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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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Ayala-Muñoz D, Macalady JL, Sánchez-España J, Falagán C, Couradeau E, Burgos WD. Microbial carbon, sulfur, iron, and nitrogen cycling linked to the potential remediation of a meromictic acidic pit lake. THE ISME JOURNAL 2022; 16:2666-2679. [PMID: 36123522 PMCID: PMC9666448 DOI: 10.1038/s41396-022-01320-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 12/15/2022]
Abstract
Cueva de la Mora is a permanently stratified acidic pit lake and a model system for extreme acid mine drainage (AMD) studies. Using a combination of amplicon sequencing, metagenomics and metatranscriptomics we performed a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling. We found that active green alga Coccomyxa onubensis dominated the upper layer and chemocline. The chemocline had activity for iron(II) oxidation carried out by populations of Ca. Acidulodesulfobacterium, Ferrovum, Leptospirillium, and Armatimonadetes. Predicted activity for iron(III) reduction was only detected in the deep layer affiliated with Proteobacteria. Activity for dissimilatory nitrogen cycling including nitrogen fixation and nitrate reduction was primarily predicted in the chemocline. Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured Thermoplasmatales dominated in the deep layer. Abundant sulfate-reducing Desulfomonile and Ca. Acidulodesulfobacterium populations were active in the chemocline. In the deep layer, uncultured populations from the bacterial phyla Actinobacteria, Chloroflexi, and Nitrospirae contributed to both sulfate reduction and sulfide oxidation. Based on this information we evaluated the potential for sulfide mineral precipitation in the deep layer as a tool for remediation. We argue that sulfide precipitation is not limited by microbial genetic potential but rather by the quantity and quality of organic carbon reaching the deep layer as well as by oxygen additions to the groundwater enabling sulfur oxidation. Addition of organic carbon and elemental sulfur should stimulate sulfate reduction and limit reoxidation of sulfide minerals.
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Affiliation(s)
- Diana Ayala-Muñoz
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, University Park, PA, 16802, USA.
| | - Jennifer L Macalady
- Department of Geosciences, The Pennsylvania State University, 211 Deike Building University Park, University Park, PA, 16802, USA
| | - Javier Sánchez-España
- Centro Nacional Instituto Geológico Minero de España (IGME), CSIC, Calera 1, 28760 Tres Cantos, Madrid, Spain
| | - Carmen Falagán
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth, PO1 2DY, UK
| | - Estelle Couradeau
- Department of Ecosystem Science and Management, The Pennsylvania State University, 50 ASI University Park, University Park, PA, 16802, USA
| | - William D Burgos
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, University Park, PA, 16802, USA.
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Wang Y, Cheng X, Wang H, Zhou J, Liu X, Tuovinen OH. The Characterization of Microbiome and Interactions on Weathered Rocks in a Subsurface Karst Cave, Central China. Front Microbiol 2022; 13:909494. [PMID: 35847118 PMCID: PMC9277220 DOI: 10.3389/fmicb.2022.909494] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Karst caves are a natural oligotrophic subsurface biosphere widely distributed in southern China. Despite the progress in bacterial and fungal diversity, the knowledge about interactions between bacteria, fungi, and minerals is still limited in caves. Hence, for the first time, we investigated the interaction between bacteria and fungi living on weathered rocks in the Heshang Cave via high-throughput sequencing of 16S rRNA and ITS1 genes, and co-occurrence analysis. The mineral compositions of weathered rocks were analyzed by X-ray diffraction. Bacterial communities were dominated by Actinobacteria (33.68%), followed by Alphaproteobacteria (8.78%), and Planctomycetia (8.73%). In contrast, fungal communities were dominated by Sordariomycetes (21.08%) and Dothideomycetes (14.06%). Mineral substrata, particularly phosphorus-bearing minerals, significantly impacted bacterial (hydroxyapatite) and fungal (fluorapatite) communities as indicated by the redundancy analysis. In comparison with fungi, the development of bacterial communities was more controlled by the environmental selection indicated by the overwhelming contribution of deterministic processes. Co-occurrence network analysis showed that all nodes were positively linked, indicating ubiquitous cooperation within bacterial groups and fungal groups, as well as between bacteria and fungi under oligotrophic conditions in the subsurface biosphere. In total, 19 bacterial ASVs and 34 fungal OTUs were identified as keystone taxa, suggesting the fundamental role of fungi in maintaining the microbial ecosystem on weathered rocks. Ascomycota was most dominant in keystone taxa, accounting for 26.42%, followed by Actinobacteria in bacteria (24.53%). Collectively, our results confirmed the highly diverse bacterial and fungal communities on weathered rocks, and their close cooperation to sustain the subsurface ecosystem. Phosphorus-bearing minerals were of significance in shaping epipetreous bacterial and fungal communities. These observations provide new knowledge about microbial interactions between bacteria, fungi, and minerals in the subterranean biosphere.
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Affiliation(s)
- Yiheng Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Jianping Zhou
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyan Liu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Olli H Tuovinen
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
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Lehosmaa K, Muotka T, Pirttilä AM, Jaakola I, Rossi PM, Jyväsjärvi J. Bacterial communities at a groundwater-surface water ecotone: gradual change or abrupt transition points along a contamination gradient? Environ Microbiol 2021; 23:6694-6706. [PMID: 34382316 DOI: 10.1111/1462-2920.15708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/11/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023]
Abstract
Microbial communities contribute greatly to groundwater quality, but the impacts of land-use practices on bacteria in groundwaters and groundwater-dependent ecosystems remain poorly known. With 16S rRNA gene amplicon sequencing, we assessed bacterial community composition at the groundwater-surface water ecotone of boreal springs impacted by urbanization and agriculture, using spring water nitrate-N as a surrogate of contamination. We also measured the rate of a key ecosystem process, organic matter decomposition. We documented a recurrent pattern across all major bacterial phyla where diversity started to decrease at unexpectedly low nitrate-N concentrations (100-300 μg L-1 ). At 400 NO3 - -N μg L-1 , 25 bacterial exact sequence variants showed a negative response, resulting in a distinct threshold in bacterial community composition. Chthonomonas, Acetobacterales and Hyphomicrobium were the most sensitive taxa, while only three taxa (Duganella, Undibacterium and Thermoanaerobaculaceae) were enriched due to increased contamination. Decomposition rate responded unimodally to increasing nitrate-N concentration, with a peak rate at ~400 NO3 - -N μg L-1 , parallelly with a major shift in bacterial community composition. Our results emphasize the utility of bacterial communities in the assessment of groundwater-dependent ecosystems. They also call for a careful reconsideration of threshold nitrate values for defining groundwater ecosystem health and protecting their microbial biodiversity.
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Affiliation(s)
- Kaisa Lehosmaa
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FI-90014, Finland
| | - Timo Muotka
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FI-90014, Finland
| | - Anna Maria Pirttilä
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FI-90014, Finland
| | - Iikka Jaakola
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FI-90014, Finland
| | - Pekka M Rossi
- Water, Energy and Environmental Engineering Research Group, University of Oulu, Oulu, FI-90014, Finland
| | - Jussi Jyväsjärvi
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FI-90014, Finland
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Compton BJ, Lagutin K, Dyer BS, Ryan J, MacKenzie A, Stott MB, Nekrasov EV, Painter GF, Vyssotski M. Isolation and Synthesis of Glycophospholipids from the extremophile
Chthonomonas calidirosea. ASIAN J ORG CHEM 2020. [DOI: 10.1002/ajoc.202000357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Benjamin J. Compton
- The Ferrier Research Institute Victoria University of Wellington P.O. Box 33–463, Lower Hutt 5046 New Zealand
| | - Kirill Lagutin
- Callaghan Innovation P.O. Box 31310, Lower Hutt 5040 New Zealand
| | - Blake S. Dyer
- GlycoSyn at Callaghan Innovation PO Box 31–310 Lower Hutt 5040 New Zealand
| | - Jason Ryan
- Callaghan Innovation P.O. Box 31310, Lower Hutt 5040 New Zealand
| | - Andrew MacKenzie
- Callaghan Innovation P.O. Box 31310, Lower Hutt 5040 New Zealand
| | - Matthew B. Stott
- School of Biological Sciences University of Canterbury Christchurch New Zealand
| | - Eduard V. Nekrasov
- Callaghan Innovation P.O. Box 31310, Lower Hutt 5040 New Zealand
- Amur Branch of Botanical Garden-Institute of the Far East Branch of the Russian Academy of Sciences Ignatyevskoe Rd. Blagoveshchensk Amurskaya Oblast 675000 Russian Federation
| | - Gavin F. Painter
- The Ferrier Research Institute Victoria University of Wellington P.O. Box 33–463, Lower Hutt 5046 New Zealand
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Chen J, Liu Y, Yang Y, Tang M, Wang R, Jiang L, Tian Y, Hu H, Zhang X, Wei Y. Bacterial community structure and gene function prediction in response to long-term running of dual graphene modified bioelectrode bioelectrochemical systems. BIORESOURCE TECHNOLOGY 2020; 309:123398. [PMID: 32325382 DOI: 10.1016/j.biortech.2020.123398] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
This work studied bacterial community structure and gene function prediction in long-term running of dual graphene modified bioelectrode bioelectrochemical systems (LT D-GM-BE BES, 2 year). The maximum power density of LT D-GM-BE BES was 99.03 ± 3.64 mW/m2, which was 3.66 times of dual control BES (D-C-BE BES), and the transfer resistance of LT GM-BE was just approximately 1/4 of control bioelectrode (C-BE). Proteobacteria and Firmicutes were dominant bacteria in long-term modified bioanode (LT GM-BA, 30.03% and 45.64%), and in long-term modified biocathode (LT GM-BC) was Armatimonadetes (47.14%) in phylum level. The dominant bacteria in LT GM-BA was Clostridium (30.56%), in GM-BC was Chthonomonas (47.14%) in genus level. Gene function related with substrate, energy metabolism and environmental adaptation were enriched. LT GM-BE was tended to enrich dominant bacteria and enrich gene to adapt to micro-environmental changes. This study would provide metagenomics information for long-term running of BES in future.
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Affiliation(s)
- Junfeng Chen
- Department of Environmental Science, School of Life Science, Qufu Normal University, Qufu 273165, PR China.
| | - Yanyan Liu
- Department of Environmental Science, School of Life Science, Qufu Normal University, Qufu 273165, PR China
| | - Yuewei Yang
- Department of Environmental Science, School of Life Science, Qufu Normal University, Qufu 273165, PR China
| | - Meizhen Tang
- Department of Environmental Science, School of Life Science, Qufu Normal University, Qufu 273165, PR China
| | - Renjun Wang
- Department of Environmental Science, School of Life Science, Qufu Normal University, Qufu 273165, PR China
| | - Liting Jiang
- Department of Environmental Science, School of Life Science, Qufu Normal University, Qufu 273165, PR China
| | - Yuping Tian
- Department of Environmental Science, School of Life Science, Qufu Normal University, Qufu 273165, PR China
| | - Hanwen Hu
- Department of Environmental Science, School of Life Science, Qufu Normal University, Qufu 273165, PR China
| | - Xiao Zhang
- Department of Environmental Science, School of Life Science, Qufu Normal University, Qufu 273165, PR China
| | - Yushan Wei
- Department of Environmental Science, School of Life Science, Qufu Normal University, Qufu 273165, PR China
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Mixotrophy drives niche expansion of verrucomicrobial methanotrophs. ISME JOURNAL 2017; 11:2599-2610. [PMID: 28777381 PMCID: PMC5649168 DOI: 10.1038/ismej.2017.112] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/07/2017] [Accepted: 05/12/2017] [Indexed: 01/26/2023]
Abstract
Aerobic methanotrophic bacteria have evolved a specialist lifestyle dependent on consumption of methane and other short-chain carbon compounds. However, their apparent substrate specialism runs contrary to the high relative abundance of these microorganisms in dynamic environments, where the availability of methane and oxygen fluctuates. In this work, we provide in situ and ex situ evidence that verrucomicrobial methanotrophs are mixotrophs. Verrucomicrobia-dominated soil communities from an acidic geothermal field in Rotokawa, New Zealand rapidly oxidised methane and hydrogen simultaneously. We isolated and characterised a verrucomicrobial strain from these soils, Methylacidiphilum sp. RTK17.1, and showed that it constitutively oxidises molecular hydrogen. Genomic analysis confirmed that this strain encoded two [NiFe]-hydrogenases (group 1d and 3b), and biochemical assays revealed that it used hydrogen as an electron donor for aerobic respiration and carbon fixation. While the strain could grow heterotrophically on methane or autotrophically on hydrogen, it grew optimally by combining these metabolic strategies. Hydrogen oxidation was particularly important for adaptation to methane and oxygen limitation. Complementary to recent findings of hydrogenotrophic growth by Methylacidiphilum fumariolicum SolV, our findings illustrate that verrucomicrobial methanotrophs have evolved to simultaneously utilise hydrogen and methane from geothermal sources to meet energy and carbon demands where nutrient flux is dynamic. This mixotrophic lifestyle is likely to have facilitated expansion of the niche space occupied by these microorganisms, allowing them to become dominant in geothermally influenced surface soils. Genes encoding putative oxygen-tolerant uptake [NiFe]-hydrogenases were identified in all publicly available methanotroph genomes, suggesting hydrogen oxidation is a general metabolic strategy in this guild.
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