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Carrión O, Larke-Mejía NL, Gibson L, Farhan Ul Haque M, Ramiro-García J, McGenity TJ, Murrell JC. Gene probing reveals the widespread distribution, diversity and abundance of isoprene-degrading bacteria in the environment. MICROBIOME 2018; 6:219. [PMID: 30526688 PMCID: PMC6286570 DOI: 10.1186/s40168-018-0607-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/25/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Approximately 500 Tg of isoprene are emitted to the atmosphere annually, an amount similar to that of methane, and despite its significant effects on the climate, very little is known about the biological degradation of isoprene in the environment. Isolation and characterisation of isoprene degraders at the molecular level has allowed the development of probes targeting isoA encoding the α-subunit of the isoprene monooxygenase. This enzyme belongs to the soluble diiron centre monooxygenase family and catalyses the first step in the isoprene degradation pathway. The use of probes targeting key metabolic genes is a successful approach in molecular ecology to study specific groups of bacteria in complex environments. Here, we developed and tested a novel isoA PCR primer set to study the distribution, abundance, and diversity of isoprene degraders in a wide range of environments. RESULTS The new isoA probes specifically amplified isoA genes from taxonomically diverse isoprene-degrading bacteria including members of the genera Rhodococcus, Variovorax, and Sphingopyxis. There was no cross-reactivity with genes encoding related oxygenases from non-isoprene degraders. Sequencing of isoA amplicons from DNA extracted from environmental samples enriched with isoprene revealed that most environments tested harboured a considerable variety of isoA sequences, with poplar leaf enrichments containing more phylogenetically diverse isoA genes. Quantification by qPCR using these isoA probes revealed that isoprene degraders are widespread in the phyllosphere, terrestrial, freshwater and marine environments. Specifically, soils in the vicinity of high isoprene-emitting trees contained the highest number of isoprene-degrading bacteria. CONCLUSION This study provides the molecular ecology tools to broaden our knowledge of the distribution, abundance and diversity of isoprene degraders in the environment, which is a fundamental step necessary to assess the impact that microbes have in mitigating the effects of this important climate-active gas.
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Affiliation(s)
- Ornella Carrión
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Nasmille L Larke-Mejía
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Lisa Gibson
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Muhammad Farhan Ul Haque
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Javier Ramiro-García
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Terry J McGenity
- School of Biological Sciences, University of Essex, Colchester, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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Rodríguez E, López JC, Prieto P, Merchán L, García-Encina PA, Lebrero R, Muñoz R. Quantitative analysis of methane monooxygenase (MMO) explains process robustness in continuous and feast-famine bioreactors treating methane. CHEMOSPHERE 2018; 212:319-329. [PMID: 30145423 DOI: 10.1016/j.chemosphere.2018.08.091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/25/2018] [Accepted: 08/18/2018] [Indexed: 06/08/2023]
Abstract
The ability of methanotrophs to rapidly respond to intentional or accidental stress conditions caused by operational failures or process fluctuations is of utmost importance to guarantee the robustness of CH4 abatement biotechnologies. In this study, the performance of a continuous and two feast-famine (5:5 days feast-famine cycles) stirred tank reactors treating diluted CH4 emissions (4-5% v/v) was comparatively assessed for 149 days. The robustness of the three bioreactors towards a 5 days CH4 deprivation episode was thoroughly evaluated at a molecular level (pmoA gene expression level) and correlated to macroscopic process performance. The bioreactors recovered their steady-state abatement performance (in terms of CH4 elimination capacity and CO2 production rate) within 1.5-2 h following CH4 supply resumption concomitantly with a maximum in pmoA gene expression, regardless of the previous operational mode. However, while methanotrophs from the continuous unit maintained higher basal levels of pmoA expression as a strategy for a rapid CH4 metabolism initiation, the strategy of the feast-famine adapted-methanotrophs consisted on a more accurate regulation of their pmoA transcripts levels along with a higher and/or more rapid induction of the pmoA gene by CH4 availability.
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Affiliation(s)
- Elisa Rodríguez
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain; Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain
| | - Juan Carlos López
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain
| | - Patricia Prieto
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain
| | - Laura Merchán
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain
| | - Pedro A García-Encina
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain; Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain
| | - Raquel Lebrero
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain; Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain; Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain.
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53
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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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54
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Khadka R, Clothier L, Wang L, Lim CK, Klotz MG, Dunfield PF. Evolutionary History of Copper Membrane Monooxygenases. Front Microbiol 2018; 9:2493. [PMID: 30420840 PMCID: PMC6215863 DOI: 10.3389/fmicb.2018.02493] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/28/2018] [Indexed: 11/30/2022] Open
Abstract
Copper membrane monooxygenases (CuMMOs) oxidize ammonia, methane and some short-chain alkanes and alkenes. They are encoded by three genes, usually in an operon of xmoCAB. We aligned xmo operons from 66 microbial genomes, including members of the Alpha-, Beta-, and Gamma-proteobacteria, Verrucomicrobia, Actinobacteria, Thaumarchaeota and the candidate phylum NC10. Phylogenetic and compositional analyses were used to reconstruct the evolutionary history of the enzyme and detect potential lateral gene transfer (LGT) events. The phylogenetic analyses showed at least 10 clusters corresponding to a combination of substrate specificity and bacterial taxonomy, but with no overriding structure based on either function or taxonomy alone. Adaptation of the enzyme to preferentially oxidize either ammonia or methane has occurred more than once. Individual phylogenies of all three genes, xmoA, xmoB and xmoC, closely matched, indicating that this operon evolved or was consistently transferred as a unit, with the possible exception of the methane monooxygenase operons in Verrucomicrobia, where the pmoB gene has a distinct phylogeny from pmoA and pmoC. Compositional analyses indicated that some clusters of xmoCAB operons (for example, the pmoCAB in gammaproteobacterial methanotrophs and the amoCAB in betaproteobacterial nitrifiers) were compositionally very different from their genomes, possibly indicating recent lateral transfer of these operons. The combined phylogenetic and compositional analyses support the hypothesis that an ancestor of the nitrifying bacterium Nitrosococcus was the donor of methane monooxygenase (pMMO) to both the alphaproteobacterial and gammaproteobacterial methanotrophs, but that before this event the gammaproteobacterial methanotrophs originally possessed another CuMMO (Pxm), which has since been lost in many species.
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Affiliation(s)
- Roshan Khadka
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Lindsay Clothier
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Lin Wang
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Chee Kent Lim
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Martin G Klotz
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Richland, WA, United States.,State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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55
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Watsuji TO, Motoki K, Hada E, Nagai Y, Takaki Y, Yamamoto A, Ueda K, Toyofuku T, Yamamoto H, Takai K. Compositional and Functional Shifts in the Epibiotic Bacterial Community of Shinkaia crosnieri Baba & Williams (a Squat Lobster from Hydrothermal Vents) during Methane-Fed Rearing. Microbes Environ 2018; 33:348-356. [PMID: 30333383 PMCID: PMC6308002 DOI: 10.1264/jsme2.me18072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The hydrothermal vent squat lobster Shinkaia crosnieri Baba & Williams harbors an epibiotic bacterial community, which is numerically and functionally dominated by methanotrophs affiliated with Methylococcaceae and thioautotrophs affiliated with Sulfurovum and Thiotrichaceae. In the present study, shifts in the phylogenetic composition and metabolic function of the epibiont community were investigated using S. crosnieri individuals, which were reared for one year in a tank fed with methane as the energy and carbon source. The results obtained indicated that indigenous predominant thioautotrophic populations, such as Sulfurovum and Thiotrichaceae members, became absent, possibly due to the lack of an energy source, and epibiotic communities were dominated by indigenous Methylococcaceae and betaproteobacterial methylotrophic members that adapted to the conditions present during rearing for 12 months with a supply of methane. Furthermore, the overall phylogenetic composition of the epibiotic community markedly changed from a composition dominated by chemolithotrophs to one enriched with cross-feeding heterotrophs in addition to methanotrophs and methylotrophs. Thus, the composition and function of the S. crosnieri epibiotic bacterial community were strongly affected by the balance between the energy and carbon sources supplied for chemosynthetic production as well as that between the production and consumption of organic compounds.
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Affiliation(s)
- Tomo-O Watsuji
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Kaori Motoki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Life Science Research Center, College of Bioresource Sciences, Nihon University.,Present Address: Department of Biological Sciences, Graduate School of Science, the University of Tokyo
| | - Emi Hada
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yukiko Nagai
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Asami Yamamoto
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Life Science Research Center, College of Bioresource Sciences, Nihon University
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University
| | | | | | - Ken Takai
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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56
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Han C, Liu B, Zhong W. Effects of transgenic Bt rice on the active rhizospheric methanogenic archaeal community as revealed by DNA-based stable isotope probing. J Appl Microbiol 2018; 125:1094-1107. [PMID: 29846995 DOI: 10.1111/jam.13939] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/16/2018] [Accepted: 05/28/2018] [Indexed: 11/29/2022]
Abstract
AIMS This study aimed to investigate the influence of planting Cry1Ab/Cry1Ac gene expressing rice (Bt rice) on rhizospheric active methanogenic archaeal communities. METHODS AND RESULTS The nontransgenic parental line was used as the control (Ck rice). DNA-based stable isotope probing (DNA-SIP) technology traced the rhizospheric active methanogens at the tillering stage. The results revealed significantly lower CH4 emission flux from Bt soil than that from Ck soil during the whole growth period. The active methanogenic community composition remained stable. The RC-I lineage (77·9-79·8%) and Methanosaetaceae (13·9-15·1%) were the predominant active methanogens in Bt and Ck rice rhizospheres. However, the abundance of functionally active methanogens in the Bt rice rhizosphere was significantly reduced. Lower levels of root exudates (that included carbohydrate and organic acids) from Bt rice were also detected at the tillering stage. CONCLUSION This study found that the genetic modification of rice reduced the potential methanogenic substrates came from plant-derived root exudates, which represented an important factor in reducing CH4 generation and active methanogenic archaeal abundance in Bt rhizosphere soil. SIGNIFICANCE AND IMPACT OF THE STUDY The effect of genetically modified (GM) insect-resistant crops on soil micro-organisms has become an issue of public concern, especially the indirect effect of plant metabolisms caused by the insertion of foreign genes. Methanogenesis, which is regarded as a critical ecological process in paddy soil, is influenced by plant root exudates; these are mainly derived from photosynthesis. The variations in root exudates across the Bt and Ck rice suggested the indirect influence of foreign gene insertion. DNA-SIP successfully traced the active methanogenic archaeal populations assimilating 13 C-labelled photosynthetic carbon and found a strong influence of planting Bt rice on active methanogens. As a consequence, we proposed that analysis of functionally active micro-organisms is more suitable for monitoring and predicting the environmental influence of GM plants.
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Affiliation(s)
- C Han
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, School of Geography Science, Nanjing Normal University - Xianlin Campus, Nanjing, Jiangsu Province, China.,Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing Normal University - Xianlin Campus, Nanjing, Jiangsu Province, China
| | - B Liu
- Ministry of Environmental Protection of the People's Republic of China, Key Laboratory of Biosafety, Nanjing Institute of Environmental Sciences, Beijing, China
| | - W Zhong
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, School of Geography Science, Nanjing Normal University - Xianlin Campus, Nanjing, Jiangsu Province, China.,Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing Normal University - Xianlin Campus, Nanjing, Jiangsu Province, China
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57
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Farhan Ul Haque M, Crombie AT, Ensminger SA, Baciu C, Murrell JC. Facultative methanotrophs are abundant at terrestrial natural gas seeps. MICROBIOME 2018; 6:118. [PMID: 29954460 PMCID: PMC6022506 DOI: 10.1186/s40168-018-0500-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/13/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Natural gas contains methane and the gaseous alkanes ethane, propane and butane, which collectively influence atmospheric chemistry and cause global warming. Methane-oxidising bacteria, methanotrophs, are crucial in mitigating emissions of methane as they oxidise most of the methane produced in soils and the subsurface before it reaches the atmosphere. Methanotrophs are usually obligate, i.e. grow only on methane and not on longer chain alkanes. Bacteria that grow on the other gaseous alkanes in natural gas such as propane have also been characterised, but they do not grow on methane. Recently, it was shown that the facultative methanotroph Methylocella silvestris grew on ethane and propane, other components of natural gas, in addition to methane. Therefore, we hypothesised that Methylocella may be prevalent at natural gas seeps and might play a major role in consuming all components of this potent greenhouse gas mixture before it is released to the atmosphere. RESULTS Environments known to be exposed to biogenic methane emissions or thermogenic natural gas seeps were surveyed for methanotrophs. 16S rRNA gene amplicon sequencing revealed that Methylocella were the most abundant methanotrophs in natural gas seep environments. New Methylocella-specific molecular tools targeting mmoX (encoding the soluble methane monooxygenase) by PCR and Illumina amplicon sequencing were designed and used to investigate various sites. Functional gene-based assays confirmed that Methylocella were present in all of the natural gas seep sites tested here. This might be due to its ability to use methane and other short chain alkane components of natural gas. We also observed the abundance of Methylocella in other environments exposed to biogenic methane, suggesting that Methylocella has been overlooked in the past as previous ecological studies of methanotrophs often used pmoA (encoding the alpha subunit of particulate methane monooxygenase) as a marker gene. CONCLUSION New biomolecular tools designed in this study have expanded our ability to detect, and our knowledge of the environmental distribution of Methylocella, a unique facultative methanotroph. This study has revealed that Methylocella are particularly abundant at natural gas seeps and may play a significant role in biogeochemical cycling of gaseous hydrocarbons.
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Affiliation(s)
- Muhammad Farhan Ul Haque
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrew T Crombie
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Calin Baciu
- Faculty of Environmental Science and Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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58
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He R, Su Y, Ma RC, Zhuang S. Characterization of toluene metabolism by methanotroph and its effect on methane oxidation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:16816-16824. [PMID: 29616477 DOI: 10.1007/s11356-018-1863-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/26/2018] [Indexed: 06/08/2023]
Abstract
Methanotrophs not only oxidize CH4, but also can oxidize a relatively broad range of other substrates, including trichloroethylene, alkanes, alkenes, and aromatic compounds. In this study, Methylosinus sporium was used as a model organism to characterize toluene metabolism by methanotrophs. Reverse transcription quantitative PCR analysis showed that toluene enhanced the mmoX expression of M. sporium. When the toluene concentration was below 2000 mg m-3, the kinetics of toluene metabolism by M. sporium conformed to the Michaelis-Menten equation (Vmax = 0.238 g gdry weight-1 h-1, K m = 545.2 mg m-3). The use of a solid-phase extraction technique followed by a gas chromatography-mass spectrometry analysis and molecular docking calculation showed that toluene was likely to primarily bind the di-iron center structural region of soluble methane monooxygenase (sMMO) hydroxylase and then be oxidized to o-cresol. Although M. sporium oxidized toluene, it did not incorporate toluene into its biomass. The coexistence of toluene and CH4 could influence CH4 oxidation, the growth of methanotrophs, and the distribution of CH4-derived carbon, which were related to the ratio of the toluene concentration to biomass. These results would be helpful to understand the metabolism of CH4 and non-methane volatile organic compounds in the environment.
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Affiliation(s)
- Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
| | - Yao Su
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Ruo-Chan Ma
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Shulin Zhuang
- Institute of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
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59
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Magnabosco C, Timmers PHA, Lau MCY, Borgonie G, Linage-Alvarez B, Kuloyo O, Alleva R, Kieft TL, Slater GF, van Heerden E, Sherwood Lollar B, Onstott TC. Fluctuations in populations of subsurface methane oxidizers in coordination with changes in electron acceptor availability. FEMS Microbiol Ecol 2018; 94:4995908. [DOI: 10.1093/femsec/fiy089] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- C Magnabosco
- Flatiron Institute Center for Computational Biology, Simons Foundation, New York, NY 10010 USA
| | - P H A Timmers
- Microbial Physiology Group, Laboratory of Microbiology, Wageningen University, Wageningen, 6700 The Netherlands
| | - M C Y Lau
- Department of Geosciences, Princeton University, Princeton, NJ 08544 USA
| | - G Borgonie
- Extreme Life Isyensya, Gentbrugge, 9050 Belgium
| | - B Linage-Alvarez
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State Bloemfontein, Free State 9300 South Africa
| | - O Kuloyo
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State Bloemfontein, Free State 9300 South Africa
- Department of Geoscience, University of Calgary, Calgary, Alberta T2N 1N4 Canada
| | - R Alleva
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544 USA
| | - T L Kieft
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM 87801 USA
| | - G F Slater
- School of Geography and Earth Sciences, McMaster University, Hamilton, Ontario L8S 4K1 Canada
| | - E van Heerden
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State Bloemfontein, Free State 9300 South Africa
- Biosaense Solutions, Bloemfontein, Free State 9300 South Africa
| | - B Sherwood Lollar
- Department of Earth Sciences, University of Toronto, Toronto, Ontario M5S 3B1 Canada
| | - T C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ 08544 USA
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60
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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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61
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Shiau YJ, Cai Y, Lin YT, Jia Z, Chiu CY. Community Structure of Active Aerobic Methanotrophs in Red Mangrove (Kandelia obovata) Soils Under Different Frequency of Tides. MICROBIAL ECOLOGY 2018; 75:761-770. [PMID: 29022063 DOI: 10.1007/s00248-017-1080-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/22/2017] [Indexed: 06/07/2023]
Abstract
Methanotrophs are important microbial communities in coastal ecosystems. They reduce CH4 emission in situ, which is influenced by soil conditions. This study aimed to understand the differences in active aerobic methanotrophic communities in mangrove forest soils experiencing different inundation frequency, i.e., in soils from tidal mangroves, distributed at lower elevations, and from dwarf mangroves, distributed at higher elevations. Labeling of pmoA gene of active methanotrophs using DNA-based stable isotope probing (DNA-SIP) revealed that methanotrophic activity was higher in the dwarf mangrove soils than in the tidal mangrove soils, possibly because of the more aerobic soil conditions. Methanotrophs affiliated with the cluster deep-sea-5 belonging to type Ib methanotrophs were the most dominant methanotrophs in the fresh mangrove soils, whereas type II methanotrophs also appeared in the fresh dwarf mangrove soils. Furthermore, Methylobacter and Methylosarcina were the most important active methanotrophs in the dwarf mangrove soils, whereas Methylomonas and Methylosarcina were more active in the tidal mangrove soils. High-throughput sequencing of the 16S ribosomal RNA (rRNA) gene also confirmed similar differences in methanotrophic communities at the different locations. However, several unclassified methanotrophic bacteria were found by 16S rRNA MiSeq sequencing in both fresh and incubated mangrove soils, implying that methanotrophic communities in mangrove forests may significantly differ from the methanotrophic communities documented in previous studies. Overall, this study showed the feasibility of 13CH4 DNA-SIP to study the active methanotrophic communities in mangrove forest soils and revealed differences in the methanotrophic community structure between coastal mangrove forests experiencing different tide frequencies.
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Affiliation(s)
- Yo-Jin Shiau
- Biodiversity Research Center, Academia Sinica, No. 128, Academia Road Section II, Nangang, Taipei, 11529, Taiwan
| | - Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science, No. 71 East Beijing Road, Nanjing, 210008, People's Republic of China
| | - Yu-Te Lin
- Biodiversity Research Center, Academia Sinica, No. 128, Academia Road Section II, Nangang, Taipei, 11529, Taiwan
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science, No. 71 East Beijing Road, Nanjing, 210008, People's Republic of China.
| | - Chih-Yu Chiu
- Biodiversity Research Center, Academia Sinica, No. 128, Academia Road Section II, Nangang, Taipei, 11529, Taiwan.
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62
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Pratscher J, Vollmers J, Wiegand S, Dumont MG, Kaster A. Unravelling the Identity, Metabolic Potential and Global Biogeography of the Atmospheric Methane-Oxidizing Upland Soil Cluster α. Environ Microbiol 2018; 20:1016-1029. [PMID: 29314604 PMCID: PMC6849597 DOI: 10.1111/1462-2920.14036] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/19/2017] [Accepted: 12/19/2017] [Indexed: 02/06/2023]
Abstract
Understanding of global methane sources and sinks is a prerequisite for the design of strategies to counteract global warming. Microbial methane oxidation in soils represents the largest biological sink for atmospheric methane. However, still very little is known about the identity, metabolic properties and distribution of the microbial group proposed to be responsible for most of this uptake, the uncultivated upland soil cluster α (USCα). Here, we reconstructed a draft genome of USCα from a combination of targeted cell sorting and metagenomes from forest soil, providing the first insights into its metabolic potential and environmental adaptation strategies. The 16S rRNA gene sequence recovered was distinctive and suggests this crucial group as a new genus within the Beijerinckiaceae, close to Methylocapsa. Application of a fluorescently labelled suicide substrate for the particulate methane monooxygenase enzyme (pMMO) coupled to 16S rRNA fluorescence in situ hybridisation (FISH) allowed for the first time a direct link of the high-affinity activity of methane oxidation to USCα cells in situ. Analysis of the global biogeography of this group further revealed its presence in previously unrecognized habitats, such as subterranean and volcanic biofilm environments, indicating a potential role of these environments in the biological sink for atmospheric methane.
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Affiliation(s)
| | - John Vollmers
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of TechnologyKarlsruheGermany
| | - Sandra Wiegand
- Department of MicrobiologyInstitute for Water and Wetland Research, Faculty of Science, Radboud UniversityNijmegenThe Netherlands
| | - Marc G. Dumont
- Biological SciencesUniversity of SouthamptonSouthamptonUK
| | - Anne‐Kristin Kaster
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of TechnologyKarlsruheGermany
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63
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Iqbal MW, Zhang Q, Yang Y, Zou C, Li L, Liang X, Wei S, Lin B. Ruminal fermentation and microbial community differently influenced by four typical subtropical forages in vitro. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2018; 4:100-108. [PMID: 30167491 PMCID: PMC6112341 DOI: 10.1016/j.aninu.2017.10.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 09/19/2017] [Accepted: 10/10/2017] [Indexed: 01/26/2023]
Abstract
The present study evaluated the effects of 4 typical subtropical forages on ruminal microbial community composition to formulate a better diet for buffalo. Corn straw silage, elephant grass, cassava residues and sugarcane tail silage were used as substrates for in vitro fermentation. Eight replicates were set up for every substrate, and fermentation was carried out in a 100-mL glass syringe, using buffalo rumen inoculum. Every replicate was anaerobically dispensed with 10 mL of rumen inoculum, 20 mL of McDougall's buffer and 200 mg of dried substrate, and placed in a water bath at 39 °C. Gas production was recorded at 0, 2, 6, 12, 24, 36, 48 and 72 h of incubation. After 24 h, fermentation was ceased for 4 replicates and samples were collected. Volatile fatty acids (VFA) concentrations were measured using gas chromatography. Microbial populations were quantified using quantitative real-time PCR (qRT-PCR), and microbial community was analyzed using high throughput sequencing technology. The results showed, cassava residues as substrate had the highest gas production, acetate, propionate and total VFA concentrations (P < 0.05), and corn straw silage had the lowest acetate:propionate ratio (P < 0.05). The lowest numbers of fungi, Ruminococcus albus and Fibrobacter succinogenes, and the highest number of protozoa were observed with cassava residues (P < 0.05). The least abundances of bacterial phyla Firmicutes, Bacteroidetes and genus Prevotella, and substantially higher abundance of phylum proteobacteria (56%) and genus Succinivibrio (52%) were observed with cassava residues. The most abundances of Methanobrevibacter gottschalkii and Entodinium were observed with cassava residues. Spearman's correlations analysis showed, Succinivibrio had strong positive correlations with propionate, butyrate, Metadinium and M. gottschalkii, indicating fermentation products were related to microbial community. In conclusion, incubation with cassava residues resulted in lower number of fiber degrading microbes but higher protozoal population because of its low fiber contents. The microbial community was highly altered by in vitro incubation with cassava residues, whereas remained similar for the other 3 high fiber containing substrates.
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Affiliation(s)
- Muhammad W. Iqbal
- College of Animal Science, Guangxi University, Nanning 530000, China
| | - Qin Zhang
- College of Animal Science, Guangxi University, Nanning 530000, China
| | - Yingbai Yang
- College of Animal Science, Guangxi University, Nanning 530000, China
| | - Caixia Zou
- College of Animal Science, Guangxi University, Nanning 530000, China
| | - Lili Li
- Buffalo Research Institute, The Chinese Academy of Agricultural Sciences, Nanning 530000, China
| | - Xin Liang
- Buffalo Research Institute, The Chinese Academy of Agricultural Sciences, Nanning 530000, China
| | - Shengju Wei
- Buffalo Research Institute, The Chinese Academy of Agricultural Sciences, Nanning 530000, China
| | - Bo Lin
- College of Animal Science, Guangxi University, Nanning 530000, China
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64
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Microbial cycling of isoprene, the most abundantly produced biological volatile organic compound on Earth. ISME JOURNAL 2018; 12:931-941. [PMID: 29463892 PMCID: PMC5864225 DOI: 10.1038/s41396-018-0072-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/26/2017] [Accepted: 12/12/2017] [Indexed: 01/28/2023]
Abstract
Isoprene (2-methyl-1,3-butadiene), the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, is highly reactive and can have diverse and often detrimental atmospheric effects, which impact on climate and health. Most isoprene is produced by terrestrial plants, but (micro)algal production is important in aquatic environments, and the relative bacterial contribution remains unknown. Soils are a sink for isoprene, and bacteria that can use isoprene as a carbon and energy source have been cultivated and also identified using cultivation-independent methods from soils, leaves and coastal/marine environments. Bacteria belonging to the Actinobacteria are most frequently isolated and identified, and Proteobacteria have also been shown to degrade isoprene. In the freshwater-sediment isolate, Rhodococcus strain AD45, initial oxidation of isoprene to 1,2-epoxy-isoprene is catalyzed by a multicomponent isoprene monooxygenase encoded by the genes isoABCDEF. The resultant epoxide is converted to a glutathione conjugate by a glutathione S-transferase encoded by isoI, and further degraded by enzymes encoded by isoGHJ. Genome sequence analysis of actinobacterial isolates belonging to the genera Rhodococcus, Mycobacterium and Gordonia has revealed that isoABCDEF and isoGHIJ are linked in an operon, either on a plasmid or the chromosome. In Rhodococcus strain AD45 both isoprene and epoxy-isoprene induce a high level of transcription of 22 contiguous genes, including isoABCDEF and isoGHIJ. Sequence analysis of the isoA gene, encoding the large subunit of the oxygenase component of isoprene monooxygenase, from isolates has facilitated the development of PCR primers that are proving valuable in investigating the ecology of uncultivated isoprene-degrading bacteria.
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65
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Schnyder E, Bodelier PLE, Hartmann M, Henneberger R, Niklaus PA. Positive diversity-functioning relationships in model communities of methanotrophic bacteria. Ecology 2018; 99:714-723. [PMID: 29323701 DOI: 10.1002/ecy.2138] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 11/01/2017] [Accepted: 12/20/2017] [Indexed: 11/11/2022]
Abstract
Biodiversity enhances ecosystem functions such as biomass production and nutrient cycling. Although the majority of the terrestrial biodiversity is hidden in soils, very little is known about the importance of the diversity of microbial communities for soil functioning. Here, we tested effects of biodiversity on the functioning of methanotrophs, a specialized group of soil bacteria that plays a key role in mediating greenhouse gas emissions from soils. Using pure strains of methanotrophic bacteria, we assembled artificial communities of different diversity levels, with which we inoculated sterile soil microcosms. To assess the functioning of these communities, we measured methane oxidation by gas chromatography throughout the experiment and determined changes in community composition and community size at several time points by quantitative PCR and sequencing. We demonstrate that microbial diversity had a positive overyielding effect on methane oxidation, in particular at the beginning of the experiment. This higher assimilation of CH4 at high diversity translated into increased growth and significantly larger communities towards the end of the study. The overyielding of mixtures with respect to CH4 consumption and community size were positively correlated. The temporal CH4 consumption profiles of strain monocultures differed, raising the possibility that temporal complementarity of component strains drove the observed community-level strain richness effects; however, the community niche metric we derived from the temporal activity profiles did not explain the observed strain richness effect. The strain richness effect also was unrelated to both the phylogenetic and functional trait diversity of mixed communities. Overall, our results suggest that positive biodiversity-ecosystem-function relationships show similar patterns across different scales and may be widespread in nature. Additionally, biodiversity is probably also important in natural methanotrophic communities for the ecosystem function methane oxidation. Therefore, maintaining soil conditions that support a high diversity of methanotrophs may help to reduce the emission of the greenhouse gas methane.
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Affiliation(s)
- Elvira Schnyder
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Martin Hartmann
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Ruth Henneberger
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Universitätstrasse 16, CH-8092, Zurich, Switzerland
| | - Pascal A Niklaus
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.,University of Zurich Research Priority Program Global Change and Biodiversity, University of Zürich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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66
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Crevecoeur S, Vincent WF, Comte J, Matveev A, Lovejoy C. Diversity and potential activity of methanotrophs in high methane-emitting permafrost thaw ponds. PLoS One 2017; 12:e0188223. [PMID: 29182670 PMCID: PMC5705078 DOI: 10.1371/journal.pone.0188223] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 11/02/2017] [Indexed: 11/27/2022] Open
Abstract
Lakes and ponds derived from thawing permafrost are strong emitters of carbon dioxide and methane to the atmosphere, but little is known about the methane oxidation processes in these waters. Here we investigated the distribution and potential activity of aerobic methanotrophic bacteria in thaw ponds in two types of eroding permafrost landscapes in subarctic Québec: peatlands and mineral soils. We hypothesized that methanotrophic community composition and potential activity differ regionally as a function of the landscape type and permafrost degradation stage, and locally as a function of depth-dependent oxygen conditions. Our analysis of pmoA transcripts by Illumina amplicon sequencing and quantitative PCR showed that the communities were composed of diverse and potentially active lineages. Type I methanotrophs, particularly Methylobacter, dominated all communities, however there was a clear taxonomic separation between the two landscape types, consistent with environmental control of community structure. In contrast, methanotrophic potential activity, measured by pmoA transcript concentrations, did not vary with landscape type, but correlated with conductivity, phosphorus and total suspended solids. Methanotrophic potential activity was also detected in low-oxygen bottom waters, where it was inversely correlated with methane concentrations, suggesting methane depletion by methanotrophs. Methanotrophs were present and potentially active throughout the water column regardless of oxygen concentration, and may therefore be resilient to future mixing and oxygenation regimes in the warming subarctic.
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Affiliation(s)
- Sophie Crevecoeur
- Département de Biologie, Centre d’études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
- * E-mail:
| | - Warwick F. Vincent
- Département de Biologie, Centre d’études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, Québec, Canada
| | - Jérôme Comte
- Département de Biologie, Centre d’études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Alex Matveev
- Département de Biologie, Centre d’études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, Québec, Canada
| | - Connie Lovejoy
- Département de Biologie, Centre d’études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
- Québec-Océan, Université Laval, Québec, Québec, Canada
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67
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Wang S, Liu Y, Liu G, Huang Y, Zhou Y. A New Primer to Amplify pmoA Gene From NC10 Bacteria in the Sediments of Dongchang Lake and Dongping Lake. Curr Microbiol 2017; 74:908-914. [PMID: 28501892 DOI: 10.1007/s00284-017-1260-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 04/28/2017] [Indexed: 11/27/2022]
Abstract
Nitrite-dependent anaerobic methane oxidation (n-damo) is catalyzed by the NC10 phylum bacterium "Candidatus Methylomirabilis oxyfera" (M. oxyfera). Generally, the pmoA gene is applied as a functional marker to test and identify NC10-like bacteria. However, it is difficult to detect the NC10 bacteria from sediments of freshwater lake (Dongchang Lake and Dongping Lake) with the previous pmoA gene primer sets. In this work, a new primer cmo208 was designed and used to amplify pmoA gene of NC10-like bacteria. A newly nested PCR approach was performed using the new primer cmo208 and the previous primers cmo182, cmo682, and cmo568 to detect the NC10 bacteria. The obtained pmoA gene sequences exhibited 85-92% nucleotide identity and 95-97% amino acid sequence identity to pmoA gene of M. oxyfera. The obtained diversity of pmoA gene sequences coincided well with the diversity of 16S rRNA sequences. These results indicated that the newly designed pmoA primer cmo208 could give one more option to detect NC10 bacteria from different environmental samples.
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MESH Headings
- Aerobiosis
- Anaerobiosis
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Cluster Analysis
- DNA Primers/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, Bacterial
- Genetic Variation
- Geologic Sediments/microbiology
- Lakes
- Phylogeny
- Polymerase Chain Reaction/methods
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Shenghui Wang
- College of Life Science, Liaocheng University, Liaocheng, 252059, People's Republic of China.
| | - Yanjun Liu
- College of Life Science, Liaocheng University, Liaocheng, 252059, People's Republic of China
| | - Guofu Liu
- College of Life Science, Liaocheng University, Liaocheng, 252059, People's Republic of China
| | - Yaru Huang
- College of Life Science, Liaocheng University, Liaocheng, 252059, People's Republic of China
| | - Yu Zhou
- College of Life Science, Liaocheng University, Liaocheng, 252059, People's Republic of China
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68
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Bessette S, Moalic Y, Gautey S, Lesongeur F, Godfroy A, Toffin L. Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic-Anoxic Interface of the Congo Deep-Sea Fan. Front Microbiol 2017; 8:715. [PMID: 28487684 PMCID: PMC5403828 DOI: 10.3389/fmicb.2017.00715] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/06/2017] [Indexed: 11/13/2022] Open
Abstract
Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3-5% organic carbon). This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB) communities at the oxic-anoxic interface of sedimentary habitats by using fluorescence in situ hybridization and comparative sequence analysis of particulate mono-oxygenase (pmoA) genes. Our findings revealed that sedimentary habitats of the recent lobe complex hosted type I and type II MOB cells and comparisons of pmoA community compositions showed variations among the different organic-rich habitats. Furthermore, the pmoA lineages were taxonomically more diverse compared to methane seep environments and were related to those found at cold seeps. Surprisingly, MOB phylogenetic lineages typical of terrestrial environments were observed at such water depth. In contrast, MOB cells or pmoA sequences were not detected at the previous lobe complex that is disconnected from the Congo River inputs.
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Affiliation(s)
- Sandrine Bessette
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
| | - Yann Moalic
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
| | - Sébastien Gautey
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
| | - Françoise Lesongeur
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
| | - Anne Godfroy
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
| | - Laurent Toffin
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
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69
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Argiroff WA, Zak DR, Lanser CM, Wiley MJ. Microbial Community Functional Potential and Composition Are Shaped by Hydrologic Connectivity in Riverine Floodplain Soils. MICROBIAL ECOLOGY 2017; 73:630-644. [PMID: 27807645 DOI: 10.1007/s00248-016-0883-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/17/2016] [Indexed: 05/12/2023]
Abstract
Riverine floodplains are ecologically and economically valuable ecosystems that are heavily threatened by anthropogenic stressors. Microbial communities in floodplain soils mediate critical biogeochemical processes, yet we understand little about the relationship between these communities and variation in hydrologic connectivity related to land management or topography. Here, we present metagenomic evidence that differences among microbial communities in three floodplain soils correspond to a long-term gradient of hydrologic connectivity. Specifically, all strictly anaerobic taxa and metabolic pathways were positively associated with increased hydrologic connectivity and flooding frequency. In contrast, most aerobic taxa and all strictly aerobic pathways were negatively related to hydrologic connectivity and flooding frequency. Furthermore, the genetic potential to metabolize organic compounds tended to decrease as hydrologic connectivity increased, which may reflect either the observed concomitant decline of soil organic matter or the parallel increase in both anaerobic taxa and pathways. A decline in soil N, accompanied by an increased genetic potential for oligotrophic N acquisition subsystems, suggests that soil nutrients also shape microbial communities in these soils. We conclude that differences among floodplain soil microbial communities can be conceptualized along a gradient of hydrologic connectivity. Additionally, we show that these differences are likely due to connectivity-related variation in flooding frequency, soil organic matter, and soil N. Our findings are particularly relevant to the restoration and management of microbially mediated biogeochemical processes in riverine floodplain wetlands.
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Affiliation(s)
- William A Argiroff
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA.
| | - Donald R Zak
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, MI, 48109, USA
| | - Christine M Lanser
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA
| | - Michael J Wiley
- School of Natural Resources and Environment, University of Michigan, 440 Church St., Ann Arbor, MI, 48109, USA
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70
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Liu H, Wu X, Li Z, Wang Q, Liu D, Liu G. Responses of soil methanogens, methanotrophs, and methane fluxes to land-use conversion and fertilization in a hilly red soil region of southern China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:8731-8743. [PMID: 28213705 DOI: 10.1007/s11356-017-8628-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/10/2017] [Indexed: 06/06/2023]
Abstract
Changes in land-uses and fertilization are important factors regulating methane (CH4) emissions from paddy soils. However, the responses of soil CH4 emissions to these factors and the underlying mechanisms remain unclear. The objective of this study was to explore the effects of land-use conversion from paddies to orchards and fertilization on soil CH4 fluxes, and the abundance and community compositions of methanogens and methanotrophs. Soil CH4 fluxes were quantified by static chamber and gas chromatography technology. Abundance and community structures of methanogens and methanotrophs (based on mcrA and pmoA genes, respectively) were determined by quantitative real-time PCR (qPCR), and terminal restriction fragment length polymorphism (TRFLP), cloning and sequence analysis, respectively. Results showed that land-use conversion from paddies to orchards dramatically decreased soil CH4 fluxes, whereas fertilization did not distinctly affect soil CH4 fluxes. Furthermore, abundance of methanogens and methanotrophs were decreased after converting paddies to orchards. Fertilization decreased the abundance of these microorganisms, but the values were not statistically significant. Moreover, land-use conversion had fatal effects on some members of the methanogenic archaea (Methanoregula and Methanosaeta), increased type II methanotrophs (Methylocystis and Methylosinus), and decreased type I methanotrophs (Methylobacter and Methylococcus). However, fertilization could only significantly affect type I methanotrophs in the orchard plots. In addition, CH4 fluxes from paddy soils were positively correlated with soil dissolved organic carbon contents and methanogens abundance, whereas CH4 fluxes in orchard plots were negatively related to methanotroph abundance. Therefore, our results suggested that land-use conversion from paddies to orchards could change the abundance and community compositions of methanogens and methanotrophs, and ultimately alter the soil CH4 fluxes. Overall, our study shed insight on the underlying mechanisms of how land-use conversion from paddies to orchards decreased CH4 emissions.
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Affiliation(s)
- Huifeng Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Xing Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- Joint Center for Global Change Studies, Beijing, 100875, China.
| | - Zongshan Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Joint Center for Global Change Studies, Beijing, 100875, China
| | - Qing Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Dan Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Guohua Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- Joint Center for Global Change Studies, Beijing, 100875, China.
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71
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Cappelletti M, Ghezzi D, Zannoni D, Capaccioni B, Fedi S. Diversity of Methane-Oxidizing Bacteria in Soils from "Hot Lands of Medolla" (Italy) Featured by Anomalous High-Temperatures and Biogenic CO 2 Emission. Microbes Environ 2016; 31:369-377. [PMID: 27645100 PMCID: PMC5158108 DOI: 10.1264/jsme2.me16087] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/13/2016] [Indexed: 11/24/2022] Open
Abstract
"Terre Calde di Medolla" (TCM) (literally, "Hot Lands of Medolla") refers to a farming area in Italy with anomalously high temperatures and diffuse emissions of biogenic CO2, which has been linked to CH4 oxidation processes from a depth of 0.7 m to the surface. We herein assessed the composition of the total bacterial community and diversity of methane-oxidizing bacteria (MOB) in soil samples collected at a depth at which the peak temperature was detected (0.6 m). Cultivation-independent methods were used, such as: i) a clone library analysis of the 16S rRNA gene and pmoA (coding for the α-subunit of the particulate methane monooxygenase) gene, and ii) Terminal Restriction Fragment Length Polymorphism (T-RFLP) fingerprinting. The 16S rRNA gene analysis assessed the predominance of Actinobacteria, Acidobacteria, Proteobacteria, and Bacillus in TCM samples collected at a depth of 0.6 m along with the presence of methanotrophs (Methylocaldum and Methylobacter) and methylotrophs (Methylobacillus). The phylogenetic analysis of pmoA sequences showed the presence of MOB affiliated with Methylomonas, Methylocystis, Methylococcus, and Methylocaldum in addition to as yet uncultivated and uncharacterized methanotrophs. Jaccard's analysis of T-RFLP profiles at different ground depths revealed a similar MOB composition in soil samples at depths of 0.6 m and 0.7 m, while this similarity was weaker between these samples and those taken at a depth of 2.5 m, in which the genus Methylocaldum was absent. These results correlate the anomalously high temperatures of the farming area of "Terre Calde di Medolla" with the presence of microbial methane-oxidizing bacteria.
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Affiliation(s)
- Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of BolognaVia Irnerio 42, 40126, BolognaItaly
| | - Daniele Ghezzi
- Department of Pharmacy and Biotechnology, University of BolognaVia Irnerio 42, 40126, BolognaItaly
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology, University of BolognaVia Irnerio 42, 40126, BolognaItaly
| | - Bruno Capaccioni
- Department of Biological, Geological and Environmental Sciences, University of BolognaPiazza di Porta S. Donato 1, 40126, BolognaItaly
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology, University of BolognaVia Irnerio 42, 40126, BolognaItaly
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72
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Pandit PS, Ranade DR, Dhakephalkar PK, Rahalkar MC. A pmoA-based study reveals dominance of yet uncultured Type I methanotrophs in rhizospheres of an organically fertilized rice field in India. 3 Biotech 2016; 6:135. [PMID: 28330207 PMCID: PMC4910840 DOI: 10.1007/s13205-016-0453-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/03/2016] [Indexed: 11/28/2022] Open
Abstract
Rice fields are one of the important sources of anthropogenic methane. Methanotrophs can oxidize up to 30 % of the produced methane and thus have a pivotal environmental role in methane mitigation. India occupies the largest region under rice cultivation; however, most of the studies done on methanotrophic communities have focused on the Northern region. We studied methanotrophic community of a flooded, organically fertilized rice field using pmoA clone library approach. Organic rice fields impose a more serious threat as they produce more methane. pmoA gene is the main functional gene which is primarily used for taxonomical analysis of methanotrophs. Our results showed that the pmoA clone libraries from two growth stages of rice were dominated by pmoA sequences which were very distant from cultivated Type Ia methanotrophic genera (80–82 % nucleotide similarity) indicative of the presence of a putatively novel genus. We designated this group of clones as ‘rice field clones’ as this also includes many pmoA sequences originating from other rice fields. Thus, our current knowledge of methanotroph diversity from Indian rice fields has been expanded revealing that a substantial portion of methanotrophic diversity is unexplored.
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Affiliation(s)
- Pranitha S Pandit
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
| | - Dilip R Ranade
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
- Microbial Culture Collection, NCCS, Sai-Trinity Building, Pashan, Pune, Maharashtra, 411021, India
| | | | - Monali C Rahalkar
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.
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73
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Bhattacharjee AS, Motlagh AM, Jetten MSM, Goel R. Methane dependent denitrification- from ecosystem to laboratory-scale enrichment for engineering applications. WATER RESEARCH 2016; 99:244-252. [PMID: 27176548 DOI: 10.1016/j.watres.2016.04.070] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/29/2016] [Accepted: 04/30/2016] [Indexed: 05/28/2023]
Abstract
Managing nitrogen and carbon cycles in engineered and natural ecosystems is an environmental challenge. In this manuscript, we report a process which connects these two cycles with immense ecological and engineering significance. Sediments, collected from Jordan River in Salt Lake City, Utah were used as seed to start a laboratory-scale denitrification coupled to anaerobic methane oxidation (n-DAMO) reactor fed with methane (CH4) and nitrite (NO2(-)). Methane (CH4)-dependent denitrification in sediments of a nutrient-impaired river was found to be in the range of 40 nmol kg(-1) d(-1) to 70 nmol kg(-1) d(-1). Post 19 months of operation of the lab scale reactor, the n-DAMO reactor achieved nitrite removal rate of 2.88 mmol L(-1) d(-1). Enrichment of n-DAMO prokaryotes was evident from the increase in 16S rRNA gene copy number of bacteria belonging to the NC10 phylum in the reactor, corroborating with increase in the oxidation rates of CH4 coupled with NO2(-)-N removal from 21 μM to 190 μM of CH4 d(-1). Based on stable isotope experiments by other researchers, nitric oxide dismutase (nod) functional gene was hypothesized to be responsible for splitting nitric oxide to nitrogen and oxygen and this internally generated oxygen is utilized by n-DAMO prokaryotes to oxidize methane gas. Primers targeting the unique nitric oxide dismutase (nod) gene were developed and tested on the enrichment culture for the first time. This revealed that n-DAMO organisms are closely related yet distinct from, the M. oxyfera which had been enriched in earlier studies. The results emphasize tremendous future promise to use these novel organisms for wastewater treatment purposes, especially to take advantage of the dissolved methane present in anaerobic digester effluents.
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Affiliation(s)
| | | | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Ramesh Goel
- Civil & Environmental Engineering, University of Utah, Salt Lake City, UT 84112, USA.
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74
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Islam T, Torsvik V, Larsen Ø, Bodrossy L, Øvreås L, Birkeland NK. Acid-Tolerant Moderately Thermophilic Methanotrophs of the Class Gammaproteobacteria Isolated From Tropical Topsoil with Methane Seeps. Front Microbiol 2016; 7:851. [PMID: 27379029 PMCID: PMC4908921 DOI: 10.3389/fmicb.2016.00851] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 05/23/2016] [Indexed: 11/13/2022] Open
Abstract
Terrestrial tropical methane seep habitats are important ecosystems in the methane cycle. Methane oxidizing bacteria play a key role in these ecosystems as they reduce methane emissions to the atmosphere. Here, we describe the isolation and initial characterization of two novel moderately thermophilic and acid-tolerant obligate methanotrophs, assigned BFH1 and BFH2 recovered from a tropical methane seep topsoil habitat. The new isolates were strictly aerobic, non-motile, coccus-shaped and utilized methane and methanol as sole carbon and energy source. Isolates grew at pH range 4.2–7.5 (optimal 5.5–6.0) and at a temperature range of 30–60°C (optimal 51–55°C). 16S rRNA gene phylogeny placed them in a well-separated branch forming a cluster together with the genus Methylocaldum as the closest relatives (93.1–94.1% sequence similarity). The genes pmoA, mxaF, and cbbL were detected, but mmoX was absent. Strains BFH1 and BFH2 are, to our knowledge, the first isolated acid-tolerant moderately thermophilic methane oxidizers of the class Gammaproteobacteria. Each strain probably denotes a novel species and they most likely represent a novel genus within the family Methylococcaceae of type I methanotrophs. Furthermore, the isolates increase our knowledge of acid-tolerant aerobic methanotrophs and signify a previously unrecognized biological methane sink in tropical ecosystems.
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Affiliation(s)
- Tajul Islam
- Department of Biology, University of Bergen Bergen, Norway
| | - Vigdis Torsvik
- Department of Biology, University of Bergen Bergen, Norway
| | - Øivind Larsen
- Department of Biology, University of BergenBergen, Norway; Uni Environment, Uni ResearchBergen, Norway
| | | | - Lise Øvreås
- Department of Biology, University of Bergen Bergen, Norway
| | - Nils-Kåre Birkeland
- Department of Biology, University of BergenBergen, Norway; Centre for Geobiology, University of BergenBergen, Norway
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75
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Yanagawa K, Tani A, Yamamoto N, Hachikubo A, Kano A, Matsumoto R, Suzuki Y. Biogeochemical Cycle of Methanol in Anoxic Deep-Sea Sediments. Microbes Environ 2016; 31:190-3. [PMID: 27301420 PMCID: PMC4912158 DOI: 10.1264/jsme2.me15204] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The biological flux and lifetime of methanol in anoxic marine sediments are largely unknown. We herein reported, for the first time, quantitative methanol removal rates in subsurface sediments. Anaerobic incubation experiments with radiotracers showed high rates of microbial methanol consumption. Notably, methanol oxidation to CO2 surpassed methanol assimilation and methanogenesis from CO2/H2 and methanol. Nevertheless, a significant decrease in methanol was not observed after the incubation, and this was attributed to the microbial production of methanol in parallel with its consumption. These results suggest that microbial reactions play an important role in the sources and sinks of methanol in subseafloor sediments.
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76
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Osudar R, Liebner S, Alawi M, Yang S, Bussmann I, Wagner D. Methane turnover and methanotrophic communities in arctic aquatic ecosystems of the Lena Delta, Northeast Siberia. FEMS Microbiol Ecol 2016; 92:fiw116. [PMID: 27230921 DOI: 10.1093/femsec/fiw116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2016] [Indexed: 01/01/2023] Open
Abstract
Large amounts of organic carbon are stored in Arctic permafrost environments, and microbial activity can potentially mineralize this carbon into methane, a potent greenhouse gas. In this study, we assessed the methane budget, the bacterial methane oxidation (MOX) and the underlying environmental controls of arctic lake systems, which represent substantial sources of methane. Five lake systems located on Samoylov Island (Lena Delta, Siberia) and the connected river sites were analyzed using radiotracers to estimate the MOX rates, and molecular biology methods to characterize the abundance and the community composition of methane-oxidizing bacteria (MOB). In contrast to the river, the lake systems had high variation in the methane concentrations, the abundance and composition of the MOB communities, and consequently, the MOX rates. The highest methane concentrations and the highest MOX rates were detected in the lake outlets and in a lake complex in a flood plain area. Though, in all aquatic systems, we detected both, Type I and II MOB, in lake systems, we observed a higher diversity including MOB, typical of the soil environments. The inoculation of soil MOB into the aquatic systems, resulting from permafrost thawing, might be an additional factor controlling the MOB community composition and potentially methanotrophic capacity.
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Affiliation(s)
- Roman Osudar
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Research Unit Potsdam, Telegrafenberg, 14473 Potsdam, Germany GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Mashal Alawi
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Sizhong Yang
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Ingeborg Bussmann
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Biological Station Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
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77
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Danilova OV, Suzina NE, Van De Kamp J, Svenning MM, Bodrossy L, Dedysh SN. A new cell morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments. ISME JOURNAL 2016; 10:2734-2743. [PMID: 27058508 DOI: 10.1038/ismej.2016.48] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/05/2016] [Accepted: 02/25/2016] [Indexed: 12/29/2022]
Abstract
Although representatives with spiral-shaped cells are described for many functional groups of bacteria, this cell morphotype has never been observed among methanotrophs. Here, we show that spiral-shaped methanotrophic bacteria do exist in nature but elude isolation by conventional approaches due to the preference for growth under micro-oxic conditions. The helical cell shape may enable rapid motility of these bacteria in water-saturated, heterogeneous environments with high microbial biofilm content, therefore offering an advantage of fast cell positioning under desired high methane/low oxygen conditions. The pmoA genes encoding a subunit of particulate methane monooxygenase from these methanotrophs form a new genus-level lineage within the family Methylococcaceae, type Ib methanotrophs. Application of a pmoA-based microarray detected these bacteria in a variety of high-latitude freshwater environments including wetlands and lake sediments. As revealed by the environmental pmoA distribution analysis, type Ib methanotrophs tend to live very near the methane source, where oxygen is scarce. The former perception of type Ib methanotrophs as being typical for thermal habitats appears to be incorrect because only a minor proportion of pmoA sequences from these bacteria originated from environments with elevated temperatures.
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Affiliation(s)
- Olga V Danilova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Natalia E Suzina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | | | - Mette M Svenning
- UiT The Arctic University of Norway, Department of Arctic and Marine Biology, Tromsø, Norway
| | | | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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78
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Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog. Appl Environ Microbiol 2016; 82:2363-2371. [PMID: 26873322 DOI: 10.1128/aem.03640-15] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/03/2016] [Indexed: 11/20/2022] Open
Abstract
The objective of this study was to characterize metabolically active, aerobic methanotrophs in an ombrotrophic peatland in the Marcell Experimental Forest, in Minnesota. Methanotrophs were investigated in the field and in laboratory incubations using DNA-stable isotope probing (SIP), expression studies on particulate methane monooxygenase (pmoA) genes, and amplicon sequencing of 16S rRNA genes. Potential rates of oxidation ranged from 14 to 17 μmol of CH4g dry weight soil(-1)day(-1) Within DNA-SIP incubations, the relative abundance of methanotrophs increased from 4% in situ to 25 to 36% after 8 to 14 days. Phylogenetic analysis of the(13)C-enriched DNA fractions revealed that the active methanotrophs were dominated by the genera Methylocystis(type II;Alphaproteobacteria),Methylomonas, and Methylovulum(both, type I;Gammaproteobacteria). In field samples, a transcript-to-gene ratio of 1 to 2 was observed for pmoA in surface peat layers, which attenuated rapidly with depth, indicating that the highest methane consumption was associated with a depth of 0 to 10 cm. Metagenomes and sequencing of cDNA pmoA amplicons from field samples confirmed that the dominant active methanotrophs were Methylocystis and Methylomonas Although type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate that members of the genera Methylomonas and Methylovulum(type I) can significantly contribute to aerobic methane oxidation in these ecosystems.
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79
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Sawakuchi HO, Bastviken D, Sawakuchi AO, Ward ND, Borges CD, Tsai SM, Richey JE, Ballester MVR, Krusche AV. Oxidative mitigation of aquatic methane emissions in large Amazonian rivers. GLOBAL CHANGE BIOLOGY 2016; 22:1075-1085. [PMID: 26872424 DOI: 10.1111/gcb.13169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 09/16/2015] [Accepted: 11/04/2015] [Indexed: 06/05/2023]
Abstract
The flux of methane (CH4 ) from inland waters to the atmosphere has a profound impact on global atmospheric greenhouse gas (GHG) levels, and yet, strikingly little is known about the dynamics controlling sources and sinks of CH4 in the aquatic setting. Here, we examine the cycling and flux of CH4 in six large rivers in the Amazon basin, including the Amazon River. Based on stable isotopic mass balances of CH4 , inputs and outputs to the water column were estimated. We determined that ecosystem methane oxidation (MOX) reduced the diffusive flux of CH4 by approximately 28-96% and varied depending on hydrologic regime and general geochemical characteristics of tributaries of the Amazon River. For example, the relative amount of MOX was maximal during high water in black and white water rivers and minimal in clear water rivers during low water. The abundance of genetic markers for methane-oxidizing bacteria (pmoA) was positively correlated with enhanced signals of oxidation, providing independent support for the detected MOX patterns. The results indicate that MOX in large Amazonian rivers can consume from 0.45 to 2.07 Tg CH4 yr(-1) , representing up to 7% of the estimated global soil sink. Nevertheless, climate change and changes in hydrology, for example, due to construction of dams, can alter this balance, influencing CH4 emissions to atmosphere.
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Affiliation(s)
- Henrique O Sawakuchi
- Center of Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário, 303, Piracicaba, SP 13400-970, Brazil
| | - David Bastviken
- Department of Thematic Studies - Environmental Change, Linköping University, Linköping, SE-581 83, Sweden
| | - André O Sawakuchi
- Departament of Sedimentary and Environmental Geology, Institute of Geosciences, University of São Paulo, Rua do Lago, 562, São Paulo, SP 05508-080, Brazil
| | - Nicholas D Ward
- Department of Geological Sciences, University of Florida, Box 112120, Gainesville, FL, 32611-2120, USA
| | - Clovis D Borges
- Center of Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário, 303, Piracicaba, SP 13400-970, Brazil
| | - Siu M Tsai
- Center of Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário, 303, Piracicaba, SP 13400-970, Brazil
| | - Jeffrey E Richey
- School of Oceanography, University of Washington, Seattle, WA, 98195-7940, USA
| | - Maria Victoria R Ballester
- Center of Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário, 303, Piracicaba, SP 13400-970, Brazil
| | - Alex V Krusche
- Center of Nuclear Energy in Agriculture, University of São Paulo, Av. Centenário, 303, Piracicaba, SP 13400-970, Brazil
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80
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Sherry A, Osborne KA, Sidgwick FR, Gray ND, Talbot HM. A temperate river estuary is a sink for methanotrophs adapted to extremes of pH, temperature and salinity. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:122-31. [PMID: 26617278 PMCID: PMC4959530 DOI: 10.1111/1758-2229.12359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 11/19/2015] [Indexed: 05/08/2023]
Abstract
River Tyne (UK) estuarine sediments harbour a genetically and functionally diverse community of methane-oxidizing bacteria (methanotrophs), the composition and activity of which were directly influenced by imposed environmental conditions (pH, salinity, temperature) that extended far beyond those found in situ. In aerobic sediment slurries methane oxidation rates were monitored together with the diversity of a functional gene marker for methanotrophs (pmoA). Under near in situ conditions (4-30°C, pH 6-8, 1-15 g l(-1) NaCl), communities were enriched by sequences affiliated with Methylobacter and Methylomonas spp. and specifically a Methylobacter psychrophilus-related species at 4-21°C. More extreme conditions, namely high temperatures ≥ 40°C, high ≥ 9 and low ≤ 5 pH, and high salinities ≥ 35 g l(-1) selected for putative thermophiles (Methylocaldum), acidophiles (Methylosoma) and haloalkaliphiles (Methylomicrobium). The presence of these extreme methanotrophs (unlikely to be part of the active community in situ) indicates passive dispersal from surrounding environments into the estuary.
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Affiliation(s)
- Angela Sherry
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kate A Osborne
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Frances R Sidgwick
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Neil D Gray
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Helen M Talbot
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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81
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Hofmann K, Pauli H, Praeg N, Wagner AO, Illmer P. Methane-cycling microorganisms in soils of a high-alpine altitudinal gradient. FEMS Microbiol Ecol 2016; 92:fiw009. [PMID: 26790465 DOI: 10.1093/femsec/fiw009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2016] [Indexed: 11/13/2022] Open
Abstract
Methanogens and methanotrophs play unique roles as producers and consumers of the greenhouse gas methane (CH4) in soils, respectively. Here, we aimed to reveal whether and to which extent methane-cyclers occur in high-alpine soils, and to assess their spatial distribution along an altitudinal gradient (2700-3500 m) in the Austrian Alps at sites located within the alpine (2700-2900 m), the alpine-nival (3000-3100 m) and the nival belts (3200-3500 m). Methanococcales and Methanocella spp. were most abundant among all quantified methanogenic guilds, whereas Methanosarcinales were not detected in the studied soil. The detected methanogens seem to be capable of persisting despite a highly oxic low-temperature environment. Methanogenic and methanotrophic activities and abundances of methanotrophs, Methanococcales and Methanocella spp. declined with altitude. Methanogenic and methanotrophic abundances were best explained by mean annual soil temperature and dissolved organic carbon, respectively. Alpine belt soils harbored significantly more methane-cyclers than those of the nival belt, indicating some influence of plant cover. Our results show that methanogens are capable of persisting in high-alpine cold soils and might help to understand future changes of these environments caused by climate warming.
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Affiliation(s)
- Katrin Hofmann
- Institute of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Harald Pauli
- Institute for Interdisciplinary Mountain Research, Austrian Academy of Sciences and Center for Global Change and Sustainability, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Nadine Praeg
- Institute of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Andreas O Wagner
- Institute of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Paul Illmer
- Institute of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
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Wang L, Pan Z, Xu H, Wang C, Gao L, Zhao P, Dong Z, Zhang J, Cui G, Wang S, Han G, Zhao H. The influence of nitrogen fertiliser rate and crop rotation on soil methane flux in rain-fed potato fields in Wuchuan County, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 537:93-99. [PMID: 26282743 DOI: 10.1016/j.scitotenv.2015.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 07/27/2015] [Accepted: 08/01/2015] [Indexed: 06/04/2023]
Abstract
As one of the important greenhouse gases, the characteristics and principles of methane exchange characteristics in cultivated lands have become hot topics in current climate change research. This study examines the influences of nitrogen fertilisation, temperature and soil water content on methane exchange characteristic and methane exchange functional gene-pmoA gene abundance based on experimental observations of methane exchange fluxes using the static chamber-gas chromatographic method and measurements of methanotroph gene copy numbers in three growing periods by real-time PCR in rain-fed potato fields. The results indicate that the rain-fed potato fields were a CH4 sink with an average annual methane absorption (negative emission) of 940.8±103.2 g CH4-C/ha/year. The cumulative methane absorption first exhibited flat and subsequently increasing trend with the increase of nitrogen fertilisation from 0~135 kg N·ha(-1). Methane cumulative absorption significantly increased with the increase of temperature when temperatures were below 19.6 °C. Methane oxidation capacity (methanotroph pmoA gene copy numbers) showed an increasing and subsequently decreasing trend with the increase of soil moisture. Crop rotation was observed to increase the methane absorption in rain-fed potato fields and nearly one time higher than that under continuous cropping. A mechanism concept model of the methane exchange in rain-fed potato fields was advanced in this paper.
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Affiliation(s)
- Liwei Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; Wuchuan Scientific Observing and Experimental Station of Agro-Environment, Ministry of Agriculture Wuchuan 011700, China
| | - Zhihua Pan
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Wuchuan Scientific Observing and Experimental Station of Agro-Environment, Ministry of Agriculture Wuchuan 011700, China.
| | - Hui Xu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Cheng Wang
- College of Agricultural and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Lin Gao
- School of Resources and Environmental, Anhui Agricultural University, Hefei 230036, China
| | - Peiyi Zhao
- Institute of Resources Environmental and Detection Technology, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Huhhot 010031, China; Wuchuan Scientific Observing and Experimental Station of Agro-Environment, Ministry of Agriculture Wuchuan 011700, China
| | - Zhiqiang Dong
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Wuchuan Scientific Observing and Experimental Station of Agro-Environment, Ministry of Agriculture Wuchuan 011700, China
| | - Jingting Zhang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Wuchuan Scientific Observing and Experimental Station of Agro-Environment, Ministry of Agriculture Wuchuan 011700, China
| | - Guohui Cui
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Wuchuan Scientific Observing and Experimental Station of Agro-Environment, Ministry of Agriculture Wuchuan 011700, China
| | - Sen Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Wuchuan Scientific Observing and Experimental Station of Agro-Environment, Ministry of Agriculture Wuchuan 011700, China
| | - Guolin Han
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Wuchuan Scientific Observing and Experimental Station of Agro-Environment, Ministry of Agriculture Wuchuan 011700, China
| | - Hui Zhao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Wuchuan Scientific Observing and Experimental Station of Agro-Environment, Ministry of Agriculture Wuchuan 011700, China
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83
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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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84
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Lee EH, Moon KE, Kim TG, Lee SD, Cho KS. Inhibitory effects of sulfur compounds on methane oxidation by a methane-oxidizing consortium. J Biosci Bioeng 2015; 120:670-6. [DOI: 10.1016/j.jbiosc.2015.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 04/07/2015] [Accepted: 04/08/2015] [Indexed: 01/10/2023]
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85
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Damm E, Rudels B, Schauer U, Mau S, Dieckmann G. Methane excess in Arctic surface water-triggered by sea ice formation and melting. Sci Rep 2015; 5:16179. [PMID: 26553610 PMCID: PMC4639778 DOI: 10.1038/srep16179] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 09/10/2015] [Indexed: 11/26/2022] Open
Abstract
Arctic amplification of global warming has led to increased summer sea ice retreat, which influences gas exchange between the Arctic Ocean and the atmosphere where sea ice previously acted as a physical barrier. Indeed, recently observed enhanced atmospheric methane concentrations in Arctic regions with fractional sea-ice cover point to unexpected feedbacks in cycling of methane. We report on methane excess in sea ice-influenced water masses in the interior Arctic Ocean and provide evidence that sea ice is a potential source. We show that methane release from sea ice into the ocean occurs via brine drainage during freezing and melting i.e. in winter and spring. In summer under a fractional sea ice cover, reduced turbulence restricts gas transfer, then seawater acts as buffer in which methane remains entrained. However, in autumn and winter surface convection initiates pronounced efflux of methane from the ice covered ocean to the atmosphere. Our results demonstrate that sea ice-sourced methane cycles seasonally between sea ice, sea-ice-influenced seawater and the atmosphere, while the deeper ocean remains decoupled. Freshening due to summer sea ice retreat will enhance this decoupling, which restricts the capacity of the deeper Arctic Ocean to act as a sink for this greenhouse gas.
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Affiliation(s)
- E Damm
- Alfred Wegener Institute Helmholtz-Centre for Polar and Marine Research P.O. Box 12061, 27515 Bremerhaven, Germany
| | - B Rudels
- Finnish Meteorological Institute, Erik Palmenin aukio 1 P.O. Box 503, FI-00101 Helsinki, Finland
| | - U Schauer
- Alfred Wegener Institute Helmholtz-Centre for Polar and Marine Research P.O. Box 12061, 27515 Bremerhaven, Germany
| | - S Mau
- University of Bremen, Section Geoscience, P.O. Box 330440, 28334 Bremen, Germany
| | - G Dieckmann
- Alfred Wegener Institute Helmholtz-Centre for Polar and Marine Research P.O. Box 12061, 27515 Bremerhaven, Germany
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86
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Wallace RJ, Rooke JA, McKain N, Duthie CA, Hyslop JJ, Ross DW, Waterhouse A, Watson M, Roehe R. The rumen microbial metagenome associated with high methane production in cattle. BMC Genomics 2015; 16:839. [PMID: 26494241 PMCID: PMC4619255 DOI: 10.1186/s12864-015-2032-0] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/08/2015] [Indexed: 02/01/2023] Open
Abstract
Background Methane represents 16 % of total anthropogenic greenhouse gas emissions. It has been estimated that ruminant livestock produce ca. 29 % of this methane. As individual animals produce consistently different quantities of methane, understanding the basis for these differences may lead to new opportunities for mitigating ruminal methane emissions. Metagenomics is a powerful new tool for understanding the composition and function of complex microbial communities. Here we have applied metagenomics to the rumen microbial community to identify differences in the microbiota and metagenome that lead to high- and low-methane-emitting cattle phenotypes. Methods Four pairs of beef cattle were selected for extreme high and low methane emissions from 72 animals, matched for breed (Aberdeen-Angus or Limousin cross) and diet (high or medium concentrate). Community analysis was carried out by qPCR of 16S and 18S rRNA genes and by alignment of Illumina HiSeq reads to the GREENGENES database. Total genomic reads were aligned to the KEGG genes databasefor functional analysis. Results Deep sequencing produced on average 11.3 Gb per sample. 16S rRNA gene abundances indicated that archaea, predominantly Methanobrevibacter, were 2.5× more numerous (P = 0.026) in high emitters, whereas among bacteria Proteobacteria, predominantly Succinivibrionaceae, were 4-fold less abundant (2.7 vs. 11.2 %; P = 0.002). KEGG analysis revealed that archaeal genes leading directly or indirectly to methane production were 2.7-fold more abundant in high emitters. Genes less abundant in high emitters included acetate kinase, electron transport complex proteins RnfC and RnfD and glucose-6-phosphate isomerase. Sequence data were assembled de novo and over 1.5 million proteins were annotated on the subsequent metagenome scaffolds. Less than half of the predicted genes matched matched a domain within Pfam. Amongst 2774 identified proteins of the 20 KEGG orthologues that correlated with methane emissions, only 16 showed 100 % identity with a publicly available protein sequence. Conclusions The abundance of archaeal genes in ruminal digesta correlated strongly with differing methane emissions from individual animals, a finding useful for genetic screening purposes. Lower emissions were accompanied by higher Succinovibrionaceae abundance and changes in acetate and hydrogen production leading to less methanogenesis, as similarly postulated for Australian macropods. Large numbers of predicted protein sequences differed between high- and low-methane-emitting cattle. Ninety-nine percent were unknown, indicating a fertile area for future exploitation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2032-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- R John Wallace
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, AB21 9SB, UK.
| | | | - Nest McKain
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, AB21 9SB, UK.
| | | | | | | | | | - Mick Watson
- Edinburgh Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.
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87
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Krause S, Niklaus PA, Badwan Morcillo S, Meima Franke M, Lüke C, Reim A, Bodelier PLE. Compositional and functional stability of aerobic methane consuming communities in drained and rewetted peat meadows. FEMS Microbiol Ecol 2015; 91:fiv119. [PMID: 26449384 DOI: 10.1093/femsec/fiv119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2015] [Indexed: 11/13/2022] Open
Abstract
The restoration of peatlands is an important strategy to counteract subsidence and loss of biodiversity. However, responses of important microbial soil processes are poorly understood. We assessed functioning, diversity and spatial organization of methanotrophic communities in drained and rewetted peat meadows with different water table management and agricultural practice. Results show that the methanotrophic diversity was similar between drained and rewetted sites with a remarkable dominance of the genus Methylocystis. Enzyme kinetics depicted no major differences, indicating flexibility in the methane (CH4) concentrations that can be used by the methanotrophic community. Short-term flooding led to temporary elevated CH4 emission but to neither major changes in abundances of methane-oxidizing bacteria (MOB) nor major changes in CH4 consumption kinetics in drained agriculturally used peat meadows. Radiolabeling and autoradiographic imaging of intact soil cores revealed a markedly different spatial arrangement of the CH4 consuming zone in cores exposed to near-atmospheric and elevated CH4. The observed spatial patterns of CH4 consumption in drained peat meadows with and without short-term flooding highlighted the spatial complexity and responsiveness of the CH4 consuming zone upon environmental change. The methanotrophic microbial community is not generally altered and harbors MOB that can cover a large range of CH4 concentrations offered due to water-table fluctuations, effectively mitigating CH4 emissions.
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Affiliation(s)
- Sascha Krause
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Pascal A Niklaus
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
| | - Sara Badwan Morcillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
| | - Marion Meima Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
| | - Claudia Lüke
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, 6525 AJ, the Netherlands
| | - Andreas Reim
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
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88
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Lammel DR, Feigl BJ, Cerri CC, Nüsslein K. Specific microbial gene abundances and soil parameters contribute to C, N, and greenhouse gas process rates after land use change in Southern Amazonian Soils. Front Microbiol 2015; 6:1057. [PMID: 26500618 PMCID: PMC4594008 DOI: 10.3389/fmicb.2015.01057] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 09/14/2015] [Indexed: 11/30/2022] Open
Abstract
Ecological processes regulating soil carbon (C) and nitrogen (N) cycles are still poorly understood, especially in the world’s largest agricultural frontier in Southern Amazonia. We analyzed soil parameters in samples from pristine rainforest and after land use change to pasture and crop fields, and correlated them with abundance of functional and phylogenetic marker genes (amoA, nirK, nirS, norB, nosZ, nifH, mcrA, pmoA, and 16S/18S rRNA). Additionally, we integrated these parameters using path analysis and multiple regressions. Following forest removal, concentrations of soil C and N declined, and pH and nutrient levels increased, which influenced microbial abundances and biogeochemical processes. A seasonal trend was observed, suggesting that abundances of microbial groups were restored to near native levels after the dry winter fallow. Integration of the marker gene abundances with soil parameters using path analysis and multiple regressions provided good predictions of biogeochemical processes, such as the fluxes of NO3, N2O, CO2, and CH4. In the wet season, agricultural soil showed the highest abundance of nitrifiers (amoA) and Archaea, however, forest soils showed the highest abundances of denitrifiers (nirK, nosZ) and high N, which correlated with increased N2O emissions. Methanogens (mcrA) and methanotrophs (pmoA) were more abundant in forest soil, but methane flux was highest in pasture sites, which was related to soil compaction. Rather than analyzing direct correlations, the data integration using multivariate tools provided a better overview of biogeochemical processes. Overall, in the wet season, land use change from forest to agriculture reduced the abundance of different functional microbial groups related to the soil C and N cycles; integrating the gene abundance data and soil parameters provided a comprehensive overview of these interactions. Path analysis and multiple regressions addressed the need for more comprehensive approaches to improve our mechanistic understanding of biogeochemical cycles.
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Affiliation(s)
- Daniel R Lammel
- Centro de Energia Nuclear na Agricultura, University of São Paulo Piracicaba, Brazil ; Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Brigitte J Feigl
- Centro de Energia Nuclear na Agricultura, University of São Paulo Piracicaba, Brazil
| | - Carlos C Cerri
- Centro de Energia Nuclear na Agricultura, University of São Paulo Piracicaba, Brazil
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
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89
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Landscape position influences microbial composition and function via redistribution of soil water across a watershed. Appl Environ Microbiol 2015; 81:8457-68. [PMID: 26431971 DOI: 10.1128/aem.02643-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/28/2015] [Indexed: 02/01/2023] Open
Abstract
Subalpine forest ecosystems influence global carbon cycling. However, little is known about the compositions of their soil microbial communities and how these may vary with soil environmental conditions. The goal of this study was to characterize the soil microbial communities in a subalpine forest watershed in central Montana (Stringer Creek Watershed within the Tenderfoot Creek Experimental Forest) and to investigate their relationships with environmental conditions and soil carbonaceous gases. As assessed by tagged Illumina sequencing of the 16S rRNA gene, community composition and structure differed significantly among three landscape positions: high upland zones (HUZ), low upland zones (LUZ), and riparian zones (RZ). Soil depth effects on phylogenetic diversity and β-diversity varied across landscape positions, being more evident in RZ than in HUZ. Mantel tests revealed significant correlations between microbial community assembly patterns and the soil environmental factors tested (water content, temperature, oxygen, and pH) and soil carbonaceous gases (carbon dioxide concentration and efflux and methane concentration). With one exception, methanogens were detected only in RZ soils. In contrast, methanotrophs were detected in all three landscape positions. Type I methanotrophs dominated RZ soils, while type II methanotrophs dominated LUZ and HUZ soils. The relative abundances of methanotroph populations correlated positively with soil water content (R = 0.72, P < 0.001) and negatively with soil oxygen (R = -0.53, P = 0.008). Our results suggest the coherence of soil microbial communities within and differences in communities between landscape positions in a subalpine forested watershed that reflect historical and contemporary environmental conditions.
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90
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Novel Methanotrophs of the Family Methylococcaceae from Different Geographical Regions and Habitats. Microorganisms 2015; 3:484-99. [PMID: 27682101 PMCID: PMC5023254 DOI: 10.3390/microorganisms3030484] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/04/2015] [Accepted: 08/07/2015] [Indexed: 11/24/2022] Open
Abstract
Terrestrial methane seeps and rice paddy fields are important ecosystems in the methane cycle. Methanotrophic bacteria in these ecosystems play a key role in reducing methane emission into the atmosphere. Here, we describe three novel methanotrophs, designated BRS-K6, GFS-K6 and AK-K6, which were recovered from three different habitats in contrasting geographic regions and ecosystems: waterlogged rice-field soil and methane seep pond sediments from Bangladesh; and warm spring sediments from Armenia. All isolates had a temperature range for growth of 8–35 °C (optimal 25–28 °C) and a pH range of 5.0–7.5 (optimal 6.4–7.0). 16S rRNA gene sequences showed that they were new gammaproteobacterial methanotrophs, which form a separate clade in the family Methylococcaceae. They fell into a cluster with thermotolerant and mesophilic growth tendency, comprising the genera Methylocaldum-Methylococcus-Methyloparacoccus-Methylogaea. So far, growth below 15 °C of methanotrophs from this cluster has not been reported. The strains possessed type I intracytoplasmic membranes. The genes pmoA, mxaF, cbbL, nifH were detected, but no mmoX gene was found. Each strain probably represents a novel species either belonging to the same novel genus or each may even represent separate genera. These isolates extend our knowledge of methanotrophic Gammaproteobacteria and their physiology and adaptation to different ecosystems.
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91
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Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions. mBio 2015; 6:e00066-15. [PMID: 25991679 PMCID: PMC4442139 DOI: 10.1128/mbio.00066-15] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhouse gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest. IMPORTANCE Wetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial communities that mediate carbon cycling in wetlands is critical to accurately predicting their responses to changes in land management and climate. Here, we studied a restored wetland and revealed substantial spatial heterogeneity in biogeochemistry, methane production, and microbial communities, largely associated with the wetland hydraulic design. We observed patterns in microbial community composition and functions correlated with biogeochemistry and methane production, including diverse microorganisms involved in methane production and consumption. We found that methanogenesis gene abundance is inversely correlated with genes from pathways exploiting other electron acceptors, yet the ubiquitous presence of genes from all these pathways suggests that diverse electron acceptors contribute to the energetic balance of the ecosystem. These investigations represent an important step toward effective management of wetlands to reduce methane flux to the atmosphere and enhance belowground carbon storage.
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92
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Lau MCY, Stackhouse BT, Layton AC, Chauhan A, Vishnivetskaya TA, Chourey K, Ronholm J, Mykytczuk NCS, Bennett PC, Lamarche-Gagnon G, Burton N, Pollard WH, Omelon CR, Medvigy DM, Hettich RL, Pfiffner SM, Whyte LG, Onstott TC. An active atmospheric methane sink in high Arctic mineral cryosols. ISME JOURNAL 2015; 9:1880-91. [PMID: 25871932 DOI: 10.1038/ismej.2015.13] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 11/21/2014] [Accepted: 01/05/2015] [Indexed: 11/09/2022]
Abstract
Methane (CH4) emission by carbon-rich cryosols at the high latitudes in Northern Hemisphere has been studied extensively. In contrast, data on the CH4 emission potential of carbon-poor cryosols is limited, despite their spatial predominance. This work employs CH4 flux measurements in the field and under laboratory conditions to show that the mineral cryosols at Axel Heiberg Island in the Canadian high Arctic consistently consume atmospheric CH4. Omics analyses present the first molecular evidence of active atmospheric CH4-oxidizing bacteria (atmMOB) in permafrost-affected cryosols, with the prevalent atmMOB genotype in our acidic mineral cryosols being closely related to Upland Soil Cluster α. The atmospheric (atm) CH4 uptake at the study site increases with ground temperature between 0 °C and 18 °C. Consequently, the atm CH4 sink strength is predicted to increase by a factor of 5-30 as the Arctic warms by 5-15 °C over a century. We demonstrate that acidic mineral cryosols are a previously unrecognized potential of CH4 sink that requires further investigation to determine its potential impact on larger scales. This study also calls attention to the poleward distribution of atmMOB, as well as to the potential influence of microbial atm CH4 oxidation, in the context of regional CH4 flux models and global warming.
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Affiliation(s)
- M C Y Lau
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - B T Stackhouse
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - A C Layton
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
| | - A Chauhan
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
| | - T A Vishnivetskaya
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
| | - K Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - J Ronholm
- Department of Natural Resource Sciences, McGill University, Ste. Anna de Bellevue, Quebec, Canada
| | - N C S Mykytczuk
- 1] Department of Natural Resource Sciences, McGill University, Ste. Anna de Bellevue, Quebec, Canada [2] Vale Living with Lakes Centre, Laurentian University, Sudbury, Ontario, Canada
| | - P C Bennett
- Department of Geological Sciences, The University of Texas at Austin, Austin, TX, USA
| | - G Lamarche-Gagnon
- Department of Natural Resource Sciences, McGill University, Ste. Anna de Bellevue, Quebec, Canada
| | - N Burton
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - W H Pollard
- Department of Geography, McGill University, Montreal, Quebec, Canada
| | - C R Omelon
- Department of Geological Sciences, The University of Texas at Austin, Austin, TX, USA
| | - D M Medvigy
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - R L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - S M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
| | - L G Whyte
- Department of Natural Resource Sciences, McGill University, Ste. Anna de Bellevue, Quebec, Canada
| | - T C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, USA
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93
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Lau E, Iv EJN, Dillard ZW, Dague RD, Semple AL, Wentzell WL. High Throughput Sequencing to Detect Differences in Methanotrophic Methylococcaceae and Methylocystaceae in Surface Peat, Forest Soil, and Sphagnum Moss in Cranesville Swamp Preserve, West Virginia, USA. Microorganisms 2015; 3:113-36. [PMID: 27682082 PMCID: PMC5023241 DOI: 10.3390/microorganisms3020113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Revised: 02/23/2015] [Accepted: 03/26/2015] [Indexed: 01/08/2023] Open
Abstract
Northern temperate forest soils and Sphagnum-dominated peatlands are a major source and sink of methane. In these ecosystems, methane is mainly oxidized by aerobic methanotrophic bacteria, which are typically found in aerated forest soils, surface peat, and Sphagnum moss. We contrasted methanotrophic bacterial diversity and abundances from the (i) organic horizon of forest soil; (ii) surface peat; and (iii) submerged Sphagnum moss from Cranesville Swamp Preserve, West Virginia, using multiplex sequencing of bacterial 16S rRNA (V3 region) gene amplicons. From ~1 million reads, >50,000 unique OTUs (Operational Taxonomic Units), 29 and 34 unique sequences were detected in the Methylococcaceae and Methylocystaceae, respectively, and 24 potential methanotrophs in the Beijerinckiaceae were also identified. Methylacidiphilum-like methanotrophs were not detected. Proteobacterial methanotrophic bacteria constitute <2% of microbiota in these environments, with the Methylocystaceae one to two orders of magnitude more abundant than the Methylococcaceae in all environments sampled. The Methylococcaceae are also less diverse in forest soil compared to the other two habitats. Nonmetric multidimensional scaling analyses indicated that the majority of methanotrophs from the Methylococcaceae and Methylocystaceae tend to occur in one habitat only (peat or Sphagnum moss) or co-occurred in both Sphagnum moss and peat. This study provides insights into the structure of methanotrophic communities in relationship to habitat type, and suggests that peat and Sphagnum moss can influence methanotroph community structure and biogeography.
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Affiliation(s)
- Evan Lau
- Department of Natural Sciences and Mathematics, West Liberty University, 208 University Drive, CUB#139, West Liberty, WV 26074, USA.
| | - Edward J Nolan Iv
- Department of Natural Sciences and Mathematics, West Liberty University, 208 University Drive, CUB#139, West Liberty, WV 26074, USA
| | - Zachary W Dillard
- Department of Natural Sciences and Mathematics, West Liberty University, 208 University Drive, CUB#139, West Liberty, WV 26074, USA.
| | - Ryan D Dague
- Department of Natural Sciences and Mathematics, West Liberty University, 208 University Drive, CUB#139, West Liberty, WV 26074, USA.
| | - Amanda L Semple
- Department of Natural Sciences and Mathematics, West Liberty University, 208 University Drive, CUB#139, West Liberty, WV 26074, USA.
| | - Wendi L Wentzell
- Department of Natural Sciences and Mathematics, West Liberty University, 208 University Drive, CUB#139, West Liberty, WV 26074, USA.
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94
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Yun J, Zhang H, Deng Y, Wang Y. Aerobic methanotroph diversity in Sanjiang wetland, Northeast China. MICROBIAL ECOLOGY 2015; 69:567-576. [PMID: 25351140 DOI: 10.1007/s00248-014-0506-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 09/25/2014] [Indexed: 06/04/2023]
Abstract
Aerobic methanotrophs present in wetlands can serve as a methane filter and thereby significantly reduce methane emissions. Sanjiang wetland is a major methane source and the second largest wetland in China, yet little is known about the characteristics of aerobic methanotrophs in this region. In the present study, we investigated the diversity and abundance of methanotrophs in marsh soils from Sanjiang wetland with three different types of vegetation by 16S ribosomal RNA (rRNA) and pmoA gene analysis. Quantitative polymerase chain reaction analysis revealed the highest number of pmoA gene copies in marsh soils vegetated with Carex lasiocarpa (10(9) g(-1) dry soil), followed by Carex meyeriana, and the least with Deyeuxia angustifolia (10(8) g(-1) dry soil). Consistent results were obtained using Sanger sequencing and pyrosequencing techniques, both indicating the codominance of Methylobacter and Methylocystis species in Sanjiang wetland. Other less abundant methanotrophy, including cultivated Methylomonas and Methylosinus genus, and uncultured clusters such as LP20 and JR-1, were also detected in the wetland. Methanotroph diversity was almost the same in three different vegetation covered soils, suggesting that vegetation types had very little influence on the methanotroph diversity. Our study gives an in-depth insight into the community composition of aerobic methanotrophs in the Sanjiang wetland.
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Affiliation(s)
- Juanli Yun
- College of Resources and Environment, University of Chinese Academy of Sciences, 19A Yuquan Road, 100049, Beijing, China
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95
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He R, Wooller MJ, Pohlman JW, Tiedje JM, Leigh MB. Methane-derived carbon flow through microbial communities in arctic lake sediments. Environ Microbiol 2015; 17:3233-50. [PMID: 25581131 DOI: 10.1111/1462-2920.12773] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/31/2014] [Indexed: 11/26/2022]
Abstract
Aerobic methane (CH4 ) oxidation mitigates CH4 release and is a significant pathway for carbon and energy flow into aquatic food webs. Arctic lakes are responsible for an increasing proportion of global CH4 emissions, but CH4 assimilation into the aquatic food web in arctic lakes is poorly understood. Using stable isotope probing (SIP) based on phospholipid fatty acids (PLFA-SIP) and DNA (DNA-SIP), we tracked carbon flow quantitatively from CH4 into sediment microorganisms from an arctic lake with an active CH4 seepage. When 0.025 mmol CH4 g(-1) wet sediment was oxidized, approximately 15.8-32.8% of the CH4 -derived carbon had been incorporated into microorganisms. This CH4 -derived carbon equated to up to 5.7% of total primary production estimates for Alaskan arctic lakes. Type I methanotrophs, including Methylomonas, Methylobacter and unclassified Methylococcaceae, were most active at CH4 oxidation in this arctic lake. With increasing distance from the active CH4 seepage, a greater diversity of bacteria incorporated CH4 -derived carbon. Actinomycetes were the most quantitatively important microorganisms involved in secondary feeding on CH4 -derived carbon. These results showed that CH4 flows through methanotrophs into the broader microbial community and that type I methanotrophs, methylotrophs and actinomycetes are important organisms involved in using CH4 -derived carbon in arctic freshwater ecosystems.
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Affiliation(s)
- Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.,Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Matthew J Wooller
- Alaska Stable Isotope Facility, Water and Environmental Research Center, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA.,School of Fisheries and Ocean Sciences, Institute of Marine Science, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - John W Pohlman
- Woods Hole Coastal and Marine Science Center, U.S. Geological Survey, Woods Hole, MA, 02543, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
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96
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Lynch RC, Darcy JL, Kane NC, Nemergut DR, Schmidt SK. Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria. Front Microbiol 2014; 5:698. [PMID: 25566214 PMCID: PMC4269115 DOI: 10.3389/fmicb.2014.00698] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 11/25/2014] [Indexed: 11/26/2022] Open
Abstract
Previous surveys of very dry Atacama Desert mineral soils have consistently revealed sparse communities of non-photosynthetic microbes. The functional nature of these microorganisms remains debatable given the harshness of the environment and low levels of biomass and diversity. The aim of this study was to gain an understanding of the phylogenetic community structure and metabolic potential of a low-diversity mineral soil metagenome that was collected from a high-elevation Atacama Desert volcano debris field. We pooled DNA extractions from over 15 g of volcanic material, and using whole genome shotgun sequencing, observed only 75-78 total 16S rRNA gene OTUs3%. The phylogenetic structure of this community is significantly under dispersed, with actinobacterial lineages making up 97.9-98.6% of the 16S rRNA genes, suggesting a high degree of environmental selection. Due to this low diversity and uneven community composition, we assembled and analyzed the metabolic pathways of the most abundant genome, a Pseudonocardia sp. (56-72% of total 16S genes). Our assembly and binning efforts yielded almost 4.9 Mb of Pseudonocardia sp. contigs, which accounts for an estimated 99.3% of its non-repetitive genomic content. This genome contains a limited array of carbohydrate catabolic pathways, but encodes for CO2 fixation via the Calvin cycle. The genome also encodes complete pathways for the catabolism of various trace gases (H2, CO and several organic C1 compounds) and the assimilation of ammonia and nitrate. We compared genomic content among related Pseudonocardia spp. and estimated rates of non-synonymous and synonymous nucleic acid substitutions between protein coding homologs. Collectively, these comparative analyses suggest that the community structure and various functional genes have undergone strong selection in the nutrient poor desert mineral soils and high-elevation atmospheric conditions.
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Affiliation(s)
- Ryan C. Lynch
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - John L. Darcy
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Diana R. Nemergut
- Environmental Studies Program, University of ColoradoBoulder, CO, USA
- Institute of Arctic and Alpine Research, University of ColoradoBoulder, CO, USA
- Department of Biology, Duke UniversityDurham, NC, USA
| | - Steve K. Schmidt
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
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97
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Lima AB, Muniz AW, Dumont MG. Activity and abundance of methane-oxidizing bacteria in secondary forest and manioc plantations of Amazonian Dark Earth and their adjacent soils. Front Microbiol 2014; 5:550. [PMID: 25374565 PMCID: PMC4205850 DOI: 10.3389/fmicb.2014.00550] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/02/2014] [Indexed: 12/20/2022] Open
Abstract
The oxidation of atmospheric CH4 in upland soils is mostly mediated by uncultivated groups of microorganisms that have been identified solely by molecular markers, such as the sequence of the pmoA gene encoding the β-subunit of the particulate methane monooxygenase enzyme. The objective of this work was to compare the activity and diversity of methanotrophs in Amazonian Dark Earth soil (ADE, Hortic Anthrosol) and their adjacent non-anthropic soil. Secondly, the effect of land use in the form of manioc cultivation was examined by comparing secondary forest and plantation soils. CH4 oxidation potentials were measured and the structure of the methanotroph communities assessed by quantitative PCR (qPCR) and amplicon pyrosequencing of pmoA genes. The oxidation potentials at low CH4 concentrations (10 ppm of volume) were relatively high in all the secondary forest sites of both ADE and adjacent soils. CH4 oxidation by the ADE soil only recently converted to a manioc plantation was also relatively high. In contrast, both the adjacent soils used for manioc cultivation and the ADE soil with a long history of agriculture displayed lower CH4 uptake rates. Amplicon pyrosequencing of pmoA genes indicated that USCα, Methylocystis and the tropical upland soil cluster (TUSC) were the dominant groups depending on the site. By qPCR analysis it was found that USCα pmoA genes, which are believed to belong to atmospheric CH4 oxidizers, were more abundant in ADE than adjacent soil. USCα pmoA genes were abundant in both forested and cultivated ADE soil, but were below the qPCR detection limit in manioc plantations of adjacent soil. The results indicate that ADE soils can harbor high abundances of atmospheric CH4 oxidizers and are potential CH4 sinks, but as in other upland soils this activity can be inhibited by the conversion of forest to agricultural plantations.
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Affiliation(s)
- Amanda B Lima
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Aleksander W Muniz
- Department of Soil Microbiology and Biogeochemistry, Brazilian Agricultural Research Corporation Manaus, Brazil
| | - Marc G Dumont
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
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98
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Vanwonterghem I, Jensen PD, Dennis PG, Hugenholtz P, Rabaey K, Tyson GW. Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters. THE ISME JOURNAL 2014; 8:2015-28. [PMID: 24739627 PMCID: PMC4184015 DOI: 10.1038/ismej.2014.50] [Citation(s) in RCA: 219] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 02/26/2014] [Accepted: 03/01/2014] [Indexed: 02/01/2023]
Abstract
A replicate long-term experiment was conducted using anaerobic digestion (AD) as a model process to determine the relative role of niche and neutral theory on microbial community assembly, and to link community dynamics to system performance. AD is performed by a complex network of microorganisms and process stability relies entirely on the synergistic interactions between populations belonging to different functional guilds. In this study, three independent replicate anaerobic digesters were seeded with the same diverse inoculum, supplied with a model substrate, α-cellulose, and operated for 362 days at a 10-day hydraulic residence time under mesophilic conditions. Selective pressure imposed by the operational conditions and model substrate caused large reproducible changes in community composition including an overall decrease in richness in the first month of operation, followed by synchronised population dynamics that correlated with changes in reactor performance. This included the synchronised emergence and decline of distinct Ruminococcus phylotypes at day 148, and emergence of a Clostridium and Methanosaeta phylotype at day 178, when performance became stable in all reactors. These data suggest that many dynamic functional niches are predictably filled by phylogenetically coherent populations over long time scales. Neutral theory would predict that a complex community with a high degree of recognised functional redundancy would lead to stochastic changes in populations and community divergence over time. We conclude that deterministic processes may play a larger role in microbial community dynamics than currently appreciated, and under controlled conditions it may be possible to reliably predict community structural and functional changes over time.
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Affiliation(s)
- Inka Vanwonterghem
- Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Queensland, Australia
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Paul D Jensen
- Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Queensland, Australia
| | - Paul G Dennis
- Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Queensland, Australia
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, Queensland, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Korneel Rabaey
- Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Queensland, Australia
- Laboratory for Microbial Ecology and Technology (LabMET), Ghent University, Ghent, Belgium
| | - Gene W Tyson
- Advanced Water Management Centre (AWMC), University of Queensland, St Lucia, Queensland, Australia
- Australian Centre for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
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99
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Abdallah RZ, Adel M, Ouf A, Sayed A, Ghazy MA, Alam I, Essack M, Lafi FF, Bajic VB, El-Dorry H, Siam R. Aerobic methanotrophic communities at the Red Sea brine-seawater interface. Front Microbiol 2014; 5:487. [PMID: 25295031 PMCID: PMC4172156 DOI: 10.3389/fmicb.2014.00487] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/28/2014] [Indexed: 01/16/2023] Open
Abstract
The central rift of the Red Sea contains 25 brine pools with different physicochemical conditions, dictating the diversity and abundance of the microbial community. Three of these pools, the Atlantis II, Kebrit and Discovery Deeps, are uniquely characterized by a high concentration of hydrocarbons. The brine-seawater interface, described as an anoxic-oxic (brine-seawater) boundary, is characterized by a high methane concentration, thus favoring aerobic methane oxidation. The current study analyzed the aerobic free–living methane-oxidizing bacterial communities that potentially contribute to methane oxidation at the brine-seawater interfaces of the three aforementioned brine pools, using metagenomic pyrosequencing, 16S rRNA pyrotags and pmoA library constructs. The sequencing of 16S rRNA pyrotags revealed that these interfaces are characterized by high microbial community diversity. Signatures of aerobic methane-oxidizing bacteria were detected in the Atlantis II Interface (ATII-I) and the Kebrit Deep Upper (KB-U) and Lower (KB-L) brine-seawater interfaces. Through phylogenetic analysis of pmoA, we further demonstrated that the ATII-I aerobic methanotroph community is highly diverse. We propose four ATII-I pmoA clusters. Most importantly, cluster 2 groups with marine methane seep methanotrophs, and cluster 4 represent a unique lineage of an uncultured bacterium with divergent alkane monooxygenases. Moreover, non-metric multidimensional scaling (NMDS) based on the ordination of putative enzymes involved in methane metabolism showed that the Kebrit interface layers were distinct from the ATII-I and DD-I brine-seawater interfaces.
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Affiliation(s)
- Rehab Z Abdallah
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt
| | - Mustafa Adel
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt
| | - Amged Ouf
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt
| | - Ahmed Sayed
- Department of Biology, American University in Cairo Cairo, Egypt
| | - Mohamed A Ghazy
- Department of Biology, American University in Cairo Cairo, Egypt
| | - Intikhab Alam
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Magbubah Essack
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Feras F Lafi
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Vladimir B Bajic
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Hamza El-Dorry
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt
| | - Rania Siam
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt ; YJ-Science and Technology Research Center, American University in Cairo Cairo, Egypt
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100
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Sorokin DY, Berben T, Melton ED, Overmars L, Vavourakis CD, Muyzer G. Microbial diversity and biogeochemical cycling in soda lakes. Extremophiles 2014; 18:791-809. [PMID: 25156418 PMCID: PMC4158274 DOI: 10.1007/s00792-014-0670-9] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/26/2014] [Indexed: 01/26/2023]
Abstract
Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art 'meta-omic' techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments.
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Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, RAS, Moscow, Russia
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Tom Berben
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Emily Denise Melton
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Lex Overmars
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Charlotte D. Vavourakis
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Gerard Muyzer
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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