151
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Cai Y, Zhou X, Shi L, Jia Z. Atmospheric Methane Oxidizers Are Dominated by Upland Soil Cluster Alpha in 20 Forest Soils of China. MICROBIAL ECOLOGY 2020; 80:859-871. [PMID: 32803363 DOI: 10.1007/s00248-020-01570-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 08/03/2020] [Indexed: 05/25/2023]
Abstract
Upland soil clusters alpha and gamma (USCα and USCγ) are considered a major biological sink of atmospheric methane and are often detected in forest and grassland soils. These clusters are phylogenetically classified using the particulate methane monooxygenase gene pmoA because of the difficulty of cultivation. Recent studies have established a direct link of pmoA genes to 16S rRNA genes based on their isolated strain or draft genomes. However, whether the results of pmoA-based assays could be largely represented by 16S rRNA gene sequencing in upland soils remains unclear. In this study, we collected 20 forest soils across China and compared methane-oxidizing bacterial (MOB) communities by high-throughput sequencing of 16S rRNA and pmoA genes using different primer sets. The results showed that 16S rRNA gene sequencing and the semi-nested polymerase chain reaction (PCR) of the pmoA gene (A189/A682r nested with a mixture of mb661 and A650) consistently revealed the dominance of USCα (accounting for more than 50% of the total MOB) in 12 forest soils. A189f/A682r successfully amplified pmoA genes (mainly RA14 of USCα) in only three forest soils. A189f/mb661 could amplify USCα (mainly JR1) in several forest soils but showed a strong preferential amplification of Methylocystis and many other type I MOB groups. A189f/A650 almost exclusively amplified USCα (mainly JR1) and largely discriminated against Methylocystis and most of the other MOB groups. The semi-nested PCR approach weakened the bias of A189f/mb661 and A189f/A650 for JR1 and balanced the coverage of all USCα members. The canonical correspondence analysis indicated that soil NH4+-N and pH were the main environmental factors affecting the MOB community of Chinese forest soils. The RA14 of the USCα group prefers to live in soils with low pH, low temperature, low elevation, high precipitation, and rich in nitrogen. JR1's preferences for temperature and elevation were opposite to RA14. Our study suggests that combining the deep sequencing of 16S rRNA and pmoA genes to characterize MOB in forest soils is the best choice.
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Affiliation(s)
- Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China
| | - Xue Zhou
- College of agricultural science and engineering, Hohai University, Nanjing, 210098, Jiangsu Province, China
| | - Limei Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China.
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152
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Chiri E, Greening C, Lappan R, Waite DW, Jirapanjawat T, Dong X, Arndt SK, Nauer PA. Termite mounds contain soil-derived methanotroph communities kinetically adapted to elevated methane concentrations. THE ISME JOURNAL 2020; 14:2715-2731. [PMID: 32709975 PMCID: PMC7784690 DOI: 10.1038/s41396-020-0722-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/07/2020] [Accepted: 07/15/2020] [Indexed: 01/29/2023]
Abstract
Termite mounds have recently been confirmed to mitigate approximately half of termite methane (CH4) emissions, but the aerobic CH4 oxidising bacteria (methanotrophs) responsible for this consumption have not been resolved. Here, we describe the abundance, composition and CH4 oxidation kinetics of the methanotroph communities in the mounds of three distinct termite species sampled from Northern Australia. Results from three independent methods employed show that methanotrophs are rare members of microbial communities in termite mounds, with a comparable abundance but distinct composition to those of adjoining soil samples. Across all mounds, the most abundant and prevalent methane monooxygenase sequences were affiliated with upland soil cluster α (USCα), with sequences homologous to Methylocystis and tropical upland soil cluster (TUSC) also detected. The reconstruction of a metagenome-assembled genome of a mound USCα representative highlighted the metabolic capabilities of this group of methanotrophs. The apparent Michaelis-Menten kinetics of CH4 oxidation in mounds were estimated from in situ reaction rates. Methane affinities of the communities were in the low micromolar range, which is one to two orders of magnitude higher than those of upland soils, but significantly lower than those measured in soils with a large CH4 source such as landfill cover soils. The rate constant of CH4 oxidation, as well as the porosity of the mound material, were significantly positively correlated with the abundance of methanotroph communities of termite mounds. We conclude that termite-derived CH4 emissions have selected for distinct methanotroph communities that are kinetically adapted to elevated CH4 concentrations. However, factors other than substrate concentration appear to limit methanotroph abundance and hence these bacteria only partially mitigate termite-derived CH4 emissions. Our results also highlight the predominant role of USCα in an environment with elevated CH4 concentrations and suggest a higher functional diversity within this group than previously recognised.
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Affiliation(s)
- Eleonora Chiri
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- School of Ecosystem and Forest Sciences, University of Melbourne, Richmond, VIC, 3121, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia.
| | - Rachael Lappan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - David W Waite
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Thanavit Jirapanjawat
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Stefan K Arndt
- School of Ecosystem and Forest Sciences, University of Melbourne, Richmond, VIC, 3121, Australia.
| | - Philipp A Nauer
- School of Ecosystem and Forest Sciences, University of Melbourne, Richmond, VIC, 3121, Australia
- School of Chemistry, Monash University, Clayton, VIC, 3800, Australia
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153
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Cox AH, Wigginton SK, Amador JA. Structure of greenhouse gas-consuming microbial communities in surface soils of a nitrogen-removing experimental drainfield. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 739:140362. [PMID: 32758972 DOI: 10.1016/j.scitotenv.2020.140362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/13/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Septic systems represent a source of greenhouse gases generated by microbial processes as wastewater constituents are degraded. Both aerobic and anerobic wastewater transformation processes can generate nitrous oxide and methane, both of which are potent greenhouse gases (GHGs). To understand how microbial communities in the surface soils above shallow drainfields contribute to methane and nitrous oxide consumption, we measured greenhouse gas surface flux and below-ground concentrations and compared them to the microbial communities present using functional genes pmoA and nosZ. These genes encode portions of particulate methane monooxygenase and nitrous oxide reductase, respectively, serving as a potential sink for the respective greenhouse gases. We assessed the surface soils above three drainfields served by a single household: an experimental layered passive N-reducing drainfield, a control conventional drainfield, and a reserve drainfield not in use but otherwise identical to the control. We found that neither GHG flux, below-ground concentration or soil properties varied among drainfield types, nor did methane oxidizing and nitrous oxide reducing communities vary by drainfield type. We found differences in pmoA and nosZ communities based on depth from the soil surface, and differences in nosZ communities based on whether the sample came from the rhizosphere or surrounding bulk soils. Type I methanotrophs (Gammaproteobacteria) were more abundant in the upper and middle portions of the soil above the drainfield. In general, we found no relationship in community composition for either gene based on GHG flux or below-ground concentration or soil properties (bulk density, organic matter, above-ground biomass). This is the first study to assess these communities in the surface soils above an experimental working drainfield, and more research is needed to understand the dynamics of greenhouse gas production and consumption in these systems.
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Affiliation(s)
- Alissa H Cox
- Department of Natural Resources Science, University of Rhode Island, 1 Greenhouse Rd, Kingston, RI 02881, USA.
| | - Sara K Wigginton
- Department of Natural Resources Science, University of Rhode Island, 1 Greenhouse Rd, Kingston, RI 02881, USA.
| | - José A Amador
- Department of Natural Resources Science, University of Rhode Island, 1 Greenhouse Rd, Kingston, RI 02881, USA.
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154
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Guggenheim C, Freimann R, Mayr MJ, Beck K, Wehrli B, Bürgmann H. Environmental and Microbial Interactions Shape Methane-Oxidizing Bacterial Communities in a Stratified Lake. Front Microbiol 2020; 11:579427. [PMID: 33178162 PMCID: PMC7593551 DOI: 10.3389/fmicb.2020.579427] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/04/2020] [Indexed: 11/13/2022] Open
Abstract
In stratified lakes, methane-oxidizing bacteria (MOB) are strongly mitigating methane fluxes to the atmosphere by consuming methane entering the water column from the sediments. MOB communities in lakes are diverse and vertically structured, but their spatio-temporal dynamics along the water column as well as physico-chemical parameters and interactions with other bacterial species that drive the community assembly have so far not been explored in depth. Here, we present a detailed investigation of the MOB and bacterial community composition and a large set of physico-chemical parameters in a shallow, seasonally stratified, and sub-alpine lake. Four highly resolved vertical profiles were sampled in three different years and during various stages of development of the stratified water column. Non-randomly assembled MOB communities were detected in all compartments. We could identify methane and oxygen gradients and physico-chemical parameters like pH, light, available copper and iron, and total dissolved nitrogen as important drivers of the MOB community structure. In addition, MOB were well-integrated into a bacterial-environmental network. Partial redundancy analysis of the relevance network of physico-chemical variables and bacteria explained up to 84% of the MOB abundances. Spatio-temporal MOB community changes were 51% congruent with shifts in the total bacterial community and 22% of variance in MOB abundances could be explained exclusively by the bacterial community composition. Our results show that microbial interactions may play an important role in structuring the MOB community along the depth gradient of stratified lakes.
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Affiliation(s)
- Carole Guggenheim
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich - Swiss Federal Institute of Technology, Zurich, Switzerland.,Department of Surface Waters - Research and Management, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Remo Freimann
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich - Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Magdalena J Mayr
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich - Swiss Federal Institute of Technology, Zurich, Switzerland.,Department of Surface Waters - Research and Management, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Karin Beck
- Department of Surface Waters - Research and Management, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Bernhard Wehrli
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich - Swiss Federal Institute of Technology, Zurich, Switzerland.,Department of Surface Waters - Research and Management, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Helmut Bürgmann
- Department of Surface Waters - Research and Management, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
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155
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Farhan Ul Haque M, Xu HJ, Murrell JC, Crombie A. Facultative methanotrophs - diversity, genetics, molecular ecology and biotechnological potential: a mini-review. MICROBIOLOGY (READING, ENGLAND) 2020; 166:894-908. [PMID: 33085587 PMCID: PMC7660913 DOI: 10.1099/mic.0.000977] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/20/2020] [Indexed: 12/18/2022]
Abstract
Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although Methylocella strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.
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Affiliation(s)
| | - Hui-Juan Xu
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andrew Crombie
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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156
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Carrier V, Svenning MM, Gründger F, Niemann H, Dessandier PA, Panieri G, Kalenitchenko D. The Impact of Methane on Microbial Communities at Marine Arctic Gas Hydrate Bearing Sediment. Front Microbiol 2020; 11:1932. [PMID: 33071992 PMCID: PMC7541813 DOI: 10.3389/fmicb.2020.01932] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 07/22/2020] [Indexed: 01/26/2023] Open
Abstract
Cold seeps are characterized by high biomass, which is supported by the microbial oxidation of the available methane by capable microorganisms. The carbon is subsequently transferred to higher trophic levels. South of Svalbard, five geological mounds shaped by the formation of methane gas hydrates, have been recently located. Methane gas seeping activity has been observed on four of them, and flares were primarily concentrated at their summits. At three of these mounds, and along a distance gradient from their summit to their outskirt, we investigated the eukaryotic and prokaryotic biodiversity linked to 16S and 18S rDNA. Here we show that local methane seepage and other environmental conditions did affect the microbial community structure and composition. We could not demonstrate a community gradient from the summit to the edge of the mounds. Instead, a similar community structure in any methane-rich sediments could be retrieved at any location on these mounds. The oxidation of methane was largely driven by anaerobic methanotrophic Archaea-1 (ANME-1) and the communities also hosted high relative abundances of sulfate reducing bacterial groups although none demonstrated a clear co-occurrence with the predominance of ANME-1. Additional common taxa were observed and their abundances were likely benefiting from the end products of methane oxidation. Among these were sulfide-oxidizing Campilobacterota, organic matter degraders, such as Bathyarchaeota, Woesearchaeota, or thermoplasmatales marine benthic group D, and heterotrophic ciliates and Cercozoa.
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Affiliation(s)
- Vincent Carrier
- Department of Arctic and Marine Biology, The Arctic University of Norway, Tromsø, Norway.,Centre for Arctic Gas Hydrate, Environment and Climate, The Arctic University of Norway, Tromsø, Norway
| | - Mette M Svenning
- Department of Arctic and Marine Biology, The Arctic University of Norway, Tromsø, Norway.,Centre for Arctic Gas Hydrate, Environment and Climate, The Arctic University of Norway, Tromsø, Norway
| | - Friederike Gründger
- Department of Bioscience, Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Helge Niemann
- Centre for Arctic Gas Hydrate, Environment and Climate, The Arctic University of Norway, Tromsø, Norway.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Pierre-Antoine Dessandier
- Centre for Arctic Gas Hydrate, Environment and Climate, The Arctic University of Norway, Tromsø, Norway
| | - Giuliana Panieri
- Centre for Arctic Gas Hydrate, Environment and Climate, The Arctic University of Norway, Tromsø, Norway
| | - Dimitri Kalenitchenko
- Centre for Arctic Gas Hydrate, Environment and Climate, The Arctic University of Norway, Tromsø, Norway
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157
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Cabrol L, Thalasso F, Gandois L, Sepulveda-Jauregui A, Martinez-Cruz K, Teisserenc R, Tananaev N, Tveit A, Svenning MM, Barret M. Anaerobic oxidation of methane and associated microbiome in anoxic water of Northwestern Siberian lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 736:139588. [PMID: 32497884 DOI: 10.1016/j.scitotenv.2020.139588] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 05/16/2023]
Abstract
Arctic lakes emit methane (CH4) to the atmosphere. The magnitude of this flux could increase with permafrost thaw but might also be mitigated by microbial CH4 oxidation. Methane oxidation in oxic water has been extensively studied, while the contribution of anaerobic oxidation of methane (AOM) to CH4 mitigation is not fully understood. We have investigated four Northern Siberian stratified lakes in an area of discontinuous permafrost nearby Igarka, Russia. Analyses of CH4 concentrations in the water column demonstrated that 60 to 100% of upward diffusing CH4 was oxidized in the anoxic layers of the four lakes. A combination of pmoA and mcrA gene qPCR and 16S rRNA gene metabarcoding showed that the same taxa, all within Methylomonadaceae and including the predominant genus Methylobacter as well as Crenothrix, could be the major methane-oxidizing bacteria (MOB) in the anoxic water of the four lakes. Correlation between Methylomonadaceae and OTUs within Methylotenera, Geothrix and Geobacter genera indicated that AOM might occur in an interaction between MOB, denitrifiers and iron-cycling partners. We conclude that MOB within Methylomonadaceae could have a crucial impact on CH4 cycling in these Siberian Arctic lakes by mitigating the majority of produced CH4 before it leaves the anoxic zone. This finding emphasizes the importance of AOM by Methylomonadaceae and extends our knowledge about CH4 cycle in lakes, a crucial component of the global CH4 cycle.
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Affiliation(s)
- Léa Cabrol
- Aix-Marseille University, Univ Toulon, CNRS, IRD, M.I.O. UM 110, Mediterranean Institute of Oceanography, Marseille, France; Institute of Ecology and Biodiversity IEB, Faculty of Sciences, Universidad de Chile, Santiago, Chile; Escuela de Ingeniería Bioquímica, Pontificia Universidad de Valparaiso, Av Brasil 2085, Valparaiso, Chile
| | - Frédéric Thalasso
- Biotechnology and Bioengineering Department, Center for Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | - Laure Gandois
- Laboratory of Functional Ecology and Environment, Université de Toulouse, CNRS, Toulouse, France
| | - Armando Sepulveda-Jauregui
- ENBEELAB, University of Magallanes, Punta Arenas, Chile; Center for Climate and Resilience Research (CR)2, Santiago, Chile
| | | | - Roman Teisserenc
- Laboratory of Functional Ecology and Environment, Université de Toulouse, CNRS, Toulouse, France
| | | | - Alexander Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Mette M Svenning
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maialen Barret
- Laboratory of Functional Ecology and Environment, Université de Toulouse, CNRS, Toulouse, France.
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158
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Semrau JD, DiSpirito AA, Obulisamy PK, Kang-Yun CS. Methanobactin from methanotrophs: genetics, structure, function and potential applications. FEMS Microbiol Lett 2020; 367:5804726. [PMID: 32166327 DOI: 10.1093/femsle/fnaa045] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/11/2020] [Indexed: 12/12/2022] Open
Abstract
Aerobic methane-oxidizing bacteria of the Alphaproteobacteria have been found to express a novel ribosomally synthesized post-translationally modified polypeptide (RiPP) termed methanobactin (MB). The primary function of MB in these microbes appears to be for copper uptake, but MB has been shown to have multiple capabilities, including oxidase, superoxide dismutase and hydrogen peroxide reductase activities, the ability to detoxify mercury species, as well as acting as an antimicrobial agent. Herein, we describe the diversity of known MBs as well as the genetics underlying MB biosynthesis. We further propose based on bioinformatics analyses that some methanotrophs may produce novel forms of MB that have yet to be characterized. We also discuss recent findings documenting that MBs play an important role in controlling copper availability to the broader microbial community, and as a result can strongly affect the activity of microbes that require copper for important enzymatic transformations, e.g. conversion of nitrous oxide to dinitrogen. Finally, we describe procedures for the detection/purification of MB, as well as potential medical and industrial applications of this intriguing RiPP.
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Affiliation(s)
- Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA 48109-2125
| | - Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | | | - Christina S Kang-Yun
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA 48109-2125
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159
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Huang D, Yang L, Xu W, Chen Q, Ko JH, Xu Q. Enhancement of the methane removal efficiency via aeration for biochar-amended landfill soil cover. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114413. [PMID: 32220690 DOI: 10.1016/j.envpol.2020.114413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/09/2020] [Accepted: 03/17/2020] [Indexed: 06/10/2023]
Abstract
Methane (CH4) mitigation of biocovers or biofilters for landfills is influenced by the bed material and oxygen availability. The improvement of active aeration for the CH4 oxidation efficiency of biochar-amended landfill soil cover was investigated over a period of 101 days. There were column 1 as the control group, column 2 with biochar amending the soil cover, and column 3 with daily active aeration besides the same biochar amendment. All groups were inoculated with enriched methane oxidation bacteria (MOB). The average CH4 removal efficiency was up to 78.6%, 85.2% and 90.6% for column 1, 2, and 3, respectively. The depth profiles of CH4 oxidation efficiencies over the whole period also showed that the stimulation of CH4 oxidation by biochar amendment was apparent in the top 35 cm but became very faint after two months. This probably was due to the rapid depletion of nitrogen nutrition caused by enhanced methanotrophic activities. While through aeration, CH4 oxidation efficiency was further improved for column 3 than column 2. This enhancement also lasted for the whole period with a reduced decline of CH4 oxidation. Finally, the major MOB Methylocystis, commonly found in the three columns, were most abundant in the top 35 cm for column 3. A more balanced ratio of MOB and more homogeneous microbial community structures across different soil depths were also the results of active aeration.
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Affiliation(s)
- Dandan Huang
- Shenzhen Engineering Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Xili, Nanshan District, Shenzhen, 518055, PR China
| | - Luning Yang
- Shenzhen Engineering Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Xili, Nanshan District, Shenzhen, 518055, PR China
| | - Wenjun Xu
- Shenzhen Engineering Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Xili, Nanshan District, Shenzhen, 518055, PR China
| | - Qindong Chen
- Shenzhen Engineering Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Xili, Nanshan District, Shenzhen, 518055, PR China
| | - Jae Hac Ko
- Department of Environmental Engineering, College of Ocean Sciences, Jeju National University, Jeju Special Self-Governing Province, 63243, Republic of Korea
| | - Qiyong Xu
- Shenzhen Engineering Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Xili, Nanshan District, Shenzhen, 518055, PR China.
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160
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Davamani V, Parameswari E, Arulmani S. Mitigation of methane gas emissions in flooded paddy soil through the utilization of methanotrophs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 726:138570. [PMID: 32305766 DOI: 10.1016/j.scitotenv.2020.138570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/30/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
The utilization of methanotrophs for reducing the global warming potential in a flooded paddy system is the progressive investigation in the recent. The field investigation was conducted in Tamil Nadu Rice Research Institute, Aduthurai. This study showed the effect of isolated methanotroph strain (MR15) on the reduction of methane emission and improvement in growth parameters and yield of paddy. The treatments included the diverse dosages of methanotroph consortium (0, 25, 50, 75 & 100%). The total seasonal methane emission varied between 1.96 and 5.04 kg ha-1 for the season of Kharif and 2.18 to 5.81 kg ha-1 for the season of Rabi owing to the footprint of methanotroph. Irrespective of treatments, the mean seasonal emission was more prominent during Rabi compared to the Kharif season. The dosage of methanotroph consortium significantly influenced not only seasonal methane emission but also the grain yield percentage, which increased over 100% Recommended Dose of Fertilizers (RDF). Application of 100% methanotroph consortium (i.e.6.25 kg ha-1) minimizes the methane emission by 60% with an increase in grain yield by 35% and lessens the usage of additional nutrients. Overall, this study showed a sign of atmospheric methane uptake with increase growth potential and yield of paddy cultivation using methanotroph consortium.
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Affiliation(s)
- Veeraswamy Davamani
- Department of Environmental Sciences, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India.
| | - Ettiyagounder Parameswari
- Department of Environmental Sciences, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | - Subramanian Arulmani
- Department of Chemistry, National Institute of Technology, Tiruchirapalli & Bannari Amman Institute of Technology, Sathyamangalam 638401, Tamil Nadu, India
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161
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Praeg N, Schwinghammer L, Illmer P. Larix decidua and additional light affect the methane balance of forest soil and the abundance of methanogenic and methanotrophic microorganisms. FEMS Microbiol Lett 2020; 366:5695738. [PMID: 31899513 DOI: 10.1093/femsle/fnz259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/31/2019] [Indexed: 11/13/2022] Open
Abstract
Due to the activity of methane-oxidizing bacteria, forest soils are usually net sinks for the greenhouse gas methane (CH4). Despite several hints that CH4 balances might be influenced by vegetation, there are only few investigations dealing with this connection. Therefore, we studied this soil-plant-microbe interaction by using mesocosm experiments with forest soil and Larix decidua, a common coniferous tree species within the Alps. Gas measurements showed that the presence of L. decidua significantly reduced CH4 oxidation of the forest soil by ∼10% (-0.95 µmol m-2 h-1 for soil vs -0.85 µmol m-2 h-1 for soil plus L. decidua) leading to an increased net CH4 balance. Increased light intensity was used to intensify the influence of the plant on the soil's CH4 balance. The increase in light intensity strengthened the effect of the plant and led to a greater reduction of CH4 oxidation. Besides, we examined the impact of L. decidua and light on the abundance of methanogens and methanotrophs in the rhizosphere as compared with bulk soil. The abundance of both methane-oxidizing bacteria and methanogenic archaea was significantly increased in the rhizosphere compared with bulk soil but no significant response of methanogens and methanotrophs upon light exposure was established.
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Affiliation(s)
- Nadine Praeg
- Universität Innsbruck, Department of Microbiology, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Larissa Schwinghammer
- Universität Innsbruck, Department of Microbiology, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Paul Illmer
- Universität Innsbruck, Department of Microbiology, Technikerstrasse 25d, A-6020 Innsbruck, Austria
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Broman E, Sun X, Stranne C, Salgado MG, Bonaglia S, Geibel M, Jakobsson M, Norkko A, Humborg C, Nascimento FJA. Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations. Front Microbiol 2020; 11:1536. [PMID: 32733420 PMCID: PMC7362727 DOI: 10.3389/fmicb.2020.01536] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/12/2020] [Indexed: 01/07/2023] Open
Abstract
Coastal zones are transitional areas between land and sea where large amounts of organic and inorganic carbon compounds are recycled by microbes. Especially shallow zones near land have been shown to be the main source for oceanic methane (CH4) emissions. Water depth has been predicted as the best explanatory variable, which is related to CH4 ebullition, but exactly how sediment methanotrophs mediates these emissions along water depth is unknown. Here, we investigated the relative abundance and RNA transcripts attributed to methane oxidation proteins of aerobic methanotrophs in the sediment of shallow coastal zones with high CH4 concentrations within a depth gradient from 10-45 m. Field sampling consisted of collecting sediment (top 0-2 cm layer) from eight stations along this depth gradient in the coastal Baltic Sea. The relative abundance and RNA transcripts attributed to the CH4 oxidizing protein (pMMO; particulate methane monooxygenase) of the dominant methanotroph Methylococcales was significantly higher in deeper costal offshore areas (36-45 m water depth) compared to adjacent shallow zones (10-28 m). This was in accordance with the shallow zones having higher CH4 concentrations in the surface water, as well as more CH4 seeps from the sediment. Furthermore, our findings indicate that the low prevalence of Methylococcales and RNA transcripts attributed to pMMO was restrained to the euphotic zone (indicated by Photosynthetically active radiation (PAR) data, photosynthesis proteins, and 18S rRNA data of benthic diatoms). This was also indicated by a positive relationship between water depth and the relative abundance of Methylococcales and pMMO. How these processes are affected by light availability requires further studies. CH4 ebullition potentially bypasses aerobic methanotrophs in shallow coastal areas, reducing CH4 availability and limiting their growth. Such mechanism could help explain their reduced relative abundance and related RNA transcripts for pMMO. These findings can partly explain the difference in CH4 concentrations between shallow and deep coastal areas, and the relationship between CH4 concentrations and water depth.
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Affiliation(s)
- Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Xiaole Sun
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Christian Stranne
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden
- Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Marco G. Salgado
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Stefano Bonaglia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Marc Geibel
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Martin Jakobsson
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden
- Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Alf Norkko
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Christoph Humborg
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Francisco J. A. Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
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163
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Tian HJ, Feng J, Zhang LM, He JZ, Liu YR. Ecological drivers of methanotrophic communities in paddy soils around mercury mining areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 721:137760. [PMID: 32169650 DOI: 10.1016/j.scitotenv.2020.137760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/04/2020] [Accepted: 03/04/2020] [Indexed: 06/10/2023]
Abstract
Methanotrophs play a crucial role in mitigating methane (CH4) emission by oxidizing produced CH4 in paddy soils; however, ecological drivers of methanotrophic community in the soils around heavy metal contaminated areas remain unclear. In this study, we evaluated the effects of heavy metal pollution and soil properties on the abundance, diversity and composition of methanotrophic community in paddy soils from two typical mercury (Hg) mining regions in southwest China. The results of random forest and structure equation models suggest that both heavy metal content and soil nutrients greatly influenced the attributes of methanotrophic community. In general, the abundance and diversity of methanotrophs were negatively related to soil Hg content, but showed positive correlation with soil organic carbon content. However, the other metals (cadmium (Cd), nickel (Ni), lead (Pb), arsenic (As), zinc (Zn)) had inconsistent associations with the microbial indexes of methanotrophic community in the soil. Elevated levels of heavy metal and nutrients in the soils shifted the community composition of methanotrophs. For example, Pb, As and Zn contents had negative associations with the relative abundance of Methylocaldum. In addition, changes in the relative abundance of ecological clusters within the co-occurrence network of methanotrophs were related to metal contents and soil properties. Together, our findings provide novel insights into understanding ecological drivers of methanotrophic community in paddy soils around Hg mining regions, with important implications for mitigating CH4 emissions in terrestrial ecosystems.
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Affiliation(s)
- Hua-Jing Tian
- 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 Sciences, Beijing 100049, China
| | - Jiao Feng
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China.
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yu-Rong Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China.
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164
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Bagnoud A, Pramateftaki P, Bogard MJ, Battin TJ, Peter H. Microbial Ecology of Methanotrophy in Streams Along a Gradient of CH 4 Availability. Front Microbiol 2020; 11:771. [PMID: 32477286 PMCID: PMC7241049 DOI: 10.3389/fmicb.2020.00771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Despite the recognition of streams and rivers as sources of methane (CH4) to the atmosphere, the role of CH4 oxidation (MOX) in these ecosystems remains poorly understood to date. Here, we measured the kinetics of MOX in stream sediments of 14 sites to resolve the ecophysiology of CH4 oxidizing bacteria (MOB) communities. The streams cover a gradient of land cover and associated physicochemical parameter and differed in stream- and porewater CH4 concentrations. Michealis–Menten kinetic parameter of MOX, maximum reaction velocity (Vmax), and CH4 concentration at half Vmax (KS) increased with CH4 supply. KS values in the micromolar range matched the CH4 concentrations measured in shallow stream sediments and indicate that MOX is mostly driven by low-affinity MOB. 16S rRNA gene sequencing identified MOB classified as Methylococcaceae and particularly Crenothrix. Their relative abundance correlated with pmoA gene counts and MOX rates, underscoring their pivotal role as CH4 oxidizers in stream sediments. Building on the concept of enterotypes, we identify two distinct groups of co-occurring MOB. While there was no taxonomic difference among the members of each cluster, one cluster contained abundant and common MOB, whereas the other cluster contained rare operational taxonomic units (OTUs) specific to a subset of streams. These integrated analyses of changes in MOB community structure, gene abundance, and the corresponding ecosystem process contribute to a better understanding of the distal controls on MOX in streams.
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Affiliation(s)
- Alexandre Bagnoud
- Stream Biofilm and Ecosystem Research Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Paraskevi Pramateftaki
- Stream Biofilm and Ecosystem Research Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matthew J Bogard
- Groupe de recherche interuniversitaire en limnologie, Département des sciences biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Tom J Battin
- Stream Biofilm and Ecosystem Research Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Hannes Peter
- Stream Biofilm and Ecosystem Research Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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165
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Hakobyan A, Zhu J, Glatter T, Paczia N, Liesack W. Hydrogen utilization by Methylocystis sp. strain SC2 expands the known metabolic versatility of type IIa methanotrophs. Metab Eng 2020; 61:181-196. [PMID: 32479801 DOI: 10.1016/j.ymben.2020.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/20/2020] [Accepted: 05/01/2020] [Indexed: 12/19/2022]
Abstract
Methane, a non-expensive natural substrate, is used by Methylocystis spp. as a sole source of carbon and energy. Here, we assessed whether Methylocystis sp. strain SC2 is able to also utilize hydrogen as an energy source. The addition of 2% H2 to the culture headspace had the most significant positive effect on the growth yield under CH4 (6%) and O2 (3%) limited conditions. The SC2 biomass yield doubled from 6.41 (±0.52) to 13.82 (±0.69) mg cell dry weight per mmol CH4, while CH4 consumption was significantly reduced. Regardless of H2 addition, CH4 utilization was increasingly redirected from respiration to fermentation-based pathways with decreasing O2/CH4 mixing ratios. Theoretical thermodynamic calculations confirmed that hydrogen utilization under oxygen-limited conditions doubles the maximum biomass yield compared to fully aerobic conditions without H2 addition. Hydrogen utilization was linked to significant changes in the SC2 proteome. In addition to hydrogenase accessory proteins, the production of Group 1d and Group 2b hydrogenases was significantly increased in both short- and long-term incubations. Both long-term incubation with H2 (37 d) and treatments with chemical inhibitors revealed that SC2 growth under hydrogen-utilizing conditions does not require the activity of complex I. Apparently, strain SC2 has the metabolic capacity to channel hydrogen-derived electrons into the quinone pool, which provides a link between hydrogen oxidation and energy production. In summary, H2 may be a promising alternative energy source in biotechnologically oriented methanotroph projects that aim to maximize biomass yield from CH4, such as the production of high-quality feed protein.
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Affiliation(s)
- Anna Hakobyan
- Research Group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jing Zhu
- Research Group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, China
| | - Timo Glatter
- Core Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Werner Liesack
- Research Group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany.
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166
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Meyer KM, Hopple AM, Klein AM, Morris AH, Bridgham SD, Bohannan BJM. Community structure - Ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function. Mol Ecol 2020; 29:1806-1819. [PMID: 32285532 DOI: 10.1111/mec.15442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 02/28/2020] [Accepted: 04/02/2020] [Indexed: 11/30/2022]
Abstract
Belowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here, we argue that this stems from at least three issues: (a) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge; (b) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge; and (c) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH4 )-cycling processes in soil samples collected along a wetland-to-upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and statistically control for environmental covariates to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high-affinity CH4 oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine-scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.
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Affiliation(s)
- Kyle M Meyer
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Anya M Hopple
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Ann M Klein
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Andrew H Morris
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Scott D Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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167
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He D, Zhang L, Dumont MG, He JS, Ren L, Chu H. The response of methanotrophs to additions of either ammonium, nitrate or urea in alpine swamp meadow soil as revealed by stable isotope probing. FEMS Microbiol Ecol 2020; 95:5498294. [PMID: 31125053 DOI: 10.1093/femsec/fiz077] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/23/2019] [Indexed: 11/13/2022] Open
Abstract
Different forms of nitrogen (N) are deposited on the Qinghai-Tibetan plateau (QTP), while their differential effects on soil methanotrophs and their activity remain elusive. We constructed microcosms amended with different N fertilizers (ammonia, nitrate and urea) using the soils sampled from a swamp meadow on the QTP. The responses of active methanotrophs to different forms of nitrogen were determined by stable isotope probing with 5% 13C-methane. At the early stage of incubation, all N fertilizers, especially urea, suppressed methane oxidation compared with the control. The methane oxidation rate increased during the incubation, suggesting an adaptation and stimulation of some methanotrophs to elevated methane. At the onset of the incubation, the type II methanotrophs Methylocystis were most abundant, but decreased during the incubation and were replaced by the type Ia methanotrophs Methylomonas. Ammonia and urea had similar effects on the methanotroph communities, both characterized by an elevation in the proportion of Methylobacter and more diverse methanotroph communities. Nitrate had less effect on the methanotroph community. Our results uncovered the active methanotrophs responding to different nitrogen forms, and suggested that urea-N might have large effects on methanotroph diversity and activity in swamp meadow soils on the QTP.
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Affiliation(s)
- Dan He
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China.,Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Liyan Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Marc G Dumont
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Jin-Sheng He
- Department of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China.,State Key Laboratory of Grassland Agro-Ecosystems, and College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Lijuan Ren
- Key Laboratory of Tropical Marine Bioresources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
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168
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Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus. Microorganisms 2020; 8:microorganisms8050768. [PMID: 32443820 PMCID: PMC7285482 DOI: 10.3390/microorganisms8050768] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 01/21/2023] Open
Abstract
The Methylocystis and Methylosinus are two of the five genera that were included in the first taxonomic framework of methanotrophic bacteria created half a century ago. Members of both genera are widely distributed in various environments and play a key role in reducing methane fluxes from soils and wetlands. The original separation of these methanotrophs in two distinct genera was based mainly on their differences in cell morphology. Further comparative studies that explored various single-gene-based phylogenies suggested the monophyletic nature of each of these genera. Current availability of genome sequences from members of the Methylocystis/Methylosinus clade opens the possibility for in-depth comparison of the genomic potentials of these methanotrophs. Here, we report the finished genome sequence of Methylocystis heyeri H2T and compare it to 23 currently available genomes of Methylocystis and Methylosinus species. The phylogenomic analysis confirmed that members of these genera form two separate clades. The Methylocystis/Methylosinus pan-genome core comprised 1173 genes, with the accessory genome containing 4941 and 11,192 genes in the shell and the cloud, respectively. Major differences between the genome-encoded environmental traits of these methanotrophs include a variety of enzymes for methane oxidation and dinitrogen fixation as well as genomic determinants for cell motility and photosynthesis.
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169
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Synergistic Effects of a Chalkophore, Methanobactin, on Microbial Methylation of Mercury. Appl Environ Microbiol 2020; 86:AEM.00122-20. [PMID: 32220843 DOI: 10.1128/aem.00122-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/24/2020] [Indexed: 11/20/2022] Open
Abstract
Microbial production of the neurotoxin methylmercury (MeHg) is a significant health and environmental concern, as it can bioaccumulate and biomagnify in the food web. A chalkophore or a copper-binding compound, termed methanobactin (MB), has been shown to form strong complexes with mercury [as Hg(II)] and also enables some methanotrophs to degrade MeHg. It is unknown, however, if Hg(II) binding with MB can also impede Hg(II) methylation by other microbes. Contrary to expectations, MB produced by the methanotroph Methylosinus trichosporium OB3b (OB3b-MB) enhanced the rate and efficiency of Hg(II) methylation more than that observed with thiol compounds (such as cysteine) by the mercury-methylating bacteria Desulfovibrio desulfuricans ND132 and Geobacter sulfurreducens PCA. Compared to no-MB controls, OB3b-MB decreased the rates of Hg(II) sorption and internalization, but increased methylation by 5- to 7-fold, suggesting that Hg(II) complexation with OB3b-MB facilitated exchange and internal transfer of Hg(II) to the HgcAB proteins required for methylation. Conversely, addition of excess amounts of OB3b-MB or a different form of MB from Methylocystis strain SB2 (SB2-MB) inhibited Hg(II) methylation, likely due to greater binding of Hg(II). Collectively, our results underscore the complex roles of microbial exogenous metal-scavenging compounds in controlling net production and bioaccumulation of MeHg in the environment.IMPORTANCE Some anaerobic microorganisms convert inorganic mercury (Hg) into the neurotoxin methylmercury, which can bioaccumulate and biomagnify in the food web. While the genetic basis of microbial mercury methylation is known, factors that control net methylmercury production in the environment are still poorly understood. Here, it is shown that mercury methylation can be substantially enhanced by one form of an exogenous copper-binding compound (methanobactin) produced by some methanotrophs, but not by another. This novel finding illustrates that complex interactions exist between microbes and that these interactions can potentially affect the net production of methylmercury in situ.
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170
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Hough M, McClure A, Bolduc B, Dorrepaal E, Saleska S, Klepac-Ceraj V, Rich V. Biotic and Environmental Drivers of Plant Microbiomes Across a Permafrost Thaw Gradient. Front Microbiol 2020; 11:796. [PMID: 32499761 PMCID: PMC7243355 DOI: 10.3389/fmicb.2020.00796] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/03/2020] [Indexed: 02/01/2023] Open
Abstract
Plant-associated microbiomes are structured by environmental conditions and plant associates, both of which are being altered by climate change. The future structure of plant microbiomes will depend on the, largely unknown, relative importance of each. This uncertainty is particularly relevant for arctic peatlands, which are undergoing large shifts in plant communities and soil microbiomes as permafrost thaws, and are potentially appreciable sources of climate change feedbacks due to their soil carbon (C) storage. We characterized phyllosphere and rhizosphere microbiomes of six plant species, and bulk peat, across a permafrost thaw progression (from intact permafrost, to partially- and fully-thawed stages) via 16S rRNA gene amplicon sequencing. We tested the hypothesis that the relative influence of biotic versus environmental filtering (the role of plant species versus thaw-defined habitat) in structuring microbial communities would differ among phyllosphere, rhizosphere, and bulk peat. Using both abundance- and phylogenetic-based approaches, we found that phyllosphere microbial composition was more strongly explained by plant associate, with little influence of habitat, whereas in the rhizosphere, plant and habitat had similar influence. Network-based community analyses showed that keystone taxa exhibited similar patterns with stronger responses to drivers. However, plant associates appeared to have a larger influence on organisms belonging to families associated with methane-cycling than the bulk community. Putative methanogens were more strongly influenced by plant than habitat in the rhizosphere, and in the phyllosphere putative methanotrophs were more strongly influenced by plant than was the community at large. We conclude that biotic effects can be stronger than environmental filtering, but their relative importance varies among microbial groups. For most microbes in this system, biotic filtering was stronger aboveground than belowground. However, for putative methane-cyclers, plant associations have a stronger influence on community composition than environment despite major hydrological changes with thaw. This suggests that plant successional dynamics may be as important as hydrological changes in determining microbial relevance to C-cycling climate feedbacks. By partitioning the degree that plant versus environmental filtering drives microbiome composition and function we can improve our ability to predict the consequences of warming for C-cycling in other arctic areas undergoing similar permafrost thaw transitions.
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Affiliation(s)
- Moira Hough
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Amelia McClure
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Benjamin Bolduc
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, United States
| | - Ellen Dorrepaal
- Climate Impacts Research Centre, Umeå University, Umeå, Sweden
| | - Scott Saleska
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Virginia Rich
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, United States
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171
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Samad MS, Lee HJ, Cerbin S, Meima-Franke M, Bodelier PLE. Niche Differentiation of Host-Associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes. Front Microbiol 2020; 11:582. [PMID: 32390961 PMCID: PMC7190982 DOI: 10.3389/fmicb.2020.00582] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 03/17/2020] [Indexed: 11/13/2022] Open
Abstract
It has been proposed that zooplankton-associated microbes provide numerous beneficial services to their "host". However, there is still a lack of understanding concerning the effect of temperature on the zooplankton microbiome. Furthermore, it is unclear to what extent the zooplankton microbiome differs from free-living and particle-associated (PA) microbes. Here, we explicitly addressed these issues by investigating (1) the differences in free-living, PA, and zooplankton associated microbes and (2) the impact of temperature on these microbes in the water column of a series of lakes artificially warmed by two power plants. High-throughput amplicon sequencing of the 16S rRNA gene showed that diversity and composition of the bacterial community associated to zooplankton, PA, and bacterioplankton varied significantly from one another, grouping in different clusters indicating niche differentiation of pelagic microbes. From the abiotic parameters measured, temperature significantly affected the diversity and composition of all analyzed microbiomes. Two phyla (e.g., Proteobacteria and Bacteroidetes) dominated in zooplankton microbiomes whereas Actinobacteria was the dominant phylum in the bacterioplankton. The microbial species richness and diversity was lower in zooplankton compared to bacterioplankton and PA. Surprisingly, genera of methane-oxidizing bacteria, methylotrophs and nitrifiers (e.g., Nitrobacter) significantly associated with the microbiome of zooplankton and PA. Our study clearly demonstrates niche differentiation of pelagic microbes and their potential link to biogeochemical cycling in freshwater systems.
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Affiliation(s)
- Md Sainur Samad
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Hyo Jung Lee
- Department of Biology, Kunsan National University, Gunsan, South Korea
| | - Slawek Cerbin
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
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172
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Draft Genome Sequences of Two Acidophilic, Mesophilic Verrucomicrobial Methanotrophs Contain Only One pmoCAB Operon. Microbiol Resour Announc 2020; 9:9/16/e00315-20. [PMID: 32299887 PMCID: PMC7163025 DOI: 10.1128/mra.00315-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methylacidimicrobium cyclopophantes 3B and Methylacidimicrobium tartarophylax 4AC are Gram-negative rod-shaped mesophilic methanotrophs isolated from soil samples with low pH at the Solfatara Crater, near Naples, Italy. The genomes of these extremophilic verrucomicrobia were sequenced using Illumina technology, and both species possess one pmoCAB operon and two xoxF genes.
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173
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Long-Term Rewetting of Three Formerly Drained Peatlands Drives Congruent Compositional Changes in Pro- and Eukaryotic Soil Microbiomes through Environmental Filtering. Microorganisms 2020; 8:microorganisms8040550. [PMID: 32290343 PMCID: PMC7232337 DOI: 10.3390/microorganisms8040550] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/02/2020] [Accepted: 04/08/2020] [Indexed: 12/16/2022] Open
Abstract
Drained peatlands are significant sources of the greenhouse gas (GHG) carbon dioxide. Rewetting is a proven strategy used to protect carbon stocks; however, it can lead to increased emissions of the potent GHG methane. The response to rewetting of soil microbiomes as drivers of these processes is poorly understood, as are the biotic and abiotic factors that control community composition. We analyzed the pro- and eukaryotic microbiomes of three contrasting pairs of minerotrophic fens subject to decade-long drainage and subsequent long-term rewetting. Abiotic soil properties including moisture, dissolved organic matter, methane fluxes, and ecosystem respiration rates were also determined. The composition of the microbiomes was fen-type-specific, but all rewetted sites showed higher abundances of anaerobic taxa compared to drained sites. Based on multi-variate statistics and network analyses, we identified soil moisture as a major driver of community composition. Furthermore, salinity drove the separation between coastal and freshwater fen communities. Methanogens were more than 10-fold more abundant in rewetted than in drained sites, while their abundance was lowest in the coastal fen, likely due to competition with sulfate reducers. The microbiome compositions were reflected in methane fluxes from the sites. Our results shed light on the factors that structure fen microbiomes via environmental filtering.
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174
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Rahalkar MC, Khatri K, Mohite J, Pandit PS, Bahulikar RA. A novel Type I methanotroph Methylolobus aquaticus gen. nov. sp. nov. isolated from a tropical wetland. Antonie van Leeuwenhoek 2020; 113:959-971. [PMID: 32270325 DOI: 10.1007/s10482-020-01410-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/30/2020] [Indexed: 11/28/2022]
Abstract
A novel gammaproteobacterial methanotroph; strain FWC3 was isolated from a tropical freshwater wetland sample collected near a beach in Western India. Strain FWC3 forms flesh pink/peach colored colonies, is non-motile, and the cells are present as diplococci, triads, tetracocci and aggregates. Strain FWC3 grows only on methane and methanol. As the 16S rRNA gene of strain FWC3 showed low similarities with other Type I methanotrophs (less than 94.3%), it was further investigated for its novelty and characterisation by a polyphasic approach. ANI indices and DDH values deduced from the draft genome of strain FWC3 (SEYW00000000.1) with the other nearest type strains (Methylocaldum marinum S8T and Methylococcus capsulatus BathT) were ~ 70% and ~ 15%, respectively. The low level similarities indicated that strain FWC3 can belong to a new genus and species. Additionally, strain FWC3 showed a unique fatty acid profile with the dominance of C16:1 ω7 and ω6c, C16:0 and C16:1 ω9c. During the characterisation of strain FWC3, a morphologically similar methanotroph, strain C50C1 was described (Ghashghavi et al. in mSphere 4:e00631-18, 2019) and named as 'Methylotetracoccus oryzae'. We found that strain FWC3 and strain C50C1 belonged to the same genus but could belong to different species based on the ANI indices and dDDH values (~ 94% and ~ 55%, respectively). However, strain C50C1 has not been deposited in two culture collections and not been validly described. Also, the 16S rRNA gene of strain C50C1 is neither available on the database nor can it be retrieved from the genome assembly. Based on the polyphasic characterisation and comparison to the other type strains of Methylococcaceae, we propose strain FWC3 (= JCM 33786T, = KCTC 72733T, = MCC 4198T) to be the type strain of a novel genus and species, for which the name Methylolobus aquaticus is proposed. Strain C50C1 (Ghashghavi et al. 2019) could represent another species ('Methylolobus oryzae').
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Affiliation(s)
- Monali C Rahalkar
- C2, Bioenergy Group, MACS Agharkar Research Institute, G. G. Agarkar Road, Pune, Maharashtra, 411004, India. .,Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India.
| | - Kumal Khatri
- C2, Bioenergy Group, MACS Agharkar Research Institute, G. G. Agarkar Road, Pune, Maharashtra, 411004, India.,Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Jyoti Mohite
- C2, Bioenergy Group, MACS Agharkar Research Institute, G. G. Agarkar Road, Pune, Maharashtra, 411004, India.,Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Pranitha S Pandit
- C2, Bioenergy Group, MACS Agharkar Research Institute, G. G. Agarkar Road, Pune, Maharashtra, 411004, India.,Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Rahul A Bahulikar
- BAIF Development Research Foundation, Central Research Station, Urulikanchan, Pune, 412202, India
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175
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Kato S, Takashino M, Igarashi K, Kitagawa W. Isolation and Genomic Characterization of a Proteobacterial Methanotroph Requiring Lanthanides. Microbes Environ 2020; 35. [PMID: 32037377 PMCID: PMC7104280 DOI: 10.1264/jsme2.me19128] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Although the bioavailability of rare earth elements (REEs, including scandium, yttrium, and 15 lanthanides) has not yet been examined in detail, methane-oxidizing bacteria (methanotrophs) were recently shown to harbor specific types of methanol dehydrogenases (XoxF-MDHs) that contain lanthanides in their active site, whereas their well-characterized counterparts (MxaF-MDHs) were Ca2+-dependent. However, lanthanide dependency in methanotrophs has not been demonstrated, except in acidic environments in which the solubility of lanthanides is high. We herein report the isolation of a lanthanide-dependent methanotroph from a circumneutral environment in which lanthanides only slightly dissolved. Methanotrophs were enriched and isolated from pond sediment using mineral medium supplemented with CaCl2 or REE chlorides. A methanotroph isolated from the cerium (Ce) chloride-supplemented culture, Methylosinus sp. strain Ce-a6, was clearly dependent on lanthanide. Strain Ce-a6 only required approximately 30 nM lanthanide chloride for its optimal growth and exhibited the ability to utilize insoluble lanthanide oxides, which may enable survival in circumneutral environments. Genome and gene expression analyses revealed that strain Ce-a6 lost the ability to produce functional MxaF-MDH, and this may have been due to a large-scale deletion around the mxa gene cluster. The present results provide evidence for lanthanide dependency as a novel survival strategy by methanotrophs in circumneutral environments.
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Affiliation(s)
- Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).,Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University
| | - Motoko Takashino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Wataru Kitagawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).,Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Computational Bio Big Data Open Innovation Laboratory (CBBD-OIL), AIST
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176
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Mayr MJ, Zimmermann M, Dey J, Brand A, Wehrli B, Bürgmann H. Growth and rapid succession of methanotrophs effectively limit methane release during lake overturn. Commun Biol 2020; 3:108. [PMID: 32144394 PMCID: PMC7060174 DOI: 10.1038/s42003-020-0838-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/19/2020] [Indexed: 11/09/2022] Open
Abstract
Lakes and reservoirs contribute substantially to atmospheric concentrations of the potent greenhouse gas methane. Lake sediments produce large amounts of methane, which accumulate in the oxygen-depleted bottom waters of stratified lakes. Climate change and eutrophication may increase the number of lakes with methane storage in the future. Whether stored methane escapes to the atmosphere during annual lake overturn is a matter of controversy and depends critically on the response of the methanotroph assemblage. Here we show, by combining 16S rRNA gene and pmoA mRNA amplicon sequencing, qPCR, CARD-FISH and potential methane-oxidation rate measurements, that the methanotroph assemblage in a mixing lake underwent both a substantial bloom and ecological succession. As a result, methane oxidation kept pace with the methane supplied from methane-rich bottom water and most methane was oxidized. This aspect of freshwater methanotroph ecology represents an effective mechanism limiting methane transfer from lakes to the atmosphere.
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Affiliation(s)
- Magdalena J Mayr
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland.,Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, 8092, Zurich, Switzerland
| | - Matthias Zimmermann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland.,Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, 8092, Zurich, Switzerland
| | - Jason Dey
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland
| | - Andreas Brand
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland.,Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, 8092, Zurich, Switzerland
| | - Bernhard Wehrli
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland.,Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, 8092, Zurich, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland.
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177
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A Novel Moderately Thermophilic Type Ib Methanotroph Isolated from an Alkaline Thermal Spring in the Ethiopian Rift Valley. Microorganisms 2020; 8:microorganisms8020250. [PMID: 32069978 PMCID: PMC7074724 DOI: 10.3390/microorganisms8020250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/09/2020] [Accepted: 02/10/2020] [Indexed: 11/23/2022] Open
Abstract
Aerobic moderately thermophilic and thermophilic methane-oxidizing bacteria make a substantial contribution in the control of global warming through biological reduction of methane emissions and have a unique capability of utilizing methane as their sole carbon and energy source. Here, we report a novel moderately thermophilic Methylococcus-like Type Ib methanotroph recovered from an alkaline thermal spring (55.4 °C and pH 8.82) in the Ethiopian Rift Valley. The isolate, designated LS7-MC, most probably represents a novel species of a new genus in the family Methylococcaceae of the class Gammaproteobacteria. The 16S rRNA gene phylogeny indicated that strain LS7-MC is distantly related to the closest described relative, Methylococcus capsulatus (92.7% sequence identity). Growth was observed at temperatures of 30–60 °C (optimal, 51–55 °C), and the cells possessed Type I intracellular membrane (ICM). The comparison of the pmoA gene sequences showed that the strain was most closely related to M.capsulatus (87.8%). Soluble methane monooxygenase (sMMO) was not detected, signifying the biological oxidation process from methane to methanol by the particulate methane monooxygenase (pMMO). The other functional genes mxaF, cbbL and nifH were detected by PCR. To our knowledge, the new strain is the first isolated moderately thermophilic methanotroph from an alkaline thermal spring of the family Methylococcaceae. Furthermore, LS7-MC represents a previously unrecognized biological methane sink in thermal habitats, expanding our knowledge of its ecological role in methane cycling and aerobic methanotrophy.
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178
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Kuloyo O, Ruff SE, Cahill A, Connors L, Zorz JK, Hrabe de Angelis I, Nightingale M, Mayer B, Strous M. Methane oxidation and methylotroph population dynamics in groundwater mesocosms. Environ Microbiol 2020; 22:1222-1237. [PMID: 32017377 PMCID: PMC7187433 DOI: 10.1111/1462-2920.14929] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/25/2020] [Indexed: 01/21/2023]
Abstract
Extraction of natural gas from unconventional hydrocarbon reservoirs by hydraulic fracturing raises concerns about methane migration into groundwater. Microbial methane oxidation can be a significant methane sink. Here, we inoculated replicated, sand‐packed, continuous mesocosms with groundwater from a field methane release experiment. The mesocosms experienced thirty‐five weeks of dynamic methane, oxygen and nitrate concentrations. We determined concentrations and stable isotope signatures of methane, carbon dioxide and nitrate and monitored microbial community composition of suspended and attached biomass. Methane oxidation was strictly dependent on oxygen availability and led to enrichment of 13C in residual methane. Nitrate did not enhance methane oxidation under oxygen limitation. Methylotrophs persisted for weeks in the absence of methane, making them a powerful marker for active as well as past methane leaks. Thirty‐nine distinct populations of methylotrophic bacteria were observed. Methylotrophs mainly occurred attached to sediment particles. Abundances of methanotrophs and other methylotrophs were roughly similar across all samples, pointing at transfer of metabolites from the former to the latter. Two populations of Gracilibacteria (Candidate Phyla Radiation) displayed successive blooms, potentially triggered by a period of methane famine. This study will guide interpretation of future field studies and provides increased understanding of methylotroph ecophysiology.
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Affiliation(s)
- Olukayode Kuloyo
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada.,Shell International Exploration and Production Inc, Westhollow Technology Center, Houston, TX, USA
| | - S Emil Ruff
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada.,Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Aaron Cahill
- The Lyell Centre, Heriot Watt University, Edinburgh, United Kingdom
| | - Liam Connors
- Biomedical Sciences Department, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jackie K Zorz
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
| | - Isabella Hrabe de Angelis
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada.,Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | | | - Bernhard Mayer
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
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179
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van Grinsven S, Sinninghe Damsté JS, Abdala Asbun A, Engelmann JC, Harrison J, Villanueva L. Methane oxidation in anoxic lake water stimulated by nitrate and sulfate addition. Environ Microbiol 2020; 22:766-782. [PMID: 31814267 PMCID: PMC7027835 DOI: 10.1111/1462-2920.14886] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 11/21/2019] [Accepted: 12/04/2019] [Indexed: 11/30/2022]
Abstract
Methanotrophic bacteria play a key role in limiting methane emissions from lakes. It is generally assumed that methanotrophic bacteria are mostly active at the oxic-anoxic transition zone in stratified lakes, where they use oxygen to oxidize methane. Here, we describe a methanotroph of the genera Methylobacter that is performing high-rate (up to 72 μM day-1 ) methane oxidation in the anoxic hypolimnion of the temperate Lacamas Lake (Washington, USA), stimulated by both nitrate and sulfate addition. Oxic and anoxic incubations both showed active methane oxidation by a Methylobacter species, with anoxic rates being threefold higher. In anoxic incubations, Methylobacter cell numbers increased almost two orders of magnitude within 3 days, suggesting that this specific Methylobacter species is a facultative anaerobe with a rapid response capability. Genomic analysis revealed adaptations to oxygen-limitation as well as pathways for mixed-acid fermentation and H2 production. The denitrification pathway was incomplete, lacking the genes narG/napA and nosZ, allowing only for methane oxidation coupled to nitrite-reduction. Our data suggest that Methylobacter can be an important driver of the conversion of methane in oxygen-limited lake systems and potentially use alternative electron acceptors or fermentation to remain active under oxygen-depleted conditions.
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Affiliation(s)
- Sigrid van Grinsven
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
| | - Alejandro Abdala Asbun
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
| | - Julia C. Engelmann
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
| | - John Harrison
- Washington State University Vancouver, School of the EnvironmentVancouverWA98686USA
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research, and Utrecht UniversityDen BurgThe Netherlands
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180
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Islam T, Larsen Ø, Birkeland NK. A Novel Cold-adapted Methylovulum species, with a High C16:1ω5c Content, Isolated from an Arctic Thermal Spring in Spitsbergen. Microbes Environ 2020; 35:ME20044. [PMID: 32536671 PMCID: PMC7511782 DOI: 10.1264/jsme2.me20044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/25/2020] [Indexed: 11/12/2022] Open
Abstract
A novel cold-adapted methane-oxidizing bacterium, termed TFB, was isolated from the thermoglacial Arctic karst spring, Trollosen, located in the South Spitsbergen National Park (Norway). The source water is cold and extremely low in phosphate and nitrate. The isolate belongs to the Methylovulum genus of gammaproteobacterial methanotrophs, with the closest phylogenetic affiliation with Methylovulum miyakonense and Methylovulum psychrotolerans (96.2 and 96.1% 16S rRNA gene sequence similarities, respectively). TFB is a strict aerobe that only grows in the presence of methane or methanol. It fixes atmospheric nitrogen and contains Type I intracellular membranes. The growth temperature range was 2-22°C, with an optimum at 13-18°C. The functional genes pmoA, mxaF, and nifH were identified by PCR, whereas mmoX and cbbL were not. C16:1ω5c was identified as the major fatty acid constituent, at an amount (>49%) not previously found in any methanotrophs, and is likely to play a major role in cold adaptation. Strain TFB may be regarded as a new psychrotolerant or psychrophilic species within the genus Methylovulum. The recovery of this cold-adapted bacterium from a neutral Arctic thermal spring increases our knowledge of the diversity and adaptation of extremophilic gammaproteobacterial methanotrophs in the candidate family "Methylomonadaceae".
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Affiliation(s)
- Tajul Islam
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Bergen Katedralskole, Kong Oscars gate 36, 5017 Bergen, Norway
| | - Øivind Larsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- NORCE Norwegian Research Centre AS, Bergen, Norway
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181
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Chen S, Wang P, Liu H, Xie W, Wan XS, Kao SJ, Phelps TJ, Zhang C. Population dynamics of methanogens and methanotrophs along the salinity gradient in Pearl River Estuary: implications for methane metabolism. Appl Microbiol Biotechnol 2019; 104:1331-1346. [DOI: 10.1007/s00253-019-10221-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/11/2019] [Accepted: 10/27/2019] [Indexed: 01/01/2023]
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182
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Thriving in Wetlands: Ecophysiology of the Spiral-Shaped Methanotroph Methylospira mobilis as Revealed by the Complete Genome Sequence. Microorganisms 2019; 7:microorganisms7120683. [PMID: 31835835 PMCID: PMC6956133 DOI: 10.3390/microorganisms7120683] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/03/2019] [Accepted: 12/09/2019] [Indexed: 12/27/2022] Open
Abstract
Candidatus Methylospira mobilis is a recently described spiral-shaped, micro-aerobic methanotroph, which inhabits northern freshwater wetlands and sediments. Due to difficulties of cultivation, it could not be obtained in a pure culture for a long time. Here, we report on the successful isolation of strain Shm1, the first axenic culture of this unique methanotroph. The complete genome sequence obtained for strain Shm1 was 4.7 Mb in size and contained over 4800 potential protein-coding genes. The array of genes encoding C1 metabolic capabilities in strain Shm1 was highly similar to that in the closely related non-motile, moderately thermophilic methanotroph Methylococcus capsulatus Bath. The genomes of both methanotrophs encoded both low- and high-affinity oxidases, which allow their survival in a wide range of oxygen concentrations. The repertoire of signal transduction systems encoded in the genome of strain Shm1, however, by far exceeded that in Methylococcus capsulatus Bath but was comparable to those in other motile gammaproteobacterial methanotrophs. The complete set of motility genes, the presence of both the molybdenum–iron and vanadium-iron nitrogenases, as well as a large number of insertion sequences were also among the features, which define environmental adaptation of Methylospira mobilis to water-saturated, micro-oxic, heterogeneous habitats depleted in available nitrogen.
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183
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Reis PCJ, Thottathil SD, Ruiz-González C, Prairie YT. Niche separation within aerobic methanotrophic bacteria across lakes and its link to methane oxidation rates. Environ Microbiol 2019; 22:738-751. [PMID: 31769176 DOI: 10.1111/1462-2920.14877] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/23/2019] [Accepted: 11/22/2019] [Indexed: 11/30/2022]
Abstract
Lake methane (CH4 ) emissions are largely controlled by aerobic methane-oxidizing bacteria (MOB) which mostly belong to the classes Alpha- and Gammaproteobacteria (Alpha- and Gamma-MOB). Despite the known metabolic and ecological differences between the two MOB groups, their main environmental drivers and their relative contribution to CH4 oxidation rates across lakes remain unknown. Here, we quantified the two MOB groups through CARD-FISH along the water column of six temperate lakes and during incubations in which we measured ambient CH4 oxidation rates. We found a clear niche separation of Alpha- and Gamma-MOB across lake water columns, which is mostly driven by oxygen concentration. Gamma-MOB appears to dominate methanotrophy throughout the water column, but Alpha-MOB may also be an important player particularly in well-oxygenated bottom waters. The inclusion of Gamma-MOB cell abundance improved environmental models of CH4 oxidation rate, explaining part of the variation that could not be explained by environmental factors alone. Altogether, our results show that MOB composition is linked to CH4 oxidation rates in lakes and that information on the MOB community can help predict CH4 oxidation rates and thus emissions from lakes.
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Affiliation(s)
- Paula C J Reis
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
| | - Shoji D Thottathil
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
| | - Clara Ruiz-González
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), Barcelona, E-08003, Spain
| | - Yves T Prairie
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
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184
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Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria. ISME JOURNAL 2019; 14:714-726. [PMID: 31796935 DOI: 10.1038/s41396-019-0561-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/09/2019] [Accepted: 11/14/2019] [Indexed: 11/08/2022]
Abstract
Copper-containing membrane monooxygenases (CuMMOs) are encoded by xmoCAB(D) gene clusters and catalyze the oxidation of methane, ammonia, or some short-chain alkanes and alkenes. In a metagenome constructed from an oilsands tailings pond we detected an xmoCABD gene cluster with <59% derived protein sequence identity to genes from known bacteria. Stable isotope probing experiments combined with a specific xmoA qPCR assay demonstrated that the bacteria possessing these genes were incapable of methane assimilation, but did grow on ethane and propane. Single-cell amplified genomes (SAGs) from propane-enriched samples were screened with the specific PCR assay to identify bacteria possessing the target gene cluster. Multiple SAGs of Betaproteobacteria belonging to the genera Rhodoferax and Polaromonas possessed homologues of the metagenomic xmoCABD gene cluster. Unexpectedly, each of these two genera also possessed other xmoCABD paralogs, representing two additional lineages in phylogenetic analyses. Metabolic reconstructions from SAGs predicted that neither bacterium encoded enzymes with the potential to support catabolic methane or ammonia oxidation, but that both were capable of higher n-alkane degradation. The involvement of the encoded CuMMOs in alkane oxidation was further suggested by reverse transcription PCR analyses, which detected elevated transcription of the xmoA genes upon enrichment of water samples with propane as the sole energy source. Enrichments, isotope incorporation studies, genome reconstructions, and gene expression studies therefore all agreed that the unknown xmoCABD operons did not encode methane or ammonia monooxygenases, but rather n-alkane monooxygenases. This study broadens the known diversity of CuMMOs and identifies these enzymes in non-nitrifying Betaproteobacteria.
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185
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Methane and Nitrous Oxide Flux after Biochar Application in Subtropical Acidic Paddy Soils under Tobacco-Rice Rotation. Sci Rep 2019; 9:17277. [PMID: 31754121 PMCID: PMC6872536 DOI: 10.1038/s41598-019-53044-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 10/28/2019] [Indexed: 12/23/2022] Open
Abstract
Biochar amendment is a good means of mitigating methane (CH4) and nitrous oxide (N2O) emissions. However, the effects of biochar amendment on N2O and CH4 reduction in soil under rotation with different soil moisture contents is not well understood. To understand CH4 and N2O flux from soil with biochar amendment under water-unsaturated and water-saturated conditions, a field experiment was conducted in a tobacco-rice rotation field in subtropical China to investigate N2O and CH4 emissions following soil amendment with tobacco straw biochar at rates of 0, 10, 40 and 80 t·ha−1 (B0, B10, B40 and B80, respectively). N2O and CH4 emissions were monitored by a closed-chamber method in the water-unsaturated tobacco (UT) and water-saturated rice (SR) seasons during the 2015 planting season. The soil pH increased from 5.4 in the control to 6.1 in the soil amended with biochar at 80 t·ha−1 in the UT season. During both the UT and SR seasons, with biochar amendment at 40 and 80 t·ha−1, the soil bulk density (BD) decreased, while the soil organic matter (SOM) and available potassium (Av. K) contents increased. N2O flux was significantly greater in UT than in SR in the controls but decreased with the application of biochar during both the UT and SR seasons. The cumulative CH4 emission decreased with the rate of biochar application and the methanotroph pmoA gene copy number in soils and increased with the methanogenic archaea 16Sr DNA gene copy number in soils during the rice-cropping season. These results indicated that biochar amendment could decrease methanogenic archaea and increase of methanotroph pmoA gene, which are the mechanistic origin for CH4 reduction.
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186
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Pérez R, Casal J, Muñoz R, Lebrero R. Polyhydroxyalkanoates production from methane emissions in Sphagnum mosses: Assessing the effect of temperature and phosphorus limitation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 688:684-690. [PMID: 31254834 DOI: 10.1016/j.scitotenv.2019.06.296] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/10/2019] [Accepted: 06/19/2019] [Indexed: 06/09/2023]
Abstract
The isolation of highly efficient methanotrophic communities is crucial for the optimization of methane bioconversion into products with a high market value such as polyhydroxyalkanoates (PHA). The research here presented aimed at enriching a methanotrophic consortium from two different inocula (Sphagnum peat moss (Sp) and Sphagnum and activated sludge (M)) able to accumulate PHA while efficiently oxidizing CH4. Moreover, the effect of the temperature and phosphorus limitation on the biodegradation rate of CH4 and the PHA accumulation potential was investigated. Higher CH4 degradation rates were obtained under P availability at increasing temperature (25, 30 and 37 °C). The biomass enriched from the mixed inoculum always exhibited a superior biodegradation performance regardless of the temperature (a maximum value of 84.3 ± 8.4 mg CH4 h-1 g biomass-1 was recorded at 37 °C). The results of the PHB production showed that phosphorus limitation is required to promote PHB accumulation, the highest PHB content being observed with the Sphagnum inoculum at 25 °C (13.6 ± 5.6%). The differential specialization of the microbial communities depending on the enrichment temperature supported the key role of this parameter on the results obtained. In all cases after the completion of the enrichment process and of the P limitation tests, Methylocystis, a type II methanotroph known for its ability to accumulate PHA, was the genus that became dominant (reaching percentages from 16 to 46% depending on the enrichment temperature). Thus, the results here obtained demonstrated for the first time the relevance of the temperature used for the enrichment of the methanotrophic bacteria to boost PHA production yields under P limiting condition, highlighting the importance of optimizing culture conditions to improve the cost-efficiency of bioprocesses based on using methane as the primary feedstock for the PHA industrial market.
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Affiliation(s)
- Rebeca Pérez
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, Valladolid University, Prado de la Magdalena, 5, Valladolid, Spain; Institute of Sustainable Processes, Valladolid University, Spain.
| | - Jesús Casal
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, Valladolid University, Prado de la Magdalena, 5, Valladolid, Spain
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, Valladolid University, Prado de la Magdalena, 5, Valladolid, Spain; Institute of Sustainable Processes, Valladolid University, Spain
| | - Raquel Lebrero
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, Valladolid University, Prado de la Magdalena, 5, Valladolid, Spain; Institute of Sustainable Processes, Valladolid University, Spain
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187
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Niche partitioning of methane-oxidizing bacteria along the oxygen-methane counter gradient of stratified lakes. ISME JOURNAL 2019; 14:274-287. [PMID: 31624343 DOI: 10.1038/s41396-019-0515-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/13/2019] [Accepted: 08/25/2019] [Indexed: 12/30/2022]
Abstract
Lakes are a significant source of atmospheric methane, although methane-oxidizing bacteria consume most methane diffusing upward from anoxic sediments. Diverse methane-oxidizing bacteria form an effective methane filter in the water column of stratified lakes, yet, niche partitioning of different methane-oxidizing bacteria along the oxygen-methane counter gradient remains poorly understood. In our study, we reveal vertical distribution patterns of active methane-oxidizing bacteria along the oxygen-methane counter gradient of four lakes, based on amplicon sequencing analysis of 16S rRNA and pmoA genes, and 16S rRNA and pmoA transcripts, and potential methane oxidation rates. Differential distribution patterns indicated that ecologically different methane-oxidizing bacteria occupied the methane-deficient and oxygen-deficient part above and below the oxygen-methane interface. The interface sometimes harbored additional taxa. Within the dominant Methylococcales, an uncultivated taxon (CABC2E06) occurred mainly under methane-deficient conditions, whereas Crenothrix-related taxa preferred oxygen-deficient conditions. Candidatus Methylomirabilis limnetica (NC10 phylum) abundantly populated the oxygen-deficient part in two of four lakes. We reason that the methane filter in lakes is structured and that methane-oxidizing bacteria may rely on niche-specific adaptations for methane oxidation along the oxygen-methane counter gradient. Niche partitioning of methane-oxidizing bacteria might support greater overall resource consumption, contributing to the high effectivity of the lacustrine methane filter.
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188
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Hua ZS, Wang YL, Evans PN, Qu YN, Goh KM, Rao YZ, Qi YL, Li YX, Huang MJ, Jiao JY, Chen YT, Mao YP, Shu WS, Hozzein W, Hedlund BP, Tyson GW, Zhang T, Li WJ. Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea. Nat Commun 2019; 10:4574. [PMID: 31594929 PMCID: PMC6783470 DOI: 10.1038/s41467-019-12574-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 09/12/2019] [Indexed: 01/10/2023] Open
Abstract
Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor. Methane metabolism by some lineages of Archaea contributes to the cycling of carbon on Earth. Here, the authors show high diversity of methyl-coenzyme M reductase (Mcr), a key enzyme associated with archaeal methane/alkane metabolism, in hot spring Archaea, and investigate their ecological roles and evolution.
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Affiliation(s)
- Zheng-Shuang Hua
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China.,Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Yu-Lin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, 999077, Hong Kong, SAR, PR China
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, 4072, QLD, Australia
| | - Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, 81310, Malaysia
| | - Yang-Zhi Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China
| | - Yan-Ling Qi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China
| | - Yu-Xian Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China
| | - Min-Jun Huang
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China
| | - Ya-Ting Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China
| | - Yan-Ping Mao
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, 999077, Hong Kong, SAR, PR China.,College of Chemistry and Environmental Engineering, Shenzhen University, 518060, Shenzhen, PR China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, 510631, Guangzhou, PR China
| | - Wael Hozzein
- Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.,Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, 65211, Egypt
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Gene W Tyson
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, 4072, QLD, Australia. .,Advanced Water Management Centre, University of Queensland, St Lucia, 4072, QLD, Australia.
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, 999077, Hong Kong, SAR, PR China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China. .,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830011, Urumqi, PR China.
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189
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Farhan Ul Haque M, Crombie AT, Murrell JC. Novel facultative Methylocella strains are active methane consumers at terrestrial natural gas seeps. MICROBIOME 2019; 7:134. [PMID: 31585550 PMCID: PMC6778391 DOI: 10.1186/s40168-019-0741-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/20/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Natural gas seeps contribute to global climate change by releasing substantial amounts of the potent greenhouse gas methane and other climate-active gases including ethane and propane to the atmosphere. However, methanotrophs, bacteria capable of utilising methane as the sole source of carbon and energy, play a significant role in reducing the emissions of methane from many environments. Methylocella-like facultative methanotrophs are a unique group of bacteria that grow on other components of natural gas (i.e. ethane and propane) in addition to methane but a little is known about the distribution and activity of Methylocella in the environment. The purposes of this study were to identify bacteria involved in cycling methane emitted from natural gas seeps and, most importantly, to investigate if Methylocella-like facultative methanotrophs were active utilisers of natural gas at seep sites. RESULTS The community structure of active methane-consuming bacteria in samples from natural gas seeps from Andreiasu Everlasting Fire (Romania) and Pipe Creek (NY, USA) was investigated by DNA stable isotope probing (DNA-SIP) using 13C-labelled methane. The 16S rRNA gene sequences retrieved from DNA-SIP experiments revealed that of various active methanotrophs, Methylocella was the only active methanotrophic genus common to both natural gas seep environments. We also isolated novel facultative methanotrophs, Methylocella sp. PC1 and PC4 from Pipe Creek, able to utilise methane, ethane, propane and various non-gaseous multicarbon compounds. Functional and comparative genomics of these new isolates revealed genomic and physiological divergence from already known methanotrophs, in particular, the absence of mxa genes encoding calcium-containing methanol dehydrogenase. Methylocella sp. PC1 and PC4 had only the soluble methane monooxygenase (sMMO) and lanthanide-dependent methanol dehydrogenase (XoxF). These are the first Alphaproteobacteria methanotrophs discovered with this reduced functional redundancy for C-1 metabolism (i.e. sMMO only and XoxF only). CONCLUSIONS Here, we provide evidence, using culture-dependent and culture-independent methods, that Methylocella are abundant and active at terrestrial natural gas seeps, suggesting that they play a significant role in the biogeochemical cycling of these gaseous alkanes. This might also be significant for the design of biotechnological strategies for controlling natural gas emissions, which are increasing globally due to unconventional exploitation of oil and gas.
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Affiliation(s)
- Muhammad Farhan Ul Haque
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.
| | - Andrew T Crombie
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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190
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Community composition and methane oxidation activity of methanotrophs associated with duckweeds in a fresh water lake. J Biosci Bioeng 2019; 128:450-455. [DOI: 10.1016/j.jbiosc.2019.04.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 11/21/2022]
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191
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Crevecoeur S, Ruiz-González C, Prairie YT, Del Giorgio PA. Large-scale biogeography and environmental regulation of methanotrophic bacteria across boreal inland waters. Mol Ecol 2019; 28:4181-4196. [PMID: 31479544 DOI: 10.1111/mec.15223] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 01/09/2023]
Abstract
Aerobic methanotrophic bacteria (methanotrophs) use methane as a source of carbon and energy, thereby mitigating net methane emissions from natural sources. Methanotrophs represent a widespread and phylogenetically complex guild, yet the biogeography of this functional group and the factors that explain the taxonomic structure of the methanotrophic assemblage are still poorly understood. Here, we used high-throughput sequencing of the 16S rRNA gene of the bacterial community to study the methanotrophic community composition and the environmental factors that influence their distribution and relative abundance in a wide range of freshwater habitats, including lakes, streams and rivers across the boreal landscape. Within one region, soil and soil water samples were additionally taken from the surrounding watersheds in order to cover the full terrestrial-aquatic continuum. The composition of methanotrophic communities across the boreal landscape showed only a modest degree of regional differentiation but a strong structuring along the hydrologic continuum from soil to lake communities, regardless of regions. This pattern along the hydrologic continuum was mostly explained by a clear niche differentiation between type I and type II methanotrophs along environmental gradients in pH, and methane concentrations. Our results suggest very different roles of type I and type II methanotrophs within inland waters, the latter likely having a terrestrial source and reflecting passive transport and dilution along the aquatic networks, but this is an unresolved issue that requires further investigation.
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Affiliation(s)
- Sophie Crevecoeur
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université du Québec à Montréal, Montréal, QC, Canada
| | - Clara Ruiz-González
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Yves T Prairie
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université du Québec à Montréal, Montréal, QC, Canada
| | - Paul A Del Giorgio
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université du Québec à Montréal, Montréal, QC, Canada
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192
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Carere CR, McDonald B, Peach HA, Greening C, Gapes DJ, Collet C, Stott MB. Hydrogen Oxidation Influences Glycogen Accumulation in a Verrucomicrobial Methanotroph. Front Microbiol 2019; 10:1873. [PMID: 31474959 PMCID: PMC6706786 DOI: 10.3389/fmicb.2019.01873] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/29/2019] [Indexed: 11/23/2022] Open
Abstract
Metabolic flexibility in aerobic methane oxidizing bacteria (methanotrophs) enhances cell growth and survival in instances where resources are variable or limiting. Examples include the production of intracellular compounds (such as glycogen or polyhydroxyalkanoates) in response to unbalanced growth conditions and the use of some energy substrates, besides methane, when available. Indeed, recent studies show that verrucomicrobial methanotrophs can grow mixotrophically through oxidation of hydrogen and methane gases via respiratory membrane-bound group 1d [NiFe] hydrogenases and methane monooxygenases, respectively. Hydrogen metabolism is particularly important for adaptation to methane and oxygen limitation, suggesting this metabolic flexibility may confer growth and survival advantages. In this work, we provide evidence that, in adopting a mixotrophic growth strategy, the thermoacidophilic methanotroph, Methylacidiphilum sp. RTK17.1 changes its growth rate, biomass yields and the production of intracellular glycogen reservoirs. Under nitrogen-fixing conditions, removal of hydrogen from the feed-gas resulted in a 14% reduction in observed growth rates and a 144% increase in cellular glycogen content. Concomitant with increases in glycogen content, the total protein content of biomass decreased following the removal of hydrogen. Transcriptome analysis of Methylacidiphilum sp. RTK17.1 revealed a 3.5-fold upregulation of the Group 1d [NiFe] hydrogenase in response to oxygen limitation and a 4-fold upregulation of nitrogenase encoding genes (nifHDKENX) in response to nitrogen limitation. Genes associated with glycogen synthesis and degradation were expressed constitutively and did not display evidence of transcriptional regulation. Collectively these data further challenge the belief that hydrogen metabolism in methanotrophic bacteria is primarily associated with energy conservation during nitrogen fixation and suggests its utilization provides a competitive growth advantage within hypoxic habitats.
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Affiliation(s)
- Carlo R. Carere
- Department of Chemical and Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Ben McDonald
- Scion, Te Papa Tipu Innovation Park, Rotorua, New Zealand
| | - Hanna A. Peach
- Geomicrobiology Research Group, Department of Geothermal Sciences, GNS Science, Taupō, New Zealand
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | | | | | - Matthew B. Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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193
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Zhao R, Wang H, Cheng X, Yun Y, Qiu X. Upland soil cluster γ dominates the methanotroph communities in the karst Heshang Cave. FEMS Microbiol Ecol 2019; 94:5107866. [PMID: 30265314 DOI: 10.1093/femsec/fiy192] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/26/2018] [Indexed: 11/13/2022] Open
Abstract
Microorganisms are thought to play a critical role in methane (CH4) consumption in karst caves and yet the presence and diversity of methane-oxidizing bacteria (MOB) remain a mystery. In Heshang Cave, CH4 concentration decreases from 1.9 ppm at the entrance to 0.65 ppm inside the cave. To explore the presence and diversity of MOB in this cave, weathered rocks and sediment samples were collected from the cave and subjected to molecular analysis. The abundances of MOB were 107-108 copies g-1 dry sample via quantification of the pmoA gene, which are comparable to or even higher than those reported in other terrestrial environments, and account for up to 20% of the total microbial communities. Phylogenetically, MOB communities were dominated by the 'high-affinity' upland soil cluster γ (USCγ), although the predominance of Type Ia MOB was also detected in the permanently waterlogged stream sediment. The estimated CH4 oxidation potential varied dramatically among samples in the range of 0.6-80 CH4 m-3 d-1. Collectively, this study provides compelling evidence that the high-affinity MOB capable of oxidizing CH4 at the atmospheric level are present in Heshang Cave, which may play an important role in the CH4 consumption, and supports karst caves as important atmospheric CH4 sinks.
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Affiliation(s)
- Rui Zhao
- State Key Laboratory of Biogeology and Environment Geology, China University of Geosciences, Wuhan 430074, P. R. China.,Now at School of Marine Science and Policy, University of Delaware, Lewes 19958, Delaware, USA
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environment Geology, China University of Geosciences, Wuhan 430074, P. R. China.,Laboratory of Basin Hydrology and Wetland Eco-restoration, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environment Geology, China University of Geosciences, Wuhan 430074, P. R. China
| | - Yuan Yun
- State Key Laboratory of Biogeology and Environment Geology, China University of Geosciences, Wuhan 430074, P. R. China
| | - Xuan Qiu
- State Key Laboratory of Biogeology and Environment Geology, China University of Geosciences, Wuhan 430074, P. R. China
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194
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Kuźniar A, Furtak K, Włodarczyk K, Stępniewska Z, Wolińska A. Methanotrophic Bacterial Biomass as Potential Mineral Feed Ingredients for Animals. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16152674. [PMID: 31357395 PMCID: PMC6696423 DOI: 10.3390/ijerph16152674] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/16/2019] [Accepted: 07/23/2019] [Indexed: 11/16/2022]
Abstract
Microorganisms play an important role in animal nutrition, as they can be used as a source of food or feed. The aim of the study was to determine the nutritional elements and fatty acids contained in the biomass of methanotrophic bacteria. Four bacterial consortia composed of Methylocystis and Methylosinus originating from Sphagnum flexuosum (Sp1), S. magellanicum (Sp2), S. fallax II (Sp3), S. magellanicum IV (Sp4), and one composed of Methylocaldum, Methylosinus, and Methylocystis that originated from coalbed rock (Sk108) were studied. Nutritional elements were determined using the flame atomic absorption spectroscopy technique after a biomass mineralization stage, whereas the fatty acid content was analyzed with the GC technique. Additionally, the growth of biomass and dynamics of methane consumption were monitored. It was found that the methanotrophic biomass contained high concentrations of K, Mg, and Fe, i.e., approx. 9.6–19.1, 2.2–7.6, and 2.4–6.6 g kg−1, respectively. Consequently, the biomass can be viewed as an appropriate feed and/or feed additive for supplementation with macroelements and certain microelements. Moreover, all consortia demonstrated higher content of unsaturated acids than saturated ones. Thus, methanotrophic bacteria seem to be a good solution, in natural supplementation of animal diets.
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Affiliation(s)
- Agnieszka Kuźniar
- Department of Biochemistry and Environmental Chemistry, The John Paul II Catholic University of Lublin, Konstantynów St. 1 I, 20-708 Lublin, Poland.
| | - Karolina Furtak
- Department of Agriculture Microbiology, Institute of Soil Sciences and Plant Cultivation State Research Institute, Czartoryskich St. 8, 24-100 Puławy, Poland
| | - Kinga Włodarczyk
- Department of Biochemistry and Environmental Chemistry, The John Paul II Catholic University of Lublin, Konstantynów St. 1 I, 20-708 Lublin, Poland
| | - Zofia Stępniewska
- Department of Biochemistry and Environmental Chemistry, The John Paul II Catholic University of Lublin, Konstantynów St. 1 I, 20-708 Lublin, Poland
| | - Agnieszka Wolińska
- Department of Biochemistry and Environmental Chemistry, The John Paul II Catholic University of Lublin, Konstantynów St. 1 I, 20-708 Lublin, Poland
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195
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Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the pmoCAB Operon of Type Ia Methanotrophs. mSystems 2019; 4:4/4/e00342-19. [PMID: 31337658 PMCID: PMC6650546 DOI: 10.1128/msystems.00342-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth’s system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the pmoCAB operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence. Understanding the interplay between genotype and phenotype is a fundamental goal of functional genomics. Methane oxidation is a microbial phenotype with global-scale significance as part of the carbon biogeochemical cycle and a sink for greenhouse gas. Microorganisms that oxidize methane (methanotrophs) are taxonomically diverse and widespread around the globe. In methanotrophic bacteria, enzymes in the methane oxidation metabolic module (KEGG module M00174, conversion of methane to formaldehyde) are encoded in four operons (pmoCAB, mmoXYZBCD, mxaFI, and xoxF). Recent reports have suggested that methanotrophs in Proteobacteria acquired methane monooxygenases through horizontal gene transfer. Here, we used a genomic meta-analysis to infer the transcriptional and translational advantages of coding sequences from the methane oxidation metabolic modules of different types of methanotrophs. By analyzing isolate and metagenome-assembled genomes from phylogenetically and geographically diverse sources, we detected an anomalous nucleotide composition bias in the coding sequences of particulate methane monooxygenase genes (pmoCAB) from type Ia methanotrophs. We found that this nucleotide bias increases the level of codon bias by decreasing the GC content in the third base of codons, a strategy that contrasts with that of other coding sequences in the module. Further codon usage analyses uncovered that codon variants of the type Ia pmoCAB coding sequences deviate from the genomic signature to match ribosomal protein-coding sequences. Subsequently, computation of transcription and translation metrics revealed that the pmoCAB coding sequences of type Ia methanotrophs optimize the usage of codon variants to maximize translation efficiency and accuracy, while minimizing the synthesis cost of transcripts and proteins. IMPORTANCE Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth’s system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the pmoCAB operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence.
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196
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Yarwood SA. The role of wetland microorganisms in plant-litter decomposition and soil organic matter formation: a critical review. FEMS Microbiol Ecol 2019; 94:5087730. [PMID: 30169564 DOI: 10.1093/femsec/fiy175] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 08/29/2018] [Indexed: 02/06/2023] Open
Abstract
New soil organic matter (SOM) models highlight the role of microorganisms in plant litter decomposition and storage of microbial-derived carbon (C) molecules. Wetlands store more C per unit area than any other ecosystem, but SOM storage mechanisms such as aggregation and metal complexes are mostly untested in wetlands. This review discusses what is currently known about the role of microorganisms in SOM formation and C sequestrations, as well as, measures of microbial communities as they relate to wetland C cycling. Studies within the last decade have yielded new insights about microbial communities. For example, microbial communities appear to be adapted to short-term fluctuations in saturation and redox and researchers have observed synergistic pairings that in some cases run counter to thermodynamic theory. Significant knowledge gaps yet to be filled include: (i) What controls microbial access to and decomposition of plant litter and SOM? (ii) How does microbial community structure shape C fate, across different wetland types? (iii) What types of plant and microbial molecules contribute to SOM accumulation? Studies examining the active microbial community directly or that utilize multi-pronged approaches are shedding new light on microbial functional potential, however, and promise to improve wetland C models in the near future.
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Affiliation(s)
- Stephanie A Yarwood
- Environmental Science and Technology Department, University of Maryland, 1204 HJ Patterson Hall, College Park, MD 20742, USA
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197
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Lau NS, Zarkasi KZ, Md Sah ASR, Shu-Chien AC. Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia. MICROBIAL ECOLOGY 2019; 78:20-32. [PMID: 30397794 DOI: 10.1007/s00248-018-1283-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/29/2018] [Indexed: 05/27/2023]
Abstract
Although freshwater biomes cover less than 1% of the Earth's surface, they have disproportionate ecological significances. Attempts to study the taxonomy and function of freshwater microbiota are currently limited to samples collected from temperate lakes. In this study, we investigated samples from the photic and aphotic of an aquaculture site (disturbed) of Temengor Lake, a tropical lake in comparison with the undisturbed site of the lake using 16S rRNA amplicon and shotgun metagenomic approaches. Vertical changes in bacterial community composition and function of the Temengor Lake metagenomes were observed. The photic water layer of Temengor Lake was dominated by typical freshwater assemblages consisting of Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, and Cyanobacteria lineages. On the other hand, the aphotic water featured in addition to Proteobacteria, Bacteroidetes, Verrucomicrobia, and two more abundant bacterial phyla that are typically ubiquitous in anoxic habitats (Chloroflexi and Firmicutes). The aphotic zone of Temengor Lake exhibited genetic potential for nitrogen and sulfur metabolisms for which terminal electron acceptors other than oxygen are used in the reactions. The aphotic water of the disturbed site also showed an overrepresentation of genes associated with the metabolism of carbohydrates, likely driven by the enrichment of nutrient resulting from aquaculture activities at the site. The results presented in this study can serve as a basis for understanding the structure and functional capacity of the microbial communities in the photic and aphotic zones/water layers of tropical man-made lakes.
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Affiliation(s)
- Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900, Bayan Lepas, Penang, Malaysia
| | - Kamarul Zaman Zarkasi
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | | | - Alexander Chong Shu-Chien
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900, Bayan Lepas, Penang, Malaysia.
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia.
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198
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Tripathi BM, Kim HM, Jung JY, Nam S, Ju HT, Kim M, Lee YK. Distinct Taxonomic and Functional Profiles of the Microbiome Associated With Different Soil Horizons of a Moist Tussock Tundra in Alaska. Front Microbiol 2019; 10:1442. [PMID: 31316487 PMCID: PMC6610311 DOI: 10.3389/fmicb.2019.01442] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/07/2019] [Indexed: 11/13/2022] Open
Abstract
Permafrost-underlain tundra soils in Northern Hemisphere are one of the largest reservoirs of terrestrial carbon, which are highly sensitive to microbial decomposition due to climate warming. However, knowledge about the taxonomy and functions of microbiome residing in different horizons of permafrost-underlain tundra soils is still limited. Here we compared the taxonomic and functional composition of microbiome between different horizons of soil cores from a moist tussock tundra ecosystem in Council, Alaska, using 16S rRNA gene and shotgun metagenomic sequencing. The composition, diversity, and functions of microbiome varied significantly between soil horizons, with top soil horizon harboring more diverse communities than sub-soil horizons. The vertical gradient in soil physico-chemical parameters were strongly associated with composition of microbial communities across permafrost soil horizons; however, a large fraction of the variation in microbial communities remained unexplained. The genes associated with carbon mineralization were more abundant in top soil horizon, while genes involved in acetogenesis, fermentation, methane metabolism (methanogenesis and methanotrophy), and N cycling were dominant in sub-soil horizons. The results of phylogenetic null modeling analysis showed that stochastic processes strongly influenced the composition of the microbiome in different soil horizons, except the bacterial community composition in top soil horizon, which was largely governed by homogeneous selection. Our study expands the knowledge on the structure and functional potential of microbiome associated with different horizons of permafrost soil, which could be useful in understanding the effects of environmental change on microbial responses in tundra ecosystems.
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Affiliation(s)
| | - Hye Min Kim
- Environmental Safety Research Institute, NeoEnBiz, Bucheon, South Korea
| | - Ji Young Jung
- Korea Polar Research Institute, Incheon, South Korea
| | - Sungjin Nam
- Korea Polar Research Institute, Incheon, South Korea
| | - Hyeon Tae Ju
- Korea Polar Research Institute, Incheon, South Korea
| | - Mincheol Kim
- Korea Polar Research Institute, Incheon, South Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon, South Korea
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199
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Deng Y, Che R, Wang F, Conrad R, Dumont M, Yun J, Wu Y, Hu A, Fang J, Xu Z, Cui X, Wang Y. Upland Soil Cluster Gamma dominates methanotrophic communities in upland grassland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 670:826-836. [PMID: 30921716 DOI: 10.1016/j.scitotenv.2019.03.299] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 05/25/2023]
Abstract
Aerobic methanotrophs in upland soils consume atmospheric methane, serving as a critical counterbalance to global warming; however, the biogeographic distribution patterns of their abundance and community composition are poorly understood, especial at a large scale. In this study, soils were sampled from 30 grasslands across >2000 km on the Qinghai-Tibetan Plateau to determine the distribution patterns of methanotrophs and their driving factors at a regional scale. Methanotroph abundance and community composition were analyzed using quantitative PCR and Illumina Miseq sequencing of pmoA genes, respectively. The pmoA gene copies ranged from 8.2 × 105 to 1.1 × 108 per gram dry soil. Among the 30 grassland soil samples, Upland Soil Cluster Gamma (USCγ) dominated the methanotroph communities in 26 samples. Jasper Ridge Cluster (JR3) was the most dominant methanotrophic cluster in two samples; while Methylocystis, cluster FWs, and Methylobacter were abundant in other two wet soil samples. Interestingly, reanalyzing the pmoA genes sequencing data from existing publications suggested that USCγ was also the main methanotrophic cluster in grassland soils in other regions, especially when their mean annual precipitation was <500 mm. Canonical Analysis of Principal Coordinates including all soil samples indicated that the methanotrophic community composition was significantly correlated with local environmental factors, among which mean annual precipitation and pH showed the strongest correlations. Variance partitioning analysis showed that environmental factors and spatial distance were significant factors affecting the community structure of methanotrophs, and environmental properties were more important factors. Collectively, these findings indicate that atmospheric methane may be mainly oxidized by USCγ in upland soils. They also highlight the key role of water availability and pH in determining the abundance and community profiles of grassland soil methanotrophs.
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Affiliation(s)
- Yongcui Deng
- School of Geography, Nanjing Normal University, 210023 Nanjing, China
| | - Rongxiao Che
- Institute of International Rivers and Eco-security, Yunnan University, 650091 Kunming, China; University of the Chinese Academy of Sciences, 100049 Beijing, China; Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Fang Wang
- University of the Chinese Academy of Sciences, 100049 Beijing, China; Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Marc Dumont
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Juanli Yun
- Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yibo Wu
- Ningbo University, 315211 Ningbo, China
| | - Ang Hu
- Hunan Agricultural University, 410128 Changsha, China
| | - Jie Fang
- School of Geography, Nanjing Normal University, 210023 Nanjing, China
| | - Zhihong Xu
- Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Xiaoyong Cui
- University of the Chinese Academy of Sciences, 100049 Beijing, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, 100101 Beijing, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China.
| | - Yanfen Wang
- University of the Chinese Academy of Sciences, 100049 Beijing, China
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200
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Ghashghavi M, Belova SE, Bodelier PLE, Dedysh SN, Kox MAR, Speth DR, Frenzel P, Jetten MSM, Lücker S, Lüke C. Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments. mSphere 2019; 4:e00631-18. [PMID: 31167950 PMCID: PMC6553558 DOI: 10.1128/msphere.00631-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 05/09/2019] [Indexed: 01/08/2023] Open
Abstract
Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the Proteobacteria, Verrucomicrobia, and NC10 phyla. Within the Proteobacteria phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs (Methylococcus and Methylocaldum) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named "Methylotetracoccus oryzae" C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C16:1ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two pmoCAB operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems.IMPORTANCE Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions.
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Affiliation(s)
- Mohammad Ghashghavi
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Svetlana E Belova
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradski Institute of Microbiology, Moscow, Russia
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Svetlana N Dedysh
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradski Institute of Microbiology, Moscow, Russia
| | - Martine A R Kox
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Daan R Speth
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Peter Frenzel
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | - Sebastian Lücker
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Claudia Lüke
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
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