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Lim J, Wehmeyer H, Heffner T, Aeppli M, Gu W, Kim PJ, Horn MA, Ho A. Resilience of aerobic methanotrophs in soils; spotlight on the methane sink under agriculture. FEMS Microbiol Ecol 2024; 100:fiae008. [PMID: 38327184 PMCID: PMC10872700 DOI: 10.1093/femsec/fiae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/09/2024] Open
Abstract
Aerobic methanotrophs are a specialized microbial group, catalyzing the oxidation of methane. Disturbance-induced loss of methanotroph diversity/abundance, thus results in the loss of this biological methane sink. Here, we synthesized and conceptualized the resilience of the methanotrophs to sporadic, recurring, and compounded disturbances in soils. The methanotrophs showed remarkable resilience to sporadic disturbances, recovering in activity and population size. However, activity was severely compromised when disturbance persisted or reoccurred at increasing frequency, and was significantly impaired following change in land use. Next, we consolidated the impact of agricultural practices after land conversion on the soil methane sink. The effects of key interventions (tillage, organic matter input, and cover cropping) where much knowledge has been gathered were considered. Pairwise comparisons of these interventions to nontreated agricultural soils indicate that the agriculture-induced impact on the methane sink depends on the cropping system, which can be associated to the physiology of the methanotrophs. The impact of agriculture is more evident in upland soils, where the methanotrophs play a more prominent role than the methanogens in modulating overall methane flux. Although resilient to sporadic disturbances, the methanotrophs are vulnerable to compounded disturbances induced by anthropogenic activities, significantly affecting the methane sink function.
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Affiliation(s)
- Jiyeon Lim
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Helena Wehmeyer
- Nestlè Research, Route du Jorat 57, CH 1000 Lausanne 26, Switzerland
| | - Tanja Heffner
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Meret Aeppli
- Environmental Engineering Institute IIE-ENAC, Laboratory SOIL, Ecole Polytechnique Fédérale de Lausanne (EPFL), Valais Wallis, CH 1950 Sion, Switzerland
| | - Wenyu Gu
- Environmental Engineering Institute IIE-ENAC, Laboratory MICROBE, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH 1015 Lausanne, Switzerland
| | - Pil Joo Kim
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Marcus A Horn
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Adrian Ho
- Nestlè Research, Route du Jorat 57, CH 1000 Lausanne 26, Switzerland
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2
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Chang J, Peng P, Farhan Ul-Haque M, Hira A, DiSpirito AA, Semrau JD. Inhibition of nitrous oxide reduction in forest soil microcosms by different forms of methanobactin. Environ Microbiol 2023; 25:2338-2350. [PMID: 37395163 DOI: 10.1111/1462-2920.16456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/14/2023] [Indexed: 07/04/2023]
Abstract
Copper plays a critical role in controlling greenhouse gas emissions as it is a key component of the particulate methane monooxygenase and nitrous oxide reductase. Some methanotrophs excrete methanobactin (MB) that has an extremely high copper affinity. As a result, MB may limit the ability of other microbes to gather copper, thereby decreasing their activity as well as impacting microbial community composition. Here, we show using forest soil microcosms that multiple forms of MB; MB from Methylosinus trichosporium OB3b (MB-OB3b) and MB from Methylocystis sp. strain SB2 (MB-SB2) increased nitrous oxide (N2 O) production as well caused significant shifts in microbial community composition. Such effects, however, were mediated by the amount of copper in the soils, with low-copper soil microcosms showing the strongest response to MB. Furthermore, MB-SB2 had a stronger effect, likely due to its higher affinity for copper. The presence of either form of MB also inhibited nitrite reduction and generally increased the presence of genes encoding for the iron-containing nitrite reductase (nirS) over the copper-dependent nitrite reductase (nirK). These data indicate the methanotrophic-mediated production of MB can significantly impact multiple steps of denitrification, as well as have broad effects on microbial community composition of forest soils.
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Affiliation(s)
- Jin Chang
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Peng Peng
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Abid Hira
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
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3
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Oh S, Cho K, Park S, Kwon MJ, Chung J, Lee S. Denitrification dynamics in unsaturated soils with different porous structures and water saturation degrees: A focus on the shift in microbial community structures. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130413. [PMID: 36436452 DOI: 10.1016/j.jhazmat.2022.130413] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Despite its environmental significance, little is known about denitrification in vadose zones owing to the complexity of such environments. Here, we investigated denitrification in unsaturated soils with different pore distributions. To this end, we performed batch-type denitrification experiments and analyzed microbial community shifts before and after possible reactions with nitrates to clarify the relevant denitrifying mechanism in the microcosms. For quantitative comparison, pore distribution in the test soil samples was characterized based on the uniformity coefficient (Cu) and water saturation degree (SD). Micro-CT analysis of the soil pore distribution confirmed that the proportion of bigger-sized pores increased with decreasing Cu. However, oxygen diffusion into the system was controlled by SD rather than Cu. Within a certain SD range (51-67%), the pore condition changed abruptly from an oxic to an anoxic state. Consequently, denitrification occurred even under unsaturated soil conditions when the SD increased beyond 51-67%. High throughput sequencing revealed that the same microbial species were potentially responsible for denitrification under both partially (SD 67%), and fully saturated (SD of 100%) conditions, implying that the mechanism of denitrification in a vadose zone, if it exists, might be possibly similar under varying conditions.
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Affiliation(s)
- Sungjik Oh
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea
| | - Kyungjin Cho
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea
| | - Saerom Park
- Urban Water Circulation Research Center, Department of Land, Water and Environment Research, Korea Institute of Civil Engineering and Building Technology (KICT), Gyeonggi-do 10223, South Korea
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Jaeshik Chung
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea.
| | - Seunghak Lee
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea; Graduate School of Energy and Environment (KU-KIST Green School), Korea University, Seoul 02841, South Korea.
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4
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Altshuler I, Raymond-Bouchard I, Magnuson E, Tremblay J, Greer CW, Whyte LG. Unique high Arctic methane metabolizing community revealed through in situ 13CH 4-DNA-SIP enrichment in concert with genome binning. Sci Rep 2022; 12:1160. [PMID: 35064149 PMCID: PMC8782848 DOI: 10.1038/s41598-021-04486-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy 13CH4 (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH4 metabolism in these high Arctic cryosols. Sequencing of 13C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-13C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and characterizing novel organisms related to specific microbial functions or biogeochemical cycles of interest. Our findings reveal a unique and active Arctic cryosol microbial community potentially involved in CH4 cycling.
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Affiliation(s)
- Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada.
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences NMBU, Universitetstunet 3, 1430, Ås, Norway.
| | - Isabelle Raymond-Bouchard
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
| | - Elisse Magnuson
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
| | - Julien Tremblay
- Energy, Mining and Environment Research Centre, National Research Council of Canada, 6100 Royalmount Ave., Montreal, QC, H4P 2R2, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
- Energy, Mining and Environment Research Centre, National Research Council of Canada, 6100 Royalmount Ave., Montreal, QC, H4P 2R2, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
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Xia F, Jiang QY, Zhu T, Zou B, Liu H, Quan ZX. Ammonium promoting methane oxidation by stimulating the Type Ia methane-oxidizing bacteria in tidal flat sediments of the Yangtze River estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148470. [PMID: 34166901 DOI: 10.1016/j.scitotenv.2021.148470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
Estuary and coastal environments have essential ecosystem functions in greenhouse gas sinks and removal of nitrogen pollution. Methane-oxidizing bacteria (MOB) and ammonia-oxidizing bacteria (AOB) communities play critical functions in the estuary's tidal flat sediments. Therefore, the effects of ammonium on MOB communities and methane on AOB communities need to be further explained. In this study, microcosm incubations with different contents of ammonium or methane were conducted for a relatively short (24 h) or long (28 days) period with tidal flat sediments from the Yangtze River estuary. Subsequently, the tagged highly degenerate primer PCR and DNA-based stable isotope probing method were employed to demonstrate the effects on MOB and AOB populations. The results indicated that the methane consumption was enhanced with ammonium supplements within 24 h of incubation. Supplement of 2 μmol/g d.w.s (μmol per gram dry weight soil) NH4+ increased the amount of MOB and its proportion to the total bacteria (p < 0.05) for 28 days incubation. The ammonium supplement increased the proportion of Methylomonas and Methylobacter based on the 16S rRNA gene. According to the functional gene analysis, the MOB primarily engaged in methane oxidation include Methylomonas, Methylobacter, Methylomicrobium, and Methylosarcina, which were associated with Type Ia MOB. It suggested that ammonium supplement may promote methane oxidation by stimulating the Type Ia MOB in tidal flat sediments of the Yangtze River estuary. The current research helps understand the effect of ammonium on methane consumption in the estuary and coastal environments.
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Affiliation(s)
- Fei Xia
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Qiu-Yue Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Ting Zhu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Bin Zou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Huan Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China.
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6
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Rahalkar MC, Khatri K, Pandit P, Bahulikar RA, Mohite JA. Cultivation of Important Methanotrophs From Indian Rice Fields. Front Microbiol 2021; 12:669244. [PMID: 34539593 PMCID: PMC8447245 DOI: 10.3389/fmicb.2021.669244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/09/2021] [Indexed: 11/15/2022] Open
Abstract
Methanotrophs are aerobic to micro-aerophilic bacteria, which oxidize and utilize methane, the second most important greenhouse gas. The community structure of the methanotrophs in rice fields worldwide has been studied mainly using culture-independent methods. Very few studies have focused on culturing methanotrophs from rice fields. We developed a unique method for the cultivation of methanotrophs from rice field samples. Here, we used a modified dilute nitrate mineral salts (dNMS) medium, with two cycles of dilution till extinction series cultivation with prolonged incubation time, and used agarose in the solid medium. The cultivation approach resulted in the isolation of methanotrophs from seven genera from the three major groups: Type Ia (Methylomonas, Methylomicrobium, and Methylocucumis), Type Ib (Methylocaldum and Methylomagnum), and Type II (Methylocystis and Methylosinus). Growth was obtained till 10–6–10–8 dilutions in the first dilution series, indicating the culturing of dominant methanotrophs. Our study was supported by 16S rRNA gene-based next-generation sequencing (NGS) of three of the rice samples. Our analyses and comparison with the global scenario suggested that the cultured members represented the major detected taxa. Strain RS1, representing a putative novel species of Methylomicrobium, was cultured; and the draft genome sequence was obtained. Genome analysis indicated that RS1 represented a new putative Methylomicrobium species. Methylomicrobium has been detected globally in rice fields as a dominant genus, although no Methylomicrobium strains have been isolated from rice fields worldwide. Ours is one of the first extensive studies on cultured methanotrophs from Indian rice fields focusing on the tropical region, and a unique method was developed. A total of 29 strains were obtained, which could be used as models for studying methane mitigation from rice fields and for environmental and biotechnological applications.
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Affiliation(s)
- Monali C Rahalkar
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Kumal Khatri
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Pranitha Pandit
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Rahul A Bahulikar
- Central Research Station, BAIF Development Research Foundation, Pune, India
| | - Jyoti A Mohite
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
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7
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Ho A, Mendes LW, Lee HJ, Kaupper T, Mo Y, Poehlein A, Bodelier PLE, Jia Z, Horn MA. Response of a methane-driven interaction network to stressor intensification. FEMS Microbiol Ecol 2021; 96:5898668. [PMID: 32857837 DOI: 10.1093/femsec/fiaa180] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/25/2020] [Indexed: 01/04/2023] Open
Abstract
Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial interaction may become relevant for community functioning under stress. However, empirical validation of the role and stressor-induced response of the interaction network remains scarce. Here, we determined the response of a complex methane-driven interaction network to a stepwise increase in NH4Cl-induced stress (0.5-4.75 g L-1, in 0.25-0.5 g L-1 increments) using enrichment of a naturally occurring complex community derived from a paddy soil in laboratory-scale incubations. Although ammonium and intermediates of ammonium oxidation are known to inhibit methane oxidation, methanotrophic activity was unexpectedly detected even in incubations with high ammonium levels, albeit rates were significantly reduced. Sequencing analysis of the 16S rRNA and pmoA genes consistently revealed divergent communities in the reference and stressed incubations. The 16S rRNA-based co-occurrence network analysis revealed that NH4Cl-induced stress intensification resulted in a less complex and modular network, likely driven by less stable interaction. Interestingly, the non-methanotrophs formed the key nodes, and appear to be relevant members of the community. Overall, stressor intensification unravels the interaction network, with adverse consequences for community functioning.
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Affiliation(s)
- Adrian Ho
- Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Lucas W Mendes
- Center of Nuclear Energy in Agriculture, University of São Paulo (CENA-USP), Avenida Centenario 303, 13416-000, Piracicaba-SP, Brazil
| | - Hyo Jung Lee
- Department of Biology, Kunsan National University, 558 Daehak-ro, Gunsan-si 54150, Republic of Korea
| | - Thomas Kaupper
- Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Yongliang Mo
- Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Xuan-Wu District, Nanjing 210008, China
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
| | - Zhongjun Jia
- Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Xuan-Wu District, Nanjing 210008, China
| | - Marcus A Horn
- Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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8
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Recovery in methanotrophic activity does not reflect on the methane-driven interaction network after peat mining. Appl Environ Microbiol 2021; 87:AEM.02355-20. [PMID: 33355115 PMCID: PMC8090869 DOI: 10.1128/aem.02355-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aerobic methanotrophs are crucial in ombrotrophic peatlands, driving the methane and nitrogen cycles. Peat mining adversely affects the methanotrophs, but activity and community composition/abundances may recover after restoration. Considering that the methanotrophic activity and growth are significantly stimulated in the presence of other microorganisms, the methane-driven interaction network, encompassing methanotrophs and non-methanotrophs (i.e., methanotrophic interactome), may also be relevant in conferring community resilience. Yet, little is known of the response and recovery of the methanotrophic interactome to disturbances. Here, we determined the recovery of the methanotrophic interactome as inferred by a co-occurrence network analysis, comparing a pristine and restored peatland. We coupled a DNA-based stable isotope probing (SIP) approach using 13C-CH4 to a co-occurrence network analysis derived from the 13C-enriched 16S rRNA gene sequences to relate the response in methanotrophic activity to the structuring of the interaction network. Methanotrophic activity and abundances recovered after peat restoration since 2000. 'Methylomonaceae' was the predominantly active methanotrophs in both peatlands, but differed in the relative abundance of Methylacidiphilaceae and Methylocystis However, bacterial community composition was distinct in both peatlands. Likewise, the methanotrophic interactome was profoundly altered in the restored peatland. Structuring of the interaction network after peat mining resulted in the loss of complexity and modularity, indicating a less connected and efficient network, which may have consequences in the event of recurring/future disturbances. Therefore, determining the response of the methane-driven interaction network, in addition to relating methanotrophic activity to community composition/abundances, provided a more comprehensive understanding of the resilience of the methanotrophs.Importance The resilience and recovery of microorganisms from disturbances are often determined with regard to their activity and community composition/abundances. Rarely has the response of the network of interacting microorganisms been considered, despite accumulating evidence showing that microbial interaction modulates community functioning. Comparing the methane-driven interaction network of a pristine and restored peatland, our findings revealed that the metabolically active microorganisms were less connected and formed less modular 'hubs' in the restored peatland, indicative of a less complex network which may have consequences with recurring disturbances and environmental changes. This also suggests that the resilience and full recovery in the methanotrophic activity and abundances do not reflect on the interaction network. Therefore, it is relevant to consider the interaction-induced response, in addition to documenting changes in activity and community composition/abundances, to provide a comprehensive understanding of the resilience of microorganisms to disturbances.
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9
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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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10
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Ding LJ, Cui HL, Nie SA, Long XE, Duan GL, Zhu YG. Microbiomes inhabiting rice roots and rhizosphere. FEMS Microbiol Ecol 2020; 95:5420819. [PMID: 30916760 DOI: 10.1093/femsec/fiz040] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/26/2019] [Indexed: 11/12/2022] Open
Abstract
Land plants directly contact soil through their roots. An enormous diversity of microbes dwelling in root-associated zones, including endosphere (inside root), rhizoplane (root surface) and rhizosphere (soil surrounding the root surface), play essential roles in ecosystem functioning and plant health. Rice is a staple food that feeds over 50% of the global population. Its root is a unique niche, which is often characterized by an oxic region (e.g. the rhizosphere) surrounded by anoxic bulk soil. This oxic-anoxic interface has been recognized as a pronounced hotspot that supports dynamic biogeochemical cycles mediated by various functional microbial groups. Considering the significance of rice production upon global food security and the methane budget, novel insights into how the overall microbial community (i.e. the microbiome) of the rice root system influences ecosystem functioning is the key to improving crop health and sustainable productivity of paddy ecosystems, and alleviating methane emissions. This mini-review summarizes the current understanding of microbial diversity of rice root-associated compartments to some extent, especially the rhizosphere, and makes a comparison of rhizosphere microbial community structures between rice and other crops/plants. Moreover, this paper describes the interactions between root-related microbiomes and rice plants, and further discusses the key factors shaping the rice root-related microbiomes.
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Affiliation(s)
- Long-Jun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hui-Ling Cui
- 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
| | - San-An Nie
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Xi-En Long
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian Province, China
| | - Gui-Lan Duan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yong-Guan Zhu
- 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.,Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian Province, China
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11
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Kim IT, Lee YE, Jeong Y, Yoo YS. A novel method to remove nitrogen from reject water in wastewater treatment plants using a methane- and methanol-dependent bacterial consortium. WATER RESEARCH 2020; 172:115512. [PMID: 31986401 DOI: 10.1016/j.watres.2020.115512] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 12/18/2019] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
This study proposes a novel method to directly treat reject water with a high ammonium content, without relying on dilution. The originality of this method resides in leveraging the coordinated action of a methane- and methanol-dependent bacterial consortium and the biogas generated from wastewater treatment facilities. Specifically, ammonium is removed through autotrophic assimilation in the glutamate cycle of methanotrophs and Methylophilus while, simultaneously, methanol generated by methanotrophs is treated through formaldehyde assimilation as Methylophilus undergo the same ribulose monophosphate cycle as methanotrophs. Using this method, the backflow of high-concentration ammonium into the wastewater treatment process was reduced to 59% in a single operation using a sequencing batch reactor at a mean influent concentration of 877.3 mg L-1. However, the removal rate temporarily declined to an average of 37.6% at a concentration of 800 mg L-1 or above, which was imputed to the influence of toxic intermediates.
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Affiliation(s)
- I-Tae Kim
- Department of Land, Water and Environment Research, Korea Institute of Civil Engineering and Building Technology, 283, Goyang-daero, Ilsanseo-gu, Goyang-si, Gyeonggi-do, 10223, South Korea.
| | - Ye-Eun Lee
- Department of Land, Water and Environment Research, Korea Institute of Civil Engineering and Building Technology, 283, Goyang-daero, Ilsanseo-gu, Goyang-si, Gyeonggi-do, 10223, South Korea; Department of Construction Environment Engineering, University of Science and Technology, 217, Gajeong-ro, Yuseong-gu, Daejeon, 34113, South Korea
| | - Yoonah Jeong
- Department of Land, Water and Environment Research, Korea Institute of Civil Engineering and Building Technology, 283, Goyang-daero, Ilsanseo-gu, Goyang-si, Gyeonggi-do, 10223, South Korea
| | - Yeong-Seok Yoo
- Department of Land, Water and Environment Research, Korea Institute of Civil Engineering and Building Technology, 283, Goyang-daero, Ilsanseo-gu, Goyang-si, Gyeonggi-do, 10223, South Korea; Department of Construction Environment Engineering, University of Science and Technology, 217, Gajeong-ro, Yuseong-gu, Daejeon, 34113, South Korea
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12
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He R, Su Y, Leewis MC, Chu YX, Wang J, Ma RC, Wu D, Zhan LT, Herriott IC, Leigh MB. Low O 2 level enhances CH 4-derived carbon flow into microbial communities in landfill cover soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113676. [PMID: 31818614 DOI: 10.1016/j.envpol.2019.113676] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/07/2019] [Accepted: 11/24/2019] [Indexed: 06/10/2023]
Abstract
CH4 oxidation in landfill cover soils plays a significant role in mitigating CH4 release to the atmosphere. Oxygen availability and the presence of co-contaminants are potentially important factors affecting CH4 oxidation rate and the fate of CH4-derived carbon. In this study, microbial populations that oxidize CH4 and the subsequent conversion of CH4-derived carbon into CO2, soil organic C and biomass C were investigated in landfill cover soils at two O2 tensions, i.e., O2 concentrations of 21% ("sufficient") and 2.5% ("limited") with and without toluene. CH4-derived carbon was primarily converted into CO2 and soil organic C in the landfill cover soils, accounting for more than 80% of CH4 oxidized. Under the O2-sufficient condition, 52.9%-59.6% of CH4-derived carbon was converted into CO2 (CECO2-C), and 29.1%-39.3% was converted into soil organic C (CEorganic-C). A higher CEorganic-C and lower CECO2-C occurred in the O2-limited environment, relative to the O2-sufficient condition. With the addition of toluene, the carbon conversion efficiency of CH4 into biomass C and organic C increased slightly, especially in the O2-limited environment. A more complex microbial network was involved in CH4 assimilation in the O2-limited environment than under the O2-sufficient condition. DNA-based stable isotope probing of the community with 13CH4 revealed that Methylocaldum and Methylosarcina had a higher relative growth rate than other type I methanotrophs in the landfill cover soils, especially at the low O2 concentration, while Methylosinus was more abundant in the treatment with both the high O2 concentration and toluene. These results indicated that O2-limited environments could prompt more CH4-derived carbon to be deposited into soils in the form of biomass C and organic C, thereby enhancing the contribution of CH4-derived carbon to soil community biomass and functionality of landfill cover soils (i.e. reduction of CO2 emission).
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Affiliation(s)
- Ruo He
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
| | - Yao Su
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China; Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Mary-Cathrine Leewis
- Institute of Arctic Biology, University of Alaska Fairbanks, Alaska, 99775, USA; US Geological Survey, Menlo Park, CA, 94025, USA
| | - Yi-Xuan Chu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jing Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo-Chan Ma
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Donglei Wu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Liang-Tong Zhan
- MOE Key Laboratory of Soft Soils and Geoenvironmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | | | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Alaska, 99775, USA
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13
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Ammonia- and Methane-Oxidizing Bacteria: The Abundance, Niches and Compositional Differences for Diverse Soil Layers in Three Flooded Paddy Fields. SUSTAINABILITY 2020. [DOI: 10.3390/su12030953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ammonia oxidizing bacteria (AOB), Ammonia oxidizing archaea (AOA) and methane oxidizing bacteria (MOB) play cogent roles in oxidation and nitrification processes, and hence have important ecological functions in several ecosystems. However, their distribution and compositional differences in different long-term flooded paddy fields (FPFs) management at different soil depths remains under-investigated. Using qPCR and phylogenetic analysis, this study investigated the abundance, niches, and compositional differences of AOA, AOB, and MOB along with their potential nitrification and oxidation rate in three soil layers from three FPFs (ShaPingBa (SPB), HeChuan (HC), and JiDi (JD)) in Chongqing, China. In all the FPFs, CH4 oxidation occurred mainly in the surface (0–3 cm) and subsurface layers (3–5 cm). A significant difference in potential methane oxidation and nitrification rates was observed among the three FPFs, in which SPB had the highest. The higher amoA genes are the marker for abundance of AOA compared to AOB while pmoA genes, which is the marker for MOB abundance and diversity, indicated their significant role in the nitrification process across the three FPFs. The phylogenetic analysis revealed that AOA were mainly composed of Nitrososphaera, Nitrosospumilus, and Nitrosotalea, while the genus Nitrosomonas accounted for the greatest proportion of AOB in the three soil layers. MOB were mainly composed of Methylocaldum and Methylocystis genera. Overall, this finding pointed to niche differences as well as suitability of the surface and subsurface soil environments for the co-occurrence of ammonia oxidation and methane oxidation in FPFs.
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14
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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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15
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Fu L, Song T, Zhang W, Zhang J, Lu Y. Stimulatory Effect of Magnetite Nanoparticles on a Highly Enriched Butyrate-Oxidizing Consortium. Front Microbiol 2018; 9:1480. [PMID: 30026737 PMCID: PMC6041394 DOI: 10.3389/fmicb.2018.01480] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/13/2018] [Indexed: 11/13/2022] Open
Abstract
Syntrophic oxidation of butyrate is catabolized by a few bacteria specialists in the presence of methanogens. In the present study, a highly enriched butyrate-oxidizing consortium was obtained from a wetland sediment in Tibetan Plateau. During continuous transfers of the enrichment, the addition of magnetite nanoparticles (nanoFe3O4) consistently enhanced butyrate oxidation and CH4 production. Molecular analysis revealed that all bacterial sequences from the consortium belonged to Syntrophomonas with the closest relative of Syntrophomonas wolfei and 96% of the archaeal sequences were related to Methanobacteria with the remaining sequences to Methanocella. Addition of graphite and carbon nanotubes for a replacement of nanoFe3O4 caused the similar stimulatory effect. Silica coating of nanoFe3O4 surface, however, completely eliminated the stimulatory effect. The control experiment with axenic cultivation of a Syntrophomonas strain and two methanogen strains showed no effect by nanoFe3O4. Together, the results in the present study support that syntrophic oxidation of butyrate is likely facilitated by direct interspecies electron transfer in the presence of conductive nanomaterials.
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Affiliation(s)
- Li Fu
- College of Urban and Environmental Sciences, Peking University, Beijing, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tianze Song
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Wei Zhang
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Jie Zhang
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, China
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16
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Rahalkar MC, Patil S, Dhakephalkar PK, Bahulikar RA. Cultivated methanotrophs associated with rhizospheres of traditional rice landraces from Western India belong to Methylocaldum and Methylocystis. 3 Biotech 2018; 8:281. [PMID: 29881659 DOI: 10.1007/s13205-018-1306-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 05/25/2018] [Indexed: 10/14/2022] Open
Abstract
Aerobic methanotrophs associated with Indian rice plants have rarely been cultivated. In the present study, we cultured aerobic methanotrophic bacteria from the rhizosphere regions of rice plants. Rhizospheric soils from seven rice landraces traditionally grown and maintained by tribal people in Jawhar region belonging to part of the Western Ghats in India, were used. Seven methanotrophic cultures were isolated from the last positive dilution (10- 4). Methanotrophs were identified by analyzing the partial methane monooxygenase gene, pmoA gene and three of these belonged to the genus Methylocaldum (gammaproteobacterial, Type I methanotrophs) and four belonged to the genus Methylocystis (alphaproteobacterial, Type II methanotrophs). We present here the first report on the cultivation of methanotrophs from Indian traditional rice landraces originating from a biodiversity hotspot.
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17
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High Temporal and Spatial Variability of Atmospheric-Methane Oxidation in Alpine Glacier Forefield Soils. Appl Environ Microbiol 2017; 83:AEM.01139-17. [PMID: 28687652 DOI: 10.1128/aem.01139-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 06/30/2017] [Indexed: 11/20/2022] Open
Abstract
Glacier forefield soils can provide a substantial sink for atmospheric CH4, facilitated by aerobic methane-oxidizing bacteria (MOB). However, MOB activity, abundance, and community structure may be affected by soil age, MOB location in different forefield landforms, and temporal fluctuations in soil physical parameters. We assessed the spatial and temporal variability of atmospheric-CH4 oxidation in an Alpine glacier forefield during the snow-free season of 2013. We quantified CH4 flux in soils of increasing age and in different landforms (sandhill, terrace, and floodplain forms) by using soil gas profile and static flux chamber methods. To determine MOB abundance and community structure, we employed pmoA gene-based quantitative PCR and targeted amplicon sequencing. Uptake of CH4 increased in magnitude and decreased in variability with increasing soil age. Sandhill soils exhibited CH4 uptake rates ranging from -3.7 to -0.03 mg CH4 m-2 day-1 Floodplain and terrace soils exhibited lower uptake rates and even intermittent CH4 emissions. Linear mixed-effects models indicated that soil age and landform were the dominating factors shaping CH4 flux, followed by cumulative rainfall (weighted sum ≤4 days prior to sampling). Of 31 MOB operational taxonomic units retrieved, ∼30% were potentially novel, and ∼50% were affiliated with upland soil clusters gamma and alpha. The MOB community structures in floodplain and terrace soils were nearly identical but differed significantly from the highly variable sandhill soil communities. We concluded that soil age and landform modulate the soil CH4 sink strength in glacier forefields and that recent rainfall affects its short-term variability. This should be taken into account when including this environment in future CH4 inventories.IMPORTANCE Oxidation of methane (CH4) in well-drained, "upland" soils is an important mechanism for the removal of this potent greenhouse gas from the atmosphere. It is largely mediated by aerobic, methane-oxidizing bacteria (MOB). Whereas there is abundant information on atmospheric-CH4 oxidation in mature upland soils, little is known about this important function in young, developing soils, such as those found in glacier forefields, where new sediments are continuously exposed to the atmosphere as a result of glacial retreat. In this field-based study, we investigated the spatial and temporal variability of atmospheric-CH4 oxidation and associated MOB communities in Alpine glacier forefield soils, aiming at better understanding the factors that shape the sink for atmospheric CH4 in this young soil ecosystem. This study contributes to the knowledge on the dynamics of atmospheric-CH4 oxidation in developing upland soils and represents a further step toward the inclusion of Alpine glacier forefield soils in global CH4 inventories.
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18
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Duan YF, Reinsch S, Ambus P, Elsgaard L, Petersen SO. Activity of Type I Methanotrophs Dominates under High Methane Concentration: Methanotrophic Activity in Slurry Surface Crusts as Influenced by Methane, Oxygen, and Inorganic Nitrogen. JOURNAL OF ENVIRONMENTAL QUALITY 2017; 46:767-775. [PMID: 28783780 DOI: 10.2134/jeq2017.02.0047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Livestock slurry is a major source of atmospheric methane (CH), but surface crusts harboring methane-oxidizing bacteria (MOB) could mediate against CH emissions. This study examined conditions for CH oxidation by in situ measurements of oxygen (O) and nitrous oxide (NO), as a proxy for inorganic N transformations, in intact crusts using microsensors. This was combined with laboratory incubations of crust material to investigate the effects of O, CH, and inorganic N on CH oxidation, using CH to trace C incorporation into lipids of MOB. Oxygen penetration into the crust was 2 to 14 mm, confining the potential for aerobic CH oxidation to a shallow layer. Nitrous oxide accumulated within or below the zone of O depletion. With 10 ppmv CH there was no O limitation on CH oxidation at O concentrations as low as 2%, whereas CH oxidation at 10 ppmv CH was reduced at ≤5% O. As hypothesized, CH oxidation was in general inhibited by inorganic N, especially NO, and there was an interaction between N inhibition and O limitation at 10 ppmv CH, as indicated by consistently stronger inhibition of CH oxidation by NH and NO at 3% compared with 20% O. Recovery of C in phospholipid fatty acids suggested that both Type I and Type II MOB were active, with Type I dominating high-concentration CH oxidation. Given the structural heterogeneity of crusts, CH oxidation activity likely varies spatially as constrained by the combined effects of CH, O, and inorganic N availability in microsites.
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19
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Hao DC, Xiao PG. Rhizosphere Microbiota and Microbiome of Medicinal Plants: From Molecular Biology to Omics Approaches. CHINESE HERBAL MEDICINES 2017. [DOI: 10.1016/s1674-6384(17)60097-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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20
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Wu Y, Wang F, Xiao X, Liu J, Wu C, Chen H, Kerr P, Shurin J. Seasonal changes in phosphorus competition and allelopathy of a benthic microbial assembly facilitate prevention of cyanobacterial blooms. Environ Microbiol 2017; 19:2483-2494. [PMID: 28464383 DOI: 10.1111/1462-2920.13781] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 04/13/2017] [Accepted: 04/23/2017] [Indexed: 12/01/2022]
Abstract
Interactions among microbes determine the prevalence of harmful algal blooms that threaten water quality. These interactions can be indirectly mediated by shared resources or consumers, or through interference by the production of allelochemicals. Allelopathic interactions and resource competition have been shown to occur among algae and associated microbes. However, little work has considered seasonal influences on ecosystem structure and function. Here, we report results of our investigations on seasonal changes in the interactions between benthic microbial assemblies and the bloom forming cyanobacterium Microcystis aeruginosa. We show that phosphorus (P) competition and allelopathy by the microbial assembly vary seasonally and inhibit growth of M. aeruginosa. The interactions per unit biomass of the microbial assembly are stronger under winter than summer conditions and inhibit the recruitment of the cyanobacteria, thereby preventing the reoccurrence of cyanobacterial blooms in the following summer. The seasonality of these interactions correlates with changes in composition, metabolic activity and functional diversity of the microbial assembly. Our findings highlight the importance of competitive and allelopathic interactions in regulating the occurrence of harmful algal blooms. Our results also imply that seasonal variation of competition and allelopathy of the microbial assembly might be beneficial to adjust aquatic ecosystem structure and function.
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Affiliation(s)
- Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, Jiangsu, 210008, China
| | - Fengwu Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, Jiangsu, 210008, China
| | - Xi Xiao
- Ocean College, Zhejiang University, 1 Zheda Road, Zhoushan, Zhejiang, 316000, China
| | - Junzhuo Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, Jiangsu, 210008, China
| | - Chenxi Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, 7 Donghu South Road, Wuhan, 430072, China
| | - Hong Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, Jiangsu, 210008, China
| | - Philip Kerr
- School of Biomedical Sciences, Charles Sturt University, Boorooma St, Wagga Wagga, NSW, 2678, Australia
| | - Jonathan Shurin
- Section of Ecology, Behavior and Evolution, University of California - San Diego, 9500 Gilman Dr, Dept 0116, La Jolla, CA, 92093, USA
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21
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Bessette S, Moalic Y, Gautey S, Lesongeur F, Godfroy A, Toffin L. Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic-Anoxic Interface of the Congo Deep-Sea Fan. Front Microbiol 2017; 8:715. [PMID: 28487684 PMCID: PMC5403828 DOI: 10.3389/fmicb.2017.00715] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/06/2017] [Indexed: 11/13/2022] Open
Abstract
Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3-5% organic carbon). This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB) communities at the oxic-anoxic interface of sedimentary habitats by using fluorescence in situ hybridization and comparative sequence analysis of particulate mono-oxygenase (pmoA) genes. Our findings revealed that sedimentary habitats of the recent lobe complex hosted type I and type II MOB cells and comparisons of pmoA community compositions showed variations among the different organic-rich habitats. Furthermore, the pmoA lineages were taxonomically more diverse compared to methane seep environments and were related to those found at cold seeps. Surprisingly, MOB phylogenetic lineages typical of terrestrial environments were observed at such water depth. In contrast, MOB cells or pmoA sequences were not detected at the previous lobe complex that is disconnected from the Congo River inputs.
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Affiliation(s)
- Sandrine Bessette
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
| | - Yann Moalic
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
| | - Sébastien Gautey
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
| | - Françoise Lesongeur
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
| | - Anne Godfroy
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
| | - Laurent Toffin
- Institut Carnot Ifremer EDROME, Centre de Bretagne, REM/EEP, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, UMR 6197, Université de Bretagne OccidentalePlouzané, France.,CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, Technopôle Brest Iroise, UMR 6197Plouzané, France
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22
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Wegener G, Kellermann MY, Elvert M. Tracking activity and function of microorganisms by stable isotope probing of membrane lipids. Curr Opin Biotechnol 2016; 41:43-52. [PMID: 27179643 DOI: 10.1016/j.copbio.2016.04.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 04/27/2016] [Accepted: 04/27/2016] [Indexed: 12/17/2022]
Abstract
Microorganisms in soils and sediments are highly abundant and phylogenetically diverse, but their specific metabolic activity and function in the environment is often not well constrained. To address this critical aspect in environmental biogeochemistry, different methods involving stable isotope probing (SIP) and detection of the isotope label in a variety of molecular compounds have been developed. Here we review recent progress in lipid-SIP, a technique that combines the assimilation of specific 13C-labeled metabolic substrates such as inorganic carbon, methane, glucose and amino acids into diagnostic membrane lipid compounds. Using the structural characteristics of certain lipid types in combination with genetic molecular techniques, the SIP approach reveals the activity and function of distinct microbial groups in the environment. More recently, deuterium labeling in the form of deuterated water (D2O) extended the lipid-SIP portfolio. Since lipid biosynthetic pathways involve hydrogen (H+) uptake from water, lipid production can be inferred from the detection of D-assimilation into these compounds. Furthermore, by combining D2O and 13C-inorganic carbon (IC) labeling in a dual-SIP approach, rates of auto- and heterotrophic carbon fixation can be estimated. We discuss the design, analytical prerequisites, data processing and interpretation of single and dual-SIP experiments and highlight a case study on anaerobic methanotrophic communities inhabiting hydrothermally heated marine sediments.
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Affiliation(s)
- Gunter Wegener
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany; MARUM Center for Marine Environmental Sciences, Leobener Straße, 28359 Bremen, Germany.
| | - Matthias Y Kellermann
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Marcus Elvert
- MARUM Center for Marine Environmental Sciences, Leobener Straße, 28359 Bremen, Germany
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23
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Wen X, Yang S, Liebner S. Evaluation and update of cutoff values for methanotrophic pmoA gene sequences. Arch Microbiol 2016; 198:629-36. [PMID: 27098810 DOI: 10.1007/s00203-016-1222-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/30/2016] [Accepted: 04/06/2016] [Indexed: 01/16/2023]
Abstract
The functional pmoA gene is frequently used to probe the diversity and phylogeny of methane-oxidizing bacteria (MOB) in various environments. Here, we compared the similarities between the pmoA gene and the corresponding 16S rRNA gene sequences of 77 described species covering gamma- and alphaproteobacterial methanotrophs (type I and type II MOB, respectively) as well as methanotrophs from the phylum Verrucomicrobia. We updated and established the weighted mean pmoA gene cutoff values on the nucleotide level at 86, 82, and 71 % corresponding to the 97, 95, and 90 % similarity of the 16S rRNA gene. Based on these cutoffs, the functional gene fragments can be entirely processed at the nucleotide level throughout software platforms such as Mothur or QIIME which provide a user-friendly and command-based alternative to amino acid-based pipelines. Type II methanotrophs are less divergent than type I both with regard to ribosomal and functional gene sequence similarity and GC content. We suggest that this agrees with the theory of different life strategies proposed for type I and type II MOB.
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Affiliation(s)
- Xi Wen
- Helmholtz Center Potsdam, GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Telegrafenberg, 14473, Potsdam, Germany.,College of Electrical Engineering, Northwest University for Nationalities, Lanzhou, 730030, China
| | - Sizhong Yang
- Helmholtz Center Potsdam, GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Telegrafenberg, 14473, Potsdam, Germany. .,State Key Laboratory of Frozen Soils Engineering, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Susanne Liebner
- Helmholtz Center Potsdam, GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Telegrafenberg, 14473, Potsdam, Germany
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24
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Wei XM, He R, Chen M, Su Y, Ma RC. Conversion of methane-derived carbon and microbial community in enrichment cultures in response to O2 availability. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:7517-7528. [PMID: 26728286 DOI: 10.1007/s11356-015-6017-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 12/22/2015] [Indexed: 06/05/2023]
Abstract
Methanotrophs not only play an important role in mitigating CH4 emissions from the environment, but also provide a large quantity of CH4-derived carbon to their habitats. In this study, the distribution of CH4-derived carbon and microbial community was investigated in a consortium enriched at three O2 tensions, i.e., the initial O2 concentrations of 2.5 % (LO-2), 5 % (LO-1), and 21 % (v/v) (HO). The results showed that compared with the O2-limiting environments (2.5 and 5 %), more CH4-derived carbon was converted into CO2 and biomass under the O2 sufficient condition (21 %). Besides biomass and CO2, a high conversion efficiency of CH4-derived carbon to dissolved organic carbon was detected in the cultures, especially in LO-2. Quantitative PCR and Miseq sequencing both showed that the abundance of methanotroph increased with the increasing O2 concentrations. Type II methanotroph Methylocystis dominated in the enrichment cultures, accounting for 54.8, 48.1, and 36.9 % of the total bacterial 16S rRNA gene sequencing reads in HO, LO-1, and LO-2, respectively. Methylotrophs, mainly including Methylophilus, Methylovorus, Hyphomicrobium, and Methylobacillus, were also abundant in the cultures. Compared with the O2 sufficient condition (21 %), higher microbial biodiversity (i.e., higher Simpson and lower Shannon indexes) was detected in LO-2 enriched at the initial O2 concentration of 2.5 %. These findings indicated that compared with the O2 sufficient condition, more CH4-derived carbon was exuded into the environments and promoted the growth of non-methanotrophic microbes in O2-limiting environments.
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Affiliation(s)
- Xiao-Meng Wei
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
| | - Min Chen
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Yao Su
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo-Chan Ma
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
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25
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Pandit PS, Rahalkar MC, Dhakephalkar PK, Ranade DR, Pore S, Arora P, Kapse N. Deciphering Community Structure of Methanotrophs Dwelling in Rice Rhizospheres of an Indian Rice Field Using Cultivation and Cultivation-Independent Approaches. MICROBIAL ECOLOGY 2016; 71:634-644. [PMID: 26547567 DOI: 10.1007/s00248-015-0697-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/26/2015] [Indexed: 06/05/2023]
Abstract
Methanotrophs play a crucial role in filtering out methane from habitats, such as flooded rice fields. India has the largest area under rice cultivation in the world; however, to the best of our knowledge, methanotrophs have not been isolated and characterized from Indian rice fields. A cultivation strategy composing of a modified medium, longer incubation time, and serial dilutions in microtiter plates was used to cultivate methanotrophs from a rice rhizosphere sample from a flooded rice field in Western India. We compared the cultured members with the uncultured community as revealed by three culture-independent methods. A novel type Ia methanotroph (Sn10-6), at the rank of a genus, and a putative novel species of a type II methanotroph (Sn-Cys) were cultivated from the terminal positive dilution (10(-6)). From lower dilution (10(-4)), a strain of Methylomonas spp. was cultivated. All the three culture-independent analyses, i.e., pmoA clone library, terminal restriction fragment length polymorphism (T-RFLP), and metagenomics approach, revealed the dominance of type I methanotrophs. Only metagenomic analysis showed significant presence of type II methanotrophs, albeit in lower proportion (37 %). All the three isolates showed relevance to the methanotrophic community as depicted by uncultured methods; however, the cultivated members might not be the most dominant ones. In conclusion, a combined cultivation and cultivation-independent strategy yielded us a broader picture of the methanotrophic community from rice rhizospheres of a flooded rice field in India.
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Affiliation(s)
- Pranitha S Pandit
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
| | - Monali C Rahalkar
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.
| | | | - Dilip R Ranade
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
- Microbial Culture Collection, NCCS, Sai-Trinity Building Garware Circle, Pashan, Pune, Maharashtra, 411021, India
| | - Soham Pore
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
| | - Preeti Arora
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
| | - Neelam Kapse
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
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26
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Knief C. Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker. Front Microbiol 2015; 6:1346. [PMID: 26696968 PMCID: PMC4678205 DOI: 10.3389/fmicb.2015.01346] [Citation(s) in RCA: 257] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/16/2015] [Indexed: 01/06/2023] Open
Abstract
Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing "unknown methanotrophic bacteria." This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.
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Affiliation(s)
- Claudia Knief
- Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, University of BonnBonn, Germany
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27
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Leng L, Chang J, Geng K, Lu Y, Ma K. Uncultivated Methylocystis Species in Paddy Soil Include Facultative Methanotrophs that Utilize Acetate. MICROBIAL ECOLOGY 2015; 70:88-96. [PMID: 25475784 DOI: 10.1007/s00248-014-0540-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 11/21/2014] [Indexed: 06/04/2023]
Abstract
Methanotrophs are crucial in regulating methane emission from rice field systems. Type II methanotrophs in particular are often observed in high abundance in paddy soil. Some cultivated species of Methylocystis are able to grow on acetate in the absence of methane. We hypothesize that the dominant type II methanotrophs in paddy soil might facultatively utilize acetate for growth, which we evaluate in the present study. The measurement of methane oxidation rates showed that the methanotrophic activity in paddy soil was inhibited by the addition of acetate compared to the continuous supplementation of methane, but the paddy soil maintained the methane oxidation capacity and recovered following methane supplementation. Terminal restriction fragment length polymorphism analysis (T-RFLP) combined with cloning and sequencing of pmoA genes showed that Methylocystis was enriched after incubation with added acetate, while the type I methanotrophs Methylocaldum/Methylococcus and Methylobacter were enriched by methane supplementation. A comparison of pmoA sequences obtained in this study with those in the public database indicated that they were globally widespread in paddy soils or in associated with rice roots. Furthermore, we performed stable isotope probing (SIP) of pmoA messenger RNA (mRNA) to investigate the assimilation of (13)C-acetate by paddy soil methanotrophs. RNA-SIP revealed that Methylocystis-related methanotrophs which shared the same genotype of the above enriched species were significantly labelled. It indicates that these methanotrophs actively assimilated the labelled acetate in paddy soil. Altogether, these results suggested that uncultivated Methylocystis species are facultative methanotrophs utilizing acetate as a secondary carbon source in paddy soil.
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Affiliation(s)
- Lingqin Leng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
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28
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He R, Wooller MJ, Pohlman JW, Tiedje JM, Leigh MB. Methane-derived carbon flow through microbial communities in arctic lake sediments. Environ Microbiol 2015; 17:3233-50. [PMID: 25581131 DOI: 10.1111/1462-2920.12773] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/31/2014] [Indexed: 11/26/2022]
Abstract
Aerobic methane (CH4 ) oxidation mitigates CH4 release and is a significant pathway for carbon and energy flow into aquatic food webs. Arctic lakes are responsible for an increasing proportion of global CH4 emissions, but CH4 assimilation into the aquatic food web in arctic lakes is poorly understood. Using stable isotope probing (SIP) based on phospholipid fatty acids (PLFA-SIP) and DNA (DNA-SIP), we tracked carbon flow quantitatively from CH4 into sediment microorganisms from an arctic lake with an active CH4 seepage. When 0.025 mmol CH4 g(-1) wet sediment was oxidized, approximately 15.8-32.8% of the CH4 -derived carbon had been incorporated into microorganisms. This CH4 -derived carbon equated to up to 5.7% of total primary production estimates for Alaskan arctic lakes. Type I methanotrophs, including Methylomonas, Methylobacter and unclassified Methylococcaceae, were most active at CH4 oxidation in this arctic lake. With increasing distance from the active CH4 seepage, a greater diversity of bacteria incorporated CH4 -derived carbon. Actinomycetes were the most quantitatively important microorganisms involved in secondary feeding on CH4 -derived carbon. These results showed that CH4 flows through methanotrophs into the broader microbial community and that type I methanotrophs, methylotrophs and actinomycetes are important organisms involved in using CH4 -derived carbon in arctic freshwater ecosystems.
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Affiliation(s)
- Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.,Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Matthew J Wooller
- Alaska Stable Isotope Facility, Water and Environmental Research Center, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA.,School of Fisheries and Ocean Sciences, Institute of Marine Science, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - John W Pohlman
- Woods Hole Coastal and Marine Science Center, U.S. Geological Survey, Woods Hole, MA, 02543, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
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29
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Milucka J, Kirf M, Lu L, Krupke A, Lam P, Littmann S, Kuypers MMM, Schubert CJ. Methane oxidation coupled to oxygenic photosynthesis in anoxic waters. ISME JOURNAL 2015; 9:1991-2002. [PMID: 25679533 DOI: 10.1038/ismej.2015.12] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/14/2014] [Accepted: 12/19/2014] [Indexed: 11/09/2022]
Abstract
Freshwater lakes represent large methane sources that, in contrast to the Ocean, significantly contribute to non-anthropogenic methane emissions to the atmosphere. Particularly mixed lakes are major methane emitters, while permanently and seasonally stratified lakes with anoxic bottom waters are often characterized by strongly reduced methane emissions. The causes for this reduced methane flux from anoxic lake waters are not fully understood. Here we identified the microorganisms and processes responsible for the near complete consumption of methane in the anoxic waters of a permanently stratified lake, Lago di Cadagno. Interestingly, known anaerobic methanotrophs could not be detected in these waters. Instead, we found abundant gamma-proteobacterial aerobic methane-oxidizing bacteria active in the anoxic waters. In vitro incubations revealed that, among all the tested potential electron acceptors, only the addition of oxygen enhanced the rates of methane oxidation. An equally pronounced stimulation was also observed when the anoxic water samples were incubated in the light. Our combined results from molecular, biogeochemical and single-cell analyses indicate that methane removal at the anoxic chemocline of Lago di Cadagno is due to true aerobic oxidation of methane fuelled by in situ oxygen production by photosynthetic algae. A similar mechanism could be active in seasonally stratified lakes and marine basins such as the Black Sea, where light penetrates to the anoxic chemocline. Given the widespread occurrence of seasonally stratified anoxic lakes, aerobic methane oxidation coupled to oxygenic photosynthesis might have an important but so far neglected role in methane emissions from lakes.
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Affiliation(s)
- Jana Milucka
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Mathias Kirf
- Department of Surface Waters-Research and Management, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Kastanienbaum, Switzerland
| | - Lu Lu
- 1] Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany [2] State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, China [3] University of Chinese Academy of Sciences, Beijing, China
| | - Andreas Krupke
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Phyllis Lam
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sten Littmann
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marcel M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carsten J Schubert
- Department of Surface Waters-Research and Management, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Kastanienbaum, Switzerland
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30
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Henneberger R, Chiri E, Bodelier PEL, Frenzel P, Lüke C, Schroth MH. Field-scale tracking of active methane-oxidizing communities in a landfill cover soil reveals spatial and seasonal variability. Environ Microbiol 2014; 17:1721-37. [PMID: 25186436 DOI: 10.1111/1462-2920.12617] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 08/31/2014] [Indexed: 01/11/2023]
Abstract
Aerobic methane-oxidizing bacteria (MOB) in soils mitigate methane (CH4 ) emissions. We assessed spatial and seasonal differences in active MOB communities in a landfill cover soil characterized by highly variable environmental conditions. Field-based measurements of CH4 oxidation activity and stable-isotope probing of polar lipid-derived fatty acids (PLFA-SIP) were complemented by microarray analysis of pmoA genes and transcripts, linking diversity and function at the field scale. In situ CH4 oxidation rates varied between sites and were generally one order of magnitude lower in winter compared with summer. Results from PLFA-SIP and pmoA transcripts were largely congruent, revealing distinct spatial and seasonal clustering. Overall, active MOB communities were highly diverse. Type Ia MOB, specifically Methylomonas and Methylobacter, were key drivers for CH4 oxidation, particularly at a high-activity site. Type II MOB were mainly active at a site showing substantial fluctuations in CH4 loading and soil moisture content. Notably, Upland Soil Cluster-gamma-related pmoA transcripts were also detected, indicating concurrent oxidation of atmospheric CH4 . Spatial separation was less distinct in winter, with Methylobacter and uncultured MOB mediating CH4 oxidation. We propose that high diversity of active MOB communities in this soil is promoted by high variability in environmental conditions, facilitating substantial removal of CH4 generated in the waste body.
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Affiliation(s)
- Ruth Henneberger
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092, Zurich, Switzerland
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31
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Gougoulias C, Clark JM, Shaw LJ. The role of soil microbes in the global carbon cycle: tracking the below-ground microbial processing of plant-derived carbon for manipulating carbon dynamics in agricultural systems. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:2362-71. [PMID: 24425529 PMCID: PMC4283042 DOI: 10.1002/jsfa.6577] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 01/06/2014] [Accepted: 01/15/2014] [Indexed: 05/04/2023]
Abstract
It is well known that atmospheric concentrations of carbon dioxide (CO2) (and other greenhouse gases) have increased markedly as a result of human activity since the industrial revolution. It is perhaps less appreciated that natural and managed soils are an important source and sink for atmospheric CO2 and that, primarily as a result of the activities of soil microorganisms, there is a soil-derived respiratory flux of CO2 to the atmosphere that overshadows by tenfold the annual CO2 flux from fossil fuel emissions. Therefore small changes in the soil carbon cycle could have large impacts on atmospheric CO2 concentrations. Here we discuss the role of soil microbes in the global carbon cycle and review the main methods that have been used to identify the microorganisms responsible for the processing of plant photosynthetic carbon inputs to soil. We discuss whether application of these techniques can provide the information required to underpin the management of agro-ecosystems for carbon sequestration and increased agricultural sustainability. We conclude that, although crucial in enabling the identification of plant-derived carbon-utilising microbes, current technologies lack the high-throughput ability to quantitatively apportion carbon use by phylogentic groups and its use efficiency and destination within the microbial metabolome. It is this information that is required to inform rational manipulation of the plant-soil system to favour organisms or physiologies most important for promoting soil carbon storage in agricultural soil.
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Affiliation(s)
- Christos Gougoulias
- Soil Research Centre, Department of Geography and Environmental Science, School of Archaeology, Geography and Environmental Science, University of ReadingRG6 6DW, United Kingdom
| | - Joanna M Clark
- Soil Research Centre, Department of Geography and Environmental Science, School of Archaeology, Geography and Environmental Science, University of ReadingRG6 6DW, United Kingdom
| | - Liz J Shaw
- Soil Research Centre, Department of Geography and Environmental Science, School of Archaeology, Geography and Environmental Science, University of ReadingRG6 6DW, United Kingdom
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32
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Li H, Chang J, Liu P, Fu L, Ding D, Lu Y. Direct interspecies electron transfer accelerates syntrophic oxidation of butyrate in paddy soil enrichments. Environ Microbiol 2014; 17:1533-47. [DOI: 10.1111/1462-2920.12576] [Citation(s) in RCA: 222] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 07/15/2014] [Accepted: 07/22/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Huijuan Li
- College of Resources and Environmental Sciences; China Agricultural University; Beijing 100193 China
| | - Jiali Chang
- College of Resources and Environmental Sciences; China Agricultural University; Beijing 100193 China
| | - Pengfei Liu
- College of Resources and Environmental Sciences; China Agricultural University; Beijing 100193 China
| | - Li Fu
- College of Resources and Environmental Sciences; China Agricultural University; Beijing 100193 China
| | - Dewen Ding
- College of Resources and Environmental Sciences; China Agricultural University; Beijing 100193 China
| | - Yahai Lu
- College of Resources and Environmental Sciences; China Agricultural University; Beijing 100193 China
- Department of Resource and Environmental Geography; College of Urban and Environmental Sciences; Peking University; Beijing 100871 China
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33
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Applications and impacts of stable isotope probing for analysis of microbial interactions. Appl Microbiol Biotechnol 2014; 98:4817-28. [PMID: 24715147 DOI: 10.1007/s00253-014-5705-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 03/17/2014] [Accepted: 03/17/2014] [Indexed: 10/25/2022]
Abstract
Probing the interactions between microbes and their environment with stable isotopes became a powerful technique over the last years. While quadruple mass spectrometry or isotope ratio mass spectrometry (IRMS) require at least 300,000 bacterial cells, analysis at the single-cell level is possible with secondary ion mass spectrometry (SIMS) or Raman microspectrometry. While SIMS needs enrichments of more than 0.1 and Raman microscopy of more than 25 at.-%, IRMS can deal with 0.0001 at.-%. To find out who eats what, one has to discern between the different species in a community. Several methods have been introduced to discern between the different taxa in microbial communities, e.g., by using fatty acids as biomarkers, density centrifugation of DNA/RNA, or fluorescent in situ hybridization (FISH) with phylogenetic probes. While the biomarker approach can be coupled with the high sensitivity of the IRMS, the DNA approach gives in general a better phylogenetic resolution of the metabolic active microbes. A combination of both is the separation via coupling of FISH-probes to magnetic beads or fluorescent assisted cell sorting (FACS) of stained cells leading to fractions which can be analyzed by IRMS. Applying these techniques over a time course can reveal the metabolic kinetics and food webs. In this review, the different methods are presented with examples and their advantages and disadvantages are discussed. An outlook on the combination of the various techniques and their applications in microbial ecology is given.
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34
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Autotrophic carbon dioxide fixation via the Calvin-Benson-Bassham cycle by the denitrifying methanotroph "Candidatus Methylomirabilis oxyfera". Appl Environ Microbiol 2014; 80:2451-60. [PMID: 24509918 DOI: 10.1128/aem.04199-13] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Methane is an important greenhouse gas and the most abundant hydrocarbon in the Earth's atmosphere. Methanotrophic microorganisms can use methane as their sole energy source and play a crucial role in the mitigation of methane emissions in the environment. "Candidatus Methylomirabilis oxyfera" is a recently described intra-aerobic methanotroph that is assumed to use nitric oxide to generate internal oxygen to oxidize methane via the conventional aerobic pathway, including the monooxygenase reaction. Previous genome analysis has suggested that, like the verrucomicrobial methanotrophs, "Ca. Methylomirabilis oxyfera" encodes and transcribes genes for the Calvin-Benson-Bassham (CBB) cycle for carbon assimilation. Here we provide multiple independent lines of evidence for autotrophic carbon dioxide fixation by "Ca. Methylomirabilis oxyfera" via the CBB cycle. The activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), a key enzyme of the CBB cycle, in cell extracts from an "Ca. Methylomirabilis oxyfera" enrichment culture was shown to account for up to 10% of the total methane oxidation activity. Labeling studies with whole cells in batch incubations supplied with either (13)CH4 or [(13)C]bicarbonate revealed that "Ca. Methylomirabilis oxyfera" biomass and lipids became significantly more enriched in (13)C after incubation with (13)C-labeled bicarbonate (and unlabeled methane) than after incubation with (13)C-labeled methane (and unlabeled bicarbonate), providing evidence for autotrophic carbon dioxide fixation. Besides this experimental approach, detailed genomic and transcriptomic analysis demonstrated an operational CBB cycle in "Ca. Methylomirabilis oxyfera." Altogether, these results show that the CBB cycle is active and plays a major role in carbon assimilation by "Ca. Methylomirabilis oxyfera" bacteria. Our results suggest that autotrophy might be more widespread among methanotrophs than was previously assumed and implies that a methanotrophic community in the environment is not necessarily revealed by (13)C-depleted lipids.
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Su Y, Xia FF, Tian BH, Li W, He R. Microbial community and function of enrichment cultures with methane and toluene. Appl Microbiol Biotechnol 2013; 98:3121-31. [PMID: 24136469 DOI: 10.1007/s00253-013-5297-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/24/2013] [Accepted: 09/26/2013] [Indexed: 11/29/2022]
Abstract
The interaction effect of co-existence of toluene and CH4 on community and activity of methanotrophs and toluene-degrading bacteria was characterized in three consortia enriched with CH4 and toluene (MT), toluene (T), and CH4 (M), respectively, in this study. The CH4 oxidation activity in the enrichment culture of MT was significantly lower than that of M at the end of the experiment (P = 0.001). The toluene degradation rate could be enhanced by continuous addition of CH4 and toluene in the initial days, but it was inhibited in the later days. Phylogenetic analysis of 16S rRNA genes showed that Proteobacteria and Bacteroidetes were dominant in the three enriched consortia, but the community of methanotrophs and toluene-degrading bacteria was significantly affected by the co-existence of CH4 and toluene. Both Methylosinus (91.8 %) and Methylocystis (8.2 %) were detected in the enrichment culture of MT, while only Methylocystis species were detected in M. The toluene-degrading bacteria including Burkholderia, Flavobacteria, Microbacterium, and Azoarcus were all detected in the enrichment culture of T. However, only Azoarcus was found in the enrichment culture of MT. Significantly higher contents of extracellular polymeric substances polysaccharose and protein in the enrichment culture of MT than that of T and M suggested that a higher environmental stress occurred in the enrichment culture of MT.
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Affiliation(s)
- Yao Su
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
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Dry/Wet cycles change the activity and population dynamics of methanotrophs in rice field soil. Appl Environ Microbiol 2013; 79:4932-9. [PMID: 23770899 DOI: 10.1128/aem.00850-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The methanotrophs in rice field soil are crucial in regulating the emission of methane. Drainage substantially reduces methane emission from rice fields. However, it is poorly understood how drainage affects microbial methane oxidation. Therefore, we analyzed the dynamics of methane oxidation rates, composition (using terminal restriction fragment length polymorphism [T-RFLP]), and abundance (using quantitative PCR [qPCR]) of methanotroph pmoA genes (encoding a subunit of particulate methane monooxygenase) and their transcripts over the season and in response to alternate dry/wet cycles in planted paddy field microcosms. In situ methane oxidation accounted for less than 15% of total methane production but was enhanced by intermittent drainage. The dry/wet alternations resulted in distinct effects on the methanotrophic communities in different soil compartments (bulk soil, rhizosphere soil, surface soil). The methanotrophic communities of the different soil compartments also showed distinct seasonal dynamics. In bulk soil, potential methanotrophic activity and transcription of pmoA were relatively low but were significantly stimulated by drainage. In contrast, however, in the rhizosphere and surface soils, potential methanotrophic activity and pmoA transcription were relatively high but decreased after drainage events and resumed after reflooding. While type II methanotrophs dominated the communities in the bulk soil and rhizosphere soil compartments (and to a lesser extent also in the surface soil), it was the pmoA of type I methanotrophs that was mainly transcribed under flooded conditions. Drainage affected the composition of the methanotrophic community only minimally but strongly affected metabolically active methanotrophs. Our study revealed dramatic dynamics in the abundance, composition, and activity of the various type I and type II methanotrophs on both a seasonal and a spatial scale and showed strong effects of dry/wet alternation cycles, which enhanced the attenuation of methane flux into the atmosphere.
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Ho A, Kerckhof FM, Luke C, Reim A, Krause S, Boon N, Bodelier PLE. Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:335-45. [PMID: 23754714 DOI: 10.1111/j.1758-2229.2012.00370.x] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/06/2012] [Accepted: 07/15/2012] [Indexed: 05/11/2023]
Abstract
Methane-oxidizing bacteria (MOB) possess the ability to use methane for energy generation and growth, thereby, providing a key ecosystem service that is highly relevant to the regulation of the global climate. MOB subgroups have different responses to key environmental controls, reflecting on their functional traits. Their unique features (C1-metabolism, unique lipids and congruence between the 16S rRNA and pmoA gene phylogeny) have facilitated numerous environmental studies, which in combination with the availability of cultured representatives, yield the most comprehensive ecological picture of any known microbial functional guild. Here, we focus on the broad MOB subgroups (type I and type II MOB), and aim to conceptualize MOB functional traits and observational characteristics derived primarily from these environmental studies to be interpreted as microbial life strategies. We focus on the functional traits, and the conditions under which these traits will render different MOB subgroups a selective advantage. We hypothesize that type I and type II MOB generally have distinct life strategies, enabling them to predominate under different conditions and maintain functionality. The ecological characteristics implicated in their adopted life strategies are discussed, and incorporated into the Competitor-Stress tolerator-Ruderal functional classification framework as put forward for plant communities. In this context, type I MOB can broadly be classified as competitor-ruderal while type II MOB fit more within the stress tolerator categories. Finally, we provide an outlook on MOB applications by exemplifying two approaches where their inferred life strategies could be exploited thereby, putting MOB into the context of microbial resource management.
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Affiliation(s)
- Adrian Ho
- Laboratory of Microbial Ecology and Technology (LabMET), Faculty of Bioscience Engineering, Coupure Links 653, B-9000 Ghent, Belgium
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Nazaries L, Murrell JC, Millard P, Baggs L, Singh BK. Methane, microbes and models: fundamental understanding of the soil methane cycle for future predictions. Environ Microbiol 2013; 15:2395-417. [DOI: 10.1111/1462-2920.12149] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 04/19/2013] [Accepted: 04/22/2013] [Indexed: 01/06/2023]
Affiliation(s)
- Loïc Nazaries
- Hawkesbury Institute for the Environment; University of Western Sydney; Building L9; Locked Bag 1797; Penrith South; NSW; 2751; Australia
| | - J. Colin Murrell
- School of Environmental Sciences; University of East Anglia; Norwich Research Park; Norwich; NR4 7TJ; UK
| | - Pete Millard
- Landcare Research; PO Box 40; Lincoln; 7604; New Zealand
| | - Liz Baggs
- Institute of Biological and Environmental Sciences; University of Aberdeen; Zoology Building; Tillydrone Avenue; Aberdeen; AB24 2TZ; Scotland; UK
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment; University of Western Sydney; Building L9; Locked Bag 1797; Penrith South; NSW; 2751; Australia
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Abstract
The methanotrophic potential in sewage treatment sludge was investigated. We detected a diverse aerobic methanotrophic community that potentially plays a significant role in mitigating methane emission in this environment. The results suggest that community structure was determined by conditions specific to the processes in a sewage treatment plant.
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Shukla AK, Upadhyay SN, Dubey SK. Current trends in trichloroethylene biodegradation: a review. Crit Rev Biotechnol 2012; 34:101-14. [PMID: 23057686 DOI: 10.3109/07388551.2012.727080] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Over the past few years biodegradation of trichloroethylene (TCE) using different microorganisms has been investigated by several researchers. In this review article, an attempt has been made to present a critical summary of the recent results related to two major processes--reductive dechlorination and aerobic co-metabolism used for TCE biodegradation. It has been shown that mainly Clostridium sp. DC-1, KYT-1, Dehalobacter, Dehalococcoides, Desulfuromonas, Desulfitobacterium, Propionibacterium sp. HK-1, and Sulfurospirillum bacterial communities are responsible for the reductive dechlorination of TCE. Efficacy of bacterial communities like Nitrosomonas, Pseudomonas, Rhodococcus, and Xanthobacter sp. etc. for TCE biodegradation under aerobic conditions has also been examined. Mixed cultures of diazotrophs and methanotrophs have been used for TCE degradation in batch and continuous cultures (biofilter) under aerobic conditions. In addition, some fungi (Trametes versicolor, Phanerochaete chrysosporium ME-446) and Actinomycetes have also been used for aerobic biodegradation of TCE. The available information on kinetics of biofiltration of TCE and its degradation end-products such as CO2 are discussed along with the available results on the diversity of bacterial community obtained using molecular biological approaches. It has emerged that there is a need to use metabolic engineering and molecular biological tools more intensively to improve the robustness of TCE degrading microbial species and assess their diversity.
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Affiliation(s)
- Awadhesh Kumar Shukla
- Department of Botany, Faculty of Science, Banaras Hindu University , Varanasi , India and
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Bodelier PLE, Bär-Gilissen MJ, Meima-Franke M, Hordijk K. Structural and functional response of methane-consuming microbial communities to different flooding regimes in riparian soils. Ecol Evol 2012; 2:106-27. [PMID: 22408730 PMCID: PMC3297182 DOI: 10.1002/ece3.34] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 08/12/2011] [Accepted: 08/17/2011] [Indexed: 02/02/2023] Open
Abstract
Climate change will lead to more extreme precipitation and associated increase of flooding events of soils. This can turn these soils from a sink into a source of atmospheric methane. The latter will depend on the balance of microbial methane production and oxidation. In the present study, the structural and functional response of methane oxidizing microbial communities was investigated in a riparian flooding gradient. Four sites differing in flooding frequency were sampled and soil-physico-chemistry as well as methane oxidizing activities, numbers and community composition were assessed. Next to this, the active community members were determined by stable isotope probing of lipids. Methane consumption as well as population size distinctly increased with flooding frequency. All methane consumption parameters (activity, numbers, lipids) correlated with soil moisture, organic matter content, and conductivity. Methane oxidizing bacteria were present and activated quickly even in seldom flooded soils. However, the active species comprised only a few representatives belonging to the genera Methylobacter, Methylosarcina, and Methylocystis, the latter being active only in permanently or regularly flooded soils. This study demonstrates that soils exposed to irregular flooding harbor a very responsive methane oxidizing community that has the potential to mitigate methane produced in these soils. The number of active species is limited and dominated by one methane oxidizing lineage. Knowledge on the characteristics of these microbes is necessary to assess the effects of flooding of soils and subsequent methane cycling therein.
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Affiliation(s)
- Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Droevendaalsesteeg 10, 6708PB Wageningen, The Netherlands
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Syntrophic oxidation of propionate in rice field soil at 15 and 30°C under methanogenic conditions. Appl Environ Microbiol 2012; 78:4923-32. [PMID: 22582054 DOI: 10.1128/aem.00688-12] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Propionate is one of the major intermediary products in the anaerobic decomposition of organic matter in wetlands and paddy fields. Under methanogenic conditions, propionate is decomposed through syntrophic interaction between proton-reducing and propionate-oxidizing bacteria and H(2)-consuming methanogens. Temperature is an important environmental regulator; yet its effect on syntrophic propionate oxidation has been poorly understood. In the present study, we investigated the syntrophic oxidation of propionate in a rice field soil at 15°C and 30°C. [U-(13)C]propionate (99 atom%) was applied to anoxic soil slurries, and the bacteria and archaea assimilating (13)C were traced by DNA-based stable isotope probing. Syntrophobacter spp., Pelotomaculum spp., and Smithella spp. were found significantly incorporating (13)C into their nucleic acids after [(13)C]propionate incubation at 30°C. The activity of Smithella spp. increased in the later stage, and concurrently that of Syntrophomonas spp. increased. Aceticlastic Methanosaetaceae and hydrogenotrophic Methanomicrobiales and Methanocellales acted as methanogenic partners at 30°C. Syntrophic oxidation of propionate also occurred actively at 15°C. Syntrophobacter spp. were significantly labeled with (13)C, whereas Pelotomaculum spp. were less active at this temperature. In addition, Methanomicrobiales, Methanocellales, and Methanosarcinaceae dominated the methanogenic community, while Methanosaetaceae decreased. Collectively, temperature markedly influenced the activity and community structure of syntrophic guilds degrading propionate in the rice field soil. Interestingly, Geobacter spp. and some other anaerobic organisms like Rhodocyclaceae, Acidobacteria, Actinobacteria, and Thermomicrobia probably also assimilated propionate-derived (13)C. The mechanisms for the involvement of these organisms remain unclear.
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Freeze-coring method for characterization of microbial community structure and function in wetland soils at high spatial resolution. Appl Environ Microbiol 2012; 78:4501-4. [PMID: 22492456 DOI: 10.1128/aem.00133-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A simple freeze-coring method was developed to obtain structurally intact cores from wetland soils. A copper tube was inserted into the wetland and filled with ethanol and dry ice to freeze the surrounding soil. Biological structure and function could be analyzed, and labile compounds such as mRNA were recovered.
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He R, Wooller MJ, Pohlman JW, Catranis C, Quensen J, Tiedje JM, Leigh MB. Identification of functionally active aerobic methanotrophs in sediments from an arctic lake using stable isotope probing. Environ Microbiol 2012; 14:1403-19. [PMID: 22429394 DOI: 10.1111/j.1462-2920.2012.02725.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Arctic lakes are a significant source of the greenhouse gas methane (CH(4) ), but the role that methane oxidizing bacteria (methanotrophs) play in limiting the overall CH(4) flux is poorly understood. Here, we used stable isotope probing (SIP) techniques to identify the metabolically active aerobic methanotrophs in upper sediments (0-1 cm) from an arctic lake in northern Alaska sampled during ice-free summer conditions. The highest CH(4) oxidation potential was observed in the upper sediment (0-1 cm depth) with 1.59 µmol g wet weight(-1) day(-1) compared with the deeper sediment samples (1-3 cm, 3-5 cm and 5-10 cm), which exhibited CH(4) oxidation potentials below 0.4 µmol g wet weight(-1) day(-1) . Both type I and type II methanotrophs were directly detected in the upper sediment total communities using targeted primer sets based on 16S rRNA genes. Sequencing of 16S rRNA genes and functional genes (pmoA and mxaF) in the (13) C-DNA from the upper sediment indicated that type I methanotrophs, mainly Methylobacter, Methylosoma, Methylomonas and Methylovulum miyakonense, dominated the assimilation of CH(4) . Methylotrophs, including the genera Methylophilus and/or Methylotenera, were also abundant in the (13) C-DNA. Our results show that a diverse microbial consortium acquired carbon from CH(4) in the sediments of this arctic lake.
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Affiliation(s)
- Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
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Yuan Q, Liu P, Lu Y. Differential responses of nirK- and nirS-carrying bacteria to denitrifying conditions in the anoxic rice field soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:113-122. [PMID: 23757237 DOI: 10.1111/j.1758-2229.2011.00311.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Denitrification occurs actively in rice field soils. In the present study, the responses of nirK and nirS denitrifier communities to nitrate addition in the anoxic rice soil were determined through molecular analyses of nitrite reductase genes nirK and nirS and 16S rRNA genes. Denitrification occurred rapidly when nitrate was added at the beginning of anoxic incubation (experiment I). The structure of nirK-type denitrifiers did not change; but their abundance as determined by quantitative (real-time) PCR increased in nitrate treatments compared with control. Both the structure and abundance of nirS denitrifiers remained unaffected in experiment I. The rate of denitrification was slowed down when nitrate was added 20 days after the onset of anoxic incubation (experiment II). The structure and abundance of nirK-type denitrifier community did not respond to nitrate addition; but the nirS community changed substantially in this experiment. The copy number of nirS genes increased by an order of magnitude in the treatments of 5 mM and 10 mM nitrate compared with control. The terminal restriction fragment length polymorphism (T-RFLP) analysis of nirS genes revealed that the 100 bp T-RF substantially increased in the nitrate treatments. Cloning and sequence analysis indicated that this T-RF had similarity of up to 90% with Herbaspirillum sp. T-RFLP profiles of the bacterial 16S rRNA genes also showed that Herbaspirillum sp. increased after nitrate amendments. Collectively, the nirK-type denitrifiers were probably active at the beginning of anaerobic incubation, while the nirS denitrifiers, especially those related with Herbaspirillum sp. probably were more active when anaerobic condition was fully developed.
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Affiliation(s)
- Quan Yuan
- College of Resources and Environmental Sciences, China Agricultural University, 100193 Beijing, China
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46
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Ke X, Lu Y. Adaptation of ammonia-oxidizing microorganisms to environment shift of paddy field soil. FEMS Microbiol Ecol 2012; 80:87-97. [DOI: 10.1111/j.1574-6941.2011.01271.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 11/10/2011] [Accepted: 11/25/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
- Xiubin Ke
- College of Resources and Environment Sciences; China Agricultural University; Beijing; China
| | - Yahai Lu
- College of Resources and Environment Sciences; China Agricultural University; Beijing; China
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Tsutsumi M, Kojima H, Fukui M. Vertical profiles of abundance and potential activity of methane-oxidizing bacteria in sediment of Lake Biwa, Japan. Microbes Environ 2011; 27:67-71. [PMID: 22200642 PMCID: PMC4036029 DOI: 10.1264/jsme2.me11285] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Vertical profiles of the abundance, community composition, and potential activity of methane-oxidizing bacteria (MOB) were investigated in the sediment of Lake Biwa. Sediment samples were obtained from two sites at different water depths. The abundance of MOB was assessed as the copy number of the pmoA gene (encoding the alpha subunit of particulate methane monooxygenase), measured with quantitative real-time PCR. Abundance of the pmoA gene peaked in the 5–8 cm layer of the sediment from both sites. MOB community composition was investigated by denaturing gradient gel electrophoresis (DGGE) analysis of pmoA and 16S rRNA genes. The band patterns observed in DGGE did not significantly differ with sediment depths or sampling sites. Sequence analysis of the DGGE bands indicated the dominance of the genus Methylobacter. Potential activity, which was measured in the presence of sufficient amounts of methane and oxygen, decreased linearly from the sediment surface to deeper layers. These results suggest that the pmoA gene copy number cannot be regarded as an indicator of aerobic MOB that retain potential activity in sediments.
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Affiliation(s)
- Masazumi Tsutsumi
- The Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan
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48
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Liu P, Qiu Q, Lu Y. Syntrophomonadaceae-affiliated species as active butyrate-utilizing syntrophs in paddy field soil. Appl Environ Microbiol 2011; 77:3884-7. [PMID: 21460111 PMCID: PMC3127591 DOI: 10.1128/aem.00190-11] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 03/23/2011] [Indexed: 11/20/2022] Open
Abstract
DNA-based stable-isotope probing was applied to identify the active microorganisms involved in syntrophic butyrate oxidation in paddy field soil. After 14 and 21 days of incubation with [U-(13)C]butyrate, the bacterial Syntrophomonadaceae and the archaeal Methanosarcinaceae and Methanocellales incorporated substantial amounts of (13)C label into their nucleic acids. Unexpectedly, members of the Planctomycetes and Chloroflexi were also labeled with (13)C by yet-unclear mechanisms.
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MESH Headings
- Butyrates/metabolism
- Carbon Isotopes/metabolism
- Chloroflexi/growth & development
- Chloroflexi/metabolism
- Cluster Analysis
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Euryarchaeota/growth & development
- Euryarchaeota/metabolism
- Genes, rRNA
- Gram-Positive Bacteria/growth & development
- Gram-Positive Bacteria/isolation & purification
- Gram-Positive Bacteria/metabolism
- Gram-Positive Bacteria/physiology
- Isotope Labeling
- Molecular Sequence Data
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
- Symbiosis
- Uridine/metabolism
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Affiliation(s)
- Pengfei Liu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Qiongfen Qiu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Yahai Lu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
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Yuan Y, Conrad R, Lu Y. Transcriptional response of methanogen mcrA genes to oxygen exposure of rice field soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:320-328. [PMID: 23761278 DOI: 10.1111/j.1758-2229.2010.00228.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Methane production in paddy soil is substantially suppressed after even a brief exposure of soil to oxygen. We hypothesized that the strong response of methanogen activity is reflected in the transcription of functional genes rather than in the composition of the community of methanogens. Therefore, we determined the community composition and the transcriptional response of methanogens in a rice field soil by targeting the mcrA gene (encoding the α subunit of methyl-coenzyme M reductase). Transcription of mcrA genes measured by quantitative PCR decreased by an order of magnitude after brief exposure to O2 . Terminal restriction fragment length polymorphism of mcrA genes and gene transcripts showed that although the community structure of methanogens did not change, the composition of transcripts dramatically responded to O2 exposure. In the beginning, transcripts of Methanocellales were the relatively most abundant, indicating resistance of these hydrogenotrophic methanogens against O2 stress. Later on, mcrA transcripts of acetoclastic methanogens became relatively more abundant coinciding with the turnover of acetate. The transcription of Methanosarcinaceae was relatively greater when acetate accumulated while Methanosaetaceae became more active when acetate concentrations decreased. In the presence of methyl fluoride, a specific inhibitor of acetoclastic methanogenesis, mcrA transcription by Methanosaetaceae was greatly suppressed while that of Methanosarcinaceae was less affected. Our study showed that in contrast to constant community structure as revealed by DNA-based fingerprinting the transcription of functional mcrA genes strongly responded to O2 stress and the presence of inhibitor CH3 F. The response patterns reflected the genomic and physiological traits of individual methanogens.
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Affiliation(s)
- Yanli Yuan
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China. Max-Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str, 35043 Marburg, Germany
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50
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Activity and diversity of methanotrophic bacteria at methane seeps in eastern Lake Constance sediments. Appl Environ Microbiol 2011; 77:2573-81. [PMID: 21335392 DOI: 10.1128/aem.02776-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The activity and community structure of aerobic methanotrophic communities were investigated at methane seeps (pockmarks) in the littoral and profundal zones of an oligotrophic freshwater lake (Lake Constance, Germany). Measurements of potential methane oxidation rates showed that sediments inside littoral pockmarks are hot spots of methane oxidation. Potential methane oxidation rates at littoral pockmark sites exceeded the rates of the surrounding sediment by 2 orders of magnitude. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the pmoA gene revealed major differences in the methanotrophic community composition between littoral pockmarks and the surrounding sediments. Clone library analysis confirmed that one distinct Methylobacter-related group dominates the community at littoral pockmarks. In profundal sediments, the differences between pockmarks and surrounding sediments were found to be less pronounced.
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