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Eam H, Ko D, Lee C, Myung J. Methylosinus trichosporium OB3b bioaugmentation unleashes polyhydroxybutyrate-accumulating potential in waste-activated sludge. Microb Cell Fact 2024; 23:160. [PMID: 38822346 PMCID: PMC11140957 DOI: 10.1186/s12934-024-02442-w] [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: 01/29/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024] Open
Abstract
BACKGROUND Wastewater treatment plants contribute approximately 6% of anthropogenic methane emissions. Methanotrophs, capable of converting methane into polyhydroxybutyrate (PHB), offer a promising solution for utilizing methane as a carbon source, using activated sludge as a seed culture for PHB production. However, maintaining and enriching PHB-accumulating methanotrophic communities poses challenges. RESULTS This study investigated the potential of Methylosinus trichosporium OB3b to bioaugment PHB-accumulating methanotrophic consortium within activated sludge to enhance PHB production. Waste-activated sludges with varying ratios of M. trichosporium OB3b (1:0, 1:1, 1:4, and 0:1) were cultivated. The results revealed substantial growth and methane consumption in waste-activated sludge with M. trichosporium OB3b-amended cultures, particularly in a 1:1 ratio. Enhanced PHB accumulation, reaching 37.1% in the same ratio culture, indicates the dominance of Type II methanotrophs. Quantification of methanotrophs by digital polymerase chain reaction showed gradual increases in Type II methanotrophs, correlating with increased PHB production. However, while initial bioaugmentation of M. trichosporium OB3b was observed, its presence decreased in subsequent cycles, indicating the dominance of other Type II methanotrophs. Microbial community analysis highlighted the successful enrichment of Type II methanotrophs-dominated cultures due to the addition of M. trichosporium OB3b, outcompeting Type I methanotrophs. Methylocystis and Methylophilus spp. were the most abundant in M. trichosporium OB3b-amended cultures. CONCLUSIONS Bioaugmentation strategies, leveraging M. trichosporium OB3b could significantly enhance PHB production and foster the enrichment of PHB-accumulating methanotrophs in activated sludge. These findings contribute to integrating PHB production in wastewater treatment plants, providing a sustainable solution for resource recovery.
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Affiliation(s)
- Hyerim Eam
- Department of Civil and Environmental Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Dayoung Ko
- Department of Civil, Urban, Earth, and Environmental Engineering, UNIST, Ulsan, 44919, Republic of Korea
| | - Changsoo Lee
- Department of Civil, Urban, Earth, and Environmental Engineering, UNIST, Ulsan, 44919, Republic of Korea
| | - Jaewook Myung
- Department of Civil and Environmental Engineering, KAIST, Daejeon, 34141, Republic of Korea.
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2
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Schmider T, Hestnes AG, Brzykcy J, Schmidt H, Schintlmeister A, Roller BRK, Teran EJ, Söllinger A, Schmidt O, Polz MF, Richter A, Svenning MM, Tveit AT. Physiological basis for atmospheric methane oxidation and methanotrophic growth on air. Nat Commun 2024; 15:4151. [PMID: 38755154 DOI: 10.1038/s41467-024-48197-1] [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: 02/13/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Atmospheric methane oxidizing bacteria (atmMOB) constitute the sole biological sink for atmospheric methane. Still, the physiological basis allowing atmMOB to grow on air is not well understood. Here we assess the ability and strategies of seven methanotrophic species to grow with air as sole energy, carbon, and nitrogen source. Four species, including three outside the canonical atmMOB group USCα, enduringly oxidized atmospheric methane, carbon monoxide, and hydrogen during 12 months of growth on air. These four species exhibited distinct substrate preferences implying the existence of multiple metabolic strategies to grow on air. The estimated energy yields of the atmMOB were substantially lower than previously assumed necessary for cellular maintenance in atmMOB and other aerobic microorganisms. Moreover, the atmMOB also covered their nitrogen requirements from air. During growth on air, the atmMOB decreased investments in biosynthesis while increasing investments in trace gas oxidation. Furthermore, we confirm that a high apparent specific affinity for methane is a key characteristic of atmMOB. Our work shows that atmMOB grow on the trace concentrations of methane, carbon monoxide, and hydrogen present in air and outlines the metabolic strategies that enable atmMOB to mitigate greenhouse gases.
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Affiliation(s)
- Tilman Schmider
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway.
| | - Anne Grethe Hestnes
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Julia Brzykcy
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096, Warsaw, Poland
| | - Hannes Schmidt
- Department of Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1030, Vienna, Austria
| | - Arno Schintlmeister
- Department of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1030, Vienna, Austria
| | - Benjamin R K Roller
- Department of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1030, Vienna, Austria
| | - Ezequiel Jesús Teran
- Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires (CIFICEN-UNCPBA-CONICET-CICPBA), Pinto, 399, Tandil (7000), Argentina
- Universidad Nacional del Centro de la Provincia de Buenos Aires, Facultad de Ciencias Exactas, Instituto de Física Arroyo Seco (IFAS), Pinto, 399, Tandil (7000), Argentina
| | - Andrea Söllinger
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Oliver Schmidt
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Martin F Polz
- Department of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1030, Vienna, Austria
| | - Andreas Richter
- Department of Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1030, Vienna, Austria
| | - Mette M Svenning
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway.
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Shen L, Ren B, Jin Y, Liu X, Jin J, Huang H, Tian M, Yang W, Yang Y, Liu J, Geng C, Bai Y, Hu Z. Effects of abrupt and gradual increase of atmospheric CO 2 concentration on methanotrophs in paddy fields. ENVIRONMENTAL RESEARCH 2023; 223:115474. [PMID: 36773639 DOI: 10.1016/j.envres.2023.115474] [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: 12/15/2022] [Revised: 01/27/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
The simulation of abrupt atmospheric CO2 increase is a common way to examine the response of soil methanotrophs to future climate change. However, atmosphere is undergoing a gradual CO2 increase, and it is unknown whether the previously reported response of methanotrophs to abrupt CO2 increase can well represent their response to the gradual increase. To improve the understanding of the effect of elevated CO2 (eCO2) on methanotrophs in paddy ecosystems, the methane oxidation potential and communities of methanotrophs were examined via open top chambers under the three following CO2 treatments: an ambient CO2 concentration (AC); an abrupt CO2 increase by 200 ppm above AC (AI); a gradual CO2 increase by 40 ppm each year until 200 ppm above AC (GI). Relative to AC treatment, AI and GI treatments significantly (p < 0.05) increased the methane oxidation rate by 43.8% and 36.7%, respectively, during rice growth period. Furthermore, the abundance of pmoA genes was significantly (p < 0.05) increased by 62.4% and 32.5%, respectively, under AI and GI treatments. However, there were no significant variations in oxidation rate or gene abundance between the two eCO2 treatments. In addition, no obvious change of overall community composition of methanotrophs was observed among treatments, while the proportions of Methylosarcina and Methylocystis significantly (p < 0.05) changed. Taken together, our results indicate similar response of methanotrophs to abrupt and gradual CO2 increase, although the magnitude of response under gradual increase was smaller and the abrupt increase may somewhat overestimate the response.
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Affiliation(s)
- Lidong Shen
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Bingjie Ren
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yuhan Jin
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Xin Liu
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jinghao Jin
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Hechen Huang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Maohui Tian
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Wangting Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yuling Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jiaqi Liu
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Caiyu Geng
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yanan Bai
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Zhenghua Hu
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
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4
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Chetri JK, Reddy KR, Green SJ. Use of methanotrophically activated biochar in novel biogeochemical cover system for carbon sequestration: Microbial characterization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153429. [PMID: 35101512 DOI: 10.1016/j.scitotenv.2022.153429] [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: 11/11/2021] [Revised: 01/05/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Biochar-amended soils have been explored to enhance microbial methane (CH4) oxidation in landfill cover systems. Recently, research priorities have expanded to include the mitigation of other components of landfill gas such as carbon dioxide (CO2) and hydrogen sulfide (H2S) along with CH4. In this study, column tests were performed to simulate the newly proposed biogeochemical cover systems, which incorporate biochar-amended soil for CH4 oxidation and basic oxygen furnace (BOF) slag for CO2 and H2S mitigation, to evaluate the effect of cover configuration on microbial CH4 oxidation and community composition. Biogeochemical covers included a biochar-amended soil (10% w/w), and methanotroph-enriched activated biochar amended soil (5% or 10% w/w) as a biocover layer or CH4 oxidation layer. The primary outcome measures of interest were CH4 oxidation rates and the structure and abundance of methane-oxidation bacteria in the covers. All column reactors were active in CH4 oxidation, but columns containing activated biochar-amended soils had higher CH4 oxidation rates (133 to 143 μg CH4 g-1 day-1) than those containing non-activated biochar-amended soil (50 μg CH4 g-1 day-1) and no-biochar soil or control soil (43 μg CH4 g-1 day-1). All treatments showed significant increases in the relative abundance of methanotrophs from an average relative abundance of 5.6% before incubation to a maximum of 45% following incubation. In activated biochar, the abundance of Type II methanotrophs, primarily Methylocystis and Methylosinus, was greater than that of Type I methanotrophs (Methylobacter) due to which activated biochar-amended soils also showed higher abundance of Type II methanotrophs. Overall, biogeochemical cover profiles showed promising potential for CH4 oxidation without any adverse effect on microbial community composition and methane oxidation. Biochar activation led to an alteration of the dominant methanotrophic communities and increased CH4 oxidation.
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Affiliation(s)
- Jyoti K Chetri
- University of Illinois at Chicago, Department of Civil, Materials, and Environmental Engineering, 842 West Taylor Street, Chicago, IL 60607, USA.
| | - Krishna R Reddy
- University of Illinois at Chicago, Department of Civil, Materials, and Environmental Engineering, 842 West Taylor Street, Chicago, IL 60607, USA.
| | - Stefan J Green
- Genomics and Microbiome Core Facility, Rush University Medical Center, 1653 W. Congress Parkway, Jelke Building, Room 444, Chicago, IL 60612, USA.
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5
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Cai Y, Yun J, Jia Z. Phylogeny and Metabolic Potential of the Methanotrophic Lineage MO3 in Beijerinckiaceae from the Paddy Soil through Metagenome-Assembled Genome Reconstruction. Microorganisms 2022; 10:microorganisms10050955. [PMID: 35630399 PMCID: PMC9145241 DOI: 10.3390/microorganisms10050955] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/22/2022] [Accepted: 04/29/2022] [Indexed: 01/27/2023] Open
Abstract
Although the study of aerobic methane-oxidizing bacteria (MOB, methanotrophs) has been carried out for more than a hundred years, there are many uncultivated methanotrophic lineages whose metabolism is largely unknown. Here, we reconstructed a nearly complete genome of a Beijerinckiaceae methanotroph from the enrichment of paddy soil by using nitrogen-free M2 medium. The methanotroph labeled as MO3_YZ.1 had a size of 3.83 Mb, GC content of 65.6%, and 3442 gene-coding regions. Based on phylogeny of pmoA gene and genome and the genomic average nucleotide identity, we confirmed its affiliation to the MO3 lineage and a close relationship to Methylocapsa. MO3_YZ.1 contained mxaF- and xoxF-type methanol dehydrogenase. MO3_YZ.1 used the serine cycle to assimilate carbon and regenerated glyoxylate through the glyoxylate shunt as it contained isocitrate lyase and complete tricarboxylic acid cycle-coding genes. The ethylmalonyl-CoA pathway and Calvin–Benson–Bassham cycle were incomplete in MO3_YZ.1. Three acetate utilization enzyme-coding genes were identified, suggesting its potential ability to utilize acetate. The presence of genes for N2 fixation, sulfur transformation, and poly-β-hydroxybutyrate synthesis enable its survival in heterogeneous habitats with fluctuating supplies of carbon, nitrogen, and sulfur.
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Affiliation(s)
- Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Correspondence: (Y.C.); (Z.J.); Tel.: +86-25-8688-1850 (Y.C.); +86-25-8688-1311 (Z.J.)
| | - Juanli Yun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Correspondence: (Y.C.); (Z.J.); Tel.: +86-25-8688-1850 (Y.C.); +86-25-8688-1311 (Z.J.)
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6
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Lin Y, Yuan J, Liu D, Kang H, Freeman C, Hu HW, Ye G, Ding W. Divergent responses of wetland methane emissions to elevated atmospheric CO 2 dependent on water table. WATER RESEARCH 2021; 205:117682. [PMID: 34592652 DOI: 10.1016/j.watres.2021.117682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Elevated atmospheric CO2 may have consequences for methane (CH4) emissions from wetlands, yet the magnitude and direction remain unpredictable, because the associated mechanisms have not been fully investigated. Here, we established an in situ macrocosm experiment to compare the effects of elevated CO2 (700 ppm) on the CH4 emissions from two wetlands: an intermittently inundated Calamagrostis angustifolia marsh and a permanently inundated Carex lasiocarpa marsh. The elevated CO2 increased CH4 emissions by 27.6-57.6% in the C. angustifolia marsh, compared to a reduction of 18.7-23.5% in the C. lasiocarpa marsh. The CO2-induced increase in CH4 emissions from the C. angustifolia marsh was paralleled with (1) increased dissolved organic carbon (DOC) released from plant photosynthesis and (2) reduced (rate of) CH4 oxidation due to a putative shift in methanotrophic community composition. In contrast, the CO2-induced decrease in CH4 emissions from the C. lasiocarpa marsh was associated with the increases in soil redox potential and pmoA gene abundance. We synthesized data from worldwide wetland ecosystems, and found that the responses of CH4 emissions to elevated CO2 was determined by the wetland water table levels and associated plant oxygen secretion capacity. In conditions with elevated CO2, plants with a high oxygen secretion capacity suppress CH4 emissions while plants with low oxygen secretion capacity stimulate CH4 emissions; both effects are mediated via a feedback loop involving shifts in activities of methanogens and methanotrophs.
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Affiliation(s)
- Yongxin Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 10049, China; Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Junji Yuan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Deyan Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul 120-749, South Korea
| | - Chris Freeman
- School of Natural Sciences, Bangor University, Gwynedd LL57 2UW, United Kingdom
| | - Hang-Wei Hu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Guiping Ye
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 10049, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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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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Wang Y, Lai CY, Wu M, Song Y, Hu S, Yuan Z, Guo J. Roles of Oxygen in Methane-dependent Selenate Reduction in a Membrane Biofilm Reactor: Stimulation or Suppression. WATER RESEARCH 2021; 198:117150. [PMID: 33910142 DOI: 10.1016/j.watres.2021.117150] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/03/2021] [Accepted: 04/10/2021] [Indexed: 05/22/2023]
Abstract
Although methane (CH4) has been proven to be able to serve as an electron donor for bio-reducing various oxidized contaminants (e.g., selenate (SeO42-)), little is known regarding the roles of oxygen in methane-based reduction processes. Here, a methane-based membrane biofilm reactor (MBfR) was established for evaluating the effects of oxygen supply rates on selenate reduction performance and microbial communities. The oxygen supply rate played a dual role (stimulatory or suppressive effect) in selenate reduction rates, depending on the presence or absence of dissolved oxygen (DO). Specifically, selenate reduction rate was substantially enhanced when an appropriate oxygen rate (e.g., 12 to 184 mg/L.d in this study) was supplied but with negligible DO. The highest selenate reduction rate (up to 34 mg-Se/L.d) was obtained under an oxygen supply rate of 184 mg/L.d. In contrast, excessive oxygen supply rate (626 mg/L.d) would significantly suppress selenate reduction rate under DO level of 3 mg/L. Accordingly, though the high oxygen supply rate (626 mg/L.d) would promote the expression of pmoA (5.9 × 109 copies g-1), the expression level of narG (a recognized gene to mediate selenate reduction) would be significantly downregulated (6.1 × 109 copies g-1), thus suppressing selenate reduction. In contrast, the expression of narG gene significantly increased to 2.8 × 1010 copies g-1, and the expression of pmoA gene could still maintain at 1.1 × 109 copies g-1 under an oxygen supply rate of 184 mg/L.d. High-throughput sequencing targeting 16S rRNA gene, pmoA, and narG collectively suggested Methylocystis acts as the major aerobic methanotroph, in synergy with Arthrobacter and Variovorax which likely jointly reduce selenate to selenite (SeO32-), and further to elemental selenium (Se0). Methylocystis was predominant in the biofilm regardless of variations of oxygen supply rates, while Arthrobacter and Variovorax were sensitive to oxygen fluctuation. These findings provide insights into the effects of oxygen on methane-dependent selenate reduction and suggest that it is feasible to achieve a higher selenate removal by regulating oxygen supply rates.
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Affiliation(s)
- Yulu Wang
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Chun-Yu Lai
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Mengxiong Wu
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Yarong Song
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Shihu Hu
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.
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Praeg N, Schwinghammer L, Illmer P. Larix decidua and additional light affect the methane balance of forest soil and the abundance of methanogenic and methanotrophic microorganisms. FEMS Microbiol Lett 2020; 366:5695738. [PMID: 31899513 DOI: 10.1093/femsle/fnz259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/31/2019] [Indexed: 11/13/2022] Open
Abstract
Due to the activity of methane-oxidizing bacteria, forest soils are usually net sinks for the greenhouse gas methane (CH4). Despite several hints that CH4 balances might be influenced by vegetation, there are only few investigations dealing with this connection. Therefore, we studied this soil-plant-microbe interaction by using mesocosm experiments with forest soil and Larix decidua, a common coniferous tree species within the Alps. Gas measurements showed that the presence of L. decidua significantly reduced CH4 oxidation of the forest soil by ∼10% (-0.95 µmol m-2 h-1 for soil vs -0.85 µmol m-2 h-1 for soil plus L. decidua) leading to an increased net CH4 balance. Increased light intensity was used to intensify the influence of the plant on the soil's CH4 balance. The increase in light intensity strengthened the effect of the plant and led to a greater reduction of CH4 oxidation. Besides, we examined the impact of L. decidua and light on the abundance of methanogens and methanotrophs in the rhizosphere as compared with bulk soil. The abundance of both methane-oxidizing bacteria and methanogenic archaea was significantly increased in the rhizosphere compared with bulk soil but no significant response of methanogens and methanotrophs upon light exposure was established.
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Affiliation(s)
- Nadine Praeg
- Universität Innsbruck, Department of Microbiology, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Larissa Schwinghammer
- Universität Innsbruck, Department of Microbiology, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Paul Illmer
- Universität Innsbruck, Department of Microbiology, Technikerstrasse 25d, A-6020 Innsbruck, Austria
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10
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He D, Zhang L, Dumont MG, He JS, Ren L, Chu H. The response of methanotrophs to additions of either ammonium, nitrate or urea in alpine swamp meadow soil as revealed by stable isotope probing. FEMS Microbiol Ecol 2020; 95:5498294. [PMID: 31125053 DOI: 10.1093/femsec/fiz077] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/23/2019] [Indexed: 11/13/2022] Open
Abstract
Different forms of nitrogen (N) are deposited on the Qinghai-Tibetan plateau (QTP), while their differential effects on soil methanotrophs and their activity remain elusive. We constructed microcosms amended with different N fertilizers (ammonia, nitrate and urea) using the soils sampled from a swamp meadow on the QTP. The responses of active methanotrophs to different forms of nitrogen were determined by stable isotope probing with 5% 13C-methane. At the early stage of incubation, all N fertilizers, especially urea, suppressed methane oxidation compared with the control. The methane oxidation rate increased during the incubation, suggesting an adaptation and stimulation of some methanotrophs to elevated methane. At the onset of the incubation, the type II methanotrophs Methylocystis were most abundant, but decreased during the incubation and were replaced by the type Ia methanotrophs Methylomonas. Ammonia and urea had similar effects on the methanotroph communities, both characterized by an elevation in the proportion of Methylobacter and more diverse methanotroph communities. Nitrate had less effect on the methanotroph community. Our results uncovered the active methanotrophs responding to different nitrogen forms, and suggested that urea-N might have large effects on methanotroph diversity and activity in swamp meadow soils on the QTP.
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Affiliation(s)
- Dan He
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China.,Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Liyan Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Marc G Dumont
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Jin-Sheng He
- Department of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China.,State Key Laboratory of Grassland Agro-Ecosystems, and College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Lijuan Ren
- Key Laboratory of Tropical Marine Bioresources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
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11
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Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus. Microorganisms 2020; 8:microorganisms8050768. [PMID: 32443820 PMCID: PMC7285482 DOI: 10.3390/microorganisms8050768] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 01/21/2023] Open
Abstract
The Methylocystis and Methylosinus are two of the five genera that were included in the first taxonomic framework of methanotrophic bacteria created half a century ago. Members of both genera are widely distributed in various environments and play a key role in reducing methane fluxes from soils and wetlands. The original separation of these methanotrophs in two distinct genera was based mainly on their differences in cell morphology. Further comparative studies that explored various single-gene-based phylogenies suggested the monophyletic nature of each of these genera. Current availability of genome sequences from members of the Methylocystis/Methylosinus clade opens the possibility for in-depth comparison of the genomic potentials of these methanotrophs. Here, we report the finished genome sequence of Methylocystis heyeri H2T and compare it to 23 currently available genomes of Methylocystis and Methylosinus species. The phylogenomic analysis confirmed that members of these genera form two separate clades. The Methylocystis/Methylosinus pan-genome core comprised 1173 genes, with the accessory genome containing 4941 and 11,192 genes in the shell and the cloud, respectively. Major differences between the genome-encoded environmental traits of these methanotrophs include a variety of enzymes for methane oxidation and dinitrogen fixation as well as genomic determinants for cell motility and photosynthesis.
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12
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Chu YX, Ma RC, Wang J, Zhu JT, Kang YR, He R. Effects of oxygen tension on the microbial community and functional gene expression of aerobic methane oxidation coupled to denitrification systems. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:12280-12292. [PMID: 31993906 DOI: 10.1007/s11356-020-07767-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
Aerobic CH4 oxidation coupled to denitrification (AME-D) can not only mitigate the emission of greenhouse gas (e.g., CH4) to the atmosphere, but also reduce NO3- and/or NO2- and alleviate nitrogen pollution. The effects of O2 tension on the community and functional gene expression of methanotrophs and denitrifiers were investigated in this study. Although higher CH4 oxidation occurred in the AME-D system with an initial O2 concentration of 21% (i.e., the O2-sufficient condition), more NO3--N was removed at the initial O2 concentration of 10% (i.e., the O2-limited environment). Type I methanotrophs, including Methylocaldum, Methylobacter, Methylococcus, Methylomonas, and Methylomicrobium, and type II methanotrophs, including Methylocystis and Methylosinus, dominated in the AME-D systems. Compared with type II methanotrophs, type I methanotrophs were more abundant in the AME-D systems. Proteobacteria and Actinobacteria were the main denitrifiers in the AME-D systems, and their compositions varied with the O2 tension. Quantitative PCR of the pmoA, nirS, and 16S rRNA genes showed that methanotrophs and denitrifiers were the main microorganisms in the AME-D systems, accounting for 46.4% and 24.1% in the O2-limited environment, respectively. However, the relative transcripts of the functional genes including pmoA, mmoX, nirK, nirS, and norZ were all less than 1%, especially the functional genes involved in denitrification under the O2-sufficient condition, likely due to the majority of the denitrifiers being dormant or even nonviable. These findings indicated that an optimal O2 concentration should be used to optimize the activity and functional gene expression of aerobic methanotrophs and denitrifiers in AME-D systems.
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Affiliation(s)
- Yi-Xuan Chu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo-Chan Ma
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jing Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jia-Tian Zhu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ya-Ru Kang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo He
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China.
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China.
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13
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Sabrekov AF, Semenov MV, Terent’eva IE, Litti YV, Il’yasov DV, Glagolev MV. The link between Soil Methane Oxidation Rate and Abundance of Methanotrophs Estimated by Quantitative PCR. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720020113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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14
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He R, Su Y, Leewis MC, Chu YX, Wang J, Ma RC, Wu D, Zhan LT, Herriott IC, Leigh MB. Low O 2 level enhances CH 4-derived carbon flow into microbial communities in landfill cover soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113676. [PMID: 31818614 DOI: 10.1016/j.envpol.2019.113676] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/07/2019] [Accepted: 11/24/2019] [Indexed: 06/10/2023]
Abstract
CH4 oxidation in landfill cover soils plays a significant role in mitigating CH4 release to the atmosphere. Oxygen availability and the presence of co-contaminants are potentially important factors affecting CH4 oxidation rate and the fate of CH4-derived carbon. In this study, microbial populations that oxidize CH4 and the subsequent conversion of CH4-derived carbon into CO2, soil organic C and biomass C were investigated in landfill cover soils at two O2 tensions, i.e., O2 concentrations of 21% ("sufficient") and 2.5% ("limited") with and without toluene. CH4-derived carbon was primarily converted into CO2 and soil organic C in the landfill cover soils, accounting for more than 80% of CH4 oxidized. Under the O2-sufficient condition, 52.9%-59.6% of CH4-derived carbon was converted into CO2 (CECO2-C), and 29.1%-39.3% was converted into soil organic C (CEorganic-C). A higher CEorganic-C and lower CECO2-C occurred in the O2-limited environment, relative to the O2-sufficient condition. With the addition of toluene, the carbon conversion efficiency of CH4 into biomass C and organic C increased slightly, especially in the O2-limited environment. A more complex microbial network was involved in CH4 assimilation in the O2-limited environment than under the O2-sufficient condition. DNA-based stable isotope probing of the community with 13CH4 revealed that Methylocaldum and Methylosarcina had a higher relative growth rate than other type I methanotrophs in the landfill cover soils, especially at the low O2 concentration, while Methylosinus was more abundant in the treatment with both the high O2 concentration and toluene. These results indicated that O2-limited environments could prompt more CH4-derived carbon to be deposited into soils in the form of biomass C and organic C, thereby enhancing the contribution of CH4-derived carbon to soil community biomass and functionality of landfill cover soils (i.e. reduction of CO2 emission).
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Affiliation(s)
- Ruo He
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
| | - Yao Su
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China; Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Mary-Cathrine Leewis
- Institute of Arctic Biology, University of Alaska Fairbanks, Alaska, 99775, USA; US Geological Survey, Menlo Park, CA, 94025, USA
| | - Yi-Xuan Chu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jing Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo-Chan Ma
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Donglei Wu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Liang-Tong Zhan
- MOE Key Laboratory of Soft Soils and Geoenvironmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | | | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Alaska, 99775, USA
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15
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Klasek S, Torres ME, Bartlett DH, Tyler M, Hong W, Colwell F. Microbial communities from Arctic marine sediments respond slowly to methane addition during
ex situ
enrichments. Environ Microbiol 2020; 22:1829-1846. [DOI: 10.1111/1462-2920.14895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/11/2019] [Accepted: 11/30/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Scott Klasek
- Department of Microbiology Oregon State University Corvallis Oregon USA
| | - Marta E. Torres
- College of Earth, Ocean, and Atmospheric Sciences Oregon State University Corvallis Oregon USA
| | - Douglas H. Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography University of California San Diego California 92093‐0202 USA
| | - Madeline Tyler
- Department of Microbiology Oregon State University Corvallis Oregon USA
| | - Wei‐Li Hong
- Centre for Arctic Gas Hydrate, Environment and Climate (CAGE), Department of Geosciences UiT The Arctic University of Norway N‐9037 Tromsø Norway
| | - Frederick Colwell
- Department of Microbiology Oregon State University Corvallis Oregon USA
- College of Earth, Ocean, and Atmospheric Sciences Oregon State University Corvallis Oregon USA
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16
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Niche partitioning of methane-oxidizing bacteria along the oxygen-methane counter gradient of stratified lakes. ISME JOURNAL 2019; 14:274-287. [PMID: 31624343 DOI: 10.1038/s41396-019-0515-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/13/2019] [Accepted: 08/25/2019] [Indexed: 12/30/2022]
Abstract
Lakes are a significant source of atmospheric methane, although methane-oxidizing bacteria consume most methane diffusing upward from anoxic sediments. Diverse methane-oxidizing bacteria form an effective methane filter in the water column of stratified lakes, yet, niche partitioning of different methane-oxidizing bacteria along the oxygen-methane counter gradient remains poorly understood. In our study, we reveal vertical distribution patterns of active methane-oxidizing bacteria along the oxygen-methane counter gradient of four lakes, based on amplicon sequencing analysis of 16S rRNA and pmoA genes, and 16S rRNA and pmoA transcripts, and potential methane oxidation rates. Differential distribution patterns indicated that ecologically different methane-oxidizing bacteria occupied the methane-deficient and oxygen-deficient part above and below the oxygen-methane interface. The interface sometimes harbored additional taxa. Within the dominant Methylococcales, an uncultivated taxon (CABC2E06) occurred mainly under methane-deficient conditions, whereas Crenothrix-related taxa preferred oxygen-deficient conditions. Candidatus Methylomirabilis limnetica (NC10 phylum) abundantly populated the oxygen-deficient part in two of four lakes. We reason that the methane filter in lakes is structured and that methane-oxidizing bacteria may rely on niche-specific adaptations for methane oxidation along the oxygen-methane counter gradient. Niche partitioning of methane-oxidizing bacteria might support greater overall resource consumption, contributing to the high effectivity of the lacustrine methane filter.
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17
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Siniscalchi LAB, Leite LR, Oliveira G, Chernicharo CAL, de Araújo JC. Illumina sequencing-based analysis of a microbial community enriched under anaerobic methane oxidation condition coupled to denitrification revealed coexistence of aerobic and anaerobic methanotrophs. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:16751-16764. [PMID: 28567677 DOI: 10.1007/s11356-017-9197-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 05/02/2017] [Indexed: 06/07/2023]
Abstract
Methane is produced in anaerobic environments, such as reactors used to treat wastewaters, and can be consumed by methanotrophs. The composition and structure of a microbial community enriched from anaerobic sewage sludge under methane-oxidation condition coupled to denitrification were investigated. Denaturing gradient gel electrophoresis (DGGE) analysis retrieved sequences of Methylocaldum and Chloroflexi. Deep sequencing analysis revealed a complex community that changed over time and was affected by methane concentration. Methylocaldum (8.2%), Methylosinus (2.3%), Methylomonas (0.02%), Methylacidiphilales (0.45%), Nitrospirales (0.18%), and Methanosarcinales (0.3%) were detected. Despite denitrifying conditions provided, Nitrospirales and Methanosarcinales, known to perform anaerobic methane oxidation coupled to denitrification (DAMO) process, were in very low abundance. Results demonstrated that aerobic and anaerobic methanotrophs coexisted in the reactor together with heterotrophic microorganisms, suggesting that a diverse microbial community was important to sustain methanotrophic activity. The methanogenic sludge was a good inoculum to enrich methanotrophs, and cultivation conditions play a selective role in determining community composition.
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Affiliation(s)
- Luciene Alves Batista Siniscalchi
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Antonio Carlos Avenue, 6627, Belo Horizonte, Minas Gerais State, 31270-901, Brazil
- Department of Engineering, Federal University of Lavras, Dr. Sylvio Menicucci Avenue, 1001, Lavras, Minas Gerais State, 37200-000, Brazil
| | - Laura Rabelo Leite
- Department of Engineering, Federal University of Lavras, Dr. Sylvio Menicucci Avenue, 1001, Lavras, Minas Gerais State, 37200-000, Brazil
| | - Guilherme Oliveira
- Genomics and Computational Biology Group, René Rachou Research Center, Oswaldo Cruz Foundation, Augusto de Lima Avenue 1715, Belo Horizonte, Minas Gerais State, 30.190-002, Brazil
- Instituto Vale de Tecnologia, Rua Boaventura da Silva, 955, Belém, Pará, 66055-090, Brazil
| | - Carlos Augusto Lemos Chernicharo
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Antonio Carlos Avenue, 6627, Belo Horizonte, Minas Gerais State, 31270-901, Brazil
| | - Juliana Calabria de Araújo
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Antonio Carlos Avenue, 6627, Belo Horizonte, Minas Gerais State, 31270-901, Brazil.
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18
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Liu H, Wu X, Li Z, Wang Q, Liu D, Liu G. Responses of soil methanogens, methanotrophs, and methane fluxes to land-use conversion and fertilization in a hilly red soil region of southern China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:8731-8743. [PMID: 28213705 DOI: 10.1007/s11356-017-8628-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/10/2017] [Indexed: 06/06/2023]
Abstract
Changes in land-uses and fertilization are important factors regulating methane (CH4) emissions from paddy soils. However, the responses of soil CH4 emissions to these factors and the underlying mechanisms remain unclear. The objective of this study was to explore the effects of land-use conversion from paddies to orchards and fertilization on soil CH4 fluxes, and the abundance and community compositions of methanogens and methanotrophs. Soil CH4 fluxes were quantified by static chamber and gas chromatography technology. Abundance and community structures of methanogens and methanotrophs (based on mcrA and pmoA genes, respectively) were determined by quantitative real-time PCR (qPCR), and terminal restriction fragment length polymorphism (TRFLP), cloning and sequence analysis, respectively. Results showed that land-use conversion from paddies to orchards dramatically decreased soil CH4 fluxes, whereas fertilization did not distinctly affect soil CH4 fluxes. Furthermore, abundance of methanogens and methanotrophs were decreased after converting paddies to orchards. Fertilization decreased the abundance of these microorganisms, but the values were not statistically significant. Moreover, land-use conversion had fatal effects on some members of the methanogenic archaea (Methanoregula and Methanosaeta), increased type II methanotrophs (Methylocystis and Methylosinus), and decreased type I methanotrophs (Methylobacter and Methylococcus). However, fertilization could only significantly affect type I methanotrophs in the orchard plots. In addition, CH4 fluxes from paddy soils were positively correlated with soil dissolved organic carbon contents and methanogens abundance, whereas CH4 fluxes in orchard plots were negatively related to methanotroph abundance. Therefore, our results suggested that land-use conversion from paddies to orchards could change the abundance and community compositions of methanogens and methanotrophs, and ultimately alter the soil CH4 fluxes. Overall, our study shed insight on the underlying mechanisms of how land-use conversion from paddies to orchards decreased CH4 emissions.
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Affiliation(s)
- Huifeng Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Xing Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- Joint Center for Global Change Studies, Beijing, 100875, China.
| | - Zongshan Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Joint Center for Global Change Studies, Beijing, 100875, China
| | - Qing Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Dan Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Guohua Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- Joint Center for Global Change Studies, Beijing, 100875, China.
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19
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Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils. Nat Commun 2016; 7:11728. [PMID: 27248847 PMCID: PMC4895445 DOI: 10.1038/ncomms11728] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/25/2016] [Indexed: 01/30/2023] Open
Abstract
Soils serve as the biological sink of the potent greenhouse gas methane with exceptionally low concentrations of ∼1.84 p.p.m.v. in the atmosphere. The as-yet-uncultivated methane-consuming bacteria have long been proposed to be responsible for this ‘high-affinity' methane oxidation (HAMO). Here we show an emerging HAMO activity arising from conventional methanotrophs in paddy soil. HAMO activity was quickly induced during the low-affinity oxidation of high-concentration methane. Activity was lost gradually over 2 weeks, but could be repeatedly regained by flush-feeding the soil with elevated methane. The induction of HAMO activity occurred only after the rapid growth of methanotrophic populations, and a metatranscriptome-wide association study suggests that the concurrent high- and low-affinity methane oxidation was catalysed by known methanotrophs rather than by the proposed novel atmospheric methane oxidizers. These results provide evidence of atmospheric methane uptake in periodically drained ecosystems that are typically considered to be a source of atmospheric methane. Atmospheric methane may be consumed by microorganisms in soil, but the mechanisms behind high-affinity methane oxidization remain poorly understood. Here, Jia et al. show that known methanotrophic bacteria are responsible for atmospheric methane uptake in periodically drained wetland ecosystems.
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20
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Wei XM, He R, Chen M, Su Y, Ma RC. Conversion of methane-derived carbon and microbial community in enrichment cultures in response to O2 availability. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:7517-7528. [PMID: 26728286 DOI: 10.1007/s11356-015-6017-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 12/22/2015] [Indexed: 06/05/2023]
Abstract
Methanotrophs not only play an important role in mitigating CH4 emissions from the environment, but also provide a large quantity of CH4-derived carbon to their habitats. In this study, the distribution of CH4-derived carbon and microbial community was investigated in a consortium enriched at three O2 tensions, i.e., the initial O2 concentrations of 2.5 % (LO-2), 5 % (LO-1), and 21 % (v/v) (HO). The results showed that compared with the O2-limiting environments (2.5 and 5 %), more CH4-derived carbon was converted into CO2 and biomass under the O2 sufficient condition (21 %). Besides biomass and CO2, a high conversion efficiency of CH4-derived carbon to dissolved organic carbon was detected in the cultures, especially in LO-2. Quantitative PCR and Miseq sequencing both showed that the abundance of methanotroph increased with the increasing O2 concentrations. Type II methanotroph Methylocystis dominated in the enrichment cultures, accounting for 54.8, 48.1, and 36.9 % of the total bacterial 16S rRNA gene sequencing reads in HO, LO-1, and LO-2, respectively. Methylotrophs, mainly including Methylophilus, Methylovorus, Hyphomicrobium, and Methylobacillus, were also abundant in the cultures. Compared with the O2 sufficient condition (21 %), higher microbial biodiversity (i.e., higher Simpson and lower Shannon indexes) was detected in LO-2 enriched at the initial O2 concentration of 2.5 %. These findings indicated that compared with the O2 sufficient condition, more CH4-derived carbon was exuded into the environments and promoted the growth of non-methanotrophic microbes in O2-limiting environments.
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Affiliation(s)
- Xiao-Meng Wei
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
| | - Min Chen
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Yao Su
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo-Chan Ma
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
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21
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Knief C. Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker. Front Microbiol 2015; 6:1346. [PMID: 26696968 PMCID: PMC4678205 DOI: 10.3389/fmicb.2015.01346] [Citation(s) in RCA: 257] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/16/2015] [Indexed: 01/06/2023] Open
Abstract
Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing "unknown methanotrophic bacteria." This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.
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Affiliation(s)
- Claudia Knief
- Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, University of BonnBonn, Germany
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Shvaleva A, Siljanen HMP, Correia A, Costa e Silva F, Lamprecht RE, Lobo-do-Vale R, Bicho C, Fangueiro D, Anderson M, Pereira JS, Chaves MM, Cruz C, Martikainen PJ. Environmental and microbial factors influencing methane and nitrous oxide fluxes in Mediterranean cork oak woodlands: trees make a difference. Front Microbiol 2015; 6:1104. [PMID: 26528257 PMCID: PMC4604323 DOI: 10.3389/fmicb.2015.01104] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 09/24/2015] [Indexed: 01/11/2023] Open
Abstract
Cork oak woodlands (montado) are agroforestry systems distributed all over the Mediterranean basin with a very important social, economic and ecological value. A generalized cork oak decline has been occurring in the last decades jeopardizing its future sustainability. It is unknown how loss of tree cover affects microbial processes that are consuming greenhouse gases in the montado ecosystem. The study was conducted under two different conditions in the natural understory of a cork oak woodland in center Portugal: under tree canopy (UC) and open areas without trees (OA). Fluxes of methane and nitrous oxide were measured with a static chamber technique. In order to quantify methanotrophs and bacteria capable of nitrous oxide consumption, we used quantitative real-time PCR targeting the pmoA and nosZ genes encoding the subunit of particulate methane mono-oxygenase and catalytic subunit of the nitrous oxide reductase, respectively. A significant seasonal effect was found on CH4 and N2O fluxes and pmoA and nosZ gene abundance. Tree cover had no effect on methane fluxes; conversely, whereas the UC plots were net emitters of nitrous oxide, the loss of tree cover resulted in a shift in the emission pattern such that the OA plots were a net sink for nitrous oxide. In a seasonal time scale, the UC had higher gene abundance of Type I methanotrophs. Methane flux correlated negatively with abundance of Type I methanotrophs in the UC plots. Nitrous oxide flux correlated negatively with nosZ gene abundance at the OA plots in contrast to that at the UC plots. In the UC soil, soil organic matter had a positive effect on soil extracellular enzyme activities, which correlated positively with the N2O flux. Our results demonstrated that tree cover affects soil properties, key enzyme activities and abundance of microorganisms and, consequently net CH4 and N2O exchange.
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Affiliation(s)
- Alla Shvaleva
- Instituto de Tecnologia Química e Biológica, Universidade Nova de LisboaOeiras, Portugal
| | - Henri M. P. Siljanen
- Department of Environmental Science, University of Eastern FinlandKuopio, Finland
| | - Alexandra Correia
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - Filipe Costa e Silva
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - Richard E. Lamprecht
- Department of Environmental Science, University of Eastern FinlandKuopio, Finland
| | - Raquel Lobo-do-Vale
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - Catarina Bicho
- Instituto de Tecnologia Química e Biológica, Universidade Nova de LisboaOeiras, Portugal
| | - David Fangueiro
- Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | | | - João S. Pereira
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - Maria M. Chaves
- Instituto de Tecnologia Química e Biológica, Universidade Nova de LisboaOeiras, Portugal
| | - Cristina Cruz
- Centre for Ecology Evolution and Environmental Changes, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
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Krause S, Niklaus PA, Badwan Morcillo S, Meima Franke M, Lüke C, Reim A, Bodelier PLE. Compositional and functional stability of aerobic methane consuming communities in drained and rewetted peat meadows. FEMS Microbiol Ecol 2015; 91:fiv119. [PMID: 26449384 DOI: 10.1093/femsec/fiv119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2015] [Indexed: 11/13/2022] Open
Abstract
The restoration of peatlands is an important strategy to counteract subsidence and loss of biodiversity. However, responses of important microbial soil processes are poorly understood. We assessed functioning, diversity and spatial organization of methanotrophic communities in drained and rewetted peat meadows with different water table management and agricultural practice. Results show that the methanotrophic diversity was similar between drained and rewetted sites with a remarkable dominance of the genus Methylocystis. Enzyme kinetics depicted no major differences, indicating flexibility in the methane (CH4) concentrations that can be used by the methanotrophic community. Short-term flooding led to temporary elevated CH4 emission but to neither major changes in abundances of methane-oxidizing bacteria (MOB) nor major changes in CH4 consumption kinetics in drained agriculturally used peat meadows. Radiolabeling and autoradiographic imaging of intact soil cores revealed a markedly different spatial arrangement of the CH4 consuming zone in cores exposed to near-atmospheric and elevated CH4. The observed spatial patterns of CH4 consumption in drained peat meadows with and without short-term flooding highlighted the spatial complexity and responsiveness of the CH4 consuming zone upon environmental change. The methanotrophic microbial community is not generally altered and harbors MOB that can cover a large range of CH4 concentrations offered due to water-table fluctuations, effectively mitigating CH4 emissions.
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Affiliation(s)
- Sascha Krause
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Pascal A Niklaus
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
| | - Sara Badwan Morcillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
| | - Marion Meima Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
| | - Claudia Lüke
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, 6525 AJ, the Netherlands
| | - Andreas Reim
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
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24
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McNamara NP, Gregg R, Oakley S, Stott A, Rahman MT, Murrell JC, Wardle DA, Bardgett RD, Ostle NJ. Soil Methane Sink Capacity Response to a Long-Term Wildfire Chronosequence in Northern Sweden. PLoS One 2015; 10:e0129892. [PMID: 26372346 PMCID: PMC4570772 DOI: 10.1371/journal.pone.0129892] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 05/15/2015] [Indexed: 11/19/2022] Open
Abstract
Boreal forests occupy nearly one fifth of the terrestrial land surface and are recognised as globally important regulators of carbon (C) cycling and greenhouse gas emissions. Carbon sequestration processes in these forests include assimilation of CO2 into biomass and subsequently into soil organic matter, and soil microbial oxidation of methane (CH4). In this study we explored how ecosystem retrogression, which drives vegetation change, regulates the important process of soil CH4 oxidation in boreal forests. We measured soil CH4 oxidation processes on a group of 30 forested islands in northern Sweden differing greatly in fire history, and collectively representing a retrogressive chronosequence, spanning 5000 years. Across these islands the build-up of soil organic matter was observed to increase with time since fire disturbance, with a significant correlation between greater humus depth and increased net soil CH4 oxidation rates. We suggest that this increase in net CH4 oxidation rates, in the absence of disturbance, results as deeper humus stores accumulate and provide niches for methanotrophs to thrive. By using this gradient we have discovered important regulatory controls on the stability of soil CH4 oxidation processes that could not have not been explored through shorter-term experiments. Our findings indicate that in the absence of human interventions such as fire suppression, and with increased wildfire frequency, the globally important boreal CH4 sink could be diminished.
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Affiliation(s)
- Niall P. McNamara
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster, United Kingdom
- * E-mail:
| | - Ruth Gregg
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster, United Kingdom
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Simon Oakley
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster, United Kingdom
| | - Andy Stott
- NERC Life Sciences Stable Isotope Facility, Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster, United Kingdom
| | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - J. Colin Murrell
- School of Environmental Science, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - David A. Wardle
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Richard D. Bardgett
- Faculty of Life Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, United Kingdom
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Nick J. Ostle
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster, United Kingdom
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
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25
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Wei XM, Su Y, Zhang HT, Chen M, He R. Responses of methanotrophic activity, community and EPS production to CH4 and O2 concentrations in waste biocover soils. WASTE MANAGEMENT (NEW YORK, N.Y.) 2015; 42:118-127. [PMID: 25921582 DOI: 10.1016/j.wasman.2015.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 03/17/2015] [Accepted: 04/05/2015] [Indexed: 06/04/2023]
Abstract
Biocover soils are known to be a good alternative material to mitigate CH4 emissions from landfills to the atmosphere. In this study, 16 treatments with four O2 concentrations (∼0%, 5%, 10% and 21%) and four CH4 concentrations (i.e. 1%, 10%, 20% and 50%) were conducted to estimate extracellular polymeric substances (EPS) production, methanotrophic activity and community in response to CH4 and O2 concentrations in waste biocover soil (WBS). When the CH4 concentration was saturated for CH4 oxidation in the WBS, the continuous exposure of CH4 above the saturated concentrations could not obviously enhance CH4 oxidation activity. In the WBS, extracellular protein (ECP) production was negatively related with the tested CH4 concentrations, while both ECP and extracellular polysaccharides (ECPS) productions were positively related with the tested O2 concentrations. Cloning and terminal restriction fragment length polymorphism analyses showed that type I methanotrophs (Methylocaldum, Methylococcaceae, Methylomicrobium and Methylobacter) and type II methanotrophs (Methylosinus) dominated in the WBS. Among them, Methylocaldum and/or Methylococcaceae were sensitive to low O2 concentrations of ∼0%. Methylobacter had propensity to grow at low O2 concentrations of ∼0% and 5%, while Methylosinus preferred environments with high concentrations of CH4 (⩾10%) and O2 (21%). In the tested five environmental variables of ECPS, O2, EPS, CH4 and ECP, only ECPS and O2 concentrations had significant effect on the methanotrophic communities. These results suggested that O2 concentration in landfill covers should be paid more attention to optimize and sustain CH4 oxidation for mitigating CH4 emission from landfills.
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Affiliation(s)
- Xiao-Meng Wei
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Yao Su
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Hong-Tao Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Min Chen
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China.
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26
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He R, Wooller MJ, Pohlman JW, Tiedje JM, Leigh MB. Methane-derived carbon flow through microbial communities in arctic lake sediments. Environ Microbiol 2015; 17:3233-50. [PMID: 25581131 DOI: 10.1111/1462-2920.12773] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/31/2014] [Indexed: 11/26/2022]
Abstract
Aerobic methane (CH4 ) oxidation mitigates CH4 release and is a significant pathway for carbon and energy flow into aquatic food webs. Arctic lakes are responsible for an increasing proportion of global CH4 emissions, but CH4 assimilation into the aquatic food web in arctic lakes is poorly understood. Using stable isotope probing (SIP) based on phospholipid fatty acids (PLFA-SIP) and DNA (DNA-SIP), we tracked carbon flow quantitatively from CH4 into sediment microorganisms from an arctic lake with an active CH4 seepage. When 0.025 mmol CH4 g(-1) wet sediment was oxidized, approximately 15.8-32.8% of the CH4 -derived carbon had been incorporated into microorganisms. This CH4 -derived carbon equated to up to 5.7% of total primary production estimates for Alaskan arctic lakes. Type I methanotrophs, including Methylomonas, Methylobacter and unclassified Methylococcaceae, were most active at CH4 oxidation in this arctic lake. With increasing distance from the active CH4 seepage, a greater diversity of bacteria incorporated CH4 -derived carbon. Actinomycetes were the most quantitatively important microorganisms involved in secondary feeding on CH4 -derived carbon. These results showed that CH4 flows through methanotrophs into the broader microbial community and that type I methanotrophs, methylotrophs and actinomycetes are important organisms involved in using CH4 -derived carbon in arctic freshwater ecosystems.
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Affiliation(s)
- Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.,Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Matthew J Wooller
- Alaska Stable Isotope Facility, Water and Environmental Research Center, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA.,School of Fisheries and Ocean Sciences, Institute of Marine Science, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - John W Pohlman
- Woods Hole Coastal and Marine Science Center, U.S. Geological Survey, Woods Hole, MA, 02543, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
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27
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Lima AB, Muniz AW, Dumont MG. Activity and abundance of methane-oxidizing bacteria in secondary forest and manioc plantations of Amazonian Dark Earth and their adjacent soils. Front Microbiol 2014; 5:550. [PMID: 25374565 PMCID: PMC4205850 DOI: 10.3389/fmicb.2014.00550] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/02/2014] [Indexed: 12/20/2022] Open
Abstract
The oxidation of atmospheric CH4 in upland soils is mostly mediated by uncultivated groups of microorganisms that have been identified solely by molecular markers, such as the sequence of the pmoA gene encoding the β-subunit of the particulate methane monooxygenase enzyme. The objective of this work was to compare the activity and diversity of methanotrophs in Amazonian Dark Earth soil (ADE, Hortic Anthrosol) and their adjacent non-anthropic soil. Secondly, the effect of land use in the form of manioc cultivation was examined by comparing secondary forest and plantation soils. CH4 oxidation potentials were measured and the structure of the methanotroph communities assessed by quantitative PCR (qPCR) and amplicon pyrosequencing of pmoA genes. The oxidation potentials at low CH4 concentrations (10 ppm of volume) were relatively high in all the secondary forest sites of both ADE and adjacent soils. CH4 oxidation by the ADE soil only recently converted to a manioc plantation was also relatively high. In contrast, both the adjacent soils used for manioc cultivation and the ADE soil with a long history of agriculture displayed lower CH4 uptake rates. Amplicon pyrosequencing of pmoA genes indicated that USCα, Methylocystis and the tropical upland soil cluster (TUSC) were the dominant groups depending on the site. By qPCR analysis it was found that USCα pmoA genes, which are believed to belong to atmospheric CH4 oxidizers, were more abundant in ADE than adjacent soil. USCα pmoA genes were abundant in both forested and cultivated ADE soil, but were below the qPCR detection limit in manioc plantations of adjacent soil. The results indicate that ADE soils can harbor high abundances of atmospheric CH4 oxidizers and are potential CH4 sinks, but as in other upland soils this activity can be inhibited by the conversion of forest to agricultural plantations.
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Affiliation(s)
- Amanda B Lima
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Aleksander W Muniz
- Department of Soil Microbiology and Biogeochemistry, Brazilian Agricultural Research Corporation Manaus, Brazil
| | - Marc G Dumont
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
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28
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Henneberger R, Chiri E, Bodelier PEL, Frenzel P, Lüke C, Schroth MH. Field-scale tracking of active methane-oxidizing communities in a landfill cover soil reveals spatial and seasonal variability. Environ Microbiol 2014; 17:1721-37. [PMID: 25186436 DOI: 10.1111/1462-2920.12617] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 08/31/2014] [Indexed: 01/11/2023]
Abstract
Aerobic methane-oxidizing bacteria (MOB) in soils mitigate methane (CH4 ) emissions. We assessed spatial and seasonal differences in active MOB communities in a landfill cover soil characterized by highly variable environmental conditions. Field-based measurements of CH4 oxidation activity and stable-isotope probing of polar lipid-derived fatty acids (PLFA-SIP) were complemented by microarray analysis of pmoA genes and transcripts, linking diversity and function at the field scale. In situ CH4 oxidation rates varied between sites and were generally one order of magnitude lower in winter compared with summer. Results from PLFA-SIP and pmoA transcripts were largely congruent, revealing distinct spatial and seasonal clustering. Overall, active MOB communities were highly diverse. Type Ia MOB, specifically Methylomonas and Methylobacter, were key drivers for CH4 oxidation, particularly at a high-activity site. Type II MOB were mainly active at a site showing substantial fluctuations in CH4 loading and soil moisture content. Notably, Upland Soil Cluster-gamma-related pmoA transcripts were also detected, indicating concurrent oxidation of atmospheric CH4 . Spatial separation was less distinct in winter, with Methylobacter and uncultured MOB mediating CH4 oxidation. We propose that high diversity of active MOB communities in this soil is promoted by high variability in environmental conditions, facilitating substantial removal of CH4 generated in the waste body.
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Affiliation(s)
- Ruth Henneberger
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092, Zurich, Switzerland
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29
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Martineau C, Pan Y, Bodrossy L, Yergeau E, Whyte LG, Greer CW. Atmospheric methane oxidizers are present and active in Canadian high Arctic soils. FEMS Microbiol Ecol 2014; 89:257-69. [PMID: 24450397 DOI: 10.1111/1574-6941.12287] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/16/2014] [Accepted: 01/16/2014] [Indexed: 01/08/2023] Open
Abstract
The melting of permafrost and the associated potential for methane emissions to the atmosphere are major concerns in the context of global warming. However, soils can also represent a significant sink for methane through the activity of methane-oxidizing bacteria (MOB). In this study, we looked at the activity, diversity, and community structure of MOB at two sampling depths within the active layer in three soils from the Canadian high Arctic. These soils had the capacity to oxidize methane at low (15 ppm) and high (1000 ppm) methane concentrations, but rates differed greatly depending on the sampling date, depth, and site. The pmoA gene sequences related to two genotypes of uncultured MOB involved in atmospheric methane oxidation, the 'upland soil cluster gamma' and the 'upland soil cluster alpha', were detected in soils with near neutral and acidic pH, respectively. Other groups of MOB, including Type I methanotrophs and the 'Cluster 1' genotype, were also detected, indicating a broader diversity of MOB than previously reported for Arctic soils. Overall, the results reported here showed that methane oxidation at both low and high methane concentrations occurs in high Arctic soils and revealed that different groups of atmospheric MOB inhabit these soils.
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30
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Dam B, Dam S, Kim Y, Liesack W. Ammonium induces differential expression of methane and nitrogen metabolism-related genes in Methylocystis sp. strain SC2. Environ Microbiol 2014; 16:3115-27. [PMID: 24373058 DOI: 10.1111/1462-2920.12367] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 12/14/2013] [Indexed: 11/30/2022]
Abstract
Nitrogen source and concentration are major determinants of methanotrophic activity, but their effect on global gene expression is poorly studied. Methylocystis sp. strain SC2 produces two isozymes of particulate methane monooxygenase. These are encoded by pmoCAB1 (low-affinity pMMO1) and pmoCAB2 (high-affinity pMMO2). We used RNA-Seq to identify strain SC2 genes that respond to standard (10 mM) and high (30 mM) NH4(+) concentrations in the medium, compared with 10 mM NO3(-). While the expression of pmoCAB1 was unaffected, pmoCAB2 was significantly downregulated (log2 fold changes of -5.0 to -6.0). Among nitrogen metabolism-related processes, genes involved in hydroxylamine detoxification (haoAB) were highly upregulated, while those for assimilatory nitrate/nitrite reduction, high-affinity ammonium uptake and nitrogen regulatory protein PII were downregulated. Differential expression of pmoCAB2 and haoAB was independently validated by end-point reverse transcription polymerase chain reaction. Methane oxidation by SC2 cells exposed to 30 mM NH4(+) was inhibited at ≤ 400 ppmv CH4 , where pMMO2 but not pMMO1 is functional. When transferred back to standard nitrogen concentration, methane oxidation capability and pmoCAB2 expression were restored. Given that Methylocystis contributes to atmospheric methane oxidation in upland soils, differential expression of pmoCAB2 explains, at least to some extent, the strong inhibitory effect of ammonium fertilizers on this activity.
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Affiliation(s)
- Bomba Dam
- Max Planck Institute for Terrestrial Microbiology, D-35043, Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35043, Marburg, Germany
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31
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Dam B, Dam S, Blom J, Liesack W. Genome analysis coupled with physiological studies reveals a diverse nitrogen metabolism in Methylocystis sp. strain SC2. PLoS One 2013; 8:e74767. [PMID: 24130670 PMCID: PMC3794950 DOI: 10.1371/journal.pone.0074767] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 07/28/2013] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Methylocystis sp. strain SC2 can adapt to a wide range of methane concentrations. This is due to the presence of two isozymes of particulate methane monooxygenase exhibiting different methane oxidation kinetics. To gain insight into the underlying genetic information, its genome was sequenced and found to comprise a 3.77 Mb chromosome and two large plasmids. PRINCIPAL FINDINGS We report important features of the strain SC2 genome. Its sequence is compared with those of seven other methanotroph genomes, comprising members of the Alphaproteobacteria, Gammaproteobacteria, and Verrucomicrobia. While the pan-genome of all eight methanotroph genomes totals 19,358 CDS, only 154 CDS are shared. The number of core genes increased with phylogenetic relatedness: 328 CDS for proteobacterial methanotrophs and 1,853 CDS for the three alphaproteobacterial Methylocystaceae members, Methylocystis sp. strain SC2 and strain Rockwell, and Methylosinus trichosporium OB3b. The comparative study was coupled with physiological experiments to verify that strain SC2 has diverse nitrogen metabolism capabilities. In correspondence to a full complement of 34 genes involved in N2 fixation, strain SC2 was found to grow with atmospheric N2 as the sole nitrogen source, preferably at low oxygen concentrations. Denitrification-mediated accumulation of 0.7 nmol (30)N2/hr/mg dry weight of cells under anoxic conditions was detected by tracer analysis. N2 production is related to the activities of plasmid-borne nitric oxide and nitrous oxide reductases. CONCLUSIONS/PERSPECTIVES Presence of a complete denitrification pathway in strain SC2, including the plasmid-encoded nosRZDFYX operon, is unique among known methanotrophs. However, the exact ecophysiological role of this pathway still needs to be elucidated. Detoxification of toxic nitrogen compounds and energy conservation under oxygen-limiting conditions are among the possible roles. Relevant features that may stimulate further research are, for example, absence of CRISPR/Cas systems in strain SC2, high number of iron acquisition systems in strain OB3b, and large number of transposases in strain Rockwell.
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Affiliation(s)
- Bomba Dam
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Somasri Dam
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Jochen Blom
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Werner Liesack
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
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32
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Partial oxidative conversion of methane to methanol through selective inhibition of methanol dehydrogenase in methanotrophic consortium from landfill cover soil. Appl Biochem Biotechnol 2013; 171:1487-99. [PMID: 23963715 DOI: 10.1007/s12010-013-0410-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 07/17/2013] [Indexed: 10/26/2022]
Abstract
Using a methanotrophic consortium (that includes Methylosinus sporium NCIMB 11126, Methylosinus trichosporium OB3b, and Methylococcus capsulatus Bath) isolated from a landfill site, the potential for partial oxidation of methane into methanol through selective inhibition of methanol dehydrogenase (MDH) over soluble methane monooxygenase (sMMO) with some selected MDH inhibitors at varied concentration range, was evaluated in batch serum bottle and bioreactor experiments. Our result suggests that MDH activity could effectively be inhibited either at 40 mM of phosphate, 100 mM of NaCl, 40 mM of NH4Cl or 50 μM of EDTA with conversion ratios (moles of CH3OH produced per mole CH4 consumed) of 58, 80, 80, and 43 %, respectively. The difference between extent of inhibition in MDH activity and sMMO activity was significantly correlated (n = 6, p < 0.05) with resultant methane to methanol conversion ratio. In bioreactor study with 100 mM of NaCl, a maximum specific methanol production rate of 9 μmol/mg h was detected. A further insight with qPCR analysis of MDH and sMMO coding genes revealed that the gene copy number continued to increase along with biomass during reactor operation irrespective of presence or absence of inhibitor, and differential inhibition among two enzymes was rather the key for methanol production.
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33
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Lüke C, Frenzel P, Ho A, Fiantis D, Schad P, Schneider B, Schwark L, Utami SR. Macroecology of methane-oxidizing bacteria: the β-diversity ofpmoAgenotypes in tropical and subtropical rice paddies. Environ Microbiol 2013; 16:72-83. [DOI: 10.1111/1462-2920.12190] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Claudia Lüke
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
- Radboud University Nijmegen; Heyendaalsweg 135 Nijmegen 6525 AJ The Netherlands
| | - Peter Frenzel
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
| | - Adrian Ho
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
- Laboratory for Microbial Ecology and Technology (LabMET); Faculty of Bioscience Engineering; Coupure Links 653 Ghent 9000 Belgium
| | - Dian Fiantis
- Department of Soil Science; Faculty of Agriculture; Andalas University; Kampus Unand Limau Manis Padang 25163 Indonesia
| | - Peter Schad
- Department Ecology and Ecosystem Management; Center of Life and Food Sciences Weihenstephan; Technische Universität München; Lehrstuhl für Bodenkunde Freising-Weihenstephan D-85350 Germany
| | - Bellinda Schneider
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
| | - Lorenz Schwark
- Institute of Geosciences; University Kiel; Ludewig-Meyn-Straße 10 Kiel 24118 Germany
- WA-OIGC; Curtin University; Perth WA 6845 Australia
| | - Sri Rahayu Utami
- Department of Soil Science; Faculty of Agriculture; Brawijaya University; Jalan Veteran Malang 65145 East Java Indonesia
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Deng Y, Cui X, Lüke C, Dumont MG. Aerobic methanotroph diversity in Riganqiao peatlands on the Qinghai-Tibetan Plateau. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:566-574. [PMID: 23864571 DOI: 10.1111/1758-2229.12046] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 02/28/2013] [Accepted: 03/01/2013] [Indexed: 06/02/2023]
Abstract
The Zoige Plateau is characterized by its high altitude, low latitude and low annual mean temperature of approximately 1°C and is a major source of atmospheric methane in the Qinghai-Tibetan Plateau. Methanotrophs play an important role in the global cycling of CH4, but the diversity, identity and activity of methanotrophs in this region are poorly characterized. Soils were collected from hummocks and hollows in the Riganqiao peatland and the methanotroph community was analysed by qPCR and sequencing methane monooxygenase (pmoA and mmoX) genes. The pmoA genes ranged between 10(7) and 10(8) copies g(-1) fresh soil, with a somewhat greater abundance in hummocks than hollows. The pmoA genes were analysed by amplicon pyrosequencing and the mmoX genes by cloning and sequencing. Methylocystis species were found to be the most abundant methanotrophs, but numerous clades were present including three novel pmoA and three novel mmoX clusters. There were differences between the methanotroph communities in the hummocks and hollows, with the most significant being an increased abundance of uncultivated type Ib methanotrophs in the hollows. The results indicate that aerobic methanotrophs are abundant in Riganqiao peatland and include previously undetected clades in this geographically isolated and distinctive environment.
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Affiliation(s)
- Yongcui Deng
- University of Chinese Academy of Sciences, 100049, Beijing, China
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Nazaries L, Murrell JC, Millard P, Baggs L, Singh BK. Methane, microbes and models: fundamental understanding of the soil methane cycle for future predictions. Environ Microbiol 2013; 15:2395-417. [DOI: 10.1111/1462-2920.12149] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 04/19/2013] [Accepted: 04/22/2013] [Indexed: 01/06/2023]
Affiliation(s)
- Loïc Nazaries
- Hawkesbury Institute for the Environment; University of Western Sydney; Building L9; Locked Bag 1797; Penrith South; NSW; 2751; Australia
| | - J. Colin Murrell
- School of Environmental Sciences; University of East Anglia; Norwich Research Park; Norwich; NR4 7TJ; UK
| | - Pete Millard
- Landcare Research; PO Box 40; Lincoln; 7604; New Zealand
| | - Liz Baggs
- Institute of Biological and Environmental Sciences; University of Aberdeen; Zoology Building; Tillydrone Avenue; Aberdeen; AB24 2TZ; Scotland; UK
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment; University of Western Sydney; Building L9; Locked Bag 1797; Penrith South; NSW; 2751; Australia
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36
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Artz RRE. Microbial Community Structure and Carbon Substrate use in Northern Peatlands. CARBON CYCLING IN NORTHERN PEATLANDS 2013. [DOI: 10.1029/2008gm000806] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Xu K, Tang Y, Ren C, Zhao K, Wang W, Sun Y. Activity, distribution, and abundance of methane-oxidizing bacteria in the near surface soils of onshore oil and gas fields. Appl Microbiol Biotechnol 2012; 97:7909-18. [DOI: 10.1007/s00253-012-4500-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Revised: 10/03/2012] [Accepted: 10/06/2012] [Indexed: 10/27/2022]
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Henneberger R, Chiri E, Blees J, Niemann H, Lehmann MF, Schroth MH. Field-scale labelling and activity quantification of methane-oxidizing bacteria in a landfill-cover soil. FEMS Microbiol Ecol 2012; 83:392-401. [DOI: 10.1111/j.1574-6941.2012.01477.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 08/15/2012] [Accepted: 08/18/2012] [Indexed: 01/20/2023] Open
Affiliation(s)
- Ruth Henneberger
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich; Zurich; Switzerland
| | - Eleonora Chiri
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich; Zurich; Switzerland
| | - Jan Blees
- Department of Environmental Sciences; University of Basel; Basel; Switzerland
| | - Helge Niemann
- Department of Environmental Sciences; University of Basel; Basel; Switzerland
| | - Moritz F. Lehmann
- Department of Environmental Sciences; University of Basel; Basel; Switzerland
| | - Martin H. Schroth
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich; Zurich; Switzerland
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Alam MS, Jia Z. Inhibition of methane oxidation by nitrogenous fertilizers in a paddy soil. Front Microbiol 2012; 3:246. [PMID: 22783249 PMCID: PMC3389332 DOI: 10.3389/fmicb.2012.00246] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 06/18/2012] [Indexed: 11/22/2022] Open
Abstract
Nitrogenous fertilizers are generally thought to have an important role in regulating methane oxidation. In this study, the effect of ammonium on methane oxidation activity was investigated in a paddy soil using urea at concentrations of 0, 50, 100, 200, and 400 μg N per gram dry weight soil (N/g.d.w.s) and ammonium sulfate at concentrations of 0, 50, and 200 μg N/g.d.w.s. The results of this study demonstrate that urea concentrations of 200 μg N/g.d.w.s. and above significantly inhibit methane oxidation activity, whereas no statistically significant difference was observed in methane oxidation activity among soil microcosms with urea concentrations of less than 200 μg N/g.d.w.s after incubation for 27 days. Similar results were obtained in a sense that methane oxidation activity was inhibited only when the ammonium sulfate concentration was 200 μg N/g.d.w.s in soil microcosms in this study. Phylogenetic analysis of pmoA genes showed that nitrogen fertilization resulted in apparent changes in the community composition of methane-oxidizing bacteria (MOB). Type I MOB displayed an increased abundance in soil microcosms amended with nitrogenous fertilizers, whereas type II MOB dominated the native soil. Furthermore, although no statistically significant relationship was observed between pmoA gene and amoA gene abundances, methane oxidation activity was significantly negatively correlated with nitrification activity in the presence of urea or ammonium sulfate. Our results indicate that the methane oxidation activity in paddy soils might be inhibited when the concentration of ammonium fertilizers is high and that the interactions between ammonia and methane oxidizers need to be further investigated.
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Affiliation(s)
- M. Saiful Alam
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese, Academy of Sciences, Nanjing, Jiangsu ProvinceP.R. China
- Graduate School of Chinese Academy of SciencesBeijing, P.R. China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese, Academy of Sciences, Nanjing, Jiangsu ProvinceP.R. China
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Linking activity, composition and seasonal dynamics of atmospheric methane oxidizers in a meadow soil. ISME JOURNAL 2011; 6:1115-26. [PMID: 22189499 DOI: 10.1038/ismej.2011.179] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Microbial oxidation is the only biological sink for atmospheric methane. We assessed seasonal changes in atmospheric methane oxidation and the underlying methanotrophic communities in grassland near Giessen (Germany), along a soil moisture gradient. Soil samples were taken from the surface layer (0-10 cm) of three sites in August 2007, November 2007, February 2008 and May 2008. The sites showed seasonal differences in hydrological parameters. Net uptake rates varied seasonally between 0 and 70 μg CH(4) m(-2) h(-1). Greatest uptake rates coincided with lowest soil moisture in spring and summer. Over all sites and seasons, the methanotrophic communities were dominated by uncultivated methanotrophs. These formed a monophyletic cluster defined by the RA14, MHP and JR1 clades, referred to as upland soil cluster alphaproteobacteria (USCα)-like group. The copy numbers of pmoA genes ranged between 3.8 × 10(5)-1.9 × 10(6) copies g(-1) of soil. Temperature was positively correlated with CH(4) uptake rates (P<0.001), but had no effect on methanotrophic population dynamics. The soil moisture was negatively correlated with CH(4) uptake rates (P<0.001), but showed a positive correlation with changes in USCα-like diversity (P<0.001) and pmoA gene abundance (P<0.05). These were greatest at low net CH(4) uptake rates during winter times and coincided with an overall increase in bacterial 16S rRNA gene abundances (P<0.05). Taken together, soil moisture had a significant but opposed effect on CH(4) uptake rates and methanotrophic population dynamics, the latter being increasingly stimulated by soil moisture contents >50 vol% and primarily related to members of the MHP clade.
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Abstract
Published pmoA primers do not match the pmoA sequence of "Candidatus Methylomirabilis oxyfera," a bacterium that performs nitrite-dependent anaerobic methane oxidation. Therefore, new pmoA primers for the detection of "Ca. Methylomirabilis oxyfera"-like methanotrophs were developed and successfully tested on freshwater samples from different habitats. These primers expand existing molecular tools for the study of methanotrophs in the environment.
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Belova SE, Baani M, Suzina NE, Bodelier PLE, Liesack W, Dedysh SN. Acetate utilization as a survival strategy of peat-inhabiting Methylocystis spp. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:36-46. [PMID: 23761229 DOI: 10.1111/j.1758-2229.2010.00180.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Representatives of the genus Methylocystis are traditionally considered to be obligately methanotrophic bacteria, which are incapable of growth on multicarbon substrates. Here, we describe a novel member of this genus, strain H2s, which represents a numerically abundant and ecologically important methanotroph population in northern Sphagnum-dominated wetlands. This isolate demonstrates a clear preference for growth on methane but is able to grow slowly on acetate in the absence of methane. Strain H2s possesses both forms of methane monooxygenase (particulate and soluble MMO) and a well-developed system of intracytoplasmic membranes (ICM). In cells grown for several transfers on acetate, these ICM are maintained, although in a reduced form, and mRNA transcripts of particulate MMO are detectable. These cells resume their growth on methane faster than those kept for the same period of time without any substrate. Growth on acetate leads to a major shift in the phospholipid fatty acid composition. The re-examination of all type strains of the validly described Methylocystis species showed that Methylocystis heyeri H2(T) and Methylocystis echinoides IMET10491(T) are also capable of slow growth on acetate. This capability might represent an important part of the survival strategy of Methylocystis spp. in environments where methane availability is variable or limited.
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Affiliation(s)
- Svetlana E Belova
- S.N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia. Max Planck Institute for terrestrial Microbiology, D-35043 Marburg, Germany. G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, 142292, Russia. Netherlands Institute of Ecology, NL3631 AC Nieuwersluis, The Netherlands
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43
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Different atmospheric methane-oxidizing communities in European beech and Norway spruce soils. Appl Environ Microbiol 2010; 76:3228-35. [PMID: 20348309 DOI: 10.1128/aem.02730-09] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Norway spruce (Picea abies) forests exhibit lower annual atmospheric methane consumption rates than do European beech (Fagus sylvatica) forests. In the current study, pmoA (encoding a subunit of membrane-bound CH(4) monooxygenase) genes from three temperate forest ecosystems with both beech and spruce stands were analyzed to assess the potential effect of tree species on methanotrophic communities. A pmoA sequence difference of 7% at the derived protein level correlated with the species-level distance cutoff value of 3% based on the 16S rRNA gene. Applying this distance cutoff, higher numbers of species-level pmoA genotypes were detected in beech than in spruce soil samples, all affiliating with upland soil cluster alpha (USCalpha). Additionally, two deep-branching genotypes (named 6 and 7) were present in various soil samples not affiliating with pmoA or amoA. Abundance of USCalpha pmoA genes was higher in beech soils and reached up to (1.2 +/- 0.2) x 10(8) pmoA genes per g of dry weight. Calculated atmospheric methane oxidation rates per cell yielded the same trend. However, these values were below the theoretical threshold necessary for facilitating cell maintenance, suggesting that USCalpha species might require alternative carbon or energy sources to thrive in forest soils. These collective results indicate that the methanotrophic diversity and abundance in spruce soils are lower than those of beech soils, suggesting that tree species-related factors might influence the in situ activity of methanotrophs.
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44
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Methanotrophic communities in Brazilian ferralsols from naturally forested, afforested, and agricultural sites. Appl Environ Microbiol 2009; 76:1307-10. [PMID: 20038707 DOI: 10.1128/aem.02282-09] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Conversion of forests to farmland permanently lowers atmospheric methane consumption due to unresolved reasons. Alphaproteobacterial methanotrophs were predominant in forested soils and gammaproteobacterial species were predominant in farmland soils of subtropical ferralsols in Brazil. The capability of atmospheric methane consumption was obliterated in farmland soils, suggesting a shift from oligotrophic to copiotrophic species.
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45
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Lüke C, Krause S, Cavigiolo S, Greppi D, Lupotto E, Frenzel P. Biogeography of wetland rice methanotrophs. Environ Microbiol 2009; 12:862-72. [DOI: 10.1111/j.1462-2920.2009.02131.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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Conrad R. The global methane cycle: recent advances in understanding the microbial processes involved. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:285-292. [PMID: 23765881 DOI: 10.1111/j.1758-2229.2009.00038.x] [Citation(s) in RCA: 406] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The global budget of atmospheric CH4 , which is on the order of 500-600 Tg CH4 per year, is mainly the result of environmental microbial processes, such as archaeal methanogenesis in wetlands, rice fields, ruminant and termite digestive systems and of microbial methane oxidation under anoxic and oxic conditions. This review highlights recent progress in the research of anaerobic CH4 oxidation, of CH4 production in the plant rhizosphere, of CH4 serving as substrate for the aquatic trophic food chain and the discovery of novel aerobic methanotrophs. It also emphasizes progress and deficiencies in our knowledge of microbial utilization of low atmospheric CH4 concentrations in soil, CH4 production in the plant canopy, intestinal methanogenesis and CH4 production in pelagic water.
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Affiliation(s)
- Ralf Conrad
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str.8, 35043 Marburg, Germany
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47
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Abell GCJ, Stralis-Pavese N, Sessitsch A, Bodrossy L. Grazing affects methanotroph activity and diversity in an alpine meadow soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:457-465. [PMID: 23765900 DOI: 10.1111/j.1758-2229.2009.00078.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The role of methane-oxidizing bacteria (MOB) in alpine environments is poorly understood, but is of importance given the abundance of alpine environments and the role of MOB in the global carbon cycle. Using a combination of approaches we examined both seasonal and land usage effects on the ecology of microbial methane oxidation in an alpine meadow soil. Analysis of the abundance and diversity of MOB demonstrated that the abundance and diversity of the dominant type II MOB, predominantly Metylocystis and relatives, was only influenced by season. Conversely type Ia MOB abundance was significantly affected by season and land usage, while diversity changes were effected predominantly by land use. Assessment of methane oxidation potential and soil physical properties demonstrated a strong link between type Ia MOB abundance and methane oxidation potential as well as a complex series of relationships between soil moisture, pH and MOB abundance, changing with season. The results of this study suggest that, while type II MOB, unaffected by land use, represent the dominant MOB, Methylobacter-related type Ia MOB appear to be responsible for the majority of methane oxidation and are strongly affected by the grazing of cattle.
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Affiliation(s)
- Guy C J Abell
- Austrian Research Centers, Department of Bioresources, A-2444 Seibersdorf, Austria
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Op den Camp HJM, Islam T, Stott MB, Harhangi HR, Hynes A, Schouten S, Jetten MSM, Birkeland NK, Pol A, Dunfield PF. Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:293-306. [PMID: 23765882 DOI: 10.1111/j.1758-2229.2009.00022.x] [Citation(s) in RCA: 288] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Aerobic methanotrophic bacteria are capable of utilizing methane as their sole energy source. They are commonly found at the oxic/anoxic interfaces of environments such as wetlands, aquatic sediments, and landfills, where they feed on methane produced in anoxic zones of these environments. Until recently, all known species of aerobic methanotrophs belonged to the phylum Proteobacteria, in the classes Gammaproteobacteria and Alphaproteobacteria. However, in 2007-2008 three research groups independently described the isolation of thermoacidophilic methanotrophs that represented a distinct lineage within the bacterial phylum Verrucomicrobia. Isolates were obtained from geothermal areas in Italy, New Zealand and Russia. They are by far the most acidophilic methanotrophs known, with a lower growth limit below pH 1. Here we summarize the properties of these novel methanotrophic Verrucomicrobia, compare them with the proteobacterial methanotrophs, propose a unified taxonomic framework for them and speculate on their potential environmental significance. New genomic and physiological data are combined with existing information to allow detailed comparison of the three strains. We propose the new genus Methylacidiphilum to encompass all three newly discovered bacteria.
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Affiliation(s)
- Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen, Toernooiveld 1, NL-6525 ED Nijmegen, The Netherlands. Department of Biology and Centre for Geobiology, University of Bergen, P.O. Box 7800, N-5020 Bergen, Norway. GNS Science, Extremophile Research Group, Private Bag 2000, 3352 Taupo, New Zealand. Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada, T2N 1N4. NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands
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Kolb S. The quest for atmospheric methane oxidizers in forest soils. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:336-46. [PMID: 23765885 DOI: 10.1111/j.1758-2229.2009.00047.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Aerobic methanotrophs in forest soils are the largest biological sink for atmospheric methane (CH4 ). Community structures in 53 soils from Europe, Russia, North and South America, Asia and New Zealand located in boreal, temperate and tropical forests were analysed and maximal abundances of 2.1 × 10(7) methanotrophs g(-1) DW were measured. In acidic soils, the most frequently detected pmoA genotypes were Upland Soil Cluster α (USCα) and Methylocystis spp. Phospholipid fatty acids that were labelled by consumption of (14/13) CH4 suggested the activity of type II methanotrophs. Cluster 1 (Methylocystaceae), USCγ and Methylocystis spp. were frequently detected genotypes in pH-neutral soils. Genotypes with ambiguous functional affiliation were co-detected (Clusters MR1, RA21, 2) and may represent aerobic methanotrophs, ammonia oxidizers or enzymes with an unknown function. The physiological traits of atmospheric CH4 oxidizers are largely unknown because organisms possessing the key forest soil pmoA genotypes (USCα, USCγ, Cluster 1) have not been cultivated. Some methanotrophic strains belonging to the family Methylocystaceae have been shown to oxidize CH4 at atmospheric mixing ratios. Methylocystis strain SC2 was found to have an alternative particulate CH4 monooxygenase responsible for CH4 oxidation at atmospheric mixing ratios. pH, forest type and temperature might be environmental factors that shape methanotrophic communities in forest soils. However, specific effects on individual species are largely unknown, and only a limited number of studies have addressed environmental controls of methanotrophic diversity, pointing to the need for future research in this area.
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Affiliation(s)
- Steffen Kolb
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
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Vecherskaya M, Dijkema C, Saad HR, Stams AJM. Microaerobic and anaerobic metabolism of a Methylocystis parvus strain isolated from a denitrifying bioreactor. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:442-449. [PMID: 23765898 DOI: 10.1111/j.1758-2229.2009.00069.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
An obligate methanotrophic bacterium, strain MTS, was isolated from a methane-fed microaerobic denitrifying bioreactor. 16S rRNA and DNA-DNA hybridization analysis revealed that this organism was most closely related to Methylocystis parvus, a Type II methanotroph, belonging to the α-subclass of the Proteobacteria. The metabolism of the bacterium under microaerobic and anaerobic conditions was studied by (13) C-NMR. (13) C-labelled poly-β-hydroxybutyrate (PHB) formation occurred in cell suspensions incubated with (13) C-labelled methane at low (5-10%) oxygen concentration. Under these conditions low levels of succinate, acetate and 2,3-butanediol were formed and excreted into the culture medium. Intracellular PHB degradation was observed in intact cells under anaerobic conditions in the absence of an exogenous carbon source during a long-term incubation of 90 days. Multiple (13) C-labelled β-hydroxybutyrate, butyrate, acetate, acetone, isopropanol, 2,3-butanediol and succinate were identified as products in in vivo(13) C-NMR spectra and in the spectra of culture medium during the dynamic PHB degradation. The isolated obligate methanotroph clearly shows a fermentative metabolism of PHB under anaerobic conditions. The excreted products may serve as substrates for denitrifying bacteria.
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Affiliation(s)
- Margarita Vecherskaya
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, the Netherlands. Laboratory of Biophysics, Wageningen University, Dreijenplein 3, 6703 HA, Wageningen, the Netherlands. Department of Biological Systems, Universidad Autónoma Metropolitana, 06960 Mexico City, Mexico
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