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Wang Y, Xue D, Chen X, Qiu Q, Chen H. Structure and Functions of Endophytic Bacterial Communities Associated with Sphagnum Mosses and Their Drivers in Two Different Nutrient Types of Peatlands. MICROBIAL ECOLOGY 2024; 87:47. [PMID: 38407642 PMCID: PMC10896819 DOI: 10.1007/s00248-024-02355-6] [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: 10/10/2023] [Accepted: 01/29/2024] [Indexed: 02/27/2024]
Abstract
Sphagnum mosses are keystone plant species in the peatland ecosystems that play a crucial role in the formation of peat, which shelters a broad diversity of endophytic bacteria with important ecological functions. In particular, methanotrophic and nitrogen-fixing endophytic bacteria benefit Sphagnum moss hosts by providing both carbon and nitrogen. However, the composition and abundance of endophytic bacteria from different species of Sphagnum moss in peatlands of different nutrient statuses and their drivers remain unclear. This study used 16S rRNA gene amplicon sequencing to examine endophytic bacterial communities in Sphagnum mosses and measured the activity of methanotrophic microbial by the 13C-CH4 oxidation rate. According to the results, the endophytic bacterial community structure varied among Sphagnum moss species and Sphagnum capillifolium had the highest endophytic bacterial alpha diversity. Moreover, chlorophyll, phenol oxidase, carbon contents, and water retention capacity strongly shaped the communities of endophytic bacteria. Finally, Sphagnum palustre in Hani (SP) had a higher methane oxidation rate than S. palustre in Taishanmiao. This result is associated with the higher average relative abundance of Methyloferula an obligate methanotroph in SP. In summary, this work highlights the effects of Sphagnum moss characteristics on the endophytic bacteriome. The endophytic bacteriome is important for Sphagnum moss productivity, as well as for carbon and nitrogen cycles in Sphagnum moss peatlands.
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Affiliation(s)
- Yue Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan Xue
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China.
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China.
| | - Xuhui Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Qiu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China
| | - Huai Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China.
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China.
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Jiang Y, Liu J, Li Y, Xiao P, Liu S, Shao J, Cai Y, Yan X, Fan L. Biochar amendment reduces biological nitrogen fixation and nitrogen use efficiency in cadmium-contaminated paddy fields. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118338. [PMID: 37379629 DOI: 10.1016/j.jenvman.2023.118338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/21/2023] [Accepted: 06/04/2023] [Indexed: 06/30/2023]
Abstract
Cadmium (Cd) contamination poses a considerable threat to human health through grain enrichment and limits biological nitrogen fixation (BNF) in paddy fields. Biochar has shown great potential for agricultural soil remediation because it inactivates Cd, but uncertainties remain as to how biochar amendments affect BNF and grain N use efficiency in paddies. To elucidate these issues, we investigated the effects of biochar amendment on the structure and function of diazotrophic bacterial communities in different rice growth stages in Cd-contaminated paddy fields, and evaluated the contribution of BNF to grain N use efficiency under biochar amendment. The results showed that biochar amendment significantly increased the abundance of diazotrophic bacteria in the tillering and jointing stages. Furthermore, the community structure of soil diazotrophic bacteria markedly changed with biochar amendment, with a significant reduction in the abundances of Euryarchaeota, Desulfobacterales (Proteobacteria), and Sphingomonadales (Bacteroidetes) in the tillering stage. Changes in the soil carbon/nitrogen (C/N) ratio was the main factor driving diazotrophic microbial community characteristics caused by the release of available C from biochar at the tillering stage, rather than the Cd. Moreover, biochar amendment increased the efficiency of BNF (especially for autotrophic N2 fixation) in the vegetative phase of rice growth. Notably, biochar amendment significantly decreased BNF efficiency during the filling stage and reduced grain N use efficiency. The limited available nutrients in biochar and the toxicity of polycyclic aromatics and phenols in biochar-derived dissolved organic matter were responsible for the varied impacts of biochar on BNF in different rice growth stages. For the first time, we report that biochar amendment in paddy soils reduces Cd toxicity but also inhibits BNF and thereby decreases N use efficiency. Therefore, before applying biochar to inactivate Cd in paddy fields, there should be a trade-off between agricultural production and ecological safety to achieve sustainable agriculture.
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Affiliation(s)
- Yuexi Jiang
- College of Environment and Ecology, Hunan Agricultural University, Changsha, Hunan, 410128, PR China
| | - Ji Liu
- College of Urban and Environmental Sciences, Central China Normal University, Wuhan, Hubei, 430079, PR China; Department of Ecohydrology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, 12587, Germany
| | - Yanyan Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and the Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, 410125, PR China
| | - Peng Xiao
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
| | - Shuang Liu
- College of Environment and Ecology, Hunan Agricultural University, Changsha, Hunan, 410128, PR China
| | - Jihai Shao
- College of Environment and Ecology, Hunan Agricultural University, Changsha, Hunan, 410128, PR China.
| | - Yixiang Cai
- College of Environment and Ecology, Hunan Agricultural University, Changsha, Hunan, 410128, PR China
| | - Xiaoqi Yan
- College of Environment and Ecology, Hunan Agricultural University, Changsha, Hunan, 410128, PR China
| | - Li Fan
- College of Environment and Ecology, Hunan Agricultural University, Changsha, Hunan, 410128, PR China
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Defining the
Sphagnum
Core Microbiome across the North American Continent Reveals a Central Role for Diazotrophic Methanotrophs in the Nitrogen and Carbon Cycles of Boreal Peatland Ecosystems. mBio 2022. [PMCID: PMC8863050 DOI: 10.1128/mbio.03714-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Peat mosses of the genus Sphagnum are ecosystem engineers that frequently predominate over photosynthetic production in boreal peatlands. Sphagnum spp. host diverse microbial communities capable of nitrogen fixation (diazotrophy) and methane oxidation (methanotrophy), thereby potentially supporting plant growth under severely nutrient-limited conditions. Moreover, diazotrophic methanotrophs represent a possible “missing link” between the carbon and nitrogen cycles, but the functional contributions of the Sphagnum-associated microbiome remain in question. A combination of metagenomics, metatranscriptomics, and dual-isotope incorporation assays was applied to investigate Sphagnum microbiome community composition across the North American continent and provide empirical evidence for diazotrophic methanotrophy in Sphagnum-dominated ecosystems. Remarkably consistent prokaryotic communities were detected in over 250 Sphagnum SSU rRNA libraries from peatlands across the United States (5 states, 17 bog/fen sites, 18 Sphagnum species), with 12 genera of the core microbiome comprising 60% of the relative microbial abundance. Additionally, nitrogenase (nifH) and SSU rRNA gene amplicon analysis revealed that nitrogen-fixing populations made up nearly 15% of the prokaryotic communities, predominated by Nostocales cyanobacteria and Rhizobiales methanotrophs. While cyanobacteria comprised the vast majority (>95%) of diazotrophs detected in amplicon and metagenome analyses, obligate methanotrophs of the genus Methyloferula (order Rhizobiales) accounted for one-quarter of transcribed nifH genes. Furthermore, in dual-isotope tracer experiments, members of the Rhizobiales showed substantial incorporation of 13CH4 and 15N2 isotopes into their rRNA. Our study characterizes the core Sphagnum microbiome across large spatial scales and indicates that diazotrophic methanotrophs, here defined as obligate methanotrophs of the rare biosphere (Methyloferula spp. of the Rhizobiales) that also carry out diazotrophy, play a keystone role in coupling of the carbon and nitrogen cycles in nutrient-poor peatlands.
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Kox MAR, Smolders AJP, Speth DR, Lamers LPM, Op den Camp HJM, Jetten MSM, van Kessel MAHJ. A Novel Laboratory-Scale Mesocosm Setup to Study Methane Emission Mitigation by Sphagnum Mosses and Associated Methanotrophs. Front Microbiol 2021; 12:652486. [PMID: 33981290 PMCID: PMC8108401 DOI: 10.3389/fmicb.2021.651103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/26/2021] [Indexed: 11/13/2022] Open
Abstract
Degraded peatlands are often rewetted to prevent oxidation of the peat, which reduces CO2 emission. However, the created anoxic conditions will boost methane (CH4) production and thus emission. Here, we show that submerged Sphagnum peat mosses in rewetted-submerged peatlands can reduce CH4 emission from peatlands with 93%. We were able to mimic the field situation in the laboratory by using a novel mesocosm set-up. By combining these with 16S rRNA gene amplicon sequencing and qPCR analysis of the pmoA and mmoX genes, we showed that submerged Sphagnum mosses act as a niche for CH4 oxidizing bacteria. The tight association between Sphagnum peat mosses and methane oxidizing bacteria (MOB) significantly reduces CH4 emissions by peatlands and can be studied in more detail in the mesocosm setup developed in this study.
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Affiliation(s)
- Martine A R Kox
- Department of Microbiology, IWWR, Radboud University, Nijmegen, Netherlands.,Department of Aquatic Ecology and Environmental Biology, IWWR, Radboud University, Nijmegen, Netherlands
| | - Alfons J P Smolders
- Department of Aquatic Ecology and Environmental Biology, IWWR, Radboud University, Nijmegen, Netherlands.,B-WARE Research Centre, Nijmegen, Netherlands
| | - Daan R Speth
- Department of Microbiology, IWWR, Radboud University, Nijmegen, Netherlands
| | - Leon P M Lamers
- Department of Aquatic Ecology and Environmental Biology, IWWR, Radboud University, Nijmegen, Netherlands
| | | | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University, Nijmegen, Netherlands
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Schmitz RA, Peeters SH, Versantvoort W, Picone N, Pol A, Jetten MSM, Op den Camp HJM. Verrucomicrobial methanotrophs: ecophysiology of metabolically versatile acidophiles. FEMS Microbiol Rev 2021; 45:6125968. [PMID: 33524112 PMCID: PMC8498564 DOI: 10.1093/femsre/fuab007] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/15/2021] [Indexed: 12/26/2022] Open
Abstract
Methanotrophs are an important group of microorganisms that counteract methane emissions to the atmosphere. Methane-oxidising bacteria of the Alpha- and Gammaproteobacteria have been studied for over a century, while methanotrophs of the phylum Verrucomicrobia are a more recent discovery. Verrucomicrobial methanotrophs are extremophiles that live in very acidic geothermal ecosystems. Currently, more than a dozen strains have been isolated, belonging to the genera Methylacidiphilum and Methylacidimicrobium. Initially, these methanotrophs were thought to be metabolically confined. However, genomic analyses and physiological and biochemical experiments over the past years revealed that verrucomicrobial methanotrophs, as well as proteobacterial methanotrophs, are much more metabolically versatile than previously assumed. Several inorganic gases and other molecules present in acidic geothermal ecosystems can be utilised, such as methane, hydrogen gas, carbon dioxide, ammonium, nitrogen gas and perhaps also hydrogen sulfide. Verrucomicrobial methanotrophs could therefore represent key players in multiple volcanic nutrient cycles and in the mitigation of greenhouse gas emissions from geothermal ecosystems. Here, we summarise the current knowledge on verrucomicrobial methanotrophs with respect to their metabolic versatility and discuss the factors that determine their diversity in their natural environment. In addition, key metabolic, morphological and ecological characteristics of verrucomicrobial and proteobacterial methanotrophs are reviewed.
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Affiliation(s)
- Rob A Schmitz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Stijn H Peeters
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Nunzia Picone
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Arjan Pol
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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Mo Y, Qi XE, Li A, Zhang X, Jia Z. Active Methanotrophs in Suboxic Alpine Swamp Soils of the Qinghai-Tibetan Plateau. Front Microbiol 2020; 11:580866. [PMID: 33281775 PMCID: PMC7689253 DOI: 10.3389/fmicb.2020.580866] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/22/2020] [Indexed: 11/29/2022] Open
Abstract
Methanotrophs are the only biofilters for reducing the flux of global methane (CH4) emissions in water-logged wetlands. However, adaptation of aerobic methanotrophs to low concentrations of oxygen and nitrogen in typical swamps, such as that of the Qinghai-Tibetan Plateau, is poorly understood. In this study, we show that Methylobacter-like methanotrophs dominate methane oxidation and nitrogen fixation under suboxic conditions in alpine swamp soils. Following incubation with 13C-CH4 and 15N-N2 for 90 days under suboxic conditions with repeated flushing using an inert gas (i.e., argon), microbial carbon and nitrogen turnover was measured in swamp soils at different depths: 0-20 cm (top), 40-60 cm (intermediate), and 60-80 cm (deep). Results show detectable methane oxidation and nitrogen fixation in all three soil depths. In particular, labeled carbon was found in CO2 enrichment (13C-CO2), and soil organic carbon (13C-SOC), whereas labeled nitrogen (15N) was detected in soil organic nitrogen (SON). The highest values of labeled isotopes were found at intermediate soil depths. High-throughput amplicon sequencing and Sanger sequencing indicated the dominance of Methylobacter-like methanotrophs in swamp soils, which comprised 21.3-24.0% of the total bacterial sequences, as measured by 13C-DNA at day 90. These results demonstrate that aerobic methanotroph Methylobacter is the key player in suboxic methane oxidation and likely catalyzes nitrogen fixation in swamp wetland soils in the Qinghai-Tibetan Plateau.
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Affiliation(s)
- Yongliang Mo
- College of Environmental Science and Engineering, China West Normal University, Nanchong, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xing-e Qi
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Aorui Li
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xinfang Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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7
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Kox MAR, van den Elzen E, Lamers LPM, Jetten MSM, van Kessel MAHJ. Microbial nitrogen fixation and methane oxidation are strongly enhanced by light in Sphagnum mosses. AMB Express 2020; 10:61. [PMID: 32236738 PMCID: PMC7109220 DOI: 10.1186/s13568-020-00994-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/16/2020] [Indexed: 12/25/2022] Open
Abstract
Peatlands have acted as C-sinks for millennia, storing large amounts of carbon, of which a significant amount is yearly released as methane (CH4). Sphagnum mosses are a key genus in many peat ecosystems and these mosses live in close association with methane-oxidizing and nitrogen-fixing microorganisms. To disentangle mechanisms which may control Sphagnum-associated methane-oxidation and nitrogen-fixation, we applied four treatments to Sphagnum mosses from a pristine peatland in Finland: nitrogen fertilization, phosphorus fertilization, CH4 addition and light. N and P fertilization resulted in nutrient accumulation in the moss tissue, but did not increase Sphagnum growth. While net CO2 fixation rates remained unaffected in the N and P treatment, net CH4 emissions decreased because of enhanced CH4 oxidation. CH4 addition did not affect Sphagnum performance in the present set-up. Light, however, clearly stimulated the activity of associated nitrogen-fixing and methane-oxidizing microorganisms, increasing N2 fixation rates threefold and CH4 oxidation rates fivefold. This underlines the strong connection between Sphagnum and associated N2 fixation and CH4 oxidation. It furthermore indicates that phototrophy is a strong control of microbial activity, which can be directly or indirectly.
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Affiliation(s)
- Martine A R Kox
- Department of Microbiology, Radboud University, Heijendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Eva van den Elzen
- Department of Aquatic Ecology and Environmental Biology, Radboud University, Heijendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Leon P M Lamers
- Department of Aquatic Ecology and Environmental Biology, Radboud University, Heijendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Heijendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Maartje A H J van Kessel
- Department of Microbiology, Radboud University, Heijendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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Bodelier PLE, Pérez G, Veraart AJ, Krause SMB. Methanotroph Ecology, Environmental Distribution and Functioning. METHANOTROPHS 2019. [DOI: 10.1007/978-3-030-23261-0_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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