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Grégoire DS, George NA, Hug LA. Microbial methane cycling in a landfill on a decadal time scale. Nat Commun 2023; 14:7402. [PMID: 37973978 PMCID: PMC10654671 DOI: 10.1038/s41467-023-43129-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Landfills generate outsized environmental footprints due to microbial degradation of organic matter in municipal solid waste, which produces the potent greenhouse gas methane. With global solid waste production predicted to increase substantially in the next few decades, there is a pressing need to better understand the temporal dynamics of biogeochemical processes that control methane cycling in landfills. Here, we use metagenomic approaches to characterize microbial methane cycling in waste that was landfilled over 39 years. Our analyses indicate that newer waste supports more diverse communities with similar composition compared to older waste, which contains lower diversity and more varied communities. Older waste contains primarily autotrophic organisms with versatile redox metabolisms, whereas newer waste is dominated by anaerobic fermenters. Methane-producing microbes are more abundant, diverse, and metabolically versatile in new waste compared to old waste. Our findings indicate that predictive models for methane emission in landfills overlook methane oxidation in the absence of oxygen, as well as certain microbial lineages that can potentially contribute to methane sinks in diverse habitats.
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Affiliation(s)
- Daniel S Grégoire
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
- Department of Chemistry, Carleton University, Ottawa, ON, K1S 5B6, Canada.
| | - Nikhil A George
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
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2
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Altshuler I, Raymond-Bouchard I, Magnuson E, Tremblay J, Greer CW, Whyte LG. Unique high Arctic methane metabolizing community revealed through in situ 13CH 4-DNA-SIP enrichment in concert with genome binning. Sci Rep 2022; 12:1160. [PMID: 35064149 PMCID: PMC8782848 DOI: 10.1038/s41598-021-04486-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy 13CH4 (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH4 metabolism in these high Arctic cryosols. Sequencing of 13C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-13C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and characterizing novel organisms related to specific microbial functions or biogeochemical cycles of interest. Our findings reveal a unique and active Arctic cryosol microbial community potentially involved in CH4 cycling.
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Affiliation(s)
- Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada.
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences NMBU, Universitetstunet 3, 1430, Ås, Norway.
| | - Isabelle Raymond-Bouchard
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
| | - Elisse Magnuson
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
| | - Julien Tremblay
- Energy, Mining and Environment Research Centre, National Research Council of Canada, 6100 Royalmount Ave., Montreal, QC, H4P 2R2, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
- Energy, Mining and Environment Research Centre, National Research Council of Canada, 6100 Royalmount Ave., Montreal, QC, H4P 2R2, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
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Adapting Macroecology to Microbiology: Using Occupancy Modeling To Assess Functional Profiles across Metagenomes. mSystems 2021; 6:e0079021. [PMID: 34874772 PMCID: PMC8651082 DOI: 10.1128/msystems.00790-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Metagenomic sequencing provides information on the metabolic capacities and taxonomic affiliations for members of a microbial community. When assessing metabolic functions in a community, missing genes in pathways can occur in two ways; the genes may legitimately be missing from the community whose DNA was sequenced, or the genes were missed during shotgun sequencing or failed to assemble, and thus the metabolic capacity of interest is wrongly absent from the sequence data. Here, we borrow and adapt occupancy modeling from macroecology to provide mathematical context to metabolic predictions from metagenomes. We review the five assumptions underlying occupancy modeling through the lens of microbial community sequence data. Using the methane cycle, we apply occupancy modeling to examine the presence and absence of methanogenesis and methanotrophy genes from nearly 10,000 metagenomes spanning global environments. We determine that methanogenesis and methanotrophy are positively correlated across environments, providing a predictive framework for assessing gene absences for these functions. We present this adaptation of macroecology’s occupancy modeling to metagenomics as a tool to quantify the uncertainty in predictions of the presence/absence of traits in environmental microbiological surveys. We further initiate a call for stronger metadata standards to accompany metagenome deposition, to enable robust statistical approaches in the future. IMPORTANCE Metagenomics is maturing rapidly as a field but is hampered by a lack of available statistical tools. A primary area of uncertainty is around missing genes or functions from a metagenomic data set. Here, we borrow an established modeling approach from macroecology and adapt it to metagenomic data sets. Rather than multiple sampling trips to a specific area to detect a species of interest (e.g., identifying a cardinal in a forest), we leverage the enormous amount of information within a metagenome and use multiple gene markers for a function of interest (e.g., subunits of an enzyme complex). We applied our adapted occupancy modeling to a case study examining methane cycling capacity. Our models show methanogens and methanotrophs are both more likely to cooccur than be present in the absence of the other guild. The lack of consistent and complete metadata is a significant hurdle for increasing the statistical rigor of metagenomic analyses.
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Liu D, Yang Y, Ai J, Li Y, Xing Y, Li J. Research on microbial structures, functions and metabolic pathways in an advanced denitrification system coupled with aerobic methane oxidation based on metagenomics. BIORESOURCE TECHNOLOGY 2021; 332:125047. [PMID: 33839509 DOI: 10.1016/j.biortech.2021.125047] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Methanotrophs can oxidize methane as the sole carbon and energy, and the resulting intermediate products can be simultaneously utilized by coexistent denitrifying bacteria to remove the nitrogen, which named Aerobic Methane Oxidation Coupled to Denitrification (AME-D). In this paper, an AME-D system was built in an improved denitrification bio-filter, to analyze the nitrogen removal efficiency and mechanism. The maximum TN removal rate reached 95.05%. As shown in Raman spectroscopy, in the effluent wave crests generated by the symmetric expansion and contraction of NO3- disappeared, and the distortion of olefin CH2 and C-OH stretching of alcohols appeared. Metagenomics revealed Methylotenera and Methylobacter were the dominated methanotrophs. There was a completed methane and nitrogen metabolism pathway with the synergism of nxrAB, narGHI, nasAB, pmo-amoABC and mmo genes. Dissimilatory reduction pathway was the primary nitrate removal pathway. Moreover, Bradyrhizobium could participate in methane and nitrogen metabolism simultaneously.
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Affiliation(s)
- Dengping Liu
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China
| | - Yanan Yang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; Sinopec Great Wall Energy and Chemical (Guizhou) Co., LTD, Zhijin, Guizhou 552100, China
| | - Jia Ai
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China
| | - Yancheng Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, Guizhou 550025, China.
| | - Yi Xing
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing 100083, China
| | - Jiang Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, Guizhou 550025, China
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5
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Murphy CL, Sheremet A, Dunfield PF, Spear JR, Stepanauskas R, Woyke T, Elshahed MS, Youssef NH. Genomic Analysis of the Yet-Uncultured Binatota Reveals Broad Methylotrophic, Alkane-Degradation, and Pigment Production Capacities. mBio 2021; 12:e00985-21. [PMID: 34006650 PMCID: PMC8262859 DOI: 10.1128/mbio.00985-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 01/18/2023] Open
Abstract
The recent leveraging of genome-resolved metagenomics has generated an enormous number of genomes from novel uncultured microbial lineages yet left many clades undescribed. Here, we present a global analysis of genomes belonging to Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. All orders in Binatota encoded the capacity for aerobic methylotrophy using methanol, methylamine, sulfomethanes, and chloromethanes as the substrates. Methylotrophy in Binatota was characterized by order-specific substrate degradation preferences, as well as extensive metabolic versatility, i.e., the utilization of diverse sets of genes, pathways, and combinations to achieve a specific metabolic goal. The genomes also encoded multiple alkane hydroxylases and monooxygenases, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids (lycopene, β- and γ-carotenes, xanthins, chlorobactenes, and spheroidenes) production. Further, the majority of genes involved in bacteriochlorophyll a, c, and d biosynthesis were identified, although absence of key genes and failure to identify a photosynthetic reaction center preclude proposing phototrophic capacities. Analysis of 16S rRNA databases showed the preferences of Binatota to terrestrial and freshwater ecosystems, hydrocarbon-rich habitats, and sponges, supporting their potential role in mitigating methanol and methane emissions, breakdown of alkanes, and their association with sponges. Our results expand the lists of methylotrophic, aerobic alkane-degrading, and pigment-producing lineages. We also highlight the consistent encountering of incomplete biosynthetic pathways in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion.IMPORTANCE A wide range of microbial lineages remain uncultured, yet little is known regarding their metabolic capacities, physiological preferences, and ecological roles in various ecosystems. We conducted a thorough comparative genomic analysis of 108 genomes belonging to the Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. We present evidence that members of the order Binatota specialize in methylotrophy and identify an extensive repertoire of genes and pathways mediating the oxidation of multiple one-carbon (C1) compounds in Binatota genomes. The occurrence of multiple alkane hydroxylases and monooxygenases in these genomes was also identified, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids production. We also report on the presence of incomplete chlorophyll biosynthetic pathways in all genomes and propose several evolutionary-grounded scenarios that could explain such a pattern. Assessment of the ecological distribution patterns of the Binatota indicates preference of its members to terrestrial and freshwater ecosystems characterized by high methane and methanol emissions, as well as multiple hydrocarbon-rich habitats and marine sponges.
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Affiliation(s)
- Chelsea L Murphy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Andriy Sheremet
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - John R Spear
- Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | | | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkley, California, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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6
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Marsh WS, Heise BW, Krzmarzick MJ, Murdoch RW, Fathepure BZ. Isolation and characterization of a halophilic Modicisalibacter sp. strain Wilcox from produced water. Sci Rep 2021; 11:6943. [PMID: 33767228 PMCID: PMC7994583 DOI: 10.1038/s41598-021-86196-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/05/2021] [Indexed: 12/11/2022] Open
Abstract
We report the isolation a halophilic bacterium that degrades both aromatic and aliphatic hydrocarbons as the sole sources of carbon at high salinity from produced water. Phylogenetic analysis of 16S rRNA-gene sequences shows the isolate is a close relative of Modicisalibacter tunisiensis isolated from an oil-field water in Tunisia. We designate our isolate as Modicisalibacter sp. strain Wilcox. Genome analysis of strain Wilcox revealed the presence of a repertoire of genes involved in the metabolism of aliphatic and aromatic hydrocarbons. Laboratory culture studies corroborated the predicted hydrocarbon degradation potential. The strain degraded benzene, toluene, ethylbenzene, and xylenes at salinities ranging from 0.016 to 4.0 M NaCl, with optimal degradation at 1 M NaCl. Also, the strain degraded phenol, benzoate, biphenyl and phenylacetate as the sole sources of carbon at 2.5 M NaCl. Among aliphatic compounds, the strain degraded n-decane and n-hexadecane as the sole sources of carbon at 2.5 M NaCl. Genome analysis also predicted the presence of many heavy metal resistance genes including genes for metal efflux pumps, transport proteins, and enzymatic detoxification. Overall, due to its ability to degrade many hydrocarbons and withstand high salt and heavy metals, strain Wilcox may prove useful for remediation of produced waters.
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Affiliation(s)
- William S Marsh
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Brenden W Heise
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Mark J Krzmarzick
- Civil and Environmental Engineering, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Robert W Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, 37996, USA
- Battelle Memorial Institute, Columbus, OH, 43201, USA
| | - Babu Z Fathepure
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA.
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7
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Islam T, Larsen Ø, Birkeland NK. A Novel Cold-adapted Methylovulum species, with a High C16:1ω5c Content, Isolated from an Arctic Thermal Spring in Spitsbergen. Microbes Environ 2020; 35:ME20044. [PMID: 32536671 PMCID: PMC7511782 DOI: 10.1264/jsme2.me20044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/25/2020] [Indexed: 11/12/2022] Open
Abstract
A novel cold-adapted methane-oxidizing bacterium, termed TFB, was isolated from the thermoglacial Arctic karst spring, Trollosen, located in the South Spitsbergen National Park (Norway). The source water is cold and extremely low in phosphate and nitrate. The isolate belongs to the Methylovulum genus of gammaproteobacterial methanotrophs, with the closest phylogenetic affiliation with Methylovulum miyakonense and Methylovulum psychrotolerans (96.2 and 96.1% 16S rRNA gene sequence similarities, respectively). TFB is a strict aerobe that only grows in the presence of methane or methanol. It fixes atmospheric nitrogen and contains Type I intracellular membranes. The growth temperature range was 2-22°C, with an optimum at 13-18°C. The functional genes pmoA, mxaF, and nifH were identified by PCR, whereas mmoX and cbbL were not. C16:1ω5c was identified as the major fatty acid constituent, at an amount (>49%) not previously found in any methanotrophs, and is likely to play a major role in cold adaptation. Strain TFB may be regarded as a new psychrotolerant or psychrophilic species within the genus Methylovulum. The recovery of this cold-adapted bacterium from a neutral Arctic thermal spring increases our knowledge of the diversity and adaptation of extremophilic gammaproteobacterial methanotrophs in the candidate family "Methylomonadaceae".
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Affiliation(s)
- Tajul Islam
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Bergen Katedralskole, Kong Oscars gate 36, 5017 Bergen, Norway
| | - Øivind Larsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- NORCE Norwegian Research Centre AS, Bergen, Norway
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8
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A novel methanotroph in the genus Methylomonas that contains a distinct clade of soluble methane monooxygenase. J Microbiol 2017; 55:775-782. [DOI: 10.1007/s12275-017-7317-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 08/25/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
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9
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Kenney GE, Sadek M, Rosenzweig AC. Copper-responsive gene expression in the methanotroph Methylosinus trichosporium OB3b. Metallomics 2016; 8:931-40. [PMID: 27087171 PMCID: PMC6195801 DOI: 10.1039/c5mt00289c] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Methanotrophic bacteria convert methane to methanol using methane monooxygenase (MMO) enzymes. In many strains, either an iron-containing soluble (sMMO) or a copper-containing particulate (pMMO) enzyme can be produced depending on copper availability; the mechanism of this copper switch has not been elucidated. A key player in methanotroph copper homeostasis is methanobactin (Mbn), a ribosomally produced, post-translationally modified natural product with a high affinity for copper. The Mbn precursor peptide is encoded within an operon that contains a range of putative transporters, regulators, and biosynthetic proteins, but the involvement of these genes in Mbn-related processes remains unclear. Extensive time-dependent qRT-PCR studies of Methylosinus trichosporium OB3b and the constitutive sMMO-producing mutant M. trichosporium OB3b PP358 show that the Mbn operon is indeed copper-regulated, providing experimental support for its bioinformatics-based identification. Moreover, the Mbn operon is co-regulated with the sMMO operon and reciprocally regulated with the pMMO operon. Within the Mbn and sMMO operons, a subset of regulatory genes exhibits a distinct and shared pattern of expression, consistent with their proposed functions as internal regulators. In addition, genome sequencing of the M. trichosporium OB3b PP358 mutant provides new evidence for the involvement of genes adjacent to the pMMO operon in methanotroph copper homeostasis.
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Affiliation(s)
- Grace E. Kenney
- Department of Molecular Biosciences, Northwestern University, Evanston,IL 60208, USA.
| | - Monica Sadek
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences, Northwestern University, Evanston,IL 60208, USA.
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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10
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Hamilton R, Kits KD, Ramonovskaya VA, Rozova ON, Yurimoto H, Iguchi H, Khmelenina VN, Sakai Y, Dunfield PF, Klotz MG, Knief C, Op den Camp HJM, Jetten MSM, Bringel F, Vuilleumier S, Svenning MM, Shapiro N, Woyke T, Trotsenko YA, Stein LY, Kalyuzhnaya MG. Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems. GENOME ANNOUNCEMENTS 2015; 3:e00515-15. [PMID: 26044417 PMCID: PMC4457054 DOI: 10.1128/genomea.00515-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 04/23/2015] [Indexed: 11/20/2022]
Abstract
Genome sequences of Methylobacter luteus, Methylobacter whittenburyi, Methylosarcina fibrata, Methylomicrobium agile, and Methylovulum miyakonense were generated. The strains represent aerobic methanotrophs typically isolated from various terrestrial ecosystems.
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Affiliation(s)
| | - K Dimitri Kits
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Victoria A Ramonovskaya
- Department of Biology of Extremophilic Microorganisms, Institute of Microbiology and Virology of National Academy of Science, Kyiv, Ukraine
| | - Olga N Rozova
- GK Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Hiroya Yurimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Japan
| | - Hiroyuki Iguchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Japan
| | - Valentina N Khmelenina
- GK Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Japan
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Martin G Klotz
- Department of Biological Sciences, 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
| | - Huub J M Op den Camp
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Françoise Bringel
- Department of Microbiology, Genomics and the Environment, Université de Strasbourg, CNRS, Strasbourg, France
| | - Stéphane Vuilleumier
- Department of Microbiology, Genomics and the Environment, Université de Strasbourg, CNRS, Strasbourg, France
| | - Mette M Svenning
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Yuri A Trotsenko
- GK Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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11
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Kong JY, Su Y, Zhang QQ, Bai Y, Xia FF, Fang CR, He R. Vertical profiles of community and activity of methanotrophs in landfill cover soils of different age. J Appl Microbiol 2013; 115:756-65. [DOI: 10.1111/jam.12263] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/29/2013] [Accepted: 05/24/2013] [Indexed: 11/30/2022]
Affiliation(s)
- J.-Y. Kong
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - Y. Su
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - Q.-Q. Zhang
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - Y. Bai
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - F.-F. Xia
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - C.-R. Fang
- School of Civil Engineering and Architecture; Zhejiang University of Science and Technology; Hangzhou China
| | - R. He
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
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12
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Bodelier PLE, Bär-Gilissen MJ, Meima-Franke M, Hordijk K. Structural and functional response of methane-consuming microbial communities to different flooding regimes in riparian soils. Ecol Evol 2012; 2:106-27. [PMID: 22408730 PMCID: PMC3297182 DOI: 10.1002/ece3.34] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 08/12/2011] [Accepted: 08/17/2011] [Indexed: 02/02/2023] Open
Abstract
Climate change will lead to more extreme precipitation and associated increase of flooding events of soils. This can turn these soils from a sink into a source of atmospheric methane. The latter will depend on the balance of microbial methane production and oxidation. In the present study, the structural and functional response of methane oxidizing microbial communities was investigated in a riparian flooding gradient. Four sites differing in flooding frequency were sampled and soil-physico-chemistry as well as methane oxidizing activities, numbers and community composition were assessed. Next to this, the active community members were determined by stable isotope probing of lipids. Methane consumption as well as population size distinctly increased with flooding frequency. All methane consumption parameters (activity, numbers, lipids) correlated with soil moisture, organic matter content, and conductivity. Methane oxidizing bacteria were present and activated quickly even in seldom flooded soils. However, the active species comprised only a few representatives belonging to the genera Methylobacter, Methylosarcina, and Methylocystis, the latter being active only in permanently or regularly flooded soils. This study demonstrates that soils exposed to irregular flooding harbor a very responsive methane oxidizing community that has the potential to mitigate methane produced in these soils. The number of active species is limited and dominated by one methane oxidizing lineage. Knowledge on the characteristics of these microbes is necessary to assess the effects of flooding of soils and subsequent methane cycling therein.
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Affiliation(s)
- Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Droevendaalsesteeg 10, 6708PB Wageningen, The Netherlands
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He R, Wooller MJ, Pohlman JW, Catranis C, Quensen J, Tiedje JM, Leigh MB. Identification of functionally active aerobic methanotrophs in sediments from an arctic lake using stable isotope probing. Environ Microbiol 2012; 14:1403-19. [PMID: 22429394 DOI: 10.1111/j.1462-2920.2012.02725.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Arctic lakes are a significant source of the greenhouse gas methane (CH(4) ), but the role that methane oxidizing bacteria (methanotrophs) play in limiting the overall CH(4) flux is poorly understood. Here, we used stable isotope probing (SIP) techniques to identify the metabolically active aerobic methanotrophs in upper sediments (0-1 cm) from an arctic lake in northern Alaska sampled during ice-free summer conditions. The highest CH(4) oxidation potential was observed in the upper sediment (0-1 cm depth) with 1.59 µmol g wet weight(-1) day(-1) compared with the deeper sediment samples (1-3 cm, 3-5 cm and 5-10 cm), which exhibited CH(4) oxidation potentials below 0.4 µmol g wet weight(-1) day(-1) . Both type I and type II methanotrophs were directly detected in the upper sediment total communities using targeted primer sets based on 16S rRNA genes. Sequencing of 16S rRNA genes and functional genes (pmoA and mxaF) in the (13) C-DNA from the upper sediment indicated that type I methanotrophs, mainly Methylobacter, Methylosoma, Methylomonas and Methylovulum miyakonense, dominated the assimilation of CH(4) . Methylotrophs, including the genera Methylophilus and/or Methylotenera, were also abundant in the (13) C-DNA. Our results show that a diverse microbial consortium acquired carbon from CH(4) in the sediments of this arctic lake.
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Affiliation(s)
- Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
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Semrau JD. Bioremediation via Methanotrophy: Overview of Recent Findings and Suggestions for Future Research. Front Microbiol 2011; 2:209. [PMID: 22016748 PMCID: PMC3191459 DOI: 10.3389/fmicb.2011.00209] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 09/24/2011] [Indexed: 01/17/2023] Open
Abstract
Microbially mediated bioremediation of polluted sites has been a subject of much research over the past 30 years, with many different compounds shown to be degraded under both aerobic and anaerobic conditions. Aerobic-mediated bioremediation commonly examines the use of methanotrophs, microorganisms that consume methane as their sole source of carbon and energy. Given the diverse environments in which methanotrophs have been found, the range of substrates they can degrade and the fact that they can be easily stimulated with the provision of methane and oxygen, these microorganisms in particular have been examined for aerobic degradation of chlorinated hydrocarbons. The physiological and phylogenetic diversity of methanotrophy, however, has increased substantially in just the past 5 years. Here in this review, the current state of knowledge of methanotrophy, particularly as it applies to pollutant degradation is summarized, and suggestions for future research provided.
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Affiliation(s)
- Jeremy D Semrau
- Department of Civil and Environmental Engineering, The University of Michigan Ann Arbor, MI, USA
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Stimulation of methanotrophic growth in cocultures by cobalamin excreted by rhizobia. Appl Environ Microbiol 2011; 77:8509-15. [PMID: 21984248 DOI: 10.1128/aem.05834-11] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanotrophs play a key role in the global carbon cycle, in which they affect methane emissions and help to sustain diverse microbial communities through the conversion of methane to organic compounds. To investigate the microbial interactions that cause positive effects on methanotrophs, cocultures were constructed using Methylovulum miyakonense HT12 and each of nine nonmethanotrophic bacteria, which were isolated from a methane-utilizing microbial consortium culture established from forest soil. Three rhizobial strains were found to strongly stimulate the growth and methane oxidation of M. miyakonense HT12 in cocultures. We purified the stimulating factor produced by Rhizobium sp. Rb122 and identified it as cobalamin. Growth stimulation by cobalamin was also observed for three other gammaproteobacterial methanotrophs. These results suggest that microbial interactions through cobalamin play an important role in methane oxidation in various ecosystems.
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