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Chaudhary DK, Seo D, Han S, Hong Y. Distribution of mercury in modern bottom sediments of the Beaufort Sea in relation to the processes of early diagenesis: Microbiological aspect. MARINE POLLUTION BULLETIN 2024; 202:116300. [PMID: 38555803 DOI: 10.1016/j.marpolbul.2024.116300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/23/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
This study investigated the contents of total mercury (THg), trace metals, and CH4 and determined the signature microbes involved in various biogeochemical processes in the sediment of the Canadian Beaufort Sea. The THg ranged between 32 and 63 μg/kg and the trace metals such as Fe, Al, Mn, and Zn were significant in distributions. The pH, SO42-, Fe2+, and redox proxy metals were crucial factors in the spatial and vertical heterogeneity of geochemical distributions. CH4 was detected only at the mud volcano site. Microbial analyses identified Clostridium, Desulfosporosinus, Desulfofustis, and Desulftiglans as the predominant Hg methylators and sulfate reducers; Nitrosopumilus and Hyphomicrobium as the major nitrifiers and denitrifiers; Methanosarcina and Methanosaeta as keystone methanogens; and Methyloceanibacter and Methyloprofundus as signature methanotrophs. Altogether, this study expands the current understanding of the microbiological and geochemical features and could be helpful in predicting ecosystem functions in the Canadian Beaufort Sea.
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Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea
| | - DongGyun Seo
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea
| | - Seunghee Han
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Gwangju 61005, Republic of Korea
| | - Yongseok Hong
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea.
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2
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Zhu X, Deng Y, Liu Y. Methylocystis dominates methane oxidation in glacier foreland soil at elevated temperature. FEMS Microbiol Lett 2024; 371:fnae011. [PMID: 38366911 DOI: 10.1093/femsle/fnae011] [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: 09/27/2023] [Revised: 12/01/2023] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
Methane-oxidizing bacteria (methanotrophs) play an important role in mitigating methane emissions in various ecological environments, including cold regions. However, the response of methanotrophs in these cold environments to extreme temperatures above the in-situ temperature has not been thoroughly explored. Therefore, this study collected soil samples from Longxiazailongba (LXZ) and Qiangyong (QY) glacier forelands and incubated them with 13CH4 at 35°C under different soil water conditions. The active methanotroph populations were identified using DNA stable isotope probing (DNA-SIP) and high throughput sequencing techniques. The results showed that the methane oxidation potential in LXZ and QY glacier foreland soils was significantly enhanced at an unusually high temperature of 35°C during microcosm incubations, where abundant substrate (methane and oxygen) was provided. Moreover, the influence of soil water conditions on this potential was observed. Interestingly, Methylocystis, a type II and mesophilic methanotroph, was detected in the unincubated in-situ soil samples and became the active and dominant methanotroph in methane oxidation at 35°C. This suggests that Methylocystis can survive at low temperatures for a prolonged period and thrive under suitable growth conditions. Furthermore, the presence of mesophilic methanotrophs in cold habitats could have potential implications for reducing greenhouse gas emissions in warming glacial environments.
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Affiliation(s)
- Xinshu Zhu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yongcui Deng
- School of Geography, Nanjing Normal University, Nanjing 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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Deng Y, Liang C, Zhu X, Zhu X, Chen L, Pan H, Xun F, Tao Y, Xing P. Methylomonadaceae was the active and dominant methanotroph in Tibet lake sediments. ISME COMMUNICATIONS 2024; 4:ycae032. [PMID: 38524764 PMCID: PMC10960969 DOI: 10.1093/ismeco/ycae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/21/2024] [Accepted: 02/29/2024] [Indexed: 03/26/2024]
Abstract
Methane (CH4), an important greenhouse gas, significantly impacts the local and global climate. Our study focused on the composition and activity of methanotrophs residing in the lakes on the Tibetan Plateau, a hotspot for climate change research. Based on the field survey, the family Methylomonadaceae had a much higher relative abundance in freshwater lakes than in brackish and saline lakes, accounting for ~92% of total aerobic methanotrophs. Using the microcosm sediment incubation with 13CH4 followed by high throughput sequencing and metagenomic analysis, we further demonstrated that the family Methylomonadaceae was actively oxidizing CH4. Moreover, various methylotrophs, such as the genera Methylotenera and Methylophilus, were detected in the 13C-labeled DNAs, which suggested their participation in CH4-carbon sequential assimilation. The presence of CH4 metabolism, such as the tetrahydromethanopterin and the ribulose monophosphate pathways, was identified in the metagenome-assembled genomes of the family Methylomonadaceae. Furthermore, they had the potential to adapt to oxygen-deficient conditions and utilize multiple electron acceptors, such as metal oxides (Fe3+), nitrate, and nitrite, for survival in the Tibet lakes. Our findings highlighted the predominance of Methylomonadaceae and the associated microbes as active CH4 consumers, potentially regulating the CH4 emissions in the Tibet freshwater lakes. These insights contributed to understanding the plateau carbon cycle and emphasized the significance of methanotrophs in mitigating climate change.
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Affiliation(s)
- Yongcui Deng
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Chulin Liang
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Xiaomeng Zhu
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Xinshu Zhu
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Lei Chen
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Hongan Pan
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Fan Xun
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ye Tao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China
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Hart R, Cardace D. Mineral Indicators of Geologically Recent Past Habitability on Mars. Life (Basel) 2023; 13:2349. [PMID: 38137950 PMCID: PMC10744562 DOI: 10.3390/life13122349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/25/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
We provide new support for habitable microenvironments in the near-subsurface of Mars, hosted in Fe- and Mg-rich rock units, and present a list of minerals that can serve as indicators of specific water-rock reactions in recent geologic paleohabitats for follow-on study. We modeled, using a thermodynamic basis without selective phase suppression, the reactions of published Martian meteorites and Jezero Crater igneous rock compositions and reasonable planetary waters (saline, alkaline waters) using Geochemist's Workbench Ver. 12.0. Solid-phase inputs were meteorite compositions for ALH 77005, Nakhla, and Chassigny, and two rock units from the Mars 2020 Perseverance rover sites, Máaz and Séítah. Six plausible Martian groundwater types [NaClO4, Mg(ClO4)2, Ca(ClO4)2, Mg-Na2(ClO4)2, Ca-Na2(ClO4)2, Mg-Ca(ClO4)2] and a unique Mars soil-water analog solution (dilute saline solution) named "Rosy Red", related to the Phoenix Lander mission, were the aqueous-phase inputs. Geophysical conditions were tuned to near-subsurface Mars (100 °C or 373.15 K, associated with residual heat from a magmatic system, impact event, or a concentration of radionuclides, and 101.3 kPa, similar to <10 m depth). Mineral products were dominated by phyllosilicates such as serpentine-group minerals in most reaction paths, but differed in some important indicator minerals. Modeled products varied in physicochemical properties (pH, Eh, conductivity), major ion activities, and related gas fugacities, with different ecological implications. The microbial habitability of pore spaces in subsurface groundwater percolation systems was interrogated at equilibrium in a thermodynamic framework, based on Gibbs Free Energy Minimization. Models run with the Chassigny meteorite produced the overall highest H2 fugacity. Models reliant on the Rosy Red soil-water analog produced the highest sustained CH4 fugacity (maximum values observed for reactant ALH 77005). In general, Chassigny meteorite protoliths produced the best yield regarding Gibbs Free Energy, from an astrobiological perspective. Occurrences of serpentine and saponite across models are key: these minerals have been observed using CRISM spectral data, and their formation via serpentinization would be consistent with geologically recent-past H2 and CH4 production and sustained energy sources for microbial life. We list index minerals to be used as diagnostic for paleo water-rock models that could have supported geologically recent-past microbial activity, and suggest their application as criteria for future astrobiology study-site selections.
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Affiliation(s)
- Roger Hart
- Department of Physics and Engineering, Community College of Rhode Island, Lincoln, RI 02865, USA
- Department of Geosciences, University of Rhode Island, Kingston, RI 02881, USA;
| | - Dawn Cardace
- Department of Geosciences, University of Rhode Island, Kingston, RI 02881, USA;
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Thangaraj S, Kim HR, Heo JM, Son S, Ryu J, Park JW, Kim JH, Kim SY, Jung HK, Kim IN. Unraveling prokaryotic diversity distribution and functional pattern on nitrogen and methane cycling in the subtropical Western North Pacific Ocean. MARINE POLLUTION BULLETIN 2023; 196:115569. [PMID: 37922593 DOI: 10.1016/j.marpolbul.2023.115569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 11/07/2023]
Abstract
Prokaryotes play an important role in marine nitrogen and methane cycles. However, their community changes and metabolic modifications to the concurrent impact of ocean warming (OW), acidification (OA), deoxygenation (OD), and anthropogenic‑nitrogen-deposition (AND) from the surface to the deep ocean remains unknown. We examined here the amplicon sequencing approach across the surface (0-200 m; SL), intermediate (200-1000 m; IL), and deep layers (1000-2200 m; DL), and characterized the simultaneous impacts of OW, OA, OD, and AND on the Western North Pacific Ocean prokaryotic changes and their functional pattern in nitrogen and methane cycles. Results showed that SL possesses higher ammonium oxidation community/metabolic composition assumably the reason for excess nitrogen input from AND and modification of their kinetic properties to OW adaptation. Expanding OD at IL showed hypoxic conditions in the oxygen minimum layer, inducing higher microbial respiration that elevates the dimerization of nitrification genes for higher nitrous oxide production. The aerobic methane-oxidation composition was dominant in SL presumably the reason for adjustment in prokaryotic optimal temperature to OW, while anaerobic oxidation composition was dominant at IL due to the evolutionary changes coupling with higher nitrification. Our findings refocus on climate-change impacts on the open ocean ecosystem from the surface to the deep-environment integrating climate-drivers as key factors for higher nitrous-oxide and methane emissions.
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Affiliation(s)
- Satheeswaran Thangaraj
- Department of Marine Science, Incheon National University, Incheon, South Korea; Freddy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel; Interuniversity Institute for Marine Sciences, Eilat, Israel; Department of Physiology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Hyo-Ryeon Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Jang-Mu Heo
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Seunghyun Son
- Cooperative Institute for Satellite Earth System Studies (CISESS) / Earth System Science Interdisciplinary Center (ESSIC), University of Maryland, USA
| | - Jongseong Ryu
- Department of Marine Biotechnology, Anyang University, Incheon, South Korea
| | - Jong-Woo Park
- Tidal Flat Research Center, National Institute of Fisheries Science, Gunsan, South Korea
| | - Ju-Hyoung Kim
- Department of Aquaculture and Aquatic Science, Kunsan National University, Gunsan, South Korea
| | - Seo-Young Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Hae-Kun Jung
- Environment and Fisheries Resources Research Division, East Sea Fisheries Institute, National Institute of Fisheries Science, Gangneung, South Korea
| | - Il-Nam Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea.
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Roldán DM, Menes RJ. Characterisation of 'Candidatus Methylobacter titanis' sp. nov., a putative novel species of Methylobacter clade 2 and their distribution in sediments of freshwater lakes in maritime Antarctica. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01840-1. [PMID: 37227602 DOI: 10.1007/s10482-023-01840-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/07/2023] [Indexed: 05/26/2023]
Abstract
Global warming has a strong impact on the polar regions, in particular, the Antarctic Peninsula and nearby islands. Methane (CH4) is a major factor in climate change and mitigation of CH4 emissions can be accomplished through microbial oxidation by methanotrophic bacteria. Understanding this biological process is crucial given the shortage of research carried out in this geographical area. The aim of this study was to characterise psychrophilic enrichment cultures of aerobic methanotrophs obtained from lake sediments of the Fildes Peninsula (King George Island, South Shetland Islands) and revealing the distribution of the genus Methylobacter in different lake sediments of the peninsula. Four stable methanotrophic enrichment cultures were obtained and analysed by metagenome-assembled genomes (MAGs). The phylogeny of methanotroph MAGs recovered from these enrichment cultures based on the 16S rRNA gene showed that K-2018 MAG008 and D1-2020 MAG004Ts clustered within the Methylobacter clade 2, with high similarity to Methylobacter tundripaludum SV96T (97.88 and 98.56% respectively). However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with M. tundripaludum were < 95% (84.8 and 85.0%, respectively) and < 70% (30.2 and 30.3%, respectively), suggesting that they represent a putative novel species for which the name 'Ca. Methylobacter titanis' is proposed. This is the first species of clade 2 of the genus Methylobacter obtained from Antarctica. The bacterial diversity assessed by 16S rRNA gene sequencing of 21 samples of different lakes (water column and sediments) revealed 54 ASVs associated with methanotrophs and the genus Methylobacter as the most abundant. These results suggest that aerobic methanotrophs belonging to the Methylobacter clade 2 would be the main responsible for CH4 oxidation in these sediments.
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Affiliation(s)
- Diego M Roldán
- Laboratorio de Ecología Microbiana Medioambiental, Microbiología, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Microbiología, Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Rodolfo Javier Menes
- Laboratorio de Ecología Microbiana Medioambiental, Microbiología, Facultad de Química, Universidad de la República, Montevideo, Uruguay.
- Laboratorio de Microbiología, Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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7
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Rafalska A, Walkiewicz A, Osborne B, Klumpp K, Bieganowski A. Variation in methane uptake by grassland soils in the context of climate change - A review of effects and mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162127. [PMID: 36764535 DOI: 10.1016/j.scitotenv.2023.162127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/19/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
Grassland soils are climate-dependent ecosystems that have a significant greenhouse gas mitigating function through their ability to store large amounts of carbon (C). However, what is often not recognized is that they can also exhibit a high methane (CH4) uptake capacity that could be influenced by future increases in atmospheric carbon dioxide (CO2) concentration and variations in temperature and water availability. While there is a wealth of information on C sequestration in grasslands there is less consensus on how climate change impacts on CH4 uptake or the underlying mechanisms involved. To address this, we assessed existing knowledge on the impact of climate change components on CH4 uptake by grassland soils. Increases in precipitation associated with soils with a high background soil moisture content generally resulted in a reduction in CH4 uptake or even net emissions, while the effect was opposite in soils with a relatively low background moisture content. Initially wet grasslands subject to the combined effects of warming and water deficits may absorb more CH4, mainly due to increased gas diffusivity. However, in the longer-term heat and drought stress may reduce the activity of methanotrophs when the mean soil moisture content is below the optimum for their survival. Enhanced plant productivity and growth under elevated CO2, increased soil moisture and changed nutrient concentrations, can differentially affect methanotrophic activity, which is often reduced by increasing N deposition. Our estimations showed that CH4 uptake in grassland soils can change from -57.7 % to +6.1 % by increased precipitation, from -37.3 % to +85.3 % by elevated temperatures, from +0.87 % to +92.4 % by decreased precipitation, and from -66.7 % to +27.3 % by elevated CO2. In conclusion, the analysis suggests that grasslands under the influence of warming and drought may absorb even more CH4, mainly because of reduced soil water contents and increased gas diffusivity.
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Affiliation(s)
- Adrianna Rafalska
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland
| | - Anna Walkiewicz
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland.
| | - Bruce Osborne
- UCD School of Agriculture and Food Science and UCD Earth Institute, University College Dublin, Belfield, 4 Dublin, Ireland
| | - Katja Klumpp
- INRAE, University of Clermont Auvergne, VetAgro Sup, UREP Unité de Recherche sur l'Ecosystème Prairial, 63000 Clermont-Ferrand, France
| | - Andrzej Bieganowski
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland
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Zhu X, Deng Y, Hernández M, Fang J, Xing P, Liu Y. Distinct responses of soil methanotrophy in hummocks and hollows to simulated glacier meltwater and temperature rise in Tibetan glacier foreland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160888. [PMID: 36521618 DOI: 10.1016/j.scitotenv.2022.160888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Glacier foreland soils are known to be essential methane (CH4) consumers. However, global warming and increased glacier meltwater have turned some foreland meadows into swamp meadows. The potential impact of this change on the function of foreland soils in methane consumption remains unclear. Therefore, we collected Tibetan glacier foreland soils in the non-melting season from typical microtopography in swamp meadows (hummock and hollow). Three soil moisture conditions (moist, saturated, and submerged) were set by adding glacier runoff water. Soil samples were then incubated in the laboratory for two weeks at 10 °C and 20 °C. About 5 % of 13CH4/12CH4 was added to the incubation bottles, and daily methane concentrations were measured. DNA stable isotope probing (DNA-SIP) and high-throughput sequencing were combined to target the active methanotroph populations. The results showed that type Ia methanotrophs, including Crenothrix, Methylobacter, and an unclassified Methylomonadaceae cluster, actively oxidized methane at 10 °C and 20 °C. There were distinct responses of methanotrophs to soil moisture rises in hummock and hollow soils, resulting in different methane oxidation potentials. In both hummock and hollow soils, the methane oxidation potential was positively correlated with temperature. Furthermore, saturated hummock soils exhibited the highest methane oxidation potential and methanotroph populations, while submerged hollow soils had the lowest. This suggests that the in-situ hummock soils, generally saturated with water, are more essential than in-situ hollows, typically submerged in water, for alleviating the global warming potential of swamp meadows in the Tibetan glacier foreland during the growing season.
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Affiliation(s)
- Xinshu Zhu
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Yongcui Deng
- School of Geography, Nanjing Normal University, Nanjing 210023, China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China.
| | - Marcela Hernández
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk NR4 7TJ, United Kingdom
| | - Jie Fang
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing 210023, China
| | - Peng Xing
- Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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Zhang S, Yan L, Cao J, Wang K, Luo Y, Hu H, Wang L, Yu R, Pan B, Yu K, Zhao J, Bao Z. Salinity significantly affects methane oxidation and methanotrophic community in Inner Mongolia lake sediments. Front Microbiol 2023; 13:1067017. [PMID: 36687579 PMCID: PMC9853545 DOI: 10.3389/fmicb.2022.1067017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Methanotrophs oxidize methane (CH4) and greatly help in mitigating greenhouse effect. Increased temperatures due to global climate change can facilitate lake salinization, particularly in the regions with cold semiarid climate. However, the effects of salinity on the CH4 oxidation activity and diversity and composition of methanotrophic community in the sediment of natural lakes at a regional scale are still unclear. Therefore, we collected lake sediment samples from 13 sites in Mongolian Plateau; CH4 oxidation activities of methanotrophs were investigated, and the diversity and abundance of methanotrophs were analyzed using real-time quantitative polymerase chain reaction and high throughput sequencing approach. The results revealed that the diversity of methanotrophic community decreased with increasing salinity, and community structure of methanotrophs was clearly different between the hypersaline sediment samples (HRS; salinity > 0.69%) and hyposaline sediment samples (HOS; salinity < 0.69%). Types II and I methanotrophs were predominant in HRS and HOS, respectively. Salinity was significantly positively correlated with the relative abundance of Methylosinus and negatively correlated with that of Methylococcus. In addition, CH4 oxidation rate and pmoA gene abundance decreased with increasing salinity, and salinity directly and indirectly affected CH4 oxidation rate via regulating the community diversity. Moreover, high salinity decreased cooperative association among methanotrophs and number of key methanotrophic species (Methylosinus and Methylococcus, e.g). These results suggested that salinity is a major driver of CH4 oxidation in lake sediments and acts by regulating the diversity of methanotrophic community and accociation among the methanotrophic species.
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Affiliation(s)
- Shaohua Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lei Yan
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Jiahui Cao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Kexin Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Ying Luo
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Haiyang Hu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lixin Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China,Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University, Hohhot, China
| | - Ruihong Yu
- Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University, Hohhot, China
| | - Baozhu Pan
- Institute of Water Resources and Hydro-electric Engineering, Xi’an University of Technology, Xi’an, Shaanxi, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Ji Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China,Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University, Hohhot, China
| | - Zhihua Bao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China,Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University, Hohhot, China,*Correspondence: Zhihua Bao, ✉
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Groult B, Bredin P, Lazar CS. Ecological processes differ in community assembly of Archaea, Bacteria and Eukaryotes in a biogeographical survey of groundwater habitats in the Quebec region (Canada). Environ Microbiol 2022; 24:5898-5910. [PMID: 36135934 DOI: 10.1111/1462-2920.16219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/19/2022] [Indexed: 01/12/2023]
Abstract
Aquifers are inhabited by microorganisms from the three major domains of life: Archaea, Eukaryotes and Bacteria. Although interest in the processes that govern the assembly of these microbial communities is growing, their study is almost systematically limited to one of the three domains of life. Archaea, Bacteria and Eukaryotes are however interconnected and essential to understand the functioning of their living ecosystems. We, therefore, conducted a spatial study of the distribution of microorganisms by sampling 35 wells spread over an area of 10,000 km2 in the Quebec region (Canada). The obtained data allowed us to define the impact of geographic distance and geochemical water composition on the microbial communities. A null model approach was used to infer the relative influence of stochastic and determinist ecological processes on the assembly of the microbial community from all three domains. We found that the organisms from these three groups are mainly governed by stochastic mechanisms. However, this apparent similarity does not reflect the differences in the processes that govern the phyla assembly. The results obtained highlight the importance of considering all the microorganisms without neglecting their individual specificities.
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Affiliation(s)
- Benjamin Groult
- Biological Sciences Department, University of Quebec in Montreal (UQAM), Montreal, Quebec, Canada
| | - Pascal Bredin
- Biological Sciences Department, University of Quebec in Montreal (UQAM), Montreal, Quebec, Canada
| | - Cassandre Sara Lazar
- Biological Sciences Department, University of Quebec in Montreal (UQAM), Montreal, Quebec, Canada
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11
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Xu Q, Du Z, Wang L, Xue K, Wei Z, Zhang G, Liu K, Lin J, Lin P, Chen T, Xiao C. The Role of Thermokarst Lake Expansion in Altering the Microbial Community and Methane Cycling in Beiluhe Basin on Tibetan Plateau. Microorganisms 2022; 10:1620. [PMID: 36014037 PMCID: PMC9412574 DOI: 10.3390/microorganisms10081620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
One of the most significant environmental changes across the Tibetan Plateau (TP) is the rapid lake expansion. The expansion of thermokarst lakes affects the global biogeochemical cycles and local climate regulation by rising levels, expanding area, and increasing water volumes. Meanwhile, microbial activity contributes greatly to the biogeochemical cycle of carbon in the thermokarst lakes, including organic matter decomposition, soil formation, and mineralization. However, the impact of lake expansion on distribution patterns of microbial communities and methane cycling, especially those of water and sediment under ice, remain unknown. This hinders our ability to assess the true impact of lake expansion on ecosystem services and our ability to accurately investigate greenhouse gas emissions and consumption in thermokarst lakes. Here, we explored the patterns of microorganisms and methane cycling by investigating sediment and water samples at an oriented direction of expansion occurred from four points under ice of a mature-developed thermokarst lake on TP. In addition, the methane concentration of each water layer was examined. Microbial diversity and network complexity were different in our shallow points (MS, SH) and deep points (CE, SH). There are differences of microbial community composition among four points, resulting in the decreased relative abundances of dominant phyla, such as Firmicutes in sediment, Proteobacteria in water, Thermoplasmatota in sediment and water, and increased relative abundance of Actinobacteriota with MS and SH points. Microbial community composition involved in methane cycling also shifted, such as increases in USCγ, Methylomonas, and Methylobacter, with higher relative abundance consistent with low dissolved methane concentration in MS and SH points. There was a strong correlation between changes in microbiota characteristics and changes in water and sediment environmental factors. Together, these results show that lake expansion has an important impact on microbial diversity and methane cycling.
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Affiliation(s)
- Qian Xu
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiheng Du
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Lei Wang
- Zhuhai Branch of State Key Laboratory of Earth Surface Processes and Resource Ecology, Beijing Normal University, Zhuhai 519087, China
| | - Kai Xue
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiqiang Wei
- Zhuhai Branch of State Key Laboratory of Earth Surface Processes and Resource Ecology, Beijing Normal University, Zhuhai 519087, China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiahui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Beijing Normal University, Beijing 100875, China
| | - Penglin Lin
- College of Geography and Environmental Science, Northwest Normal University, Lanzhou 730070, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Cunde Xiao
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Beijing Normal University, Beijing 100875, China
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12
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Diversity and Composition of Methanotroph Communities in Caves. Microbiol Spectr 2022; 10:e0156621. [PMID: 35943259 PMCID: PMC9430973 DOI: 10.1128/spectrum.01566-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Methane oxidizing microorganisms (methanotrophs) are ubiquitous in the environment and represent a major sink for the greenhouse gas methane (CH4). Recent studies have demonstrated methanotrophs are abundant and contribute to CH4 dynamics in caves. However, very little is known about what controls the distribution and abundance of methanotrophs in subterranean ecosystems. Here, we report a survey of soils collected from > 20 caves in North America to elucidate the factors shaping cave methanotroph communities. Using 16S rRNA sequencing, we recovered methanotrophs from nearly all (98%) of the samples, including cave sites where CH4 concentrations were at or below detection limits (≤0.3 ppmv). We identified a core methanotroph community among caves comprised of high-affinity methanotrophs. Although associated with local-scale mineralogy, methanotroph composition did not systematically vary between the entrances and interior of caves, where CH4 concentrations varied. We also observed methanotrophs are able to disperse readily between cave systems showing these organisms have low barriers to dispersal. Lastly, the relative abundance of methanotrophs was positively correlated with cave-air CH4 concentrations, suggesting these microorganisms contribute to CH4 flux in subterranean ecosystems. IMPORTANCE Recent observations have shown the atmospheric greenhouse gas methane (CH4) is consumed by microorganisms (methanotrophs) in caves at rates comparable to CH4 oxidation in surface soils. Caves are abundant in karst landscapes that comprise 14% of Earth’s land surface area, and therefore may represent a potentially important, but overlooked, CH4 sink. We sampled cave soils to gain a better understand the community composition and structure of cave methanotrophs. Our results show the members of the USC-γ clade are dominant in cave communities and can easily disperse through the environment, methanotroph relative abundance was correlated with local scale mineralogy of soils, and the relative abundance of methanotrophs was positively correlated with CH4 concentrations in cave air.
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13
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Impact of interannual and multidecadal trends on methane-climate feedbacks and sensitivity. Nat Commun 2022; 13:3592. [PMID: 35739128 PMCID: PMC9226131 DOI: 10.1038/s41467-022-31345-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/01/2022] [Indexed: 11/29/2022] Open
Abstract
We estimate the causal contributions of spatiotemporal changes in temperature (T) and precipitation (Pr) to changes in Earth’s atmospheric methane concentration (CCH4) and its isotope ratio δ13CH4 over the last four decades. We identify oscillations between positive and negative feedbacks, showing that both contribute to increasing CCH4. Interannually, increased emissions via positive feedbacks (e.g. wetland emissions and wildfires) with higher land surface air temperature (LSAT) are often followed by increasing CCH4 due to weakened methane sink via atmospheric •OH, via negative feedbacks with lowered sea surface temperatures (SST), especially in the tropics. Over decadal time scales, we find alternating rate-limiting factors for methane oxidation: when CCH4 is limiting, positive methane-climate feedback via direct oceanic emissions dominates; when •OH is limiting, negative feedback is favoured. Incorporating the interannually increasing CCH4 via negative feedbacks gives historical methane-climate feedback sensitivity ≈ 0.08 W m−2 °C−1, much higher than the IPCC AR6 estimate. Record-breaking rates of increasing atmospheric methane concentrations in 2020 and 2021 are alarming, but puzzling, in view of declining methane emissions from fossil fuel in 2020. The authors show that interannual variation of both positive and negative feedbacks contribute positively to the rising methane concentration.
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Wang J, Chu YX, Schäfer H, Tian G, He R. CS 2 increasing CH 4-derived carbon emissions and active microbial diversity in lake sediments. ENVIRONMENTAL RESEARCH 2022; 208:112678. [PMID: 34999031 DOI: 10.1016/j.envres.2022.112678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/24/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Lakes are important methane (CH4) sources to the atmosphere, especially eutrophic lakes with cyanobacterial blooms accompanied by volatile sulfur compound (VSC) emissions. CH4 oxidation is a key strategy to mitigate CH4 emission from lakes. In this study, we characterized the fate of CH4-derived carbon and active microbial communities in lake sediments with CS2 used as a typical VSC, based on the investigation of CH4 and VSC fluxes from Meiliang Bay in Lake Taihu. Stable isotope probing microcosm incubation showed that the efficiency of CH4-derived carbon incorporated into organic matter was 21.1% in the sediment with CS2 existence, which was lower than that without CS2 (27.3%). SO42--S was the main product of CS2 oxidation under aerobic condition, accounting for 59.3-62.7% of the input CS2-S. CS2 and CH4 coexistence led to a decrease of methanotroph and methylotroph abundances and stimulated the production of extracellular polymeric substances. CS2 and its metabolites including total sulfur, SO42- and acid volatile sulfur acted as the main drivers influencing the active microbial community structure in the sediments. Compared with α-proteobacteria methanotrophs, γ-proteobacteria methanotrophs Methylomicrobium, Methylomonas, Crenothrix and Methylosarcina were more dominant in the sediments. CH4-derived carbon mainly flowed into methylotrophs in the first stage. With CH4 consumption, more CH4-derived carbon flowed into non-methylotrophs. CS2 could prompt more CH4-derived carbon flowing into non-methanotrophs and non-methylotrophs, such as sulfur-metabolizing bacteria. These findings can help elucidate the influence of VSCs on microorganisms and provide insights to carbon fluxes from eutrophic lake systems.
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Affiliation(s)
- Jing Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Yi-Xuan Chu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Hendrik Schäfer
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Guangming Tian
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo He
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China.
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15
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Roldán DM, Carrizo D, Sánchez-García L, Menes RJ. Diversity and Effect of Increasing Temperature on the Activity of Methanotrophs in Sediments of Fildes Peninsula Freshwater Lakes, King George Island, Antarctica. Front Microbiol 2022; 13:822552. [PMID: 35369426 PMCID: PMC8969513 DOI: 10.3389/fmicb.2022.822552] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
Global warming has a strong impact on polar regions. Particularly, the Antarctic Peninsula and nearby islands have experienced a marked warming trend in the past 50 years. Therefore, higher methane (CH4) emissions from this area could be expected in the future. Since mitigation of these emissions can be carried out by microbial oxidation, understanding this biological process is crucial since to our knowledge, no related studies have been performed in this area before. In this work, the aerobic CH4 oxidation potential of five freshwater lake sediments of Fildes Peninsula (King George Island, South Shetland Islands) was determined with values from 0.07 to 10 μmol CH4 gdw–1 day–1 and revealed up to 100-fold increase in temperature gradients (5, 10, 15, and 20°C). The structure and diversity of the bacterial community in the sediments were analyzed by next-generation sequencing (Illumina MiSeq) of 16S rRNA and pmoA genes. A total of 4,836 ASVs were identified being Proteobacteria, Actinobacteriota, Acidobacteriota, and Bacteroidota the most abundant phyla. The analysis of the pmoA gene identified 200 ASVs of methanotrophs, being Methylobacter Clade 2 (Type I, family Methylococcaceae) the main responsible of the aerobic CH4 oxidation. Moreover, both approaches revealed the presence of methanotrophs of the classes Gammaproteobacteria (families Methylococcaceae and Crenotrichaceae), Alphaproteobacteria (family Methylocystaceae), Verrucomicrobia (family Methylacidiphilaceae), and the candidate phylum of anaerobic methanotrophs Methylomirabilota. In addition, bacterial phospholipid fatty acids (PLFA) biomarkers were studied as a proxy for aerobic methane-oxidizing bacteria and confirmed these results. Methanotrophic bacterial diversity was significantly correlated with pH. In conclusion, our findings suggest that aerobic methanotrophs could mitigate in situ CH4 emissions in a future scenario with higher temperatures in this climate-sensitive area. This study provides new insights into the diversity of methanotrophs, as well as the influence of temperature on the CH4 oxidation potential in sediments of freshwater lakes in polar regions of the southern hemisphere.
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Affiliation(s)
- Diego M. Roldán
- Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Microbiología, Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Daniel Carrizo
- Centro de Astrobiología, Consejo Superior de Investigaciones Científicas-Instituto Nacional de Técnica Aeroespacial (CSIC-INTA), Madrid, Spain
| | - Laura Sánchez-García
- Centro de Astrobiología, Consejo Superior de Investigaciones Científicas-Instituto Nacional de Técnica Aeroespacial (CSIC-INTA), Madrid, Spain
| | - Rodolfo Javier Menes
- Laboratorio de Ecología Microbiana Medioambiental, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Microbiología, Unidad Asociada del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- *Correspondence: Rodolfo Javier Menes,
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16
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Metabolic flexibility of aerobic methanotrophs under anoxic conditions in Arctic lake sediments. THE ISME JOURNAL 2022; 16:78-90. [PMID: 34244610 PMCID: PMC8692461 DOI: 10.1038/s41396-021-01049-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 06/19/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023]
Abstract
Methane (CH4) emissions from Arctic lakes are a large and growing source of greenhouse gas to the atmosphere with critical implications for global climate. Because Arctic lakes are ice covered for much of the year, understanding the metabolic flexibility of methanotrophs under anoxic conditions would aid in characterizing the mechanisms responsible for limiting CH4 emissions from high-latitude regions. Using sediments from an active CH4 seep in Lake Qalluuraq, Alaska, we conducted DNA-based stable isotope probing (SIP) in anoxic mesocosms and found that aerobic Gammaproteobacterial methanotrophs dominated in assimilating CH4. Aerobic methanotrophs were also detected down to 70 cm deep in sediments at the seep site, where anoxic conditions persist. Metagenomic analyses of the heavy DNA from 13CH4-SIP incubations showed that these aerobic methanotrophs had the capacity to generate intermediates such as methanol, formaldehyde, and formate from CH4 oxidation and to oxidize formaldehyde in the tetrahydromethanopterin (H4MPT)-dependent pathway under anoxic conditions. The high levels of Fe present in sediments, combined with Fe and CH4 profiles in the persistent CH4 seep site, suggested that oxidation of CH4, or, more specifically, its intermediates such as methanol and formaldehyde might be coupled to iron reduction. Aerobic methanotrophs also possessed genes associated with nitrogen and hydrogen metabolism, which might provide potentially alternative energy conservation options under anoxic conditions. These results expand the known metabolic spectrum of aerobic methanotrophs under anoxic conditions and necessitate the re-assessment of the mechanisms underlying CH4 oxidation in the Arctic, especially under lakes that experience extended O2 limitations during ice cover.
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17
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Microbial Succession under Freeze-Thaw Events and Its Potential for Hydrocarbon Degradation in Nutrient-Amended Antarctic Soil. Microorganisms 2021; 9:microorganisms9030609. [PMID: 33809442 PMCID: PMC8000410 DOI: 10.3390/microorganisms9030609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/24/2022] Open
Abstract
The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze–thaw cycle (FTC) alternating between −20 and 4 °C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.
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18
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Kallistova AY, Kadnikov VV, Savvichev AS, Rusanov II, Dvornikov YA, Leibman MO, Khomutov AV, Ravin NV, Pimenov NV. Comparative Study of Methanogenic Pathways in the Sediments of Thermokarst and Polygenetic Yamal Lakes. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721020065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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19
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Changes in planktonic and sediment bacterial communities under the highly regulated dam in the mid-part of the Three Gorges Reservoir. Appl Microbiol Biotechnol 2021; 105:839-852. [PMID: 33404832 DOI: 10.1007/s00253-020-11047-3] [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] [Received: 06/24/2020] [Revised: 10/21/2020] [Accepted: 12/09/2020] [Indexed: 10/22/2022]
Abstract
Bacterial communities play an important role in the biogeochemical cycle in reservoir ecosystems. However, the dynamic changes in both planktonic and sediment bacterial communities in a highly regulated dam reservoir remain unclear. This study investigated the temporal distribution patterns of bacterial communities in a transition section of the Three Gorges Reservoir (TGR) using Illumina MiSeq sequencing. Results suggested that in comparison to the planktonic bacteria, sediment bacteria contributed more to the reservoir microbial communities, accounting for 97% of the 7434 OTUs. The Shannon diversity index in the water (3.22~5.68) was generally lower than that in the sediment (6.72~7.56). In the high water level period (January and March), Proteobacteria, Actinobacteria, Cyanobacteria, and Firmicutes were the most abundant phyla, whereas in the low water level period (May, July, and September), the dominant phyla were Proteobacteria, Actinobacteria, and Bacteroidetes. Sediment samples were dominated by Proteobacteria, Chloroflexi, and Acidobacteria. Principal coordinate analysis of the bacterioplankton communities showed greater sensitivity to monthly changes than that of the sediment bacterial communities. Network analysis suggested that in comparison to planktonic bacterial communities, sediment bacterial communities were more complex and stable. The linear relationship between the CH4/CO2 ratio, water level, and relative abundance of methanotrophs highlighted the potential methane-oxidizing process in the mid-part of the TGR. Moreover, the potential impact of dam regulation on the bacterial communities was revealed by the significant relationship between abundant phyla and the inflow of the TGR. KEY POINTS: • Bacterioplankton communities showed great sensitivity to monthly changes. • Potential methane-oxidizing process was revealed in this representative area. • Water inflow regulated by dam has significant effects on dominant bacterioplankton.
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20
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In 't Zandt MH, Liebner S, Welte CU. Roles of Thermokarst Lakes in a Warming World. Trends Microbiol 2020; 28:769-779. [PMID: 32362540 DOI: 10.1016/j.tim.2020.04.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/10/2020] [Accepted: 04/01/2020] [Indexed: 11/27/2022]
Abstract
Permafrost covers a quarter of the northern hemisphere land surface and contains twice the amount of carbon that is currently present in the atmosphere. Future climate change is expected to reduce its near-surface cover by over 90% by the end of the 21st century, leading to thermokarst lake formation. Thermokarst lakes are point sources of carbon dioxide and methane which release long-term carbon stocks into the atmosphere, thereby initiating a positive climate feedback potentially contributing up to a 0.39°C rise of surface air temperatures by 2300. This review describes the potential role of thermokarst lakes in a warming world and the microbial mechanisms that underlie their contributions to the global greenhouse gas budget.
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Affiliation(s)
- Michiel H In 't Zandt
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands; Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS, Utrecht, the Netherlands
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Section 3.7 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; University of Potsdam, Institute of Biochemistry and Biology, 14469 Potsdam, Germany
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands; Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
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21
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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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22
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Kallistova AY, Savvichev AS, Rusanov II, Pimenov NV. Thermokarst Lakes, Ecosystems with Intense Microbial Processes of the Methane Cycle. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261719060043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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23
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Reis PCJ, Thottathil SD, Ruiz-González C, Prairie YT. Niche separation within aerobic methanotrophic bacteria across lakes and its link to methane oxidation rates. Environ Microbiol 2019; 22:738-751. [PMID: 31769176 DOI: 10.1111/1462-2920.14877] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/23/2019] [Accepted: 11/22/2019] [Indexed: 11/30/2022]
Abstract
Lake methane (CH4 ) emissions are largely controlled by aerobic methane-oxidizing bacteria (MOB) which mostly belong to the classes Alpha- and Gammaproteobacteria (Alpha- and Gamma-MOB). Despite the known metabolic and ecological differences between the two MOB groups, their main environmental drivers and their relative contribution to CH4 oxidation rates across lakes remain unknown. Here, we quantified the two MOB groups through CARD-FISH along the water column of six temperate lakes and during incubations in which we measured ambient CH4 oxidation rates. We found a clear niche separation of Alpha- and Gamma-MOB across lake water columns, which is mostly driven by oxygen concentration. Gamma-MOB appears to dominate methanotrophy throughout the water column, but Alpha-MOB may also be an important player particularly in well-oxygenated bottom waters. The inclusion of Gamma-MOB cell abundance improved environmental models of CH4 oxidation rate, explaining part of the variation that could not be explained by environmental factors alone. Altogether, our results show that MOB composition is linked to CH4 oxidation rates in lakes and that information on the MOB community can help predict CH4 oxidation rates and thus emissions from lakes.
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Affiliation(s)
- Paula C J Reis
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
| | - Shoji D Thottathil
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
| | - Clara Ruiz-González
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), Barcelona, E-08003, Spain
| | - Yves T Prairie
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
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24
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Seto M, Noguchi K, Cappellen PV. Potential for Aerobic Methanotrophic Metabolism on Mars. ASTROBIOLOGY 2019; 19:1187-1195. [PMID: 31173512 PMCID: PMC6785171 DOI: 10.1089/ast.2018.1943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 05/07/2019] [Indexed: 06/09/2023]
Abstract
Observational evidence supports the presence of methane (CH4) in the martian atmosphere on the order of parts per billion by volume (ppbv). Here, we assess whether aerobic methanotrophy is a potentially viable metabolism in the martian upper regolith, by calculating metabolic energy gain rates under assumed conditions of martian surface temperature, pressure, and atmospheric composition. Using kinetic parameters for 19 terrestrial aerobic methanotrophic strains, we show that even under the imposed low temperature and pressure extremes (180-280 K and 6-11 hPa), methane oxidation by oxygen (O2) should in principle be able to generate the minimum energy production rate required to support endogenous metabolism (i.e., cellular maintenance). Our results further indicate that the corresponding metabolic activity would be extremely low, with cell doubling times in excess of 4000 Earth years at the present-day ppbv-level CH4 mixing ratios in the atmosphere of Mars. Thus, while aerobic methanotrophic microorganisms similar to those found on Earth could theoretically maintain their vital functions, they are unlikely to constitute prolific members of hypothetical martian soil communities.
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Affiliation(s)
- Mayumi Seto
- Department of Chemistry, Biology, and Environmental Sciences, Faculty of Science, Nara Women's University, Nara, Japan
| | - Katsuyuki Noguchi
- Department of Chemistry, Biology, and Environmental Sciences, Faculty of Science, Nara Women's University, Nara, Japan
| | - Philippe Van Cappellen
- Ecohydrology Research Group, Department of Earth and Environmental Sciences, Water Institute, University of Waterloo, Waterloo, Canada
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25
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Reddy KR, Rai RK, Green SJ, Chetri JK. Effect of temperature on methane oxidation and community composition in landfill cover soil. J Ind Microbiol Biotechnol 2019; 46:1283-1295. [PMID: 31317292 DOI: 10.1061/(asce)ee.1943-7870.0001712] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/11/2019] [Indexed: 05/26/2023]
Abstract
Municipal solid waste (MSW) landfills are the third largest anthropogenic source of methane (CH4) emissions in the United States. The majority of CH4 generated in landfills is converted to carbon dioxide (CO2) by CH4-oxidizing bacteria (MOB) present in the landfill cover soil, whose activity is controlled by various environmental factors including temperature. As landfill temperature can fluctuate substantially seasonally, rates of CH4 oxidation can also vary, and this could lead to incomplete oxidation. This study aims at analyzing the effect of temperature on CH4 oxidation potential and microbial community structure of methanotrophs in laboratory-based studies of landfill cover soil and cultivated consortia. Soil and enrichment cultures were incubated at temperatures ranging from 6 to 70 °C, and rates of CH4 oxidation were measured, and the microbial community structure was analyzed using 16S rRNA gene amplicon sequencing and shotgun metagenome sequencing. CH4 oxidation occurred at temperatures from 6 to 50 °C in soil microcosm tests, and 6-40 °C in enrichment culture batch tests; maximum rates of oxidation were obtained at 30 °C. A corresponding shift in the soil microbiota was observed, with a transition from putative psychrophilic to thermophilic methanotrophs with increasing incubation temperature. A strong shift in methanotrophic community structure was observed above 30 °C. At temperatures up to 30 °C, methanotrophs from the genus Methylobacter were dominant in soils and enrichment cultures; at a temperature of 40 °C, putative thermophilic methanotrophs from the genus Methylocaldum become dominant. Maximum rate measurements of nearly 195 μg CH4 g-1 day-1 were observed in soil incubations, while observed maximum rates in enrichments were significantly lower, likely as a result of diffusion limitations. This study demonstrates that temperature is a critical factor affecting rates of landfill soil CH4 oxidation in vitro and that changing rates of CH4 oxidation are in part driven by changes in methylotroph community structure.
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Affiliation(s)
- Krishna R Reddy
- Department of Civil and Materials Engineering, University of Illinois at Chicago, 842 West Taylor Street, Chicago, IL, 60607, USA.
| | - Raksha K Rai
- Department of Civil and Materials Engineering, University of Illinois at Chicago, 842 West Taylor Street, Chicago, IL, 60607, USA
| | - Stefan J Green
- Department of Biological Sciences, Sequencing Core, Resources Center, University of Illinois at Chicago, 835 S. Wolcott, Chicago, IL, 60612, USA
| | - Jyoti K Chetri
- Department of Civil and Materials Engineering, University of Illinois at Chicago, 842 West Taylor Street, Chicago, IL, 60607, USA
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26
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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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27
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Zakharenko AS, Galachyants YP, Morozov IV, Shubenkova OV, Morozov AA, Ivanov VG, Pimenov NV, Krasnopeev AY, Zemskaya TI. Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal. MICROBIAL ECOLOGY 2019; 78:269-285. [PMID: 30483839 DOI: 10.1007/s00248-018-1299-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
We have assessed the diversity of bacteria near oil-methane (area I) and methane (area II) seeps in the pelagic zone of Lake Baikal using massive parallel sequencing of 16S rRNA, pmoA, and mxaF gene fragments amplified from total DNA. At depths from the surface to 100 m, sequences belonging to Cyanobacteria dominated. In the communities to a depth of 200 m of the studied areas, Proteobacteria dominated the deeper layers of the water column. Alphaproteobacteria sequences were predominant in the community near the oil-methane seep, while the community near the methane seep was characterized by the prevalence of Alpha- and Gammaproteobacteria. Among representatives of these classes, type I methanotrophs prevailed in the 16S rRNA gene libraries from the near-bottom area, and type II methanotrophs were detected in minor quantities at different depths. In the analysis of the libraries of the pmoA and mxaF functional genes, we observed the different taxonomic composition of methanotrophic bacteria in the surface and deep layers of the water column. All pmoA sequences from area I were type II methanotrophs and were detected at a depth of 300 m, while sequences of type I methanotrophs were the most abundant in deep layers of the water column of area II. All mxaF gene sequences belonged to Methylobacterium representatives. Based on comparative analyses of 16S rRNA, pmoA, and mxaF gene fragment libraries, we suggest that there must be a wider spectrum of functional genes facilitating methane oxidation that were not detected with the primers used.
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Affiliation(s)
- Aleksandra S Zakharenko
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia.
| | - Yuriy P Galachyants
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Igor V Morozov
- Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Olga V Shubenkova
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Alexey A Morozov
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Vyacheslav G Ivanov
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Nikolay V Pimenov
- Research Center of Biotechnology, Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Andrey Y Krasnopeev
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Tamara I Zemskaya
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
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28
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A Quick-Look Method for Initial Evaluation of Gas Hydrate Stability below Subaqueous Permafrost. GEOSCIENCES 2019. [DOI: 10.3390/geosciences9080329] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Many studies demonstrated the coexistence of subaqueous permafrost and gas hydrate. Subaqueous permafrost could be a factor affecting the formation/dissociation of gas hydrate. Here, we propose a simple empirical approach that allows estimating the steady-state conditions for gas hydrate stability in the presence of subaqueous permafrost. This approach was derived for pressure, temperature, and salinity conditions typical of subaqueous permafrost in marine (brine) and lacustrine (freshwater) environments.
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29
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Reddy KR, Rai RK, Green SJ, Chetri JK. Effect of temperature on methane oxidation and community composition in landfill cover soil. J Ind Microbiol Biotechnol 2019; 46:1283-1295. [PMID: 31317292 DOI: 10.1007/s10295-019-02217-y] [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: 02/27/2019] [Accepted: 07/11/2019] [Indexed: 11/30/2022]
Abstract
Municipal solid waste (MSW) landfills are the third largest anthropogenic source of methane (CH4) emissions in the United States. The majority of CH4 generated in landfills is converted to carbon dioxide (CO2) by CH4-oxidizing bacteria (MOB) present in the landfill cover soil, whose activity is controlled by various environmental factors including temperature. As landfill temperature can fluctuate substantially seasonally, rates of CH4 oxidation can also vary, and this could lead to incomplete oxidation. This study aims at analyzing the effect of temperature on CH4 oxidation potential and microbial community structure of methanotrophs in laboratory-based studies of landfill cover soil and cultivated consortia. Soil and enrichment cultures were incubated at temperatures ranging from 6 to 70 °C, and rates of CH4 oxidation were measured, and the microbial community structure was analyzed using 16S rRNA gene amplicon sequencing and shotgun metagenome sequencing. CH4 oxidation occurred at temperatures from 6 to 50 °C in soil microcosm tests, and 6-40 °C in enrichment culture batch tests; maximum rates of oxidation were obtained at 30 °C. A corresponding shift in the soil microbiota was observed, with a transition from putative psychrophilic to thermophilic methanotrophs with increasing incubation temperature. A strong shift in methanotrophic community structure was observed above 30 °C. At temperatures up to 30 °C, methanotrophs from the genus Methylobacter were dominant in soils and enrichment cultures; at a temperature of 40 °C, putative thermophilic methanotrophs from the genus Methylocaldum become dominant. Maximum rate measurements of nearly 195 μg CH4 g-1 day-1 were observed in soil incubations, while observed maximum rates in enrichments were significantly lower, likely as a result of diffusion limitations. This study demonstrates that temperature is a critical factor affecting rates of landfill soil CH4 oxidation in vitro and that changing rates of CH4 oxidation are in part driven by changes in methylotroph community structure.
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Affiliation(s)
- Krishna R Reddy
- Department of Civil and Materials Engineering, University of Illinois at Chicago, 842 West Taylor Street, Chicago, IL, 60607, USA.
| | - Raksha K Rai
- Department of Civil and Materials Engineering, University of Illinois at Chicago, 842 West Taylor Street, Chicago, IL, 60607, USA
| | - Stefan J Green
- Department of Biological Sciences, Sequencing Core, Resources Center, University of Illinois at Chicago, 835 S. Wolcott, Chicago, IL, 60612, USA
| | - Jyoti K Chetri
- Department of Civil and Materials Engineering, University of Illinois at Chicago, 842 West Taylor Street, Chicago, IL, 60607, USA
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30
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Lew S, Glińska-Lewczuk K. Environmental controls on the abundance of methanotrophs and methanogens in peat bog lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:1201-1211. [PMID: 30248845 DOI: 10.1016/j.scitotenv.2018.07.141] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/11/2018] [Accepted: 07/11/2018] [Indexed: 06/08/2023]
Abstract
The aim of the present study was to identify the factors that influence the composition of methanogens and methanotrophs in the background prokaryotic community in peat bog lakes. We hypothesized that the microbial composition is a function of the physicochemical conditions of the water and a function of depth-dependent oxygen (DO) concentrations. To address this aim, we collected water samples from subsurface and near-bottom layers, representing oxic and anoxic conditions in 4 peat bog lakes in NE Poland. The structure of methanogenic Archaea and methane-oxidizing bacteria (MOB) was determined with double labeled-fluorescence in situ hybridization (DOPE-FISH). The results showed significant differences in Procaryota communities between the oxic (subsurface) and suboxic/anoxic (near-bottom) layers in peat bog lakes (t-test, p < 0.05). The methanogens from the Archaea domain were observed in anoxic periods, while methanotrophs were present regardless of water depth and season. The abundance of methanogens was inversely correlated with DO and CO2. Methanotrophs adapted better to the changing habitat conditions. The nonmetrical multidimensional scaling (NMS) and partial least square regression (PLS-R) models showed that the methanotrophs in subsurface layers are positively associated with temperature, DOC, and TON while negatively associated with pH. The DO availability is not a prerequisite condition for the presence of methanothrophs. The most important factors for MOB at the bottom were CO2 and TON. Due to a significant role of methanotrophs in the control of the methane emission flux rates, there is a need for further research on factors responsible for methanotroph development in peat bog lakes.
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Affiliation(s)
- Sylwia Lew
- University of Warmia and Mazury in Olsztyn, Department of Microbiology and Mycology, Oczapowskiego str. 1a, 10-719 Olsztyn, Poland.
| | - Katarzyna Glińska-Lewczuk
- University of Warmia and Mazury in Olsztyn, Department of Water Resources, Climatology and Environmental Management, Plac Łódzki 2, 10-719 Olsztyn, Poland.
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31
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de Jong AEE, In 't Zandt MH, Meisel OH, Jetten MSM, Dean JF, Rasigraf O, Welte CU. Increases in temperature and nutrient availability positively affect methane-cycling microorganisms in Arctic thermokarst lake sediments. Environ Microbiol 2018; 20:4314-4327. [PMID: 29968310 PMCID: PMC6334529 DOI: 10.1111/1462-2920.14345] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/27/2018] [Accepted: 06/27/2018] [Indexed: 11/30/2022]
Abstract
Arctic permafrost soils store large amounts of organic matter that is sensitive to temperature increases and subsequent microbial degradation to methane (CH4) and carbon dioxide (CO2). Here, we studied methanogenic and methanotrophic activity and community composition in thermokarst lake sediments from Utqiag˙vik (formerly Barrow), Alaska. This experiment was carried out under in situ temperature conditions (4°C) and the IPCC 2013 Arctic climate change scenario (10°C) after addition of methanogenic and methanotrophic substrates for nearly a year. Trimethylamine (TMA) amendment with warming showed highest maximum CH4production rates, being 30% higher at 10°C than at 4°C. Maximum methanotrophic rates increased by up to 57% at 10°C compared to 4°C. 16S rRNA gene sequencing indicated high relative abundance of Methanosarcinaceae in TMA amended incubations, and for methanotrophic incubations Methylococcaeae were highly enriched. Anaerobic methanotrophic activity with nitrite or nitrate as electron acceptor was not detected. This study indicates that the methane cycling microbial community can adapt to temperature increases and that their activity is highly dependent on substrate availability.
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Affiliation(s)
- Anniek E E de Jong
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Michiel H In 't Zandt
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Ove H Meisel
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands.,Department of Earth Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Joshua F Dean
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands.,Department of Earth Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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32
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Variation in Soil Methane Fluxes and Comparison between Two Forests in China. FORESTS 2018. [DOI: 10.3390/f9040204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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33
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Crevecoeur S, Vincent WF, Comte J, Matveev A, Lovejoy C. Diversity and potential activity of methanotrophs in high methane-emitting permafrost thaw ponds. PLoS One 2017; 12:e0188223. [PMID: 29182670 PMCID: PMC5705078 DOI: 10.1371/journal.pone.0188223] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 11/02/2017] [Indexed: 11/27/2022] Open
Abstract
Lakes and ponds derived from thawing permafrost are strong emitters of carbon dioxide and methane to the atmosphere, but little is known about the methane oxidation processes in these waters. Here we investigated the distribution and potential activity of aerobic methanotrophic bacteria in thaw ponds in two types of eroding permafrost landscapes in subarctic Québec: peatlands and mineral soils. We hypothesized that methanotrophic community composition and potential activity differ regionally as a function of the landscape type and permafrost degradation stage, and locally as a function of depth-dependent oxygen conditions. Our analysis of pmoA transcripts by Illumina amplicon sequencing and quantitative PCR showed that the communities were composed of diverse and potentially active lineages. Type I methanotrophs, particularly Methylobacter, dominated all communities, however there was a clear taxonomic separation between the two landscape types, consistent with environmental control of community structure. In contrast, methanotrophic potential activity, measured by pmoA transcript concentrations, did not vary with landscape type, but correlated with conductivity, phosphorus and total suspended solids. Methanotrophic potential activity was also detected in low-oxygen bottom waters, where it was inversely correlated with methane concentrations, suggesting methane depletion by methanotrophs. Methanotrophs were present and potentially active throughout the water column regardless of oxygen concentration, and may therefore be resilient to future mixing and oxygenation regimes in the warming subarctic.
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Affiliation(s)
- Sophie Crevecoeur
- Département de Biologie, Centre d’études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
- * E-mail:
| | - Warwick F. Vincent
- Département de Biologie, Centre d’études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, Québec, Canada
| | - Jérôme Comte
- Département de Biologie, Centre d’études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Alex Matveev
- Département de Biologie, Centre d’études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, Québec, Canada
| | - Connie Lovejoy
- Département de Biologie, Centre d’études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
- Québec-Océan, Université Laval, Québec, Québec, Canada
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34
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Stackhouse B, Lau MCY, Vishnivetskaya T, Burton N, Wang R, Southworth A, Whyte L, Onstott TC. Atmospheric CH 4 oxidation by Arctic permafrost and mineral cryosols as a function of water saturation and temperature. GEOBIOLOGY 2017; 15:94-111. [PMID: 27474434 DOI: 10.1111/gbi.12193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 05/09/2016] [Indexed: 06/06/2023]
Abstract
The response of methanotrophic bacteria capable of oxidizing atmospheric CH4 to climate warming is poorly understood, especially for those present in Arctic mineral cryosols. The atmospheric CH4 oxidation rates were measured in microcosms incubated at 4 °C and 10 °C along a 1-m depth profile and over a range of water saturation conditions for mineral cryosols containing type I and type II methanotrophs from Axel Heiberg Island (AHI), Nunavut, Canada. The cryosols exhibited net consumption of ~2 ppmv CH4 under all conditions, including during anaerobic incubations. Methane oxidation rates increased with temperature and decreased with increasing water saturation and depth, exhibiting the highest rates at 10 °C and 33% saturation at 5 cm depth (260 ± 60 pmol CH4 gdw-1 d-1 ). Extrapolation of the CH4 oxidation rates to the field yields net CH4 uptake fluxes ranging from 11 to 73 μmol CH4 m-2 d-1 , which are comparable to field measurements. Stable isotope mass balance indicates ~50% of the oxidized CH4 is incorporated into the biomass regardless of temperature or saturation. Future atmospheric CH4 uptake rates at AHI with increasing temperatures will be determined by the interplay of increasing CH4 oxidation rates vs. water saturation and the depth to the water table during summer thaw.
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Affiliation(s)
- B Stackhouse
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - M C Y Lau
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - T Vishnivetskaya
- The Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
| | - N Burton
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - R Wang
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - A Southworth
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - L Whyte
- Department of Natural Resource Sciences, McGill University, Montreal, QC, Canada
| | - T C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, USA
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Ho A, Angel R, Veraart AJ, Daebeler A, Jia Z, Kim SY, Kerckhof FM, Boon N, Bodelier PLE. Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System. Front Microbiol 2016; 7:1285. [PMID: 27602021 PMCID: PMC4993757 DOI: 10.3389/fmicb.2016.01285] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/04/2016] [Indexed: 11/13/2022] Open
Abstract
Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes.
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Affiliation(s)
- Adrian Ho
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Roey Angel
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna Vienna, Austria
| | - Annelies J Veraart
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Anne Daebeler
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna Vienna, Austria
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
| | - Sang Yoon Kim
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Frederiek-Maarten Kerckhof
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University Ghent, Belgium
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
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Denikina NN, Dzyuba EV, Bel’kova NL, Khanaev IV, Feranchuk SI, Makarov MM, Granin NG, Belikov SI. The first case of disease of the sponge Lubomirskia baicalensis: Investigation of its microbiome. BIOL BULL+ 2016; 43:263-270. [DOI: 10.1134/s106235901603002x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2024]
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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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Leewis MC, Uhlik O, Leigh MB. Synergistic Processing of Biphenyl and Benzoate: Carbon Flow Through the Bacterial Community in Polychlorinated-Biphenyl-Contaminated Soil. Sci Rep 2016; 6:22145. [PMID: 26915282 PMCID: PMC4768254 DOI: 10.1038/srep22145] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/08/2016] [Indexed: 11/18/2022] Open
Abstract
Aerobic mineralization of PCBs, which are toxic and persistent organic pollutants, involves the upper (biphenyl, BP) and lower (benzoate, BZ) degradation pathways. The activity of different members of the soil microbial community in performing one or both pathways, and their synergistic interactions during PCB biodegradation, are not well understood. This study investigates BP and BZ biodegradation and subsequent carbon flow through the microbial community in PCB-contaminated soil. DNA stable isotope probing (SIP) was used to identify the bacterial guilds involved in utilizing 13C-biphenyl (unchlorinated analogue of PCBs) and/or 13C-benzoate (product/intermediate of BP degradation and analogue of chlorobenzoates). By performing SIP with two substrates in parallel, we reveal microbes performing the upper (BP) and/or lower (BZ) degradation pathways, and heterotrophic bacteria involved indirectly in processing carbon derived from these substrates (i.e. through crossfeeding). Substrate mineralization rates and shifts in relative abundance of labeled taxa suggest that BP and BZ biotransformations were performed by microorganisms with different growth strategies: BZ-associated bacteria were fast growing, potentially copiotrophic organisms, while microbes that transform BP were oligotrophic, slower growing, organisms. Our findings provide novel insight into the functional interactions of soil bacteria active in processing biphenyl and related aromatic compounds in soil, revealing how carbon flows through a bacterial community.
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Affiliation(s)
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czech Republic
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
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Gugliandolo C, Michaud L, Lo Giudice A, Lentini V, Rochera C, Camacho A, Maugeri TL. Prokaryotic Community in Lacustrine Sediments of Byers Peninsula (Livingston Island, Maritime Antarctica). MICROBIAL ECOLOGY 2016; 71:387-400. [PMID: 26337826 DOI: 10.1007/s00248-015-0666-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/18/2015] [Indexed: 06/05/2023]
Abstract
Byers Peninsula (Livingston Island, Antarctica), the largest seasonally ice-free region of the Maritime Antarctica, holds a large number of lakes, ponds, and streams. The prokaryotic structure and bacterial diversity in sediment samples collected during the 2008-2009 austral summer from five inland lakes, two coastal lakes, and an estuarine site were analyzed by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) and 16S rRNA 454 tag pyrosequencing techniques, respectively. Differently from inland lakes, which range around the oligotrophic status, coastal lakes are eutrophic environments, enriched by nutrient inputs from marine animals. Although the prokaryotic abundances (estimated as DAPI stained cells) in sediment samples were quite similar among inland and coastal lakes, Bacteria always far dominated over Archaea. Despite the phylogenetic analysis indicated that most of sequences were affiliated to a few taxonomic groups, mainly referred to Proteobacteria, Bacteroidetes, and Actinobacteria, their relative abundances greatly differed from each site. Differences in bacterial composition showed that lacustrine sediments were more phyla rich than the estuarine sediment. Proteobacterial classes in lacustrine samples were dominated by Betaproteobacteria (followed by Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria), while in the estuarine sample, they were mainly related to Gammaproteobacteria (followed by Deltaproteobacteria, Epsilonproteobacteria, Alphaproteobacteria, and Betaproteobacteria). Higher number of sequences of Alphaproteobacteria, Cyanobacteria, Verrucomicrobia, and Planctomycetes were observed in sediments of inland lakes compared to those of coastal lakes, whereas Chloroflexi were relatively more abundant in the sediments of coastal eutrophic lakes. As demonstrated by the great number of dominant bacterial genera, bacterial diversity was higher in the sediments of inland lakes than that in coastal lakes. Ilumatobacter (Actinobacteria), Gp16 (Acidobacteria), and Gemmatimonas (Gemmatimonadetes) were recovered as dominant genera in both inland and coastal lakes, but not in the estuarine sample, indicating that they may be useful markers of Antarctic lakes. The proximity to the sea, the different lake depths and the external or internal origin of the nutrient sources shape the bacterial communities composition in lacustrine sediments of Byers Peninsula.
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Affiliation(s)
- Concetta Gugliandolo
- Research Centre for Extreme Environments and Extremophiles, Department of Biological and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres 31, 98166, Messina, Italy.
| | - Luigi Michaud
- Research Centre for Extreme Environments and Extremophiles, Department of Biological and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Angelina Lo Giudice
- Research Centre for Extreme Environments and Extremophiles, Department of Biological and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres 31, 98166, Messina, Italy
- Institute for Coastal Marine Environment, National Research Council (IAMC-CNR), Spianata San Raineri 86, 98122, Messina, Italy
| | - Valeria Lentini
- Research Centre for Extreme Environments and Extremophiles, Department of Biological and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Carlos Rochera
- Cavanilles Institute for Biodiversity and Evolutionary Biology and Department of Microbiology and Ecology, Campus de Burjassot, University of Valencia, E-46100, Burjassot, Spain
| | - Antonio Camacho
- Cavanilles Institute for Biodiversity and Evolutionary Biology and Department of Microbiology and Ecology, Campus de Burjassot, University of Valencia, E-46100, Burjassot, Spain
| | - Teresa Luciana Maugeri
- Research Centre for Extreme Environments and Extremophiles, Department of Biological and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres 31, 98166, Messina, Italy
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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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Aerobic and nitrite-dependent methane-oxidizing microorganisms in sediments of freshwater lakes on the Yunnan Plateau. Appl Microbiol Biotechnol 2014; 99:2371-81. [PMID: 25698510 DOI: 10.1007/s00253-014-6141-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 09/24/2014] [Accepted: 10/06/2014] [Indexed: 10/24/2022]
Abstract
Both aerobic methane-oxidizing bacteria (MOB) and nitrite-dependent anaerobic methane oxidation (n-damo) bacteria can play an important role in mitigating the methane emission produced in anoxic sediment layers to the atmosphere. However, the environmental factors regulating the distribution of these methane-oxidizing microorganisms in lacustrine ecosystems remain essentially unclear. The present study investigated the distribution of aerobic MOB and n-damo bacteria in sediments of various freshwater lakes on the Yunnan Plateau (China). Quantitative PCR assay and clone library analysis illustrated the spatial variations in the abundances and structures of aerobic MOB and n-damo bacterial communities. Type I MOB (Methylosoma and Methylobacter) and type II MOB (Methylocystis) were detected, while type I MOB was more abundant than type II MOB. Lake sediments n-damo bacterial communities were composed of novel Methylomirabilis oxyfera-like pmoA genes. Lake sediments in the same geographic region could share a relatively similar aerobic MOB community structure. Moreover, Pearson's correlation analysis indicated that n-damo pmoA gene diversity showed a positive correlation with the ratio of organic matter to total nitrogen in lake sediment.
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42
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Chen R, Wang Y, Wei S, Wang W, Lin X. Windrow composting mitigated CH4emissions: characterization of methanogenic and methanotrophic communities in manure management. FEMS Microbiol Ecol 2014; 90:575-86. [DOI: 10.1111/1574-6941.12417] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/11/2014] [Accepted: 08/13/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ruirui Chen
- State Key Laboratory of Soil and Sustainable Agriculture; Institute of Soil Science; Chinese Academy of Sciences; Nanjing China
| | - Yiming Wang
- State Key Laboratory of Soil and Sustainable Agriculture; Institute of Soil Science; Chinese Academy of Sciences; Nanjing China
| | - Shiping Wei
- State Key Laboratory of Soil and Sustainable Agriculture; Institute of Soil Science; Chinese Academy of Sciences; Nanjing China
| | - Wei Wang
- State Key Laboratory of Soil and Sustainable Agriculture; Institute of Soil Science; Chinese Academy of Sciences; Nanjing China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture; Institute of Soil Science; Chinese Academy of Sciences; Nanjing China
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Yun J, Ju Y, Deng Y, Zhang H. Bacterial community structure in two permafrost wetlands on the Tibetan Plateau and Sanjiang Plain, China. MICROBIAL ECOLOGY 2014; 68:360-369. [PMID: 24718907 DOI: 10.1007/s00248-014-0415-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/31/2014] [Indexed: 06/03/2023]
Abstract
Permafrost wetlands are important methane emission sources and fragile ecosystems sensitive to climate change. Presently, there remains a lack of knowledge regarding bacterial communities, especially methanotrophs in vast areas of permafrost on the Tibetan Plateau in Northwest China and the Sanjiang Plain (SJ) in Northeast China. In this study, 16S rRNA-based quantitative PCR (qPCR) and 454 pyrosequencing were used to identify bacterial communities in soils sampled from a littoral wetland of Lake Namco on the Tibetan Plateau (NMC) and an alluvial wetland on the SJ. Additionally, methanotroph-specific primers targeting particulate methane monooxygenase subunit A gene (pmoA) were used for qPCR and pyrosequencing analysis of methanotrophic community structure in NMC soils. qPCR analysis revealed the presence of 10(10) 16S rRNA gene copies per gram of wet soil in both wetlands, with 10(8) pmoA copies per gram of wet soil in NMC. The two permafrost wetlands showed similar bacterial community compositions, which differed from those reported in other cold environments. Proteobacteria, Actinobacteria , and Chloroflexi were the most abundant phyla in both wetlands, whereas Acidobacteria was prevalent in the acidic wetland SJ only. These four phyla constituted more than 80 % of total bacterial community diversity in permafrost wetland soils, and Methylobacter of type I methanotrophs was overwhelmingly dominant in NMC soils. This study is the first major bacterial sequencing effort of permafrost in the NMC and SJ wetlands, which provides fundamental data for further studies of microbial function in extreme ecosystems under climate change scenarios.
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Affiliation(s)
- Juanli Yun
- College of Resources and Environment, University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
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Su Y, Zhang X, Xia FF, Zhang QQ, Kong JY, Wang J, He R. Diversity and activity of methanotrophs in landfill cover soils with and without landfill gas recovery systems. Syst Appl Microbiol 2014; 37:200-7. [DOI: 10.1016/j.syapm.2013.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/17/2013] [Accepted: 10/21/2013] [Indexed: 11/15/2022]
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Osman OA, Gudasz C, Bertilsson S. Diversity and abundance of aromatic catabolic genes in lake sediments in response to temperature change. FEMS Microbiol Ecol 2014; 88:468-81. [PMID: 24597511 DOI: 10.1111/1574-6941.12312] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 02/15/2014] [Accepted: 02/24/2014] [Indexed: 11/29/2022] Open
Abstract
The abundance and composition of genes involved in the catabolism of aromatic compounds provide important information on the biodegradation potential of organic pollutants and naturally occurring compounds in the environment. We studied catechol 2, 3 dioxygenase (C23O) and benzylsuccinate synthase (bssA) genes coding for key enzymes of aerobic and anaerobic degradation of aromatic compounds in experimental incubations with sediments from two contrasting lakes; humic lake Svarttjärn and eutrophic Vallentunasjön, respectively. Sediment cores from both lakes were incubated continuously for 5 months at constant temperatures ranging from 1.0 to 21.0 °C. The difference in C23O gene composition of the sediment analyzed at the end of the experiment was larger between lakes, than among temperature treatments within each lake. The abundance of C23O gene copies and measured respiration was positively correlated with temperature in Vallentunasjön, whereas putative C23O genes were present in lower concentrations in Svarttjärn sediments. Putative bssA genes were only detected in Svarttjärn. For both lakes, the two catabolic genes were most abundant in the surface sediment. The results emphasize the important role of temperature and nutrient availability in controlling the functional potential of sediment microorganisms and reveal differences between systems with contrasting trophic status. A better understanding of catabolic pathways and enzymes will enable more accurate forecasting of the functional properties of ecosystems under various scenarios of environmental change.
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Affiliation(s)
- Omneya A Osman
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Bacterial genome replication at subzero temperatures in permafrost. ISME JOURNAL 2013; 8:139-49. [PMID: 23985750 DOI: 10.1038/ismej.2013.140] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 06/21/2013] [Accepted: 07/10/2013] [Indexed: 11/08/2022]
Abstract
Microbial metabolic activity occurs at subzero temperatures in permafrost, an environment representing ∼25% of the global soil organic matter. Although much of the observed subzero microbial activity may be due to basal metabolism or macromolecular repair, there is also ample evidence for cellular growth. Unfortunately, most metabolic measurements or culture-based laboratory experiments cannot elucidate the specific microorganisms responsible for metabolic activities in native permafrost, nor, can bulk approaches determine whether different members of the microbial community modulate their responses as a function of changing subzero temperatures. Here, we report on the use of stable isotope probing with (13)C-acetate to demonstrate bacterial genome replication in Alaskan permafrost at temperatures of 0 to -20 °C. We found that the majority (80%) of operational taxonomic units detected in permafrost microcosms were active and could synthesize (13)C-labeled DNA when supplemented with (13)C-acetate at temperatures of 0 to -20 °C during a 6-month incubation. The data indicated that some members of the bacterial community were active across all of the experimental temperatures, whereas many others only synthesized DNA within a narrow subzero temperature range. Phylogenetic analysis of (13)C-labeled 16S rRNA genes revealed that the subzero active bacteria were members of the Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes and Proteobacteria phyla and were distantly related to currently cultivated psychrophiles. These results imply that small subzero temperature changes may lead to changes in the active microbial community, which could have consequences for biogeochemical cycling in permanently frozen systems.
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Evidence of microbial regulation of biogeochemical cycles from a study on methane flux and land use change. Appl Environ Microbiol 2013; 79:4031-40. [PMID: 23624469 DOI: 10.1128/aem.00095-13] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbes play an essential role in ecosystem functions, including carrying out biogeochemical cycles, but are currently considered a black box in predictive models and all global biodiversity debates. This is due to (i) perceived temporal and spatial variations in microbial communities and (ii) lack of ecological theory explaining how microbes regulate ecosystem functions. Providing evidence of the microbial regulation of biogeochemical cycles is key for predicting ecosystem functions, including greenhouse gas fluxes, under current and future climate scenarios. Using functional measures, stable-isotope probing, and molecular methods, we show that microbial (community diversity and function) response to land use change is stable over time. We investigated the change in net methane flux and associated microbial communities due to afforestation of bog, grassland, and moorland. Afforestation resulted in the stable and consistent enhancement in sink of atmospheric methane at all sites. This change in function was linked to a niche-specific separation of microbial communities (methanotrophs). The results suggest that ecological theories developed for macroecology may explain the microbial regulation of the methane cycle. Our findings provide support for the explicit consideration of microbial data in ecosystem/climate models to improve predictions of biogeochemical cycles.
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