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Wutkowska M, Daebeler A. Draft genomes of three aerobic methanotrophs from a temperate eutrophic fishpond. Microbiol Resour Announc 2024; 13:e0015224. [PMID: 38526089 PMCID: PMC11008168 DOI: 10.1128/mra.00152-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 03/15/2024] [Indexed: 03/26/2024] Open
Abstract
Here we introduce draft genomes of three methanotrophs belonging to the Methylococcaceae, a family of typically fast-growing methane oxidizers. Methylobacter sp. Wu1, Methylomicrobium sp. Wu6, and Methylobacter sp. Wu8 were cultured from the top sediment collected from a shore of a eutrophic fishpond in the southern Czech Republic.
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Affiliation(s)
- Magdalena Wutkowska
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
| | - Anne Daebeler
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
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2
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Patil SK, Islam T, Tveit A, Hodson A, Øvreås L. Targeting methanotrophs and isolation of a novel psychrophilic Methylobacter species from a terrestrial Arctic alkaline methane seep in Lagoon Pingo, Central Spitsbergen (78° N). Antonie Van Leeuwenhoek 2024; 117:60. [PMID: 38517574 PMCID: PMC10959801 DOI: 10.1007/s10482-024-01953-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/19/2024] [Indexed: 03/24/2024]
Abstract
The microbial diversity associated with terrestrial groundwater seepage through permafrost soils is tightly coupled to the geochemistry of these fluids. Terrestrial alkaline methane seeps from Lagoon Pingo, Central Spitsbergen (78°N) in Norway, with methane-saturated and oxygen-limited groundwater discharge providing a potential habitat for methanotrophy. Here, we report on the microbial community's comparative analyses and distribution patterns at two sites close to Lagoon Pingo's methane emission source. To target methane-oxidizing bacteria from this system, we analysed the microbial community pattern of replicate samples from two sections near the main methane seepage source. DNA extraction, metabarcoding and subsequent sequencing of 16S rRNA genes revealed microbial communities where the major prokaryotic phyla were Pseudomonadota (42-47%), Gemmatimonadota (4-14%) and Actinobacteriota (7-11%). Among the Pseudomonadota, members of the genus Methylobacter were present at relative abundances between 1.6 and 4.7%. Enrichment targeting the methane oxidising bacteria was set up using methane seep sediments as inoculum and methane as the sole carbon and energy source, and this resulted in the isolation of a novel psychrophilic methane oxidizer, LS7-T4AT. The optimum growth temperature for the isolate was 13 °C and the pH optimum was 8.0. The morphology of cells was short rods, and TEM analysis revealed intracytoplasmic membranes arranged in stacks, a distinctive feature for Type I methanotrophs in the family Methylomonadaceae of the class Gammaproteobacteria. The strain belongs to the genus Methylobacter based on high 16S rRNA gene similarity to the psychrophilic species of Methylobacter psychrophilus Z-0021T (98.95%), the psychrophilic strain Methylobacter sp. strain S3L5C (99.00%), and the Arctic mesophilic species of Methylobacter tundripaludum SV96T (99.06%). The genome size of LS7-T4AT was 4,338,157 bp with a G + C content of 47.93%. The average nucleotide identities (ANIb) of strain LS7-T4AT to 10 isolated strains of genus Methylobacter were between 75.54 and 85.51%, lower than the species threshold of 95%. The strain LS7-T4AT represents a novel Arctic species, distinct from other members of the genus Methylobacter, for which the name Methylobacter svalbardensis sp. nov. is proposed. The type of strain is LS7-T4AT (DSMZ:114308, JCM:39463).
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Affiliation(s)
- Shalaka K Patil
- Department of Biological Sciences, University of Bergen, Postboks 7803, 5020, Bergen, Norway.
| | - Tajul Islam
- Department of Biological Sciences, University of Bergen, Postboks 7803, 5020, Bergen, Norway
| | - Alexander Tveit
- Department of Arctic and Marine Biology, The Arctic University of Tromsø, 9037, Tromsø, Norway
| | - Andrew Hodson
- University Centre in Svalbard, 9171, Longyearbyen, Norway
| | - Lise Øvreås
- Department of Biological Sciences, University of Bergen, Postboks 7803, 5020, Bergen, Norway
- University Centre in Svalbard, 9171, Longyearbyen, Norway
- Bjerknes Centre for Climate Research, Jahnebakken 5, 5007, Bergen, Norway
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3
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Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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Goraj W, Pytlak A, Grządziel J, Gałązka A, Stępniewska Z, Szafranek-Nakonieczna A. Dynamics of Methane-Consuming Biomes from Wieliczka Formation: Environmental and Enrichment Studies. BIOLOGY 2023; 12:1420. [PMID: 37998019 PMCID: PMC10669130 DOI: 10.3390/biology12111420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023]
Abstract
The rocks surrounding Wieliczka salt deposits are an extreme, deep subsurface ecosystem that as we studied previously harbors many microorganisms, including methanotrophs. In the presented research bacterial community structure of the Wieliczka Salt Mine was determined as well as the methanotrophic activity of the natural microbiome. Finally, an enrichment culture of methane-consuming methanotrophs was obtained. The research material used in this study consisted of rocks surrounding salt deposits in the Wieliczka Salt Mine. DNA was extracted directly from the pristine rock material, as well as from rocks incubated in an atmosphere containing methane and mineral medium, and from a methanotrophic enrichment culture from this ecosystem. As a result, the study describes the composition of the microbiome in the rocks surrounding the salt deposits, while also explaining how biodiversity changes during the enrichment culture of the methanotrophic bacterial community. The contribution of methanotrophic bacteria ranged from 2.614% in the environmental sample to 64.696% in the bacterial culture. The methanotrophic enrichment culture was predominantly composed of methanotrophs from the genera Methylomonas (48.848%) and Methylomicrobium (15.636%) with methane oxidation rates from 3.353 ± 0.105 to 4.200 ± 0.505 µmol CH4 mL-1 day-1.
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Affiliation(s)
- Weronika Goraj
- Department of Biology and Biotechnology of Microorganisms, Faculty of Medicine, The John Paul II Catholic University of Lublin, Str. Konstantynów 1I, 20-708 Lublin, Poland;
| | - Anna Pytlak
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-280 Lublin, Poland;
| | - Jarosław Grządziel
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation–State Research Institute (IUNG-PIB), Czartoryskich 8, 24-100 Puławy, Poland; (J.G.); (A.G.)
| | - Anna Gałązka
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation–State Research Institute (IUNG-PIB), Czartoryskich 8, 24-100 Puławy, Poland; (J.G.); (A.G.)
| | - Zofia Stępniewska
- Department of Biochemistry and Environmental Chemistry, The John Paul II Catholic University of Lublin, Konstantynów 1 I, 20-708 Lublin, Poland;
| | - Anna Szafranek-Nakonieczna
- Department of Biology and Biotechnology of Microorganisms, Faculty of Medicine, The John Paul II Catholic University of Lublin, Str. Konstantynów 1I, 20-708 Lublin, Poland;
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Liu Y, Zhang B, Zhang Y, Shen Y, Cheng C, Yuan W, Guo P. Organic Matter Decomposition in River Ecosystems: Microbial Interactions Influenced by Total Nitrogen and Temperature in River Water. MICROBIAL ECOLOGY 2023; 85:1236-1252. [PMID: 35501499 DOI: 10.1007/s00248-022-02013-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/11/2022] [Indexed: 05/10/2023]
Abstract
Microbes contribute to the organic matter decomposition (OMD) in river ecosystems. This study considers two aspects of OMD in river ecosystems which have not been examined in scientific studies previously, and these are the microbial interactions in OMD and the influence of environmental factors on microbial interactions. Cotton strip (CS), as a substitute for organic matter, was introduced to Luanhe River Basin in China. The results of CS assay, microbial sequencing, and redundancy analysis (RDA) showed that CS selectively enriched bacterial and fungal groups related to cellulose decomposition, achieving cotton strip decomposition (CSD). Bacterial phylum Proteobacteria and fungal phyla Rozellomycota and Ascomycota were the dominant groups associated with CSD. Network analysis and Mantel test results indicated that bacteria and fungi on CS cooperatively formed an interaction network to achieve the CSD. In the network, modules 2 and 4 were significantly positively associated with CSD, which were considered as the key modules in this study. The key modules were mainly composed of phyla Proteobacteria and Ascomycota, indicating that microbes in key modules were the effective decomposers of CS. Although keystone taxa were not directly associated with CSD, they may regulate the genera in key modules to achieve the CSD, since some keystone taxa were linked with the microbial genera associated with CSD in the key modules. Total nitrogen (TN) and temperature in water were the dominant environmental factors positively influenced CSD. The key modules 2 and 4 were positively influenced by water temperature and TN in water, respectively, and two keystone taxa were positively associated with TN. This profoundly revealed that water temperature and TN influenced the OMD through acting on the keystone taxa and key modules in microbial interactions. The research findings help us to understand the microbial interactions influenced by environmental factors in OMD in river ecosystems.
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Affiliation(s)
- Yibo Liu
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, 130012, People's Republic of China
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun, 130012, People's Republic of China
| | - Baiyu Zhang
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John' s, NL, A1B 3X5, Canada
| | - Yixin Zhang
- Department of Landscape Architecture, Gold Mantis School of Architecture, Soochow University, Suzhou, China
| | - Yanping Shen
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, 130012, People's Republic of China
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun, 130012, People's Republic of China
| | - Cheng Cheng
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, 130012, People's Republic of China
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun, 130012, People's Republic of China
| | - Weilin Yuan
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, 130012, People's Republic of China
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun, 130012, People's Republic of China
| | - Ping Guo
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, 130012, People's Republic of China.
- Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun, 130012, People's Republic of China.
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Cre/ lox-Mediated CRISPRi Library Reveals Core Genome of a Type I Methanotroph Methylotuvimicrobium buryatense 5GB1C. Appl Environ Microbiol 2023; 89:e0188322. [PMID: 36622175 PMCID: PMC9888281 DOI: 10.1128/aem.01883-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Methanotrophs play key roles in global methane cycling and are promising platforms for methane bioconversion. However, major gaps existing in fundamental knowledge undermines understanding of these methane-consuming microorganisms. To associate genes with a phenotype at the genome-wide level, we developed a Cre/lox-mediated method for constructing a large-scale CRISPRi library in a model methanotroph Methylotuvimicrobium buryatense 5GB1C. The efficiency of this Cre mediated integration method was up to a level of 105 CFU/μg DNA. Targeting 4,100 predicted protein-coding genes, our CRISPRi pooled screening uncovered 788 core genes for the growth of strain 5GB1C using methane. The core genes are highly consistent with the gene knockout results, indicating the reliability of the CRISPRi screen. Insights from the core genes include that annotated isozymes generally exist in metabolic pathways and many core genes are hypothetical genes. This work not only provides functional genomic data for both fundamental research and metabolic engineering of methanotrophs, but also offers a method for CRISPRi library construction. IMPORTANCE Due to their key role in methane cycling and their industrial potential, methanotrophs have drawn increasing attention. Genome-wide experimental approaches for gene-phenotype mapping accelerate our understanding and engineering of a bacterium. However, these approaches are still unavailable in methanotrophs. This work has two significant implications. First, the core genes identified here provide functional genetic basics for complete reconstruction of the metabolic network and afford more clues for knowledge gaps. Second, the Cre-mediated knock-in method developed in this work enables large-scale DNA library construction in methanotrophs; the CRISPRi library can be used to screen the genes associated with special culture conditions.
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Yao X, Wang J, Hu B. How methanotrophs respond to pH: A review of ecophysiology. Front Microbiol 2023; 13:1034164. [PMID: 36687570 PMCID: PMC9853399 DOI: 10.3389/fmicb.2022.1034164] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/09/2022] [Indexed: 01/08/2023] Open
Abstract
Varying pH globally affects terrestrial microbial communities and biochemical cycles. Methanotrophs effectively mitigate methane fluxes in terrestrial habitats. Many methanotrophs grow optimally at neutral pH. However, recent discoveries show that methanotrophs grow in strongly acidic and alkaline environments. Here, we summarize the existing knowledge on the ecophysiology of methanotrophs under different pH conditions. The distribution pattern of diverse subgroups is described with respect to their relationship with pH. In addition, their responses to pH stress, consisting of structure-function traits and substrate affinity traits, are reviewed. Furthermore, we propose a putative energy trade-off model aiming at shedding light on the adaptation mechanisms of methanotrophs from a novel perspective. Finally, we take an outlook on methanotrophs' ecophysiology affected by pH, which would offer new insights into the methane cycle and global climate change.
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Affiliation(s)
- Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China,Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China,*Correspondence: Baolan Hu ✉
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8
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Yun J, Crombie AT, Ul Haque MF, Cai Y, Zheng X, Wang J, Jia Z, Murrell JC, Wang Y, Du W. Revealing the community and metabolic potential of active methanotrophs by targeted metagenomics in the Zoige wetland of the Tibetan Plateau. Environ Microbiol 2021; 23:6520-6535. [PMID: 34390603 DOI: 10.1111/1462-2920.15697] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/27/2021] [Accepted: 07/27/2021] [Indexed: 01/21/2023]
Abstract
The Zoige wetland of the Tibetan Plateau is one of the largest alpine wetlands in the world and a major emission source of methane. Methane oxidation by methanotrophs can counteract the global warming effect of methane released in the wetlands. Understanding methanotroph activity, diversity and metabolism at the molecular level can guide the isolation of the uncultured microorganisms and inform strategy-making decisions and policies to counteract global warming in this unique ecosystem. Here we applied DNA stable isotope probing using 13 C-labelled methane to label the genomes of active methanotrophs, examine the methane oxidation potential and recover metagenome-assembled genomes (MAGs) of active methanotrophs. We found that gammaproteobacteria of type I methanotrophs are responsible for methane oxidation in the wetland. We recovered two phylogenetically novel methanotroph MAGs distantly related to extant Methylobacter and Methylovulum. They belong to type I methanotrophs of gammaproteobacteria, contain both mxaF and xoxF types of methanol dehydrogenase coding genes, and participate in methane oxidation via H4 MPT and RuMP pathways. Overall, the community structure of active methanotrophs and their methanotrophic pathways revealed by DNA-SIP metagenomics and retrieved methanotroph MAGs highlight the importance of methanotrophs in suppressing methane emission in the wetland under the scenario of global warming.
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Affiliation(s)
- Juanli Yun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Andrew T Crombie
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, 210008, China
| | - Xiaowei Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian Wang
- 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, Jiangsu Province, 210008, China
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 10049, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 10049, China
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9
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Abstract
Methanotrophic bacteria represent a potential route to methane utilization and mitigation of methane emissions. In the first step of their metabolic pathway, aerobic methanotrophs use methane monooxygenases (MMOs) to activate methane, oxidizing it to methanol. There are two types of MMOs: a particulate, membrane-bound enzyme (pMMO) and a soluble, cytoplasmic enzyme (sMMO). The two MMOs are completely unrelated, with different architectures, metal cofactors, and mechanisms. The more prevalent of the two, pMMO, is copper-dependent, but the identity of its copper active site remains unclear. By contrast, sMMO uses a diiron active site, the catalytic cycle of which is well understood. Here we review the current state of knowledge for both MMOs, with an emphasis on recent developments and emerging hypotheses. In addition, we discuss obstacles to developing expression systems, which are needed to address outstanding questions and to facilitate future protein engineering efforts.
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Affiliation(s)
- Christopher W Koo
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA.
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Schmitz RA, Peeters SH, Versantvoort W, Picone N, Pol A, Jetten MSM, Op den Camp HJM. Verrucomicrobial methanotrophs: ecophysiology of metabolically versatile acidophiles. FEMS Microbiol Rev 2021; 45:6125968. [PMID: 33524112 PMCID: PMC8498564 DOI: 10.1093/femsre/fuab007] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/15/2021] [Indexed: 12/26/2022] Open
Abstract
Methanotrophs are an important group of microorganisms that counteract methane emissions to the atmosphere. Methane-oxidising bacteria of the Alpha- and Gammaproteobacteria have been studied for over a century, while methanotrophs of the phylum Verrucomicrobia are a more recent discovery. Verrucomicrobial methanotrophs are extremophiles that live in very acidic geothermal ecosystems. Currently, more than a dozen strains have been isolated, belonging to the genera Methylacidiphilum and Methylacidimicrobium. Initially, these methanotrophs were thought to be metabolically confined. However, genomic analyses and physiological and biochemical experiments over the past years revealed that verrucomicrobial methanotrophs, as well as proteobacterial methanotrophs, are much more metabolically versatile than previously assumed. Several inorganic gases and other molecules present in acidic geothermal ecosystems can be utilised, such as methane, hydrogen gas, carbon dioxide, ammonium, nitrogen gas and perhaps also hydrogen sulfide. Verrucomicrobial methanotrophs could therefore represent key players in multiple volcanic nutrient cycles and in the mitigation of greenhouse gas emissions from geothermal ecosystems. Here, we summarise the current knowledge on verrucomicrobial methanotrophs with respect to their metabolic versatility and discuss the factors that determine their diversity in their natural environment. In addition, key metabolic, morphological and ecological characteristics of verrucomicrobial and proteobacterial methanotrophs are reviewed.
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Affiliation(s)
- Rob A Schmitz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Stijn H Peeters
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Nunzia Picone
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Arjan Pol
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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11
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Poghosyan L, Koch H, Frank J, van Kessel MAHJ, Cremers G, van Alen T, Jetten MSM, Op den Camp HJM, Lücker S. Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in two sequential rapid sand filters. WATER RESEARCH 2020; 185:116288. [PMID: 32810745 DOI: 10.1016/j.watres.2020.116288] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/17/2020] [Accepted: 08/09/2020] [Indexed: 05/22/2023]
Abstract
Elevated concentrations of ammonium and methane in groundwater are often associated with microbiological, chemical and sanitary problems during drinking water production and distribution. To avoid their accumulation, raw water in the Netherlands and many other countries is purified by sand filtration. These drinking water filtration systems select for microbial communities that mediate the biodegradation of organic and inorganic compounds. In this study, the top layers and wall biofilm of a Dutch drinking water treatment plant (DWTP) were sampled from the filtration units of the plant over three years. We used high-throughput sequencing in combination with differential coverage and sequence composition-based binning to recover 56 near-complete metagenome-assembled genomes (MAGs) with an estimated completion of ≥70% and with ≤10% redundancy. These MAGs were used to characterize the microbial communities involved in the conversion of ammonia and methane. The methanotrophic microbial communities colonizing the wall biofilm (WB) and the granular material of the primary rapid sand filter (P-RSF) were dominated by members of the Methylococcaceae and Methylophilaceae. The abundance of these bacteria drastically decreased in the secondary rapid sand filter (S-RSF) samples. In all samples, complete ammonia-oxidizing (comammox) Nitrospira were the most abundant nitrifying guild. Clade A comammox Nitrospira dominated the P-RSF, while clade B was most abundant in WB and S-RSF, where ammonium concentrations were much lower. In conclusion, the knowledge obtained in this study contributes to understanding the role of microorganisms in the removal of carbon and nitrogen compounds during drinking water production. We furthermore found that drinking water treatment plants represent valuable model systems to study microbial community function and interaction.
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Affiliation(s)
- Lianna Poghosyan
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Hanna Koch
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Jeroen Frank
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Maartje A H J van Kessel
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Geert Cremers
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Theo van Alen
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands.
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Islam MM, Le T, Daggumati SR, Saha R. Investigation of microbial community interactions between Lake Washington methanotrophs using -------genome-scale metabolic modeling. PeerJ 2020; 8:e9464. [PMID: 32655999 PMCID: PMC7333651 DOI: 10.7717/peerj.9464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/10/2020] [Indexed: 11/21/2022] Open
Abstract
Background The role of methane in global warming has become paramount to the environment and the human society, especially in the past few decades. Methane cycling microbial communities play an important role in the global methane cycle, which is why the characterization of these communities is critical to understand and manipulate their behavior. Methanotrophs are a major player in these communities and are able to oxidize methane as their primary carbon source. Results Lake Washington is a freshwater lake characterized by a methane-oxygen countergradient that contains a methane cycling microbial community. Methanotrophs are a major part of this community involved in assimilating methane from lake water. Two significant methanotrophic species in this community are Methylobacter and Methylomonas. In this work, these methanotrophs are computationally studied via developing highly curated genome-scale metabolic models. Each model was then integrated to form a community model with a multi-level optimization framework. The competitive and mutualistic metabolic interactions among Methylobacter and Methylomonas were also characterized. The community model was next tested under carbon, oxygen, and nitrogen limited conditions in addition to a nutrient-rich condition to observe the systematic shifts in the internal metabolic pathways and extracellular metabolite exchanges. Each condition showed variations in the methane oxidation pathway, pyruvate metabolism, and the TCA cycle as well as the excretion of formaldehyde and carbon di-oxide in the community. Finally, the community model was simulated under fixed ratios of these two members to reflect the opposing behavior in the two-member synthetic community and in sediment-incubated communities. The community simulations predicted a noticeable switch in intracellular carbon metabolism and formaldehyde transfer between community members in sediment-incubated vs. synthetic condition. Conclusion In this work, we attempted to predict the response of a simplified methane cycling microbial community from Lake Washington to varying environments and also provide an insight into the difference of dynamics in sediment-incubated microcosm community and synthetic co-cultures. Overall, this study lays the ground for in silico systems-level studies of freshwater lake ecosystems, which can drive future efforts of understanding, engineering, and modifying these communities for dealing with global warming issues.
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Affiliation(s)
- Mohammad Mazharul Islam
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Tony Le
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Shardhat R Daggumati
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Rajib Saha
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States of America
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13
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van Grinsven S, Sinninghe Damsté JS, Harrison J, Villanueva L. Impact of Electron Acceptor Availability on Methane-Influenced Microorganisms in an Enrichment Culture Obtained From a Stratified Lake. Front Microbiol 2020; 11:715. [PMID: 32477281 PMCID: PMC7240106 DOI: 10.3389/fmicb.2020.00715] [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: 06/20/2019] [Accepted: 03/27/2020] [Indexed: 12/26/2022] Open
Abstract
Methanotrophs are of major importance in limiting methane emissions from lakes. They are known to preferably inhabit the oxycline of stratified water columns, often assumed due to an intolerance to atmospheric oxygen concentrations, but little is known on the response of methanotrophs to different oxygen concentrations as well as their preference for different electron acceptors. In this study, we enriched a methanotroph of the Methylobacter genus from the oxycline and the anoxic water column of a stratified lake, which was also present in the oxic water column in the winter. We tested the response of this Methylobacter-dominated enrichment culture to different electron acceptors, i.e., oxygen, nitrate, sulfate, and humic substances, and found that, in contrast to earlier results with water column incubations, oxygen was the preferred electron acceptor, leading to methane oxidation rates of 45–72 pmol cell−1 day−1. Despite the general assumption of methanotrophs preferring microaerobic conditions, methane oxidation was most efficient under high oxygen concentrations (>600 μM). Low (<30 μM) oxygen concentrations still supported methane oxidation, but no methane oxidation was observed with trace oxygen concentrations (<9 μM) or under anoxic conditions. Remarkably, the presence of nitrate stimulated methane oxidation rates under oxic conditions, raising the methane oxidation rates by 50% when compared to oxic incubations with ammonium. Under anoxic conditions, no net methane consumption was observed; however, methanotroph abundances were two to three times higher in incubations with nitrate and sulfate compared to anoxic incubations with ammonium as the nitrogen source. Metagenomic sequencing revealed the absence of a complete denitrification pathway in the dominant methanotroph Methylobacter, but the most abundant methylotroph Methylotenera seemed capable of denitrification, which can possibly play a role in the enhanced methane oxidation rates under nitrate-rich conditions.
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Affiliation(s)
- Sigrid van Grinsven
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Utrecht, Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Utrecht, Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - John Harrison
- School of the Environment, Washington State University Vancouver, Vancouver, WA, United States
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Utrecht, Netherlands
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14
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van Grinsven S, Sinninghe Damsté JS, Abdala Asbun A, Engelmann JC, Harrison J, Villanueva L. Methane oxidation in anoxic lake water stimulated by nitrate and sulfate addition. Environ Microbiol 2020; 22:766-782. [PMID: 31814267 PMCID: PMC7027835 DOI: 10.1111/1462-2920.14886] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 11/21/2019] [Accepted: 12/04/2019] [Indexed: 11/30/2022]
Abstract
Methanotrophic bacteria play a key role in limiting methane emissions from lakes. It is generally assumed that methanotrophic bacteria are mostly active at the oxic-anoxic transition zone in stratified lakes, where they use oxygen to oxidize methane. Here, we describe a methanotroph of the genera Methylobacter that is performing high-rate (up to 72 μM day-1 ) methane oxidation in the anoxic hypolimnion of the temperate Lacamas Lake (Washington, USA), stimulated by both nitrate and sulfate addition. Oxic and anoxic incubations both showed active methane oxidation by a Methylobacter species, with anoxic rates being threefold higher. In anoxic incubations, Methylobacter cell numbers increased almost two orders of magnitude within 3 days, suggesting that this specific Methylobacter species is a facultative anaerobe with a rapid response capability. Genomic analysis revealed adaptations to oxygen-limitation as well as pathways for mixed-acid fermentation and H2 production. The denitrification pathway was incomplete, lacking the genes narG/napA and nosZ, allowing only for methane oxidation coupled to nitrite-reduction. Our data suggest that Methylobacter can be an important driver of the conversion of methane in oxygen-limited lake systems and potentially use alternative electron acceptors or fermentation to remain active under oxygen-depleted conditions.
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Affiliation(s)
- Sigrid van Grinsven
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
| | - Alejandro Abdala Asbun
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
| | - Julia C. Engelmann
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
| | - John Harrison
- Washington State University Vancouver, School of the EnvironmentVancouverWA98686USA
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
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15
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López JC, Porca E, Collins G, Clifford E, Quijano G, Muñoz R. Ammonium influences kinetics and structure of methanotrophic consortia. WASTE MANAGEMENT (NEW YORK, N.Y.) 2019; 89:345-353. [PMID: 31079748 DOI: 10.1016/j.wasman.2019.04.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 04/02/2019] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
The literature is conflicted on the influence of ammonium on the kinetics and microbial ecology of methanotrophy. In this study, methanotrophic cultures were enriched, under ammonium concentrations ranging from 0 to 200 mM, from an inoculum comprising leachate and top-cover soil from a landfill. Specific CH4 biodegradation rates were highest (7.8 × 10-4 ± 6.0 × 10-5 gCH4 gX-1 h-1) in cultures enriched at 4 mM NH4+, which were mainly dominated by type II methanotrophs belonging to Methylocystis spp. Lower specific CH4 oxidation rates (average values of 1.8-3.6 × 10-4 gCH4 gX-1 h-1) were achieved by cultures enriched at higher NH4+ concentrations (20 and 80 mM), and had higher affinity for CH4 compared to 4 mM enrichments. These lower affinities were attributed to lower diversity dominated by type I methanotrophs, of the Methylosarcina, Methylobacter and Methylomicrobium genera, encountered with increasing concentrations of NH4+. The study indicates that CH4 oxidation biotechnologies applied at low NH4+ concentrations can support efficient abatement of CH4 and high diversity of methanotrophic consortia, whilst enriching type II methanotrophs.
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Affiliation(s)
- Juan C López
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Estefanía Porca
- Microbial Communities Laboratory, School of Natural Sciences, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland; Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland
| | - Gavin Collins
- Microbial Communities Laboratory, School of Natural Sciences, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland; Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland
| | - Eoghan Clifford
- Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland; College of Engineering and Informatics, National University of Ireland Galway, University Road, Galway H91 F677, Ireland
| | - Guillermo Quijano
- Laboratory for Research on Advanced Processes for Water Treatment, Instituto de Ingeniería, Unidad Académica Juriquilla, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Querétaro 76230, Mexico
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Institute of Sustainable Proceses, University of Valladolid, Spain.
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16
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Rahalkar MC, Khatri K, Pandit PS, Dhakephalkar PK. A putative novel Methylobacter member (KRF1) from the globally important Methylobacter clade 2: cultivation and salient draft genome features. Antonie van Leeuwenhoek 2019; 112:1399-1408. [PMID: 30968234 DOI: 10.1007/s10482-019-01262-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/02/2019] [Indexed: 11/28/2022]
Abstract
Methane oxidation by methanotrophs is a very important environmental process in the mitigation of methane. Methylobacter (Mtb.) clade 2 members have been reported as dominant methane oxidisers in soils and sediments worldwide. We enriched and purified a methanotroph from a tropical rice field soil sample from India. The highly enriched culture showed the presence of motile, long and thick rods (3-5 µm × 0.9-1.2 µm) and minor presence of short, thin rods. The culture was purified on agarose medium and formed yellow colonies which showed the presence of only thick and long rods, henceforth termed as strain KRF1. Based on 16S rRNA gene sequence analysis, strain KRF1 shows close phylogenetic affiliation to Methylobacter tundripaludum SV96T (98.6% similarity). Due to the taxonomic novelty, and being the first member of Mtb. related to Mtb. tundripaludum from the tropics, the draft genome was sequenced. From the blastx analysis of the contigs, it was clear that the culture still had contamination of another organism, a Methylophilus species. The data binned in two clear bins: Mtb. related contigs and Methylophilus-related contigs. The binned draft genome of KRF1 shows features including the typical pathways for methane metabolism, denitrification and the presence of molybdenum iron and vanadium-iron nitrogenase genes. KRF1 is phylogenetically distinct from the five strains of Mtb. tundripaludum including SV96T, Lake Washington strains and OWC strains, showing ~ 26% DDH and ~ 81% ANIb values and a unique position in a phylogenomic tree. Subsequently, KRF1 has been completely purified from its methylotrophic partner and a pure culture has been established and maintained in a WDCM approved culture collection, the MACS Collection of Microorganisms (as MCM 1471). KRF1 is thus the first cultured member of a putative novel species of Methylobacter clade 2 isolated from the tropics.
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Affiliation(s)
- Monali C Rahalkar
- C2, Bioenergy Group, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India. .,Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India.
| | - Kumal Khatri
- C2, Bioenergy Group, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.,Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Pranitha S Pandit
- C2, Bioenergy Group, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.,Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Prashant K Dhakephalkar
- C2, Bioenergy Group, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.,Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
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17
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Esparza M, Jedlicki E, González C, Dopson M, Holmes DS. Effect of CO 2 Concentration on Uptake and Assimilation of Inorganic Carbon in the Extreme Acidophile Acidithiobacillus ferrooxidans. Front Microbiol 2019; 10:603. [PMID: 31019493 PMCID: PMC6458275 DOI: 10.3389/fmicb.2019.00603] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/11/2019] [Indexed: 02/01/2023] Open
Abstract
This study was motivated by surprising gaps in the current knowledge of microbial inorganic carbon (Ci) uptake and assimilation at acidic pH values (pH < 3). Particularly striking is the limited understanding of the differences between Ci uptake mechanisms in acidic versus circumneutral environments where the Ci predominantly occurs either as a dissolved gas (CO2) or as bicarbonate (HCO3 -), respectively. In order to gain initial traction on the problem, the relative abundance of transcripts encoding proteins involved in Ci uptake and assimilation was studied in the autotrophic, polyextreme acidophile Acidithiobacillus ferrooxidans whose optimum pH for growth is 2.5 using ferrous iron as an energy source, although they are able to grow at pH 5 when using sulfur as an energy source. The relative abundance of transcripts of five operons (cbb1-5) and one gene cluster (can-sulP) was monitored by RT-qPCR and, in selected cases, at the protein level by Western blotting, when cells were grown under different regimens of CO2 concentration in elemental sulfur. Of particular note was the absence of a classical bicarbonate uptake system in A. ferrooxidans. However, bioinformatic approaches predict that sulP, previously annotated as a sulfate transporter, is a novel type of bicarbonate transporter. A conceptual model of CO2 fixation was constructed from combined bioinformatic and experimental approaches that suggests strategies for providing ecological flexibility under changing concentrations of CO2 and provides a portal to elucidating Ci uptake and regulation in acidic conditions. The results could advance the understanding of industrial bioleaching processes to recover metals such as copper at acidic pH. In addition, they may also shed light on how chemolithoautotrophic acidophiles influence the nutrient and energy balance in naturally occurring low pH environments.
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Affiliation(s)
- Mario Esparza
- Laboratorio de Biominería, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Eugenia Jedlicki
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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18
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Smith GJ, Angle JC, Solden LM, Borton MA, Morin TH, Daly RA, Johnston MD, Stefanik KC, Wolfe R, Gil B, Wrighton KC. Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland. mBio 2018; 9:e00815-18. [PMID: 30401770 PMCID: PMC6222125 DOI: 10.1128/mbio.00815-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 10/01/2018] [Indexed: 11/20/2022] Open
Abstract
Microbial carbon degradation and methanogenesis in wetland soils generate a large proportion of atmospheric methane, a highly potent greenhouse gas. Despite their potential to mitigate greenhouse gas emissions, knowledge about methane-consuming methanotrophs is often limited to lower-resolution single-gene surveys that fail to capture the taxonomic and metabolic diversity of these microorganisms in soils. Here our objective was to use genome-enabled approaches to investigate methanotroph membership, distribution, and in situ activity across spatial and seasonal gradients in a freshwater wetland near Lake Erie. 16S rRNA gene analyses demonstrated that members of the methanotrophic Methylococcales were dominant, with the dominance largely driven by the relative abundance of four taxa, and enriched in oxic surface soils. Three methanotroph genomes from assembled soil metagenomes were assigned to the genus Methylobacter and represented the most abundant methanotrophs across the wetland. Paired metatranscriptomes confirmed that these Old Woman Creek (OWC) Methylobacter members accounted for nearly all the aerobic methanotrophic activity across two seasons. In addition to having the capacity to couple methane oxidation to aerobic respiration, these new genomes encoded denitrification potential that may sustain energy generation in soils with lower dissolved oxygen concentrations. We further show that Methylobacter members that were closely related to the OWC members were present in many other high-methane-emitting freshwater and soil sites, suggesting that this lineage could participate in methane consumption in analogous ecosystems. This work contributes to the growing body of research suggesting that Methylobacter may represent critical mediators of methane fluxes in freshwater saturated sediments and soils worldwide.IMPORTANCE Here we used soil metagenomics and metatranscriptomics to uncover novel members within the genus Methylobacter We denote these closely related genomes as members of the lineage OWC Methylobacter Despite the incredibly high microbial diversity in soils, here we present findings that unexpectedly showed that methane cycling was primarily mediated by a single genus for both methane production ("Candidatus Methanothrix paradoxum") and methane consumption (OWC Methylobacter). Metatranscriptomic analyses revealed that decreased methanotrophic activity rather than increased methanogenic activity possibly contributed to the greater methane emissions that we had previously observed in summer months, findings important for biogeochemical methane models. Although members of this Methylococcales order have been cultivated for decades, multi-omic approaches continue to illuminate the methanotroph phylogenetic and metabolic diversity harbored in terrestrial and marine ecosystems.
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Affiliation(s)
- Garrett J Smith
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Jordan C Angle
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Lindsey M Solden
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Mikayla A Borton
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
- Environmental Science Graduate Program, The Ohio State University, Columbus, Ohio, USA
| | - Timothy H Morin
- Department of Environmental Resources Engineering, State University of New York College of Environmental Science and Forestry, Syracuse, New York, USA
| | - Rebecca A Daly
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Michael D Johnston
- National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Kay C Stefanik
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Civil and Environmental Engineering and Geodetic Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Richard Wolfe
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Bohrer Gil
- Environmental Science Graduate Program, The Ohio State University, Columbus, Ohio, USA
- Department of Civil and Environmental Engineering and Geodetic Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Kelly C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
- Environmental Science Graduate Program, The Ohio State University, Columbus, Ohio, USA
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19
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Matheus Carnevali PB, Herbold CW, Hand KP, Priscu JC, Murray AE. Distinct Microbial Assemblage Structure and Archaeal Diversity in Sediments of Arctic Thermokarst Lakes Differing in Methane Sources. Front Microbiol 2018; 9:1192. [PMID: 29930542 PMCID: PMC6000721 DOI: 10.3389/fmicb.2018.01192] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 05/16/2018] [Indexed: 12/04/2022] Open
Abstract
Developing a microbial ecological understanding of Arctic thermokarst lake sediments in a geochemical context is an essential first step toward comprehending the contributions of these systems to greenhouse gas emissions, and understanding how they may shift as a result of long term changes in climate. In light of this, we set out to study microbial diversity and structure in sediments from four shallow thermokarst lakes in the Arctic Coastal Plain of Alaska. Sediments from one of these lakes (Sukok) emit methane (CH4) of thermogenic origin, as expected for an area with natural gas reserves. However, sediments from a lake 10 km to the North West (Siqlukaq) produce CH4 of biogenic origin. Sukok and Siqlukaq were chosen among the four lakes surveyed to test the hypothesis that active CH4-producing organisms (methanogens) would reflect the distribution of CH4 gas levels in the sediments. We first examined the structure of the little known microbial community inhabiting the thaw bulb of arctic thermokarst lakes near Barrow, AK. Molecular approaches (PCR-DGGE and iTag sequencing) targeting the SSU rRNA gene and rRNA molecule were used to profile diversity, assemblage structure, and identify potentially active members of the microbial assemblages. Overall, the potentially active (rRNA dominant) fraction included taxa that have also been detected in other permafrost environments (e.g., Bacteroidetes, Actinobacteria, Nitrospirae, Chloroflexi, and others). In addition, Siqlukaq sediments were unique compared to the other sites, in that they harbored CH4-cycling organisms (i.e., methanogenic Archaea and methanotrophic Bacteria), as well as bacteria potentially involved in N cycling (e.g., Nitrospirae) whereas Sukok sediments were dominated by taxa typically involved in photosynthesis and biogeochemical sulfur (S) transformations. This study revealed a high degree of archaeal phylogenetic diversity in addition to CH4-producing archaea, which spanned nearly the phylogenetic extent of currently recognized Archaea phyla (e.g., Euryarchaeota, Bathyarchaeota, Thaumarchaeota, Woesearchaeota, Pacearchaeota, and others). Together these results shed light on expansive bacterial and archaeal diversity in Arctic thermokarst lakes and suggest important differences in biogeochemical potential in contrasting Arctic thermokarst lake sediment ecosystems.
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Affiliation(s)
| | - Craig W Herbold
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Kevin P Hand
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - John C Priscu
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
| | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
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20
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Mateos-Rivera A, Islam T, Marshall IPG, Schreiber L, Øvreås L. High-quality draft genome of the methanotroph Methylovulum psychrotolerans Str. HV10-M2 isolated from plant material at a high-altitude environment. Stand Genomic Sci 2018; 13:10. [PMID: 29686747 PMCID: PMC5898042 DOI: 10.1186/s40793-018-0314-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 04/04/2018] [Indexed: 11/10/2022] Open
Abstract
Here we present the genome of Methylovulum psychrotolerans strain HV10-M2, a methanotroph isolated from Hardangervidda national park (Norway). This strain represents the second of the two validly published species genus with a sequenced genome. The other is M. miyakonense HT12, which is the type strain of the species and the type species of the genus Methylovulum. We present the genome of M. psychrotolerants str. HV10-M2 and discuss the differences between M. psychrotolerans and M. miyakonense. The genome size of M. psychrotolerans str. HV10-M2 is 4,923,400 bp and contains 4415 protein-coding genes, 50 RNA genes and an average GC content of 50.88%.
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Affiliation(s)
- Alejandro Mateos-Rivera
- 1Department of Biology, University of Bergen, Bergen, Norway.,2Faculty of Engineering and Science, Western Norway University of Applied Sciences, Sogndal, Norway
| | - Tajul Islam
- 1Department of Biology, University of Bergen, Bergen, Norway
| | - Ian P G Marshall
- 3Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Lars Schreiber
- 3Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.,5Present address: Energy, Mining and Environment, National Research Council, Montreal, QC Canada
| | - Lise Øvreås
- 1Department of Biology, University of Bergen, Bergen, Norway.,4UNIS, the University Centre in Svalbard, Longyearbyen, Norway
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21
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Martinez-Cruz K, Leewis MC, Herriott IC, Sepulveda-Jauregui A, Anthony KW, Thalasso F, Leigh MB. Anaerobic oxidation of methane by aerobic methanotrophs in sub-Arctic lake sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:23-31. [PMID: 28686892 DOI: 10.1016/j.scitotenv.2017.06.187] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 06/20/2017] [Accepted: 06/22/2017] [Indexed: 05/25/2023]
Abstract
Anaerobic oxidation of methane (AOM) is a biological process that plays an important role in reducing the CH4 emissions from a wide range of ecosystems. Arctic and sub-Arctic lakes are recognized as significant contributors to global methane (CH4) emission, since CH4 production is increasing as permafrost thaws and provides fuels for methanogenesis. Methanotrophy, including AOM, is critical to reducing CH4 emissions. The identity, activity, and metabolic processes of anaerobic methane oxidizers are poorly understood, yet this information is critical to understanding CH4 cycling and ultimately to predicting future CH4 emissions. This study sought to identify the microorganisms involved in AOM in sub-Arctic lake sediments using DNA- and phospholipid-fatty acid (PLFA)- based stable isotope probing. Results indicated that aerobic methanotrophs belonging to the genus Methylobacter assimilate carbon from CH4, either directly or indirectly. Other organisms that were found, in minor proportions, to assimilate CH4-derived carbon were methylotrophs and iron reducers, which might indicate the flow of CH4-derived carbon from anaerobic methanotrophs into the broader microbial community. While various other taxa have been reported in the literature to anaerobically oxidize methane in various environments (e.g. ANME-type archaea and Methylomirabilis Oxyfera), this report directly suggest that Methylobacter can perform this function, expanding our understanding of CH4 oxidation in anaerobic lake sediments.
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Affiliation(s)
- Karla Martinez-Cruz
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA; Biotechnology and Bioengineering Department, Cinvestav, 2508 IPN Av, 07360, Mexico City, Mexico.
| | - Mary-Cathrine Leewis
- Institute of Arctic Biology, University of Alaska Fairbanks, 930 N Koyukuk Dr, 99775Fairbanks, AK, USA.
| | - Ian Charold Herriott
- Institute of Arctic Biology, University of Alaska Fairbanks, 930 N Koyukuk Dr, 99775Fairbanks, AK, USA.
| | - Armando Sepulveda-Jauregui
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA.
| | - Katey Walter Anthony
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA.
| | - Frederic Thalasso
- Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, 306 Tanana Loop, 99775 Fairbanks, AK, USA; Biotechnology and Bioengineering Department, Cinvestav, 2508 IPN Av, 07360, Mexico City, Mexico.
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, 930 N Koyukuk Dr, 99775Fairbanks, AK, USA.
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22
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Quorum Sensing in a Methane-Oxidizing Bacterium. J Bacteriol 2017; 199:JB.00773-16. [PMID: 27994019 DOI: 10.1128/jb.00773-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/15/2016] [Indexed: 12/12/2022] Open
Abstract
Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Dissecting the molecular details of how these organisms interact in the environment may increase our understanding of how they perform this important ecological role. Many bacterial species use quorum sensing (QS) systems to regulate gene expression in a cell density-dependent manner. We have identified a QS system in the genome of Methylobacter tundripaludum, a dominant methane oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA). We determined that M. tundripaludum produces primarily N-3-hydroxydecanoyl-l-homoserine lactone (3-OH-C10-HSL) and that its production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by QS in this methane oxidizer using transcriptome sequencing (RNA-seq) and discovered that this system regulates the expression of a putative nonribosomal peptide synthetase biosynthetic gene cluster. Finally, we detected an extracellular factor that is produced by M. tundripaludum in a QS-dependent manner. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium.IMPORTANCE Aerobic methanotrophs are critical for sequestering carbon from the potent greenhouse gas methane in the environment, yet the mechanistic details of chemical interactions in methane-oxidizing bacterial communities are not well understood. Understanding these interactions is important in order to maintain, and potentially optimize, the functional potential of the bacteria that perform this vital ecosystem function. In this work, we identify a quorum sensing system in the aerobic methanotroph Methylobacter tundripaludum and use both chemical and genetic methods to characterize this system at the molecular level.
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Zhu J, Wang Q, Yuan M, Tan GYA, Sun F, Wang C, Wu W, Lee PH. Microbiology and potential applications of aerobic methane oxidation coupled to denitrification (AME-D) process: A review. WATER RESEARCH 2016; 90:203-215. [PMID: 26734780 DOI: 10.1016/j.watres.2015.12.020] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/10/2015] [Accepted: 12/12/2015] [Indexed: 06/05/2023]
Abstract
Aerobic methane oxidation coupled to denitrification (AME-D) is an important link between the global methane and nitrogen cycles. This mini-review updates discoveries regarding aerobic methanotrophs and denitrifiers, as a prelude to spotlight the microbial mechanism and the potential applications of AME-D. Until recently, AME-D was thought to be accomplished by a microbial consortium where denitrifying bacteria utilize carbon intermediates, which are excreted by aerobic methanotrophs, as energy and carbon sources. Potential carbon intermediates include methanol, citrate and acetate. This mini-review presents microbial thermodynamic estimations and postulates that methanol is the ideal electron donor for denitrification, and may serve as a trophic link between methanotrophic bacteria and denitrifiers. More excitingly, new discoveries have revealed that AME-D is not only confined to the conventional synergism between methanotrophic bacteria and denitrifiers. Specifically, an obligate aerobic methanotrophic bacterium, Methylomonas denitrificans FJG1, has been demonstrated to couple partial denitrification with methane oxidation, under hypoxia conditions, releasing nitrous oxide as a terminal product. This finding not only substantially advances the understanding of AME-D mechanism, but also implies an important but unknown role of aerobic methanotrophs in global climate change through their influence on both the methane and nitrogen cycles in ecosystems. Hence, further investigation on AME-D microbiology and mechanism is essential to better understand global climate issues and to develop niche biotechnological solutions. This mini-review also presents traditional microbial techniques, such as pure cultivation and stable isotope probing, and powerful microbial techniques, such as (meta-) genomics and (meta-) transcriptomics, for deciphering linked methane oxidation and denitrification. Although AME-D has immense potential for nitrogen removal from wastewater, drinking water and groundwater, bottlenecks and potential issues are also discussed.
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Affiliation(s)
- Jing Zhu
- Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Qian Wang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Mengdong Yuan
- Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Giin-Yu Amy Tan
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Faqian Sun
- Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Cheng Wang
- Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Weixiang Wu
- Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
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24
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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: 259] [Impact Index Per Article: 28.8] [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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25
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Kits KD, Campbell DJ, Rosana AR, Stein LY. Diverse electron sources support denitrification under hypoxia in the obligate methanotroph Methylomicrobium album strain BG8. Front Microbiol 2015; 6:1072. [PMID: 26500622 PMCID: PMC4594100 DOI: 10.3389/fmicb.2015.01072] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 09/18/2015] [Indexed: 11/30/2022] Open
Abstract
Aerobic methane-oxidizing bacteria (MOB) are a diverse group of microorganisms that are ubiquitous in natural environments. Along with anaerobic MOB and archaea, aerobic methanotrophs are critical for attenuating emission of methane to the atmosphere. Clearly, nitrogen availability in the form of ammonium and nitrite have strong effects on methanotrophic activity and their natural community structures. Previous findings show that nitrite amendment inhibits the activity of some cultivated methanotrophs; however, the physiological pathways that allow some strains to transform nitrite, expression of gene inventories, as well as the electron sources that support this activity remain largely uncharacterized. Here we show that Methylomicrobium album strain BG8 utilizes methane, methanol, formaldehyde, formate, ethane, ethanol, and ammonia to support denitrification activity under hypoxia only in the presence of nitrite. We also demonstrate that transcript abundance of putative denitrification genes, nirS and one of two norB genes, increased in response to nitrite. Furthermore, we found that transcript abundance of pxmA, encoding the alpha subunit of a putative copper-containing monooxygenase, increased in response to both nitrite and hypoxia. Our results suggest that expression of denitrification genes, found widely within genomes of aerobic methanotrophs, allow the coupling of substrate oxidation to the reduction of nitrogen oxide terminal electron acceptors under oxygen limitation. The present study expands current knowledge of the metabolic flexibility of methanotrophs by revealing that a diverse array of electron donors support nitrite reduction to nitrous oxide under hypoxia.
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Affiliation(s)
- K Dimitri Kits
- Department of Biological Sciences, Faculty of Science, University of Alberta Edmonton, AB, Canada
| | - Dustin J Campbell
- Department of Biological Sciences, Faculty of Science, University of Alberta Edmonton, AB, Canada
| | - Albert R Rosana
- Department of Biological Sciences, Faculty of Science, University of Alberta Edmonton, AB, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, Faculty of Science, University of Alberta Edmonton, AB, Canada
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26
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Methylotrophs in natural habitats: current insights through metagenomics. Appl Microbiol Biotechnol 2015; 99:5763-79. [PMID: 26051673 DOI: 10.1007/s00253-015-6713-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/15/2015] [Accepted: 05/19/2015] [Indexed: 01/10/2023]
Abstract
The focus of this review is on the recent data from the omics approaches, measuring the presence of methylotrophs in natural environments. Both Bacteria and Archaea are considered. The data are discussed in the context of the current knowledge on the biochemistry of methylotrophy and the physiology of cultivated methylotrophs. One major issue discussed is the recent metagenomic data pointing toward the activity of "aerobic" methanotrophs, such as Methylobacter, in microoxic or hypoxic conditions. A related issue of the metabolic distinction between aerobic and "anaerobic" methylotrophy is addressed in the light of the genomic and metagenomic data for respective organisms. The role of communities, as opposed to single-organism activities in environmental cycling of single-carbon compounds, such as methane, is also discussed. In addition, the emerging issue of the role of non-traditional methylotrophs in global metabolism of single-carbon compounds and the role of methylotrophy pathways in non-methylotrophs is briefly mentioned.
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27
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Tveit AT, Urich T, Frenzel P, Svenning MM. Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming. Proc Natl Acad Sci U S A 2015; 112:E2507-16. [PMID: 25918393 PMCID: PMC4434766 DOI: 10.1073/pnas.1420797112] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arctic permafrost soils store large amounts of soil organic carbon (SOC) that could be released into the atmosphere as methane (CH4) in a future warmer climate. How warming affects the complex microbial network decomposing SOC is not understood. We studied CH4 production of Arctic peat soil microbiota in anoxic microcosms over a temperature gradient from 1 to 30 °C, combining metatranscriptomic, metagenomic, and targeted metabolic profiling. The CH4 production rate at 4 °C was 25% of that at 25 °C and increased rapidly with temperature, driven by fast adaptations of microbial community structure, metabolic network of SOC decomposition, and trophic interactions. Below 7 °C, syntrophic propionate oxidation was the rate-limiting step for CH4 production; above this threshold temperature, polysaccharide hydrolysis became rate limiting. This change was associated with a shift within the functional guild for syntrophic propionate oxidation, with Firmicutes being replaced by Bacteroidetes. Correspondingly, there was a shift from the formate- and H2-using Methanobacteriales to Methanomicrobiales and from the acetotrophic Methanosarcinaceae to Methanosaetaceae. Methanogenesis from methylamines, probably stemming from degradation of bacterial cells, became more important with increasing temperature and corresponded with an increased relative abundance of predatory protists of the phylum Cercozoa. We concluded that Arctic peat microbiota responds rapidly to increased temperatures by modulating metabolic and trophic interactions so that CH4 is always highly produced: The microbial community adapts through taxonomic shifts, and cascade effects of substrate availability cause replacement of functional guilds and functional changes within taxa.
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Affiliation(s)
- Alexander Tøsdal Tveit
- Department of Arctic and Marine Biology, University of Tromsø The Arctic University of Norway, 9037 Tromsø, Norway;
| | - Tim Urich
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria; Austrian Polar Research Institute, 1090, Vienna, Austria; and
| | - Peter Frenzel
- Department of Biochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Mette Marianne Svenning
- Department of Arctic and Marine Biology, University of Tromsø The Arctic University of Norway, 9037 Tromsø, Norway;
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28
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Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response. ISME JOURNAL 2014; 9:1119-29. [PMID: 25333464 DOI: 10.1038/ismej.2014.203] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 09/11/2014] [Accepted: 09/22/2014] [Indexed: 11/08/2022]
Abstract
We report observations on the dynamics of bacterial communities in response to methane stimulus in laboratory microcosm incubations prepared with lake sediment samples. We first measured taxonomic compositions of long-term enrichment cultures and determined that, although dominated by Methylococcaceae types, these cultures also contained accompanying types belonging to a limited number of bacterial taxa, methylotrophs and non-methylotrophs. We then followed the short-term community dynamics, in two oxygen tension regimens (150 μM and 15 μM), observing rapid loss of species diversity. In all microcosms, a single type of Methylobacter represented the major methane-oxidizing partner. The accompanying members of the communities revealed different trajectories in response to different oxygen tensions, with Methylotenera species being the early responders to methane stimulus under both conditions. The communities in both conditions were convergent in terms of their assemblage, suggesting selection for specific taxa. Our results support prior observations from metagenomics on distribution of carbon from methane among diverse bacterial populations and further suggest that communities are likely responsible for methane cycling, rather than a single type of microbe.
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29
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Quaiser A, Bodi X, Dufresne A, Naquin D, Francez AJ, Dheilly A, Coudouel S, Pedrot M, Vandenkoornhuyse P. Unraveling the stratification of an iron-oxidizing microbial mat by metatranscriptomics. PLoS One 2014; 9:e102561. [PMID: 25033299 PMCID: PMC4102501 DOI: 10.1371/journal.pone.0102561] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/19/2014] [Indexed: 02/02/2023] Open
Abstract
A metatranscriptomic approach was used to study community gene expression in a naturally occurring iron-rich microbial mat. Total microbial community RNA was reversely transcribed and sequenced by pyrosequencing. Characterization of expressed gene sequences provided accurate and detailed information of the composition of the transcriptionally active community and revealed phylogenetic and functional stratifications within the mat. Comparison of 16S rRNA reads and delineation of OTUs showed significantly lower values of metatranscriptomic-based richness and diversity in the upper parts of the mat than in the deeper regions. Taxonomic affiliation of rRNA sequences and mRNA genome recruitments indicated that iron-oxidizing bacteria affiliated to the genus Leptothrix, dominated the community in the upper layers of the mat. Surprisingly, type I methanotrophs contributed to the majority of the sequences in the deep layers of the mat. Analysis of mRNA expression patterns showed that genes encoding the three subunits of the particulate methane monooxygenase (pmoCAB) were the most highly expressed in our dataset. These results provide strong hints that iron-oxidation and methane-oxidation occur simultaneously in microbial mats and that both groups of microorganisms are major players in the functioning of this ecosystem.
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Affiliation(s)
- Achim Quaiser
- Université de Rennes 1, CNRS UMR6553 EcoBio, Rennes, France
- * E-mail:
| | - Xavier Bodi
- Université de Rennes 1, CNRS UMR6553 EcoBio, Rennes, France
| | | | - Delphine Naquin
- CNRS FRC3115 Centre de Recherches de Gif-sur-Yvette, Gif sur Yvette, France
| | | | - Alexandra Dheilly
- Université de Rennes 1, CNRS UMS3343 OSUR, Plateforme génomique environnementale et fonctionnelle, Rennes, France
| | - Sophie Coudouel
- Université de Rennes 1, CNRS UMS3343 OSUR, Plateforme génomique environnementale et fonctionnelle, Rennes, France
| | - Mathieu Pedrot
- Université de Rennes 1, CNRS UMR6118 Géosciences, Rennes, France
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Abstract
Recent advances in meta-omics and particularly metatranscriptomic approaches have enabled detailed studies of the structure and function of microbial communities in many ecosystems. Molecular analyses of peat soils, ecosystems important to the global carbon balance, are still challenging due to the presence of coextracted substances that inhibit enzymes used in downstream applications. We sampled layers at different depths from two high-Arctic peat soils in Svalbard for metatranscriptome preparation. Here we show that enzyme inhibition in the preparation of metatranscriptomic libraries can be circumvented by linear amplification of diluted template RNA. A comparative analysis of mRNA-enriched and nonenriched metatranscriptomes showed that mRNA enrichment resulted in a 2-fold increase in the relative abundance of mRNA but biased the relative distribution of mRNA. The relative abundance of transcripts for cellulose degradation decreased with depth, while the transcripts for hemicellulose debranching increased, indicating that the polysaccharide composition of the peat was different in the deeper and older layers. Taxonomic annotation revealed that Actinobacteria and Bacteroidetes were the dominating polysaccharide decomposers. The relative abundances of 16S rRNA and mRNA transcripts of methanogenic Archaea increased substantially with depth. Acetoclastic methanogenesis was the dominating pathway, followed by methanogenesis from formate. The relative abundances of 16S rRNA and mRNA assigned to the methanotrophic Methylococcaceae, primarily Methylobacter, increased with depth. In conclusion, linear amplification of total RNA and deep sequencing constituted the preferred method for metatranscriptomic preparation to enable high-resolution functional and taxonomic analyses of the active microbiota in Arctic peat soil.
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31
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Johnson KA, Ve T, Larsen Ø, Pedersen RB, Lillehaug JR, Jensen HB, Helland R, Karlsen OA. CorA is a copper repressible surface-associated copper(I)-binding protein produced in Methylomicrobium album BG8. PLoS One 2014; 9:e87750. [PMID: 24498370 PMCID: PMC3912023 DOI: 10.1371/journal.pone.0087750] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 12/30/2013] [Indexed: 11/18/2022] Open
Abstract
CorA is a copper repressible protein previously identified in the methanotrophic bacterium Methylomicrobium album BG8. In this work, we demonstrate that CorA is located on the cell surface and binds one copper ion per protein molecule, which, based on X-ray Absorption Near Edge Structure analysis, is in the reduced state (Cu(I)). The structure of endogenously expressed CorA was solved using X-ray crystallography. The 1.6 Å three-dimensional structure confirmed the binding of copper and revealed that the copper atom was coordinated in a mononuclear binding site defined by two histidines, one water molecule, and the tryptophan metabolite, kynurenine. This arrangement of the copper-binding site is similar to that of its homologous protein MopE* from Metylococcus capsulatus Bath, confirming the importance of kynurenine for copper binding in these proteins. Our findings show that CorA has an overall fold similar to MopE, including the unique copper(I)-binding site and most of the secondary structure elements. We suggest that CorA plays a role in the M. album BG8 copper acquisition.
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Affiliation(s)
- Kenneth A. Johnson
- Norwegian Structural Biology Centre, Faculty of Science, University of Tromsø, Tromsø, Norway
| | - Thomas Ve
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Øivind Larsen
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Rolf B. Pedersen
- Department of Earth Science - Centre for Geobiology, University of Bergen, Bergen, Norway
| | | | - Harald B. Jensen
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Ronny Helland
- Norwegian Structural Biology Centre, Faculty of Science, University of Tromsø, Tromsø, Norway
| | - Odd A. Karlsen
- Department of Molecular Biology, University of Bergen, Bergen, Norway
- * E-mail:
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32
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刘 建. The Application of High-Throughput Sequencing Technologies in the Research of Wetland Microbiology. INTERNATIONAL JOURNAL OF ECOLOGY 2014. [DOI: 10.12677/ije.2014.34009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Urich T, Lanzén A, Stokke R, Pedersen RB, Bayer C, Thorseth IH, Schleper C, Steen IH, Øvreas L. Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics. Environ Microbiol 2013; 16:2699-710. [DOI: 10.1111/1462-2920.12283] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 08/23/2013] [Accepted: 09/09/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Tim Urich
- Division of Archaea Biology and Ecogenomics; Department of Ecogenomics and Systems Biology; University of Vienna; 1090 Vienna Austria
- Centre for Geobiology; University of Bergen; 5007 Bergen Norway
| | - Anders Lanzén
- Centre for Geobiology; University of Bergen; 5007 Bergen Norway
- Department of Biology; University of Bergen; 5020 Bergen Norway
| | - Runar Stokke
- Centre for Geobiology; University of Bergen; 5007 Bergen Norway
- Department of Biology; University of Bergen; 5020 Bergen Norway
| | | | - Christoph Bayer
- Division of Archaea Biology and Ecogenomics; Department of Ecogenomics and Systems Biology; University of Vienna; 1090 Vienna Austria
| | - Ingunn H. Thorseth
- Centre for Geobiology; University of Bergen; 5007 Bergen Norway
- Department of Earth Science; University of Bergen; 5020 Bergen Norway
| | - Christa Schleper
- Division of Archaea Biology and Ecogenomics; Department of Ecogenomics and Systems Biology; University of Vienna; 1090 Vienna Austria
- Centre for Geobiology; University of Bergen; 5007 Bergen Norway
| | - Ida H. Steen
- Centre for Geobiology; University of Bergen; 5007 Bergen Norway
- Department of Biology; University of Bergen; 5020 Bergen Norway
| | - Lise Øvreas
- Centre for Geobiology; University of Bergen; 5007 Bergen Norway
- Department of Biology; University of Bergen; 5020 Bergen Norway
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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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35
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Dumont MG, Pommerenke B, Casper P. Using stable isotope probing to obtain a targeted metatranscriptome of aerobic methanotrophs in lake sediment. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:757-764. [PMID: 24115627 DOI: 10.1111/1758-2229.12078] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 04/23/2013] [Accepted: 06/19/2013] [Indexed: 06/02/2023]
Abstract
In this study, we demonstrate the possibility of obtaining a targeted metatranscriptome from a functional group of microorganisms using a stable isotope probing (SIP) approach. Methanotrophs in lake sediment were labelled using (13)CH4, and both labelled and unlabelled-RNA were isolated and sequenced by 454 pyrosequencing. The unlabelled metatranscriptome had a large diversity of bacterial, archaeal, eukaryotic and viral sequences as expected from a diverse sediment community. In contrast, the labelled-RNA metatranscriptome was dominated by methanotroph sequences, particularly from Methylococcaceae. Transcripts of the methane monooxygenase genes pmoCAB were the most abundant in this metatranscriptome, and the pathway of methane oxidation to CO2 could be traced, as well as many steps in the ribulose monophosphate pathway for carbon assimilation. A high abundance of mRNA transcripts for proteins related to motility was detected, suggesting an importance for methanotrophs in lake sediments. This combination of SIP and metatranscriptomics should be broadly applicable, and will enhance the detection and identification of mRNA from target organisms.
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Affiliation(s)
- Marc G Dumont
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany
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36
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Rivers AR, Sharma S, Tringe SG, Martin J, Joye SB, Moran MA. Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. ISME JOURNAL 2013; 7:2315-29. [PMID: 23902988 DOI: 10.1038/ismej.2013.129] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 06/29/2013] [Accepted: 07/01/2013] [Indexed: 02/01/2023]
Abstract
The Deepwater Horizon blowout released a massive amount of oil and gas into the deep ocean between April and July 2010, stimulating microbial blooms of petroleum-degrading bacteria. To understand the metabolic response of marine microorganisms, we sequenced ≈ 66 million community transcripts that revealed the identity of metabolically active microbes and their roles in petroleum consumption. Reads were assigned to reference genes from ≈ 2700 bacterial and archaeal taxa, but most assignments (39%) were to just six genomes representing predominantly methane- and petroleum-degrading Gammaproteobacteria. Specific pathways for the degradation of alkanes, aromatic compounds and methane emerged from the metatranscriptomes, with some transcripts assigned to methane monooxygenases representing highly divergent homologs that may degrade either methane or short alkanes. The microbial community in the plume was less taxonomically and functionally diverse than the unexposed community below the plume; this was due primarily to decreased species evenness resulting from Gammaproteobacteria blooms. Surprisingly, a number of taxa (related to SAR11, Nitrosopumilus and Bacteroides, among others) contributed equal numbers of transcripts per liter in both the unexposed and plume samples, suggesting that some groups were unaffected by the petroleum inputs and blooms of degrader taxa, and may be important for re-establishing the pre-spill microbial community structure.
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Affiliation(s)
- Adam R Rivers
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
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37
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Li M, Jain S, Baker BJ, Taylor C, Dick GJ. Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume. Environ Microbiol 2013; 16:60-71. [PMID: 23826624 DOI: 10.1111/1462-2920.12182] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 05/10/2013] [Accepted: 06/03/2013] [Indexed: 12/30/2022]
Abstract
Particulate membrane-associated hydrocarbon monooxygenases (pHMOs) are critical components of the aerobic degradation pathway for low molecular weight hydrocarbons, including the potent greenhouse gas methane. Here, we analysed pHMO gene diversity in metagenomes and metatranscriptomes of hydrocarbon-rich hydrothermal plumes in the Guaymas Basin (GB) and nearby background waters in the deep Gulf of California. Seven distinct phylogenetic groups of pHMO were present and transcriptionally active in both plume and background waters, including several that are undetectable with currently available polymerase chain reaction (PCR) primers. The seven groups of pHMOs included those related to a putative ethane oxidizing Methylococcaceae-like group, a group of the SAR324 Deltaproteobacteria, three deep-sea clades (Deep sea-1/symbiont-like, Deep sea-2/PS-80 and Deep sea-3/OPU3) within gammaproteobacterial methanotrophs, one clade related to Group Z and one unknown group. Differential abundance of pHMO gene transcripts in plume and background suggests niche differentiation between groups. Corresponding 16S rRNA genes reflected similar phylogenetic and transcriptomic abundance trends. The novelty of transcriptionally active pHMOs we recovered from a hydrocarbon-rich hydrothermal plume suggests there are significant gaps in our knowledge of the diversity and function of these enzymes in the environment.
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Affiliation(s)
- Meng Li
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
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38
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Khmelenina VN, Beck DAC, Munk C, Davenport K, Daligault H, Erkkila T, Goodwin L, Gu W, Lo CC, Scholz M, Teshima H, Xu Y, Chain P, Bringel F, Vuilleumier S, DiSpirito A, Dunfield P, Jetten MSM, Klotz MG, Knief C, Murrell JC, Op den Camp HJM, Sakai Y, Semrau J, Svenning M, Stein LY, Trotsenko YA, Kalyuzhnaya MG. Draft Genome Sequence of Methylomicrobium buryatense Strain 5G, a Haloalkaline-Tolerant Methanotrophic Bacterium. GENOME ANNOUNCEMENTS 2013; 1:e00053-13. [PMID: 23814105 PMCID: PMC3695433 DOI: 10.1128/genomea.00053-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/08/2013] [Indexed: 11/20/2022]
Abstract
Robust growth of the gammaproteobacterium Methylomicrobium buryatense strain 5G on methane makes it an attractive system for CH4-based biocatalysis. Here we present a draft genome sequence of the strain that will provide a valuable framework for metabolic engineering of the core pathways for the production of valuable chemicals from methane.
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Affiliation(s)
- Valentina N. Khmelenina
- GK Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - David A. C. Beck
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- eScience Institute, University of Washington, Seattle, Washington, USA
| | - Christine Munk
- Los Alamos National Laboratory, Joint Genome Institute, Biosciences Division Genome Science B6, Los Alamos, New Mexico, USA
| | - Karen Davenport
- Los Alamos National Laboratory, Joint Genome Institute, Biosciences Division Genome Science B6, Los Alamos, New Mexico, USA
| | - Hajnalka Daligault
- Los Alamos National Laboratory, Joint Genome Institute, Biosciences Division Genome Science B6, Los Alamos, New Mexico, USA
| | - Tracy Erkkila
- Los Alamos National Laboratory, Joint Genome Institute, Biosciences Division Genome Science B6, Los Alamos, New Mexico, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Joint Genome Institute, Biosciences Division Genome Science B6, Los Alamos, New Mexico, USA
| | - Wei Gu
- Los Alamos National Laboratory, Joint Genome Institute, Biosciences Division Genome Science B6, Los Alamos, New Mexico, USA
| | - Chien-Chi Lo
- Los Alamos National Laboratory, Joint Genome Institute, Biosciences Division Genome Science B6, Los Alamos, New Mexico, USA
| | - Matthew Scholz
- Los Alamos National Laboratory, Joint Genome Institute, Biosciences Division Genome Science B6, Los Alamos, New Mexico, USA
| | - Hazuki Teshima
- Los Alamos National Laboratory, Joint Genome Institute, Biosciences Division Genome Science B6, Los Alamos, New Mexico, USA
| | - Yan Xu
- Los Alamos National Laboratory, Joint Genome Institute, Biosciences Division Genome Science B6, Los Alamos, New Mexico, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Joint Genome Institute, Biosciences Division Genome Science B6, Los Alamos, New Mexico, USA
| | - Francoise Bringel
- Equipe Adaptations et Interactions Microbiennes dans l’Environnement, UMR 7156 UdS–CNRS Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, Strasbourg, France
| | - Stéphane Vuilleumier
- Equipe Adaptations et Interactions Microbiennes dans l’Environnement, UMR 7156 UdS–CNRS Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, Strasbourg, France
| | - Alan DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Peter Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Mike S. M. Jetten
- Department of Microbiology, Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Martin G. Klotz
- Department of Biology, University of North Carolina, Charlotte, North Carolina, USA
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation–Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Huub J. M. Op den Camp
- Department of Microbiology, Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Jeremy Semrau
- Department of Civil & Environmental Engineering, the University of Michigan, Ann Arbor, Michigan, USA
| | - Mette Svenning
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø, Norway
| | - Lisa Y. Stein
- OMeGA, the Organization for Methanotrophic Genome Analysis, Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Yuri A. Trotsenko
- GK Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
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Ho A, Kerckhof FM, Luke C, Reim A, Krause S, Boon N, Bodelier PLE. Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:335-45. [PMID: 23754714 DOI: 10.1111/j.1758-2229.2012.00370.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/06/2012] [Accepted: 07/15/2012] [Indexed: 05/11/2023]
Abstract
Methane-oxidizing bacteria (MOB) possess the ability to use methane for energy generation and growth, thereby, providing a key ecosystem service that is highly relevant to the regulation of the global climate. MOB subgroups have different responses to key environmental controls, reflecting on their functional traits. Their unique features (C1-metabolism, unique lipids and congruence between the 16S rRNA and pmoA gene phylogeny) have facilitated numerous environmental studies, which in combination with the availability of cultured representatives, yield the most comprehensive ecological picture of any known microbial functional guild. Here, we focus on the broad MOB subgroups (type I and type II MOB), and aim to conceptualize MOB functional traits and observational characteristics derived primarily from these environmental studies to be interpreted as microbial life strategies. We focus on the functional traits, and the conditions under which these traits will render different MOB subgroups a selective advantage. We hypothesize that type I and type II MOB generally have distinct life strategies, enabling them to predominate under different conditions and maintain functionality. The ecological characteristics implicated in their adopted life strategies are discussed, and incorporated into the Competitor-Stress tolerator-Ruderal functional classification framework as put forward for plant communities. In this context, type I MOB can broadly be classified as competitor-ruderal while type II MOB fit more within the stress tolerator categories. Finally, we provide an outlook on MOB applications by exemplifying two approaches where their inferred life strategies could be exploited thereby, putting MOB into the context of microbial resource management.
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Affiliation(s)
- Adrian Ho
- Laboratory of Microbial Ecology and Technology (LabMET), Faculty of Bioscience Engineering, Coupure Links 653, B-9000 Ghent, Belgium
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40
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Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8. GENOME ANNOUNCEMENTS 2013; 1:e0017013. [PMID: 23580712 PMCID: PMC3624686 DOI: 10.1128/genomea.00170-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The complete genome sequence of Methylomicrobium album strain BG8, a methane-oxidizing gammaproteobacterium isolated from freshwater, is reported. Aside from a conserved inventory of genes for growth on single-carbon compounds, M. album BG8 carries a range of gene inventories for additional carbon and nitrogen transformations but no genes for growth on multicarbon substrates or for N fixation.
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41
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Beck DAC, Kalyuzhnaya MG, Malfatti S, Tringe SG, Glavina Del Rio T, Ivanova N, Lidstrom ME, Chistoserdova L. A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae. PeerJ 2013; 1:e23. [PMID: 23638358 PMCID: PMC3628875 DOI: 10.7717/peerj.23] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 01/09/2013] [Indexed: 11/20/2022] Open
Abstract
We investigated microbial communities active in methane oxidation in lake sediment at different oxygen tensions and their response to the addition of nitrate, via stable isotope probing combined with deep metagenomic sequencing. Communities from a total of four manipulated microcosms were analyzed, supplied with 13C-methane in, respectively, ambient air, ambient air with the addition of nitrate, nitrogen atmosphere and nitrogen atmosphere with the addition of nitrate, and these were compared to the community from an unamended sediment sample. We found that the major group involved in methane oxidation in both aerobic and microaerobic conditions were members of the family Methylococcaceae, dominated by species of the genus Methylobacter, and these were stimulated by nitrate in aerobic but not microaerobic conditions. In aerobic conditions, we also noted a pronounced response to both methane and nitrate by members of the family Methylophilaceae that are non-methane-oxidizing methylotrophs, and predominantly by the members of the genus Methylotenera. The relevant abundances of the Methylococcaceae and the Methylophilaceae and their coordinated response to methane and nitrate suggest that these species may be engaged in cooperative behavior, the nature of which remains unknown.
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Affiliation(s)
- David A C Beck
- Department of Chemical Engineering and eScience Institute, University of Washington , Seattle, WA , USA
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42
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Abstract
Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria, organisms that live on methane gas as their sole carbon source. Understanding pMMO function has important implications for bioremediation applications and for the development of new, environmentally friendly catalysts for the direct conversion of methane to methanol. Crystal structures of pMMOs from three different methanotrophs reveal a trimeric architecture, consisting of three copies each of the pmoB, pmoA, and pmoC subunits. There are three distinct metal centers in each protomer of the trimer, mononuclear and dinuclear copper sites in the periplasmic regions of pmoB and a mononuclear site within the membrane that can be occupied by copper or zinc. Various models for the pMMO active site have been proposed within these structural constraints, including dicopper, tricopper, and diiron centers. Biochemical and spectroscopic data on pMMO and recombinant soluble fragments, denoted spmoB proteins, indicate that the active site involves copper and is located at the site of the dicopper center in the pmoB subunit. Initial spectroscopic evidence for O(2) binding at this site has been obtained. Despite these findings, questions remain about the active site identity and nuclearity and will be the focus of future studies.
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Affiliation(s)
- Megen A. Culpepper
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA
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43
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Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms. ISME JOURNAL 2012; 7:299-311. [PMID: 22955232 PMCID: PMC3554415 DOI: 10.1038/ismej.2012.99] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A substantial part of the Earths' soil organic carbon (SOC) is stored in Arctic permafrost peatlands, which represent large potential sources for increased emissions of the greenhouse gases CH4 and CO2 in a warming climate. The microbial communities and their genetic repertoire involved in the breakdown and mineralisation of SOC in these soils are, however, poorly understood. In this study, we applied a combined metagenomic and metatranscriptomic approach on two Arctic peat soils to investigate the identity and the gene pool of the microbiota driving the SOC degradation in the seasonally thawed active layers. A large and diverse set of genes encoding plant polymer-degrading enzymes was found, comparable to microbiotas from temperate and subtropical soils. This indicates that the metabolic potential for SOC degradation in Arctic peat is not different from that of other climatic zones. The majority of these genes were assigned to three bacterial phyla, Actinobacteria, Verrucomicrobia and Bacteroidetes. Anaerobic metabolic pathways and the fraction of methanogenic archaea increased with peat depth, evident for a gradual transition from aerobic to anaerobic lifestyles. A population of CH4-oxidising bacteria closely related to Methylobacter tundripaludum was the dominating active group of methanotrophs. Based on the in-depth characterisation of the microbes and their genes, we conclude that these Arctic peat soils will turn into CO2 sources owing to increased active layer depth and prolonged growing season. However, the extent of future CH4 emissions will critically depend on the response of the methanotrophic bacteria.
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Complete sequence analysis of two methanotroph-specific repABC-containing plasmids from Methylocystis sp. strain SC2. Appl Environ Microbiol 2012; 78:4373-9. [PMID: 22504811 DOI: 10.1128/aem.00628-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete nucleotide sequences of two large, low-copy-number plasmids of 229.6 kb (pBSC2-1) and 143.5 kb (pBSC2-2) were determined during assembly of the whole-genome shotgun sequences of the methane-oxidizing bacterium Methylocystis sp. strain SC2. The physical existence of the two plasmids in strain SC2 was confirmed by pulsed-field gel electrophoresis followed by Southern hybridization. Both plasmids have a conserved replication module of the repABC system and carry genes involved in their faithful maintenance and conjugation. In addition, they contain genes that might be involved in essential metabolic processes. These include several heavy metal resistance genes and copper transport genes in pBSC2-1 and a complete nitrous oxide reductase operon and a pmoC singleton in pBSC2-2, the latter encoding the PmoC subunit of particulate methane monooxygenase.
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45
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Vuilleumier S, Khmelenina VN, Bringel F, Reshetnikov AS, Lajus A, Mangenot S, Rouy Z, Op den Camp HJM, Jetten MSM, Dispirito AA, Dunfield P, Klotz MG, Semrau JD, Stein LY, Barbe V, Médigue C, Trotsenko YA, Kalyuzhnaya MG. Genome sequence of the haloalkaliphilic methanotrophic bacterium Methylomicrobium alcaliphilum 20Z. J Bacteriol 2012; 194:551-2. [PMID: 22207753 PMCID: PMC3256673 DOI: 10.1128/jb.06392-11] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 10/21/2011] [Indexed: 11/20/2022] Open
Abstract
Methylomicrobium strains are widespread in saline environments. Here, we report the complete genome sequence of Methylomicrobium alcaliphilum 20Z, a haloalkaliphilic methanotrophic bacterium, which will provide the basis for detailed characterization of the core pathways of both single-carbon metabolism and responses to osmotic and high-pH stresses. Final assembly of the genome sequence revealed that this bacterium contains a 128-kb plasmid, making M. alcaliphilum 20Z the first methanotrophic bacterium of known genome sequence for which a plasmid has been reported.
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Affiliation(s)
- Stéphane Vuilleumier
- Équipe Adaptations et Interactions Microbiennes dans l’Environnement, Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France
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46
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Nelson OW, Garrity GM. Genome sequences published outside of Standards in Genomic Sciences, October – November 2011. Stand Genomic Sci 2011. [DOI: 10.4056/sigs.2404675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Oranmiyan W. Nelson
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| | - George M. Garrity
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
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