipids were phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, diphosphatidylglycerol, some unidentified phospholipids and glycolipids, and other unknown polar lipids. Strain IT6T has a genome size of 2.19 Mbp and a G+C content of 40.70 mol%. Relative evolutionary divergence using 120 conserved single-copy marker genes (bac120) and phylogenetic analyses based on bac120 and 16S rRNA gene sequences showed that strain IT6T is affiliated with members of the proposed order 'Methylacidiphilales' of the class Verrucomicrobiia in the phylum Verrucomicrobiota. It shared a 16S rRNA gene sequence identity of >96 % with cultivated isolates in the genus 'Methylacidiphilum' of the family 'Methylacidiphilaceae', which are thermoacidophilic methane-oxidizing bacteria. 'Methylacidiphilum sp.' Phi (100 %), 'Methylacidiphilum infernorum' V4 (99.02 %) and 'Methylacidiphilum sp.' RTK17.1 (99.02 %) were its closest relatives. Its physiological and genomic properties were consistent with those of other isolated 'Methylacidiphilum' species. Based on these results, we propose the name Methylacidiphilum caldifontis gen. nov., sp. nov. to accommodate strain IT6T (=KCTC 92103T=JCM 39288T). We also formally propose that the names Methylacidiphilaceae fam. nov. and Methylacidiphilales ord. nov. to accommodate the genus Methylacidiphilum gen. nov.
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Affiliation(s)
- Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Yongman Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Chanmee Seo
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Andrea Strazzulli
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126, Naples, Italy
| | - Song-Gun Kim
- University of Science and Technology, Yuseong-gu, Daejeon 305-850, Republic of Korea
- Biological Resource Center/ Korean Collection for Type Culture (KCTC), Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
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19
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Hwang Y, Na JG, Lee SJ. Transcriptional regulation of soluble methane monooxygenase via enhancer-binding protein derived from Methylosinus sporium 5. Appl Environ Microbiol 2023; 89:e0210422. [PMID: 37668365 PMCID: PMC10537576 DOI: 10.1128/aem.02104-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/07/2023] [Indexed: 09/06/2023] Open
Abstract
Methane is a major greenhouse gas, and methanotrophs regulate the methane level in the carbon cycle. Soluble methane monooxygenase (sMMO) is expressed in various methanotroph genera, including Alphaproteobacteria and Gammaproteobacteria, and catalyzes the hydroxylation of methane to methanol. It has been proposed that MmoR regulates the expression of sMMO as an enhancer-binding protein under copper-limited conditions; however, details on this transcriptional regulation remain limited. Herein, we elucidate the transcriptional pathway of sMMO depending on copper ion concentration, which affects the interaction of MmoR and sigma factor. MmoR and sigma-54 (σ54) from Methylosinus sporium 5 were successfully overexpressed in Escherichia coli and purified to investigate sMMO transcription in methanotrophs. The results indicated that σ54 binds to a promoter positioned -24 (GG) and -12 (TGC) upstream between mmoG and mmoX1. The binding affinity and selectivity are lower (Kd = 184.6 ± 6.2 nM) than those of MmoR. MmoR interacts with the upstream activator sequence (UAS) with a strong binding affinity (Kd = 12.5 ± 0.5 nM). Mutational studies demonstrated that MmoR has high selectivity to its binding partner (ACA-xx-TGT). Titration assays have demonstrated that MmoR does not coordinate with copper ions directly; however, its binding affinity to UAS decreases in a low-copper-containing medium. MmoR strongly interacts with adenosine triphosphate (Kd = 62.8 ± 0.5 nM) to generate RNA polymerase complex. This study demonstrated that the binding events of both MmoR and σ54 that regulate transcription in M. sporium 5 depend on the copper ion concentration. IMPORTANCE This study provides biochemical evidence of transcriptional regulation of soluble methane monooxygenase (sMMO) in methanotrophs that control methane levels in ecological systems. Previous studies have proposed transcriptional regulation of MMOs, including sMMO and pMMO, while we provide further evidence to elucidate its mechanism using a purified enhancer-binding protein (MmoR) and transcription factor (σ54). The characterization studies of σ54 and MmoR identified the promoter binding sites and enhancer-binding sequences essential for sMMO expression. Our findings also demonstrate that MmoR functions as a trigger for sMMO expression due to the high specificity and selectivity for enhancer-binding sequences. The UV-visible spectrum of purified MmoR suggested an iron coordination like other GAF domain, and that ATP is essential for the initiation of enhancer elements. Binding assays indicated that these interactions are blocked by the copper ion. These results provide novel insights into gene regulation of methanotrophs.
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Affiliation(s)
- Yunha Hwang
- Department of Chemistry, Jeonbuk National University , Jeonju, South Korea
| | - Jeong-Geol Na
- Department of Chemical Engineering, Sogang University , Seoul, South Korea
| | - Seung Jae Lee
- Department of Chemistry, Jeonbuk National University , Jeonju, South Korea
- Institute of Molecular Biology and Genetics, Jeonbuk National University , Jeonju, South Korea
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20
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Dedysh SN. Describing difficult-to-culture bacteria: Taking a shortcut or investing time to discover something new? Syst Appl Microbiol 2023; 46:126439. [PMID: 37413783 DOI: 10.1016/j.syapm.2023.126439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/17/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Despite the growing interest in isolating representatives of poorly studied and as-yet-uncultivated bacterial phylogenetic groups, these microorganisms remain difficult objects for taxonomic studies. The time required for describing one of these fastidious bacteria is commonly measured in several years. What is even more problematic, many routine laboratory tests, which were originally developed for fast-growing and fast-responding microorganisms, are not fully suitable for many environmentally relevant, slow-growing bacteria. Standard techniques used in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. A common practice of preparing taxonomic descriptions that report a minimal set of features to name a newly isolated organism deepens a gap between microbial ecologists and taxonomists. By contrast, investing time in detailed analysis of cell biology and experimental verification of genome-encoded capabilities of newly isolated microorganisms opens a window for novel, unexpected findings, which may shape our ideas about the functional role of these microbes in the environment.
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Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
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21
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Ratnadevi CM, Erikstad HA, Kruse T, Birkeland NK. Methylacidiphilum kamchatkense gen. nov., sp. nov., an extremely acidophilic and moderately thermophilic methanotroph belonging to the phylum Verrucomicrobiota. Int J Syst Evol Microbiol 2023; 73. [PMID: 37755432 DOI: 10.1099/ijsem.0.006060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
The thermo-acidophilic aerobic methanotrophic Verrucomicrobia bacterium, designated strain Kam1T was isolated from an acidic geothermal mud spring in Kamchatka, Russia. Kam1T is Gram-stain-negative, with non-motile cells and non-spore-forming rods, and a diameter of 0.45-0.65 µm and length of 0.8-1.0 µm. Its growth is optimal at the temperature of 55 °C (range, 37-60 °C) and pH of 2.5 (range, pH 1-6), and its maximal growth rate is ~0.11 h-1 (doubling time ~6.3 h). Its cell wall contains peptidoglycan with meso-diaminopimelic acid. In addition to growing on methane and methanol, strain Kam1T grows on acetone and 2-propanol. Phylogenetically, it forms a distinct group together with other Methylacidiphilum strains and with the candidate genus Methylacidimicrobium as a sister group. These findings support the classification of the strain Kam1T as a representative of a novel species and genus of the phylum Verrucomicrobiota. For this strain, we propose the name Methylacidiphilum kamchatkense sp. nov. as the type species within Methylacidiphilum gen. nov. Strain Kam1T (JCM 30608T=KCTC 4682T) is the type strain.
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Affiliation(s)
| | - Helge-André Erikstad
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway
| | - Thomas Kruse
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway
- Present address: NORCE, Industrial biotechnology, Prof. Olav Hanssensvei 15, 4021 Stavanger, Norway
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22
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Huang J, Zhao W, Ju J, Liu S, Ye J, Long Y. The existence of ferric hydroxide links the carbon and nitrogen cycles by promoting nitrite-coupled methane anaerobic oxidation. WATER RESEARCH 2023; 243:120192. [PMID: 37454463 DOI: 10.1016/j.watres.2023.120192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 07/18/2023]
Abstract
Microorganism-mediated anaerobic oxidation of methane can efficiently mitigate methane atmospheric emissions and is a key process linking the biogeochemical cycles of carbon, nitrogen, and iron. The results showed that methane oxidation and nitrite removal rates in the CF were 1.12 and 1.28 times higher than those in CK, respectively, suggesting that ferric hydroxide can enhance nitrite-driven AOM. The biochemical process was mediated by the enrichment of methanogens, methanotrophs, and denitrifiers. Methanobacterium and Methanosarcina were positively correlated with Fe3+ and Fe2+, whereas Methylocystis and Methylocaldum were positively correlated with methane, and denitrifiers were positively correlated with nitrite. Metagenomic analysis revealed that the genes related to methane oxidation, nitrogen reduction, and heme c-type cytochrome were upregulated in CF, indicating that a synergistic action of bacteria and methanogens drove AOM via diverse metabolic pathways, within which ferric hydroxide played a crucial role. This study provides novel insights into the synergistic mechanism of ferric iron and nitrite-driven AOM.
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Affiliation(s)
- Juan Huang
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Wurong Zhao
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinwei Ju
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Suifen Liu
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinshao Ye
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yan Long
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China.
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23
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Houghton KM, Carere CR, Stott MB, McDonald IR. Thermophilic methane oxidation is widespread in Aotearoa-New Zealand geothermal fields. Front Microbiol 2023; 14:1253773. [PMID: 37720161 PMCID: PMC10502179 DOI: 10.3389/fmicb.2023.1253773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023] Open
Abstract
Geothermal areas represent substantial point sources for greenhouse gas emissions such as methane. While it is known that methanotrophic microorganisms act as a biofilter, decreasing the efflux of methane in most soils to the atmosphere, the diversity and the extent to which methane is consumed by thermophilic microorganisms in geothermal ecosystems has not been widely explored. To determine the extent of biologically mediated methane oxidation at elevated temperatures, we set up 57 microcosms using soils from 14 Aotearoa-New Zealand geothermal fields and show that moderately thermophilic (>40°C) and thermophilic (>60°C) methane oxidation is common across the region. Methane oxidation was detected in 54% (n = 31) of the geothermal soil microcosms tested at temperatures up to 75°C (pH 1.5-8.1), with oxidation rates ranging from 0.5 to 17.4 μmol g-1 d-1 wet weight. The abundance of known aerobic methanotrophs (up to 60.7% Methylacidiphilum and 11.2% Methylothermus) and putative anaerobic methanotrophs (up to 76.7% Bathyarchaeota) provides some explanation for the rapid rates of methane oxidation observed in microcosms. However, not all methane oxidation was attributable to known taxa; in some methane-consuming microcosms we detected methanotroph taxa in conditions outside of their known temperature range for growth, and in other examples, we observed methane oxidation in the absence of known methanotrophs through 16S rRNA gene sequencing. Both of these observations suggest unidentified methane oxidizing microorganisms or undescribed methanotrophic syntrophic associations may also be present. Subsequent enrichment cultures from microcosms yielded communities not predicted by the original diversity studies and showed rates inconsistent with microcosms (≤24.5 μmol d-1), highlighting difficulties in culturing representative thermophilic methanotrophs. Finally, to determine the active methane oxidation processes, we attempted to elucidate metabolic pathways from two enrichment cultures actively oxidizing methane using metatranscriptomics. The most highly expressed genes in both enrichments (methane monooxygenases, methanol dehydrogenases and PqqA precursor peptides) were related to methanotrophs from Methylococcaceae, Methylocystaceae and Methylothermaceae. This is the first example of using metatranscriptomics to investigate methanotrophs from geothermal environments and gives insight into the metabolic pathways involved in thermophilic methanotrophy.
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Affiliation(s)
- Karen M. Houghton
- Te Pū Ao | GNS Science, Wairakei Research Centre, Taupō, New Zealand
- Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
| | - Carlo R. Carere
- Te Pū Ao | GNS Science, Wairakei Research Centre, Taupō, New Zealand
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
| | - Matthew B. Stott
- Te Pū Ao | GNS Science, Wairakei Research Centre, Taupō, New Zealand
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
| | - Ian R. McDonald
- Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
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24
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Jensen S, Siljanen HM, Dörsch P. Activity and abundance of methanotrophic bacteria in a northern mountainous gradient of wetlands. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:206-215. [PMID: 36786058 PMCID: PMC10464705 DOI: 10.1111/1758-2229.13137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/23/2022] [Indexed: 05/06/2023]
Abstract
Methane uptake and diversity of methanotrophic bacteria was investigated across six hydrologically connected wetlands in a mountainous forest landscape upstream of lake Langtjern, southern Norway. From floodplain through shrubs, forest and sedges to a Sphagnum covered site, growing season CH4 production was insufficiently consumed to balance release into the atmosphere. Emission increased by soil moisture ranging 0.6-6.8 mg CH4 m-2 h-1 . Top soils of all sites consumed CH4 including at the lowest 78 ppmv CH4 supplied, thus potentially oxidizing 17-51 nmol CH4 g-1 dw h-1 , with highest Vmax 440 nmol g-1 dw h-1 under Sphagnum and lowest Km 559 nM under hummocked Carex. Nine genera and several less understood type I and type II methanotrophs were detected by the key functional gene pmoA involved in methane oxidation. Microarray signal intensities from all sites revealed Methylococcus, the affiliated Lake Washington cluster, Methylocaldum, a Japanese rice cluster, Methylosinus, Methylocystis and the affiliated Peat264 cluster. Notably enriched by site was a floodplain Methylomonas and a Methylocapsa-affiliated watershed cluster in the Sphagnum site. The climate sensitive water table was shown to be a strong controlling factor highlighting its link with the CH4 cycle in elevated wetlands.
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Affiliation(s)
- Sigmund Jensen
- Department of Biological SciencesUniversity of BergenBergenNorway
| | - Henri M.P. Siljanen
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandKuopioFinland
| | - Peter Dörsch
- Norwegian University of Life SciencesFaculty for Environmental Sciences and Natural Resource ManagementNorway
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25
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Podosokorskaya OA, Elcheninov AG, Novikov AA, Merkel AY, Kublanov IV. Fontisphaera persica gen. nov., sp. nov., a thermophilic hydrolytic bacterium from a hot spring of Baikal lake region, and proposal of Fontisphaeraceae fam. nov., and Limisphaeraceae fam. nov. within the Limisphaerales ord. nov. (Verrucomicrobiota). Syst Appl Microbiol 2023; 46:126438. [PMID: 37263084 DOI: 10.1016/j.syapm.2023.126438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/25/2023] [Accepted: 05/24/2023] [Indexed: 06/03/2023]
Abstract
A novel facultatively anaerobic moderately thermophilic bacterium, strain B-154 T, was isolated from a terrestrial hot spring in the Baikal lake region (Russian Federation). Gram-negative, motile, spherical cells were present singly, in pairs, or aggregates, and reproduced by binary fission. The strain grew at 30-57 °C and within a pH range of 5.1-8.4 with the optimum at 50 °C and pH 6.8-7.1. Strain B-154 T was a chemoorganoheterotroph, growing on mono-, di- and polysaccharides (xylan, starch, galactan, galactomannan, glucomannan, xyloglucan, pullulan, arabinan, lichenan, beta-glucan, pachyman, locust bean gum, xanthan gum). It did not require sodium chloride or yeast extract for growth. Major cellular fatty acids were anteiso-C15:0, iso-C16:0 and iso-C14:0. The respiratory quinone was MK-7. The complete genome of strain B-154 T was 4.73 Mbp in size; its G + C content was 61%. According to the phylogenomic analysis strain B-154 T forms a separate family-level phylogenetic lineage. Moreover, together with Limisphaera ngatamarikiensis and "Pedosphaera parvula" this strain forms a separate order-level phylogenetic lineage within Verrucomicrobiae class. Hence, we propose a novel order, Limisphaerales ord. nov., with two families Limisphaeraceae fam. nov. and Fontisphaeraceae fam. nov., and a novel genus and species Fontisphaera persica gen. nov., sp. nov. with type strain B-154 T. Ecogenomic analysis showed that representatives of the Limisphaerales are widespread in various environments. Although some of them were detected in hot springs the majority of Limisphaerales (54% of the studied metagenome-assembled genomes) were found in marine habitats. This study allowed a better understanding of physiology and ecology of Verrucomicrobiota - a rather understudied bacterial phylum.
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Affiliation(s)
- Olga A Podosokorskaya
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia.
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
| | - Andrei A Novikov
- Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
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26
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Schmitz RA, Peeters SH, Mohammadi SS, Berben T, van Erven T, Iosif CA, van Alen T, Versantvoort W, Jetten MSM, Op den Camp HJM, Pol A. Simultaneous sulfide and methane oxidation by an extremophile. Nat Commun 2023; 14:2974. [PMID: 37221165 DOI: 10.1038/s41467-023-38699-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/11/2023] [Indexed: 05/25/2023] Open
Abstract
Hydrogen sulfide (H2S) and methane (CH4) are produced in anoxic environments through sulfate reduction and organic matter decomposition. Both gases diffuse upwards into oxic zones where aerobic methanotrophs mitigate CH4 emissions by oxidizing this potent greenhouse gas. Although methanotrophs in myriad environments encounter toxic H2S, it is virtually unknown how they are affected. Here, through extensive chemostat culturing we show that a single microorganism can oxidize CH4 and H2S simultaneously at equally high rates. By oxidizing H2S to elemental sulfur, the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV alleviates the inhibitory effects of H2S on methanotrophy. Strain SolV adapts to increasing H2S by expressing a sulfide-insensitive ba3-type terminal oxidase and grows as chemolithoautotroph using H2S as sole energy source. Genomic surveys revealed putative sulfide-oxidizing enzymes in numerous methanotrophs, suggesting that H2S oxidation is much more widespread in methanotrophs than previously assumed, enabling them to connect carbon and sulfur cycles in novel ways.
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Affiliation(s)
- Rob A Schmitz
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, 8092, Zurich, Switzerland
| | - Stijn H Peeters
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Sepehr S Mohammadi
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Tom Berben
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Timo van Erven
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Carmen A Iosif
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Theo van Alen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands.
| | - Arjan Pol
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
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Yang L, Zhang S, Lv X, Liu Y, Guo S, Hu X, Manirakiza B. Vallisneria natans decreased CH 4 fluxes in wetlands: Interactions among plant physiological status, nutrients and epiphytic bacterial community. ENVIRONMENTAL RESEARCH 2023; 224:115547. [PMID: 36822529 DOI: 10.1016/j.envres.2023.115547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/13/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Submerged macrophytes provide niches for epiphytic microbes (including aerobic methanotrophs) growth. However, little is known about the impacts of submerged macrophytes growth status and nutrients loadings on methanotroph community and methane release in wetlands. In the present study, methane fluxes, bacterial and methanotroph community in epiphytic biofilm, and environmental parameters were investigated during Vallisneria natans senescence in wetlands under low (VnL) and high (VnH) nutrients for seven weeks. Relative conductivity and concentration of H2O2, total chlorophyll and malondialdehyde were higher in leaves of V. natans in VnH than VnL at the same sampling time. Nutrients loading increased methane fluxes in treatments with or without (Control) macrophytes, while healthy V. natans plants reduced the methane flux and nutrients concentration in water columns. CH4 fluxes were positively correlated to temperature and COD (p < 0.05). Methane oxidation rates were 3.04-31.68 μmol methane mg-1 fresh weight of V. natans leaves - epiphytic biofilm within 1 h. Proteobacteria, Cyanobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, Actinobacteria and Acidobacteria were dominant phylum in all epiphytic biofilms. The mean abundances of pmoA/16S rRNA were higher in VnL than VnH. According to Illumina sequencing results of pmoA gene, γ-proteobacteria and α-proteobacteria were the dominant methanotroph class in epiphytic biofilm from VnH and VnL, respectively. Among seven detected methanotrophic genera, Methylomonas was significantly higher in VnH than VnL. Network analysis revealed that there were much closer relationships between the environmental parameters and epiphytic bacterial community in VnH than in VnL. COD and MDA were negatively correlated with Methyloglobulus, Methylosarcina, Methylobacter and Methylocystis, but positively correlated with Methylomonas and Methylosinus. This study highlights that methanotrophs in epiphytic biofilm play important roles in methane-oxidizing, which can be affected by plant physiological status and environmental parameters.
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Affiliation(s)
- Liu Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, PR China; College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Songhe Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, PR China; College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Xin Lv
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, PR China; College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yuansi Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, PR China; College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Shaozhuang Guo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, PR China; College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Xiuren Hu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, PR China; College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Benjamin Manirakiza
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, PR China; College of Environment, Hohai University, Nanjing, 210098, PR China
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28
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Hwangbo M, Shao Y, Hatzinger PB, Chu KH. Acidophilic methanotrophs: Occurrence, diversity, and possible bioremediation applications. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 37041665 DOI: 10.1111/1758-2229.13156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
Methanotrophs have been identified and isolated from acidic environments such as wetlands, acidic soils, peat bogs, and groundwater aquifers. Due to their methane (CH4 ) utilization as a carbon and energy source, acidophilic methanotrophs are important in controlling the release of atmospheric CH4 , an important greenhouse gas, from acidic wetlands and other environments. Methanotrophs have also played an important role in the biodegradation and bioremediation of a variety of pollutants including chlorinated volatile organic compounds (CVOCs) using CH4 monooxygenases via a process known as cometabolism. Under neutral pH conditions, anaerobic bioremediation via carbon source addition is a commonly used and highly effective approach to treat CVOCs in groundwater. However, complete dechlorination of CVOCs is typically inhibited at low pH. Acidophilic methanotrophs have recently been observed to degrade a range of CVOCs at pH < 5.5, suggesting that cometabolic treatment may be an option for CVOCs and other contaminants in acidic aquifers. This paper provides an overview of the occurrence, diversity, and physiological activities of methanotrophs in acidic environments and highlights the potential application of these organisms for enhancing contaminant biodegradation and bioremediation.
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Affiliation(s)
- Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
| | - Yiru Shao
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
| | - Paul B Hatzinger
- Aptim Federal Services, LLC, 17 Princess Road, Lawrenceville, New Jersey, USA
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
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Hodgskiss LH, Melcher M, Kerou M, Chen W, Ponce-Toledo RI, Savvides SN, Wienkoop S, Hartl M, Schleper C. Unexpected complexity of the ammonia monooxygenase in archaea. THE ISME JOURNAL 2023; 17:588-599. [PMID: 36721060 PMCID: PMC10030591 DOI: 10.1038/s41396-023-01367-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 02/02/2023]
Abstract
Ammonia oxidation, as the first step of nitrification, constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase, is lacking, in particular for the environmentally abundant ammonia-oxidizing archaea (AOA). Here the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Besides the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modeling and in-gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase but also reveals clear differences in extracellular domains of the enzyme. These data open avenues for further structure-function studies of this ecologically important nitrification complex.
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Affiliation(s)
- Logan H Hodgskiss
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Michael Melcher
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Melina Kerou
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Weiqiang Chen
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter (VBC), Vienna, Austria
| | - Rafael I Ponce-Toledo
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Stefanie Wienkoop
- Molecular Systems Biology Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Markus Hartl
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter (VBC), Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Unit, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.
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García-Maldonado JQ, Latisnere-Barragán H, Escobar-Zepeda A, Cadena S, Ramírez-Arenas PJ, Vázquez-Juárez R, Rojas-Contreras M, López-Cortés A. Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities. Microorganisms 2023; 11:microorganisms11030812. [PMID: 36985385 PMCID: PMC10059902 DOI: 10.3390/microorganisms11030812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023] Open
Abstract
Knowledge regarding the diversity of methanogenic archaeal communities in hypersaline environments is limited because of the lack of efficient cultivation efforts as well as their low abundance and metabolic activities. In this study, we explored the microbial communities in hypersaline microbial mats. Bioinformatic analyses showed significant differences among the archaeal community structures for each studied site. Taxonomic assignment based on 16S rRNA and methyl coenzyme-M reductase (mcrA) gene sequences, as well as metagenomic analysis, corroborated the presence of Methanosarcinales. Furthermore, this study also provided evidence for the presence of Methanobacteriales, Methanomicrobiales, Methanomassiliicoccales, Candidatus Methanofastidiosales, Methanocellales, Methanococcales and Methanopyrales, although some of these were found in extremely low relative abundances. Several mcrA environmental sequences were significantly different from those previously reported and did not match with any known methanogenic archaea, suggesting the presence of specific environmental clusters of methanogenic archaea in Guerrero Negro. Based on functional inference and the detection of specific genes in the metagenome, we hypothesised that all four methanogenic pathways were able to occur in these environments. This study allowed the detection of extremely low-abundance methanogenic archaea, which were highly diverse and with unknown physiology, evidencing the presence of all methanogenic metabolic pathways rather than the sheer existence of exclusively methylotrophic methanogenic archaea in hypersaline environments.
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Affiliation(s)
- José Q García-Maldonado
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Mérida 97310, Yucatán, Mexico
| | - Hever Latisnere-Barragán
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| | | | - Santiago Cadena
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Patricia J Ramírez-Arenas
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| | - Ricardo Vázquez-Juárez
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| | - Maurilia Rojas-Contreras
- Departamento de Agronomía, Universidad Autónoma de Baja California Sur, La Paz 23080, Baja California Sur, Mexico
| | - Alejandro López-Cortés
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
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31
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Yao X, Wang J, Hu B. How methanotrophs respond to pH: A review of ecophysiology. Front Microbiol 2023; 13:1034164. [PMID: 36687570 PMCID: PMC9853399 DOI: 10.3389/fmicb.2022.1034164] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/09/2022] [Indexed: 01/08/2023] Open
Abstract
Varying pH globally affects terrestrial microbial communities and biochemical cycles. Methanotrophs effectively mitigate methane fluxes in terrestrial habitats. Many methanotrophs grow optimally at neutral pH. However, recent discoveries show that methanotrophs grow in strongly acidic and alkaline environments. Here, we summarize the existing knowledge on the ecophysiology of methanotrophs under different pH conditions. The distribution pattern of diverse subgroups is described with respect to their relationship with pH. In addition, their responses to pH stress, consisting of structure-function traits and substrate affinity traits, are reviewed. Furthermore, we propose a putative energy trade-off model aiming at shedding light on the adaptation mechanisms of methanotrophs from a novel perspective. Finally, we take an outlook on methanotrophs' ecophysiology affected by pH, which would offer new insights into the methane cycle and global climate change.
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Affiliation(s)
- Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China,Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China,*Correspondence: Baolan Hu ✉
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32
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Khmelenina VN, But SY, Rozova ON, Oshkin IY, Pimenov NV, Dedysh SN. Genome Editing in Methanotrophic Bacteria: Potential Targets and Available Tools. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722602196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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33
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Liu F, Ji M, Xiao L, Wang X, Diao Y, Dan Y, Wang H, Sang W, Zhang Y. Organics composition and microbial analysis reveal the different roles of biochar and hydrochar in affecting methane oxidation from paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:157036. [PMID: 35772551 DOI: 10.1016/j.scitotenv.2022.157036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Biochar and hydrochar, as valuable and eco-friendly soil remediation materials from greenwaste, have potential to enhance methane oxidation in paddy soil. But the mechanism of biomass carbon on the improvement of methane-oxidizing bacteria communities in paddy soil has not been adequately elucidated. In the present study, the effect of different-temperature rice straw-based biomass carbon (RB400, RB600, RH250 and RH300) on methane oxidation were investigated by analyzing the soil dissolved organic matter (DOM), physicochemical properties and changes in microbial community structure. The results of the 17-day incubation experiment showed that the methane oxidation rate increased under all types of biomass carbon in the first 6 days. The enhancement of methane oxidation rate was more pronounced for biochar compared to hydrochar, with RB600 being the most effective treatment. The result of excitation-emission matrix (EEM) fluorescence spectroscopy showed that less DOM were released from the soil in the biochar treatments compared to the hydrochar treatments and protein-like were detected only in the hydrochar group. Microbial analysis further showed that hydrochar inhibited the growth of Bacillus, Methylobacter, and Methylocystis, while RB600 significantly increased the relative abundance of methanotrophs (responsible for methane oxidation), such as Methylocystis and Methylobacter, which was consistent with their different effects on the methane oxidation rate. Moreover, from the analysis of principal component analysis (PCA) and canonical correspondence analysis (CCA), Methylobacter and Methylocystis were negatively respond to H/C of biomass carbon. The present study provides a deeper understanding of the effect of biomass carbon obtained by different processes on methane oxidation when applied to soil from the perspective of organic matter and microbial communities.
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Affiliation(s)
- Feihong Liu
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Mengyuan Ji
- Department of Biology, University of Padua, 35131 Padova, Italy
| | - Lurui Xiao
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xiaoxia Wang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yinzhu Diao
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yitong Dan
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Huan Wang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Wenjing Sang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China.
| | - Yalei Zhang
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
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Abstract
Wetlands are the major natural source of methane, an important greenhouse gas. The sulfur and methane cycles in wetlands are linked—e.g., a strong sulfur cycle can inhibit methanogenesis. Although there has historically been a clear distinction drawn between methane and sulfur oxidizers, here, we isolated a methanotroph that also performed respiratory oxidization of sulfur compounds. We experimentally demonstrated that thiotrophy and methanotrophy are metabolically compatible, and both metabolisms could be expressed simultaneously in a single microorganism. These findings suggest that mixotrophic methane/sulfur-oxidizing bacteria are a previously overlooked component of environmental methane and sulfur cycles. This creates a framework for a better understanding of these redox cycles in natural and engineered wetlands. Natural and anthropogenic wetlands are major sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic bacteria at the oxic–anoxic interface, a zone of intense redox cycling of carbon, sulfur, and nitrogen compounds. Here, we report on the isolation of an aerobic methanotrophic bacterium, ‘Methylovirgula thiovorans' strain HY1, which possesses metabolic capabilities never before found in any methanotroph. Most notably, strain HY1 is the first bacterium shown to aerobically oxidize both methane and reduced sulfur compounds for growth. Genomic and proteomic analyses showed that soluble methane monooxygenase and XoxF-type alcohol dehydrogenases are responsible for methane and methanol oxidation, respectively. Various pathways for respiratory sulfur oxidation were present, including the Sox–rDsr pathway and the S4I system. Strain HY1 employed the Calvin–Benson–Bassham cycle for CO2 fixation during chemolithoautotrophic growth on reduced sulfur compounds. Proteomic and microrespirometry analyses showed that the metabolic pathways for methane and thiosulfate oxidation were induced in the presence of the respective substrates. Methane and thiosulfate could therefore be independently or simultaneously oxidized. The discovery of this versatile bacterium demonstrates that methanotrophy and thiotrophy are compatible in a single microorganism and underpins the intimate interactions of methane and sulfur cycles in oxic–anoxic interface environments.
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35
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Prasitwuttisak W, Hoshiko Y, Maeda T, Haraguchi A, Yanagawa K. Microbial Community Structures and Methanogenic Functions in Wetland Peat Soils. Microbes Environ 2022; 37. [PMID: 35851269 PMCID: PMC9530717 DOI: 10.1264/jsme2.me22004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methane metabolism in wetlands involves diverse groups of bacteria and archaea, which are responsible for the biological decomposition of organic matter under certain anoxic conditions. Recent advances in environmental omics revealed the phylogenetic diversity of novel microbial lineages, which have not been previously placed in the traditional tree of life. The present study aimed to verify the key players in methane production, either well-known archaeal members or recently identified lineages, in peat soils collected from wetland areas in Japan. Based on an analysis of microbial communities using 16S rRNA gene sequencing and the molecular cloning of the functional gene, mcrA, a marker gene for methanogenesis, methanogenic archaea belonging to Methanomicrobiales, Methanosarcinales, Methanobacteriales, and Methanomassiliicoccales were detected in anoxic peat soils, suggesting the potential of CH4 production in this natural wetland. “Candidatus Bathyarchaeia”, archaea with vast metabolic capabilities that is widespread in anoxic environments, was abundant in subsurface peat soils (up to 96% of the archaeal community) based on microbial gene quantification by qPCR. These results emphasize the importance of discovering archaea members outside of traditional methanogenic lineages that may have significant functions in the wetland biogeochemical cycle.
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Affiliation(s)
| | - Yuki Hoshiko
- Department of Biological Functions Engineering, Graduate School of Life Sciences and Systems Engineering, Kyushu Institute of Technology
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Sciences and Systems Engineering, Kyushu Institute of Technology
| | - Akira Haraguchi
- Faculty of Environmental Engineering, The University of Kitakyushu
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36
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Schmitz RA, Mohammadi SS, van Erven T, Berben T, Jetten MSM, Pol A, Op den Camp HJM. Methanethiol Consumption and Hydrogen Sulfide Production by the Thermoacidophilic Methanotroph Methylacidiphilum fumariolicum SolV. Front Microbiol 2022; 13:857442. [PMID: 35422776 PMCID: PMC9003020 DOI: 10.3389/fmicb.2022.857442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Methanotrophs aerobically oxidize methane to carbon dioxide to make a living and are known to degrade various other short chain carbon compounds as well. Volatile organic sulfur compounds such as methanethiol (CH3SH) are important intermediates in the sulfur cycle. Although volatile organic sulfur compounds co-occur with methane in various environments, little is known about how these compounds affect methanotrophy. The enzyme methanethiol oxidase catalyzing the oxidation of methanethiol has been known for decades, but only recently the mtoX gene encoding this enzyme was identified in a methylotrophic bacterium. The presence of a homologous gene in verrucomicrobial methanotrophs prompted us to examine how methanotrophs cope with methanethiol. Here, we show that the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV consumes methanethiol and produces H2S, which is concurrently oxidized. Consumption of methanethiol is required since methanethiol inhibits methane oxidation. Cells incubated with ∼15 μM methanethiol from the start clearly showed inhibition of growth. After depletion of methanethiol, growth resumed within 1 day. Genes encoding a putative methanethiol oxidase were found in a variety of methanotrophs. Therefore, we hypothesize that methanethiol degradation is a widespread detoxification mechanism in methanotrophs in a range of environments.
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Affiliation(s)
- Rob A Schmitz
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands.,Environmental Chemistry, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland
| | - Sepehr S Mohammadi
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
| | - Timo van Erven
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
| | - Tom Berben
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
| | - Arjan Pol
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
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37
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Roldán DM, Carrizo D, Sánchez-García L, Menes RJ. Diversity and Effect of Increasing Temperature on the Activity of Methanotrophs in Sediments of Fildes Peninsula Freshwater Lakes, King George Island, Antarctica. Front Microbiol 2022; 13:822552. [PMID: 35369426 PMCID: PMC8969513 DOI: 10.3389/fmicb.2022.822552] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
Global warming has a strong impact on polar regions. Particularly, the Antarctic Peninsula and nearby islands have experienced a marked warming trend in the past 50 years. Therefore, higher methane (CH4) emissions from this area could be expected in the future. Since mitigation of these emissions can be carried out by microbial oxidation, understanding this biological process is crucial since to our knowledge, no related studies have been performed in this area before. In this work, the aerobic CH4 oxidation potential of five freshwater lake sediments of Fildes Peninsula (King George Island, South Shetland Islands) was determined with values from 0.07 to 10 μmol CH4 gdw–1 day–1 and revealed up to 100-fold increase in temperature gradients (5, 10, 15, and 20°C). The structure and diversity of the bacterial community in the sediments were analyzed by next-generation sequencing (Illumina MiSeq) of 16S rRNA and pmoA genes. A total of 4,836 ASVs were identified being Proteobacteria, Actinobacteriota, Acidobacteriota, and Bacteroidota the most abundant phyla. The analysis of the pmoA gene identified 200 ASVs of methanotrophs, being Methylobacter Clade 2 (Type I, family Methylococcaceae) the main responsible of the aerobic CH4 oxidation. Moreover, both approaches revealed the presence of methanotrophs of the classes Gammaproteobacteria (families Methylococcaceae and Crenotrichaceae), Alphaproteobacteria (family Methylocystaceae), Verrucomicrobia (family Methylacidiphilaceae), and the candidate phylum of anaerobic methanotrophs Methylomirabilota. In addition, bacterial phospholipid fatty acids (PLFA) biomarkers were studied as a proxy for aerobic methane-oxidizing bacteria and confirmed these results. Methanotrophic bacterial diversity was significantly correlated with pH. In conclusion, our findings suggest that aerobic methanotrophs could mitigate in situ CH4 emissions in a future scenario with higher temperatures in this climate-sensitive area. This study provides new insights into the diversity of methanotrophs, as well as the influence of temperature on the CH4 oxidation potential in sediments of freshwater lakes in polar regions of the southern hemisphere.
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Affiliation(s)
- Diego M. Roldán
- Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Microbiología, Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Daniel Carrizo
- Centro de Astrobiología, Consejo Superior de Investigaciones Científicas-Instituto Nacional de Técnica Aeroespacial (CSIC-INTA), Madrid, Spain
| | - Laura Sánchez-García
- Centro de Astrobiología, Consejo Superior de Investigaciones Científicas-Instituto Nacional de Técnica Aeroespacial (CSIC-INTA), Madrid, Spain
| | - Rodolfo Javier Menes
- Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Microbiología, Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- *Correspondence: Rodolfo Javier Menes,
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Variable Inhibition of Nitrous Oxide Reduction in Denitrifying Bacteria by Different Forms of Methanobactin. Appl Environ Microbiol 2022; 88:e0234621. [PMID: 35285718 DOI: 10.1128/aem.02346-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aerobic methanotrophic activity is highly dependent on copper availability, and methanotrophs have developed multiple strategies to collect copper. Specifically, when copper is limiting (ambient concentrations less than 1 μM), some methanotrophs produce and secret a small modified peptide (less than 1,300 Da) termed methanobactin (MB) that binds copper with high affinity. As MB is secreted into the environment, other microbes that require copper for their metabolism may be inhibited as MB may make copper unavailable; e.g., inhibition of denitrifiers as complete conversion nitrate to dinitrogen involves multiple enzymes, some of which are copper-dependent. Of key concern is inhibition of the copper-dependent nitrous oxide reductase (NosZ), the only known enzyme capable of converting nitrous oxide (N2O) to dinitrogen. Herein, we show that different forms of MB differentially affect copper uptake and N2O reduction by Pseudomonas stutzeri strain DCP-Ps1 (that expresses clade I NosZ) and Dechloromonas aromatica strain RCB (that expresses clade II NosZ). Specifically, in the presence of MB from Methylocystis sp. strain SB2 (SB2-MB), copper uptake and nosZ expression were more significantly reduced than in the presence of MB from Methylosinus trichosporium OB3b (OB3b-MB). Further, N2O accumulation increased more significantly for both P. stutzeri strain DCP-Ps1 and D. aromatica strain RCB in the presence of SB2-MB versus OB3b-MB. These data illustrate that copper competition between methanotrophs and denitrifying bacteria can be significant and that the extent of such competition is dependent on the form of MB that methanotrophs produce. IMPORTANCE Herein, it was demonstrated that the different forms of methanobactin differentially enhance N2O emissions from Pseudomonas stutzeri strain DCP-Ps1 (harboring clade I nitrous oxide reductase) and Dechloromonas aromatica strain RCB (harboring clade II nitrous oxide reductase). This work contributes to our understanding of how aerobic methanotrophs compete with denitrifiers for the copper uptake and also suggests how MBs prevent copper collection by denitrifiers, thus downregulating expression of nitrous oxide reductase. This study provides critical information for enhanced understanding of microbe-microbe interactions that are important for the development of better predictive models of net greenhouse gas emissions (i.e., methane and nitrous oxide) that are significantly controlled by microbial activity.
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Kochetkova TV, Podosokorskaya OA, Elcheninov AG, Kublanov IV. Diversity of Thermophilic Prokaryotes Inhabiting Russian Natural Hot Springs. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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40
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Wang Z, Fang W, Peng W, Wu P, Wang B. Recent Computational Insights into the Oxygen Activation by Copper-Dependent Metalloenzymes. Top Catal 2022. [DOI: 10.1007/s11244-021-01444-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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41
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Rhizosphere Diazotrophs and Other Bacteria Associated with Native and Encroaching Legumes in the Succulent Karoo Biome in South Africa. Microorganisms 2022; 10:microorganisms10020216. [PMID: 35208671 PMCID: PMC8880511 DOI: 10.3390/microorganisms10020216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/04/2021] [Accepted: 12/23/2021] [Indexed: 12/10/2022] Open
Abstract
Total and diazotrophic bacteria were assessed in the rhizosphere soils of native and encroaching legumes growing in the Succulent Karoo Biome (SKB), South Africa. These were Calobota sericea, Lessertia diffusa, Vachellia karroo, and Wiborgia monoptera, of Fabaceae family near Springbok (Northern Cape Province) and neighboring refugia of the Fynbos biome for C. sericea for comparison purposes. Metabarcoding approach using 16S rRNA gene revealed Actinobacteria (26.7%), Proteobacteria (23.6%), Planctomycetes, and Acidobacteria (10%), while the nifH gene revealed Proteobacteria (70.3%) and Cyanobacteria (29.5%) of the total sequences recovered as the dominant phyla. Some of the diazotrophs measured were assigned to families; Phyllobacteriaceae (39%) and Nostocaceae (24.4%) (all legumes), Rhodospirillaceae (7.9%), Bradyrhizobiaceae (4.6%) and Methylobacteriaceae (3%) (C. sericea, V. karroo, W. monoptera), Rhizobiaceae (4.2%; C. sericea, L. diffusa, V. Karroo), Microchaetaceae (4%; W. monoptera, V. karroo), Scytonemataceae (3.1%; L. diffusa, W. monoptera), and Pseudomonadaceae (2.7%; V. karroo) of the total sequences recovered. These families have the potential to fix the atmospheric nitrogen. While some diazotrophs were specific or shared across several legumes, a member of Mesorhizobium species was common in all rhizosphere soils considered. V. karroo had statistically significantly higher Alpha and distinct Beta-diversity values, than other legumes, supporting its influence on soil microbes. Overall, this work showed diverse bacteria that support plant life in harsh environments such as the SKB, and shows how they are influenced by legumes.
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42
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Genome Sequence of a Thermoacidophilic Methanotroph Belonging to the Verrucomicrobiota Phylum from Geothermal Hot Springs in Yellowstone National Park: A Metagenomic Assembly and Reconstruction. Microorganisms 2022; 10:microorganisms10010142. [PMID: 35056591 PMCID: PMC8779874 DOI: 10.3390/microorganisms10010142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 02/04/2023] Open
Abstract
Verrucomicrobiotal methanotrophs are thermoacidophilic methane oxidizers that have been isolated from volcanic and geothermal regions of the world. We used a metagenomic approach that entailed obtaining the whole genome sequence of a verrucomicrobiotal methanotroph from a microbial consortium enriched from samples obtained from Nymph Lake (89.9 °C, pH 2.73) in Yellowstone National Park in the USA. To identify and reconstruct the verrucomicrobiotal genome from Illumina NovaSeq 6000 sequencing data, we constructed a bioinformatic pipeline with various combinations of de novo assembly, alignment, and binning algorithms. Based on the marker gene (pmoA), we identified and assembled the Candidatus Methylacidiphilum sp. YNP IV genome (2.47 Mbp, 2392 ORF, and 41.26% GC content). In a comparison of average nucleotide identity between Ca. Methylacidiphilum sp. YNP IV and Ca. Methylacidiphilum fumariolicum SolV, its closest 16S rRNA gene sequence relative, is lower than 95%, suggesting that Ca. Methylacidiphilum sp. YNP IV can be regarded as a different species. The Ca. Methylacidiphilum sp. YNP IV genome assembly showed most of the key genes for methane metabolism, the CBB pathway for CO2 fixation, nitrogen fixation and assimilation, hydrogenases, and rare earth elements transporter, as well as defense mechanisms. The assembly and reconstruction of a thermoacidophilic methanotroph belonging to the Verrucomicrobiota phylum from a geothermal environment adds further evidence and knowledge concerning the diversity of biological methane oxidation and on the adaptation of this geochemically relevant reaction in extreme environments.
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Rokubacteria in Northern Peatlands: Habitat Preferences and Diversity Patterns. Microorganisms 2021; 10:microorganisms10010011. [PMID: 35056460 PMCID: PMC8780371 DOI: 10.3390/microorganisms10010011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 01/04/2023] Open
Abstract
Rokubacteria is a phylogenetic clade of as-yet-uncultivated prokaryotes, which are detected in diverse terrestrial habitats and are commonly addressed as members of the rare biosphere. This clade was originally described as a candidate phylum; however, based on the results of comparative genome analysis, was later defined as the order-level lineage, Rokubacteriales, within the phylum Methylomirabilota. The physiology and lifestyles of these bacteria are poorly understood. A dataset of 16S rRNA gene reads retrieved from four boreal raised bogs and six eutrophic fens was examined for the presence of the Rokubacteriales; the latter were detected exclusively in fens. Their relative abundance varied between 0.2 and 4% of all bacteria and was positively correlated with pH, total nitrogen content, and availability of Ca and Mg. To test an earlier published hypothesis regarding the presence of methanotrophic capabilities in Rokubacteria, peat samples were incubated with 10% methane for four weeks. No response to methane availability was detected for the Rokubacteriales, while clear a increase in relative abundance was observed for the conventional Methylococcales methanotrophs. The search for methane monooxygenase encoding genes in 60 currently available Rokubacteriales metagenomes yielded negative results, although copper-containing monooxygenases were encoded by some members of this order. This study suggests that peat-inhabiting Rokubacteriales are neutrophilic non-methanotrophic bacteria that colonize nitrogen-rich wetlands.
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Peat-Inhabiting Verrucomicrobia of the Order Methylacidiphilales Do Not Possess Methanotrophic Capabilities. Microorganisms 2021; 9:microorganisms9122566. [PMID: 34946166 PMCID: PMC8706344 DOI: 10.3390/microorganisms9122566] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 01/04/2023] Open
Abstract
Methanotrophic verrucomicrobia of the order Methylacidiphilales are known as extremely acidophilic, thermophilic or mesophilic bacteria that inhabit acidic geothermal ecosystems. The occurrence of verrucomicrobial methanotrophs in other types of acidic environments remains an open question. Notably, Methylacidiphilales-affiliated 16S rRNA gene sequences are commonly retrieved from acidic (pH 3.5–5.5) peatlands. In this study, we compared the patterns of verrucomicrobial diversity in four acidic raised bogs and six neutral fens located in European North Russia. Methylacidiphilales-like 16S rRNA gene reads displaying 83–86% similarity to 16S rRNA gene sequences of currently described verrucomicrobial methanotrophs were recovered exclusively from raised bogs. Laboratory incubation of peat samples with 10% methane for 3 weeks resulted in the pronounced increase of a relative abundance of alphaproteobacterial methanotrophs, while no response was detected for Methylacidiphilales-affiliated bacteria. Three metagenome-assembled genomes (MAGs) of peat-inhabiting Methylacidiphilales bacteria were reconstructed and examined for the presence of genes encoding methane monooxygenase enzymes and autotrophic carbon fixation pathways. None of these genomic determinants were detected in assembled MAGs. Metabolic reconstructions predicted a heterotrophic metabolism, with a potential to hydrolyze several plant-derived polysaccharides. As suggested by our analysis, peat-inhabiting representatives of the Methylacidiphilales are acidophilic aerobic heterotrophs, which comprise a sister family of the methanotrophic Methylacidiphilaceae.
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Two TonB-dependent transporters in Methylosinus trichosporium OB3b are responsible for uptake of different forms of methanobactin and are involved in the canonical 'copper switch'. Appl Environ Microbiol 2021; 88:e0179321. [PMID: 34669437 DOI: 10.1128/aem.01793-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Copper is an important component of methanotrophic physiology as it controls the expression and activity of alternative forms of methane monooxygenase (MMO). To collect copper, some methanotrophs secrete a chalkophore or copper-binding compound called methanobactin (MB). MB is a ribosomally synthesized post-translationally modified polypeptide (RiPP) that, after binding copper, is collected by MbnT, a TonB-dependent transporter (TBDT). Structurally different forms of MB have been characterized, and here we show that different forms of MB are collected by specific TBDTs. Further, we report that in the model methanotroph, Methylosinus trichosporium OB3b, expression of the TBDT required for uptake of a different MB made by Methylocystis sp. strain SB2 (MB-SB2), is induced in the presence of MB-SB2, suggesting that methanotrophs have developed specific machinery and regulatory systems to actively take up MB from other methanotrophs for copper collection. Moreover, the canonical "copper-switch" in Ms. trichosporium OB3b that controls expression of alternative MMOs is apparent if one of the two TBDTs required for MB-OB3b and MB-SB2 uptake is knocked out, but is disrupted if both TBDTs are knocked out. These data indicate that MB uptake, including the uptake of exogenous MB, plays an important role in the copper switch in M. trichosporium OB3b and thus overall activity. Based on these data, we propose a revised model for the "copper-switch" in this methanotroph that involves MB uptake. IMPORTANCE In this study, we demonstrate that different TonB-dependent transporters (TBDTs) in the model methanotroph Methylosinus trichosporium OB3b are responsible for uptake of either endogenous MB or exogenous MB. Interestingly, the presence of exogenous MB induces expression of its specific TBDT in M. trichosporium OB3b, suggesting that this methanotroph is able to actively take up MB produced by others. This work contributes to our understanding of how microbes collect and compete for copper, and also helps inform how such uptake coordinates the expression of different forms of methane monooxygenase. Such studies are likely to be very important to develop a better understanding of methanotrophic interactions via synthesis and secretion of secondary metabolites such as methanobactin and thus provide additional means whereby these microbes can be manipulated for a variety of environmental and industrial purposes.
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Bussmann I, Horn F, Hoppert M, Klings KW, Saborowski A, Warnstedt J, Liebner S. Methylomonas albis sp. nov. and Methylomonas fluvii sp. nov.: Two cold-adapted methanotrophs from the river Elbe and emended description of the species Methylovulum psychrotolerans. Syst Appl Microbiol 2021; 44:126248. [PMID: 34624710 DOI: 10.1016/j.syapm.2021.126248] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/16/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
Three strains of methanotrophic bacteria (EbAT, EbBT and Eb1) were isolated from the River Elbe, Germany. These Gram-negative, rod-shaped or coccoid cells contain intracytoplasmic membranes perpendicular to the cell surface. Colonies and liquid cultures appeared bright-pink. The major cellular fatty acids were 12:0 and 14:0, in addition in Eb1 the FA 16:1ω5t was also dominant. Methane and methanol were utilized as sole carbon sources by EbBT and Eb1, while EbAT could not use methanol. All strains oxidize methane using the particulate methane monooxygenase. Both strains contain an additional soluble methane monooxygenase. The strains grew optimally at 15-25 °C and at pH 6 and 8. Based on 16S rRNA gene analysis recovered from the full genome, the phylogenetic position of EbAT is robustly outside any species clade with its closest relatives being Methylomonas sp. MK1 (98.24%) and Methylomonas sp. 11b (98.11%). Its closest type strain is Methylomonas methanica NCIMB11130 (97.91%). The 16S rRNA genes of EbBT are highly similar to Methylomonas methanica strains with Methylomonas methanica R-45371 as the closest relative (99.87% sequence identity). However, average nucleotide identity (ANI) and digital DNA-DNA-hybridization (dDDH) values reveal it as distinct species. The DNA G + C contents were 51.07 mol% and 51.5 mol% for EbAT and EbBT, and 50.7 mol% for Eb1, respectively. Strains EbAT and EbBT are representing two novel species within the genus Methylomonas. For strain EbAT we propose the name Methylomonas albis sp. nov (LMG 29958, JCM 32282) and for EbBT, we propose the name Methylomonas fluvii sp. nov (LMG 29959, JCM 32283). Eco-physiological descriptions for both strains are provided. Strain Eb1 (LMG 30323, JCM 32281) is a member of the species Methylovulum psychrotolerans. This genus is so far only represented by two isolates but Eb1 is the first isolate from a temperate environment; so, an emended description of the species is given.
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Affiliation(s)
- Ingeborg Bussmann
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Marine Station Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Michael Hoppert
- University of Göttingen, Institute of Microbiology and Genetics, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Karl-Walter Klings
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Marine Station Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Anke Saborowski
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Julia Warnstedt
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Marine Station Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; University of Potsdam, Institute of Biochemistry and Biology, 14469 Potsdam, Germany
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Martin G, Rissanen AJ, Garcia SL, Mehrshad M, Buck M, Peura S. Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes. Front Microbiol 2021; 12:669937. [PMID: 34456882 PMCID: PMC8397446 DOI: 10.3389/fmicb.2021.669937] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/30/2021] [Indexed: 11/21/2022] Open
Abstract
Boreal lakes and ponds produce two-thirds of the total natural methane emissions above the latitude of 50° North. These lake emissions are regulated by methanotrophs which can oxidize up to 99% of the methane produced in the sediments and the water column. Despite their importance, the diversity and distribution of the methanotrophs in lakes are still poorly understood. Here, we used shotgun metagenomic data to explore the diversity and distribution of methanotrophs in 40 oxygen-stratified water bodies in boreal and subarctic areas in Europe and North America. In our data, gammaproteobacterial methanotrophs (order Methylococcales) generally dominated the methanotrophic communities throughout the water columns. A recently discovered lineage of Methylococcales, Candidatus Methylumidiphilus, was present in all the studied water bodies and dominated the methanotrophic community in lakes with a high relative abundance of methanotrophs. Alphaproteobacterial methanotrophs were the second most abundant group of methanotrophs. In the top layer of the lakes, characterized by low CH4 concentration, their abundance could surpass that of the gammaproteobacterial methanotrophs. These results support the theory that the alphaproteobacterial methanotrophs have a high affinity for CH4 and can be considered stress-tolerant strategists. In contrast, the gammaproteobacterial methanotrophs are competitive strategists. In addition, relative abundances of anaerobic methanotrophs, Candidatus Methanoperedenaceae and Candidatus Methylomirabilis, were strongly correlated, suggesting possible co-metabolism. Our data also suggest that these anaerobic methanotrophs could be active even in the oxic layers. In non-metric multidimensional scaling, alpha- and gammaproteobacterial methanotrophs formed separate clusters based on their abundances in the samples, except for the gammaproteobacterial Candidatus Methylumidiphilus, which was separated from these two clusters. This may reflect similarities in the niche and environmental requirements of the different genera within alpha- and gammaproteobacterial methanotrophs. Our study confirms the importance of O2 and CH4 in shaping the methanotrophic communities and suggests that one variable cannot explain the diversity and distribution of the methanotrophs across lakes. Instead, we suggest that the diversity and distribution of freshwater methanotrophs are regulated by lake-specific factors.
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Affiliation(s)
- Gaëtan Martin
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Antti J. Rissanen
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
| | - Sarahi L. Garcia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sari Peura
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Biofilms for Turbidity Mitigation in Oil Sands End Pit Lakes. Microorganisms 2021; 9:microorganisms9071443. [PMID: 34361879 PMCID: PMC8307862 DOI: 10.3390/microorganisms9071443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 01/04/2023] Open
Abstract
End pit lakes (EPLs) have been proposed as a method of reclaiming oil sands fluid fine tailings (FFT), which consist primarily of process-affected water and clay- and silt-sized particles. Base Mine Lake (BML) is the first full-scale demonstration EPL and contains thick deposits of FFT capped with water. Because of the fine-grained nature of FFT, turbidity generation and mitigation in BML are issues that may be detrimental to the development of an aquatic ecosystem in the water cap. Laboratory mixing experiments were conducted to investigate the effect of mudline biofilms made up of microbial communities indigenous to FFT on mitigating turbidity in EPLs. Four mixing speeds were tested (80, 120, 160, and 200 rpm), all of which are above the threshold velocity required to initiate erosion of FFT in BML. These mixing speeds were selected to evaluate (i) the effectiveness of biofilms in mitigating turbidity and (ii) the mixing speed required to 'break' the biofilms. The impact of biofilm age (10 weeks versus 20 weeks old) on turbidity mitigation was also evaluated. Diverse microbial communities in the biofilms included photoautotrophs, namely cyanobacteria and Chlorophyta (green algae), as well as a number of heterotrophs such as Gammaproteobacteria, Desulfobulbia, and Anaerolineae. Biofilms reduced surface water turbidity by up to 99%, depending on the biofilm age and mixing speed. Lifting and layering in the older biofilms resulted in weaker attachment to the FFT; as such, younger biofilms performed better than older biofilms. However, older biofilms still reduced turbidity by 69% to 95%, depending on the mixing speed. These results indicate that biostabilization is a promising mechanism for turbidity mitigation in EPLs.
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Shubenkova OV, Zakharenko AS, Galach’yants YP, Kalmychkov GV, Ivanov VG, Khabuev AV, Pogodaeva TV, Chernitsyna SM, Zemskaya TI. Effect of Methanol and Mineral Nitrogen Compounds on the Composition of Methanotrophic Enrichments from the Sediments of a Lake Baikal Methane Seep. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721040123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Awala SI, Gwak JH, Kim YM, Kim SJ, Strazzulli A, Dunfield PF, Yoon H, Kim GJ, Rhee SK. Verrucomicrobial methanotrophs grow on diverse C3 compounds and use a homolog of particulate methane monooxygenase to oxidize acetone. ISME JOURNAL 2021; 15:3636-3647. [PMID: 34158629 PMCID: PMC8630023 DOI: 10.1038/s41396-021-01037-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 11/26/2022]
Abstract
Short-chain alkanes (SCA; C2-C4) emitted from geological sources contribute to photochemical pollution and ozone production in the atmosphere. Microorganisms that oxidize SCA and thereby mitigate their release from geothermal environments have rarely been studied. In this study, propane-oxidizing cultures could not be grown from acidic geothermal samples by enrichment on propane alone, but instead required methane addition, indicating that propane was co-oxidized by methanotrophs. “Methylacidiphilum” isolates from these enrichments did not grow on propane as a sole energy source but unexpectedly did grow on C3 compounds such as 2-propanol, acetone, and acetol. A gene cluster encoding the pathway of 2-propanol oxidation to pyruvate via acetol was upregulated during growth on 2-propanol. Surprisingly, this cluster included one of three genomic operons (pmoCAB3) encoding particulate methane monooxygenase (PMO), and several physiological tests indicated that the encoded PMO3 enzyme mediates the oxidation of acetone to acetol. Acetone-grown resting cells oxidized acetone and butanone but not methane or propane, implicating a strict substrate specificity of PMO3 to ketones instead of alkanes. Another PMO-encoding operon, pmoCAB2, was induced only in methane-grown cells, and the encoded PMO2 could be responsible for co-metabolic oxidation of propane to 2-propanol. In nature, propane probably serves primarily as a supplemental growth substrate for these bacteria when growing on methane.
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Affiliation(s)
- Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Yong-Man Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - So-Jeong Kim
- Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Republic of Korea
| | - Andrea Strazzulli
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126, Naples, Italy
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Hyeokjun Yoon
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju, 61186, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea.
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