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Yang WT, Wang WQ, Shen LD, Bai YN, Liu X, Tian MH, Wang C, Feng YF, Liu Y, Yang YL, Liu JQ, Geng CY. Potential role of nitrite-dependent anaerobic methane oxidation in methane consumption and nitrogen removal in Chinese paddy fields. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156534. [PMID: 35679939 DOI: 10.1016/j.scitotenv.2022.156534] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/20/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Nitrite-dependent anaerobic methane oxidation (n-damo), catalyzed by bacteria closely related to Candidatus Methylomirabilis oxyfera, links the global carbon and nitrogen cycles. Currently, the contribution of n-damo in controlling methane emissions and nitrogen removal, and the key regulatory factors of this process in Chinese paddy fields are poorly known. Here, soil samples from 20 paddy fields located in different climate zones across China were collected to examine the n-damo activity and bacterial communities. The n-damo activity and bacterial abundance varied from 1.05 to 5.97 nmol CH4 g-1 (dry soil) d-1 and 2.59 × 105 to 2.50 × 107 copies g-1 dry soil, respectively. Based on the n-damo activity, it was estimated that approximately 0.91 Tg CH4 and 2.17 Tg N could be consumed annually via n-damo in Chinese paddy soils. The spatial variations in n-damo activity and community structure of n-damo bacteria were significantly (p < 0.05) affected by the soil ammonium content, labile organic carbon content and pH. Furthermore, significant differences in n-damo activity, bacterial abundance and community composition were observed among different climate zones. The n-damo activity was found to be positively correlated with the mean annual air temperature. Taken together, our results demonstrated the potential importance of n-damo in both methane consumption and nitrogen removal in Chinese paddy soils, and this process was regulated by local soil and climatic factors.
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Affiliation(s)
- Wang-Ting Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Wei-Qi Wang
- Key Laboratory of Humid Subtropical Eco-geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Ya-Nan Bai
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Xin Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Mao-Hui Tian
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Chun Wang
- Key Laboratory of Humid Subtropical Eco-geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Yan-Fang Feng
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210044, China
| | - Yang Liu
- Information Center, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yu-Ling Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Jia-Qi Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Cai-Yu Geng
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
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Methane utilizing plant growth-promoting microbial diversity analysis of flooded paddy ecosystem of India. World J Microbiol Biotechnol 2021; 37:56. [PMID: 33619649 DOI: 10.1007/s11274-021-03018-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/01/2021] [Indexed: 01/10/2023]
Abstract
Methane utilizing bacteria (MUB) are known to inhabit the flooded paddy ecosystem where they play an important role in regulating net methane (CH4) emission. We hypothesize that efficient MUB having plant growth-promoting (PGP) attributes can be used for developing novel bio-inoculant for flooded paddy ecosystem which might not only reduce methane emission but also assist in improving the plant growth parameters. Hence, soil and plant samples were collected from the phyllosphere, rhizosphere, and non-rhizosphere of five rice-growing regions of India at the tillering stage and investigated for efficient methane-oxidizing and PGP bacteria. Based on the monooxygenase activity and percent methane utilization on NMS medium with methane as the sole C source, 123 isolates were identified and grouped phylogenetically into 13 bacteria and 2 yeast genera. Among different regions, a significantly higher number of isolates were obtained from lowland flooded paddy ecosystems of Aduthurai (33.33%) followed by Ernakulum (20.33%) and Brahmaputra valley (19.51%) as compared to upland irrigated regions of Gaya (17.07%) and Varanasi (8.94%). Among sub-samples, a significantly higher number of isolates were found inhabiting the phyllosphere (58.54%) followed by non-rhizosphere (25.20%) and rhizosphere (15.45%). Significantly higher utilization of methane and PGP attributes were observed in 30 isolates belonging to genera Hyphomicrobium, Burkholderia, Methylobacterium, Paenibacillus, Pseudomonas, Rahnella, and Meyerozyma. M. oryzae MNL7 showed significantly better growth with 74.33% of CH4 utilization at the rate of 302.9 ± 5.58 and exhibited half-maximal growth rate, Ks of 1.92 ± 0.092 mg CH4 L-1. Besides the ability to utilize CH4, P. polymyxa MaAL70 possessed PGP attributes such as solubilization of P, K, and Zn, fixation of atmospheric N and production of indole acetic acid (IAA). Both these promising isolates can be explored in the future for developing novel biofertilizers for flooded paddies.
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Zhu P, Cheng M, Pei D, Liu Y, Yan X. Methylomonas rhizoryzae sp. nov., a type I methanotroph isolated from the rhizosphere soil of rice. Antonie van Leeuwenhoek 2020; 113:2167-2176. [PMID: 33145620 DOI: 10.1007/s10482-020-01487-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/19/2020] [Indexed: 10/23/2022]
Abstract
A gammaproteobacterial methanotroph, strain GJ1T, was isolated from a rhizosphere soil sample of rice in Nanjing, China. The cells were Gram-negative, motile rods with a single polar flagellum, and they contained type I intracytoplasmic membranes. The cells formed pink colonies. The strain possessed both the particulate methane monooxygenase enzyme (pMMO) and the soluble methane monooxygenase enzyme (sMMO). pxmABC, encoding a divergent methane monooxygenase (pXMO), and nifH, which encodes dinitrogenase reductase, were also present. Methane and methanol were utilized as sole carbon sources, while other carbon sources, including acetate, pyruvate, succinate, citrate, malate, glucose, urea, methylamine, ethanol and formate, could not be utilized by strain GJ1T. Cell grew optimally at 25-33 °C (range 16-37 °C), pH 6.0-8.0 (range 5.5-8.5) and 0-1.2% NaCl (no growth above 1.5% NaCl). Phylogenetic analyses based on the 16S rRNA gene, pmoA and nifH showed that the isolate belongs to the genus Methylomonas of the family Methylococcaceae within the class Gammaproteobacteria. The major quinone was determined to be MQ-8, and the major fatty acids were observed to be C16:1 and C14:0. The genome size of strain GJ1T is about 4.55 Mb, and the DNA G + C content of the strain was determined to be 53.67 mol% within the range of the genus Methylomonas (47-58 mol%) reported at present. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain GJ1T and Methylomonas koyamae Fw12E-YT among the genus Methylomonas were the highest, and they were only 74.66% and 21.40%, respectively. In consequence, results of phenotypic characterization and phylogenetic analyses support strain GJ1T as a novel species within the genus Methylomonas, namely, Methylomonas rhizoryzae sp. nov.. The type strain is GJ1T (= ACCC 61706).
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Affiliation(s)
- Pingping Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Minggen Cheng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Dongmei Pei
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yongchuang Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Frindte K, Maarastawi SA, Lipski A, Hamacher J, Knief C. Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai. Int J Syst Evol Microbiol 2017; 67:4507-4514. [PMID: 28984554 DOI: 10.1099/ijsem.0.002319] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three gammaproteobacterial methanotrophic strains (73aT, 175 and 114) were isolated from stems of rice plants. All strains are Gram-negative, motile and grow on methane or methanol as sole carbon sources. They oxidize methane using the particulate methane monooxygenase. Strains 114 and 175 possess additionally a soluble methane monooxygenase. All strains contain significant amounts of the cellular fatty acids C16 : 0, C16 : 1ω6c and C16 : 1ω7c, typical for type Ib methanotrophs. Characteristic for strains 114 and 175 are high amounts of C14 : 0 and C16 : 1ω6c , while strain 73aT contains high quantities of C16 : 1ω5c. 16S rRNA gene sequence analyses showed that strains 114 and 175 are most closely related to Methylomagnum ishizawai (≥99.6 % sequence identity). Strain 73aT is representing a new genus within the family Methylococcaceae, most closely related to Methylococcus capsulatus (94.3 % sequence identity). Phylogenetic analysis of the PmoA sequence indicates that strain 73aT represents rice paddy cluster I (RPCI), which has almost exclusively been detected in rice ecosystems. The G+C content of strain 73aT is 61.0 mol%, while strains 114 and 175 have a G+C content of 63.3 mol%. Strain 73aT (=LMG 29185T, =VKM B-2986T) represents the type strain of a novel species and genus, for which the name Methyloterricola oryzae gen. nov., sp. nov. is proposed and a description is provided. Strains 175 (=LMG 28717, VKM B-2989) and 114 are members of the species Methylomagnum ishizawai. This genus was so far only represented by one isolate, so an amended description of the species is given.
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Affiliation(s)
- Katharina Frindte
- Molecular Biology of the Rhizosphere, Institute of Crop Science and Resource Conservation, University of Bonn, Nussallee 13, 53115 Bonn, Germany
| | - Sarah A Maarastawi
- Molecular Biology of the Rhizosphere, Institute of Crop Science and Resource Conservation, University of Bonn, Nussallee 13, 53115 Bonn, Germany
| | - André Lipski
- Food Microbiology and Hygiene, Institute of Nutritional and Food Sciences, University of Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Joachim Hamacher
- Plant Diseases and Crop Protection, Institute of Crop Science and Resource Conservation, University of Bonn, Nussallee 9, 53115 Bonn, Germany
| | - Claudia Knief
- Molecular Biology of the Rhizosphere, Institute of Crop Science and Resource Conservation, University of Bonn, Nussallee 13, 53115 Bonn, Germany
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Ghashghavi M, Jetten MSM, Lüke C. Survey of methanotrophic diversity in various ecosystems by degenerate methane monooxygenase gene primers. AMB Express 2017; 7:162. [PMID: 28831762 PMCID: PMC5567572 DOI: 10.1186/s13568-017-0466-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/17/2017] [Indexed: 01/07/2023] Open
Abstract
Methane is the second most important greenhouse gas contributing to about 20% of global warming. Its mitigation is conducted by methane oxidizing bacteria that act as a biofilter using methane as their energy and carbon source. Since their first discovery in 1906, methanotrophs have been studied using a complementary array of methods. One of the most used molecular methods involves PCR amplification of the functional gene marker for the diagnostic of copper and iron containing particulate methane monooxygenase. To investigate the diversity of methanotrophs and to extend their possible molecular detection, we designed a new set of degenerate methane monooxygenase primers to target an 850 nucleotide long sequence stretch from pmoC to pmoA. The primers were based on all available full genomic pmoCAB operons. The newly designed primers were tested on various pure cultures, enrichment cultures and environmental samples using PCR. The results demonstrated that this primer set has the ability to correctly amplify the about 850 nucleotide long pmoCA product from Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobia and the NC10 phyla methanotrophs. The new primer set will thus be a valuable tool to screen ecosystems and can be applied in conjunction with previously used pmoA primers to extend the diversity of currently known methane-oxidizing bacteria.
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Krause S, Niklaus PA, Badwan Morcillo S, Meima Franke M, Lüke C, Reim A, Bodelier PLE. Compositional and functional stability of aerobic methane consuming communities in drained and rewetted peat meadows. FEMS Microbiol Ecol 2015; 91:fiv119. [PMID: 26449384 DOI: 10.1093/femsec/fiv119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2015] [Indexed: 11/13/2022] Open
Abstract
The restoration of peatlands is an important strategy to counteract subsidence and loss of biodiversity. However, responses of important microbial soil processes are poorly understood. We assessed functioning, diversity and spatial organization of methanotrophic communities in drained and rewetted peat meadows with different water table management and agricultural practice. Results show that the methanotrophic diversity was similar between drained and rewetted sites with a remarkable dominance of the genus Methylocystis. Enzyme kinetics depicted no major differences, indicating flexibility in the methane (CH4) concentrations that can be used by the methanotrophic community. Short-term flooding led to temporary elevated CH4 emission but to neither major changes in abundances of methane-oxidizing bacteria (MOB) nor major changes in CH4 consumption kinetics in drained agriculturally used peat meadows. Radiolabeling and autoradiographic imaging of intact soil cores revealed a markedly different spatial arrangement of the CH4 consuming zone in cores exposed to near-atmospheric and elevated CH4. The observed spatial patterns of CH4 consumption in drained peat meadows with and without short-term flooding highlighted the spatial complexity and responsiveness of the CH4 consuming zone upon environmental change. The methanotrophic microbial community is not generally altered and harbors MOB that can cover a large range of CH4 concentrations offered due to water-table fluctuations, effectively mitigating CH4 emissions.
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Affiliation(s)
- Sascha Krause
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Pascal A Niklaus
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
| | - Sara Badwan Morcillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
| | - Marion Meima Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
| | - Claudia Lüke
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, 6525 AJ, the Netherlands
| | - Andreas Reim
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
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Pump J, Pratscher J, Conrad R. Colonization of rice roots with methanogenic archaea controls photosynthesis-derived methane emission. Environ Microbiol 2015; 17:2254-60. [PMID: 25367104 DOI: 10.1111/1462-2920.12675] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 11/28/2022]
Abstract
The methane emitted from rice fields originates to a large part (up to 60%) from plant photosynthesis and is formed on the rice roots by methanogenic archaea. To investigate to which extent root colonization controls methane (CH4 ) emission, we pulse-labeled rice microcosms with (13) CO2 to determine the rates of (13) CH4 emission exclusively derived from photosynthates. We also measured emission of total CH4 ((12+13) CH4 ), which was largely produced in the soil. The total abundances of archaea and methanogens on the roots and in the soil were analysed by quantitative polymerase chain reaction of the archaeal 16S rRNA gene and the mcrA gene coding for a subunit of the methyl coenzyme M reductase respectively. The composition of archaeal and methanogenic communities was determined with terminal restriction fragment length polymorphism (T-RFLP). During the vegetative growth stages, emission rates of (13) CH4 linearly increased with the abundance of methanogenic archaea on the roots and then decreased during the last plant growth stage. Rates of (13) CH4 emission and the abundance of methanogenic archaea were lower when the rice was grown in quartz-vermiculite with only 10% rice soil. Rates of total CH4 emission were not systematically related to the abundance of methanogenic archaea in soil plus roots. The composition of the archaeal communities was similar under all conditions; however, the analysis of mcrA genes indicated that the methanogens differed between the soil and root. Our results support the hypothesis that rates of photosynthesis-driven CH4 emission are limited by the abundance of methanogens on the roots.
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Affiliation(s)
- Judith Pump
- Department of Biogeochemistry, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Jennifer Pratscher
- Department of Biogeochemistry, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Ralf Conrad
- Department of Biogeochemistry, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
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Franchini AG, Henneberger R, Aeppli M, Zeyer J. Methane dynamics in an alpine fen: a field-based study on methanogenic and methanotrophic microbial communities. FEMS Microbiol Ecol 2014; 91:fiu032. [PMID: 25789997 DOI: 10.1093/femsec/fiu032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Wetlands are important sources of the greenhouse gas methane (CH4). We provide an in situ study of CH4 dynamics in the permanently submerged soil of a Swiss alpine fen. Physico-chemical pore water analyses were combined with structural and microbiological analyses of soil cores at high vertical resolution down to 50 cm depth. Methanotrophs and methanogens were active throughout the depth profile, and highest abundance of active methanotrophs and methanogens [6.1 × 10(5) and 1.1 × 10(7) pmoA and mcrA transcripts (g soil)(-1), respectively] was detected in the uppermost 2 cm of the soil. Active methanotrophic communities in the near-surface zone, dominated by viable mosses, varied from the communities in the deeper zones, but further changes with depth were not pronounced. Apart from a distinct active methanogenic community in the uppermost sample, a decrease of acetoclastic Methanosaetaceae with depth was observed in concomitance with decreasing root surface area. Overall, root surface area correlated with mcrA transcript abundance and CH4 pore water concentrations, which peaked (137.1 μM) at 10 to 15 cm depth. Our results suggest that stimulation of methanogenesis by root exudates of vascular plants had a stronger influence on CH4 dynamics than stimulation of CH4 oxidation by O2 input.
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Affiliation(s)
- Alessandro G Franchini
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Ruth Henneberger
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Meret Aeppli
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Josef Zeyer
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
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Henneberger R, Chiri E, Bodelier PEL, Frenzel P, Lüke C, Schroth MH. Field-scale tracking of active methane-oxidizing communities in a landfill cover soil reveals spatial and seasonal variability. Environ Microbiol 2014; 17:1721-37. [PMID: 25186436 DOI: 10.1111/1462-2920.12617] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 08/31/2014] [Indexed: 01/11/2023]
Abstract
Aerobic methane-oxidizing bacteria (MOB) in soils mitigate methane (CH4 ) emissions. We assessed spatial and seasonal differences in active MOB communities in a landfill cover soil characterized by highly variable environmental conditions. Field-based measurements of CH4 oxidation activity and stable-isotope probing of polar lipid-derived fatty acids (PLFA-SIP) were complemented by microarray analysis of pmoA genes and transcripts, linking diversity and function at the field scale. In situ CH4 oxidation rates varied between sites and were generally one order of magnitude lower in winter compared with summer. Results from PLFA-SIP and pmoA transcripts were largely congruent, revealing distinct spatial and seasonal clustering. Overall, active MOB communities were highly diverse. Type Ia MOB, specifically Methylomonas and Methylobacter, were key drivers for CH4 oxidation, particularly at a high-activity site. Type II MOB were mainly active at a site showing substantial fluctuations in CH4 loading and soil moisture content. Notably, Upland Soil Cluster-gamma-related pmoA transcripts were also detected, indicating concurrent oxidation of atmospheric CH4 . Spatial separation was less distinct in winter, with Methylobacter and uncultured MOB mediating CH4 oxidation. We propose that high diversity of active MOB communities in this soil is promoted by high variability in environmental conditions, facilitating substantial removal of CH4 generated in the waste body.
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Affiliation(s)
- Ruth Henneberger
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092, Zurich, Switzerland
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10
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Krause S, Meima-Franke M, Hefting MM, Bodelier PLE. Spatial patterns of methanotrophic communities along a hydrological gradient in a riparian wetland. FEMS Microbiol Ecol 2013; 86:59-70. [PMID: 23397906 DOI: 10.1111/1574-6941.12091] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 02/06/2013] [Accepted: 02/06/2013] [Indexed: 11/30/2022] Open
Abstract
Microbial communities display a variety of biogeographical patterns mainly driven by large-scale environmental gradients. Here, we analysed the spatial distribution of methane-oxidizing bacteria (MOB) and methane oxidation in a strongly fluctuating environment. We investigated whether the spatial variability of the MOB community can be explained by an environmental gradient and whether this changes with different plot sizes. We applied a pmoA-specific microarray to detect MOB, measured methane oxidation, methane emissions and soil properties. All variables were measured in a 10 × 10 m, 1 × 1 m and 20 × 20 cm plot and interpreted using a geostatistical approach. Methane oxidation as well as MOB displayed spatial patterns reflected in the underlying flooding gradient. Overlapping and contrasting spatial patterns for type I and type II MOB suggested different ecological life strategies. With smaller plot size, the environmental gradient could not explain the variability in the data and local factors became more important. In conclusion, environmental gradients can generally explain variability in microbial spatial patterns; however, we think that this does not contribute to a mechanistic explanation for microbial diversity because the relevant scales for microorganisms are much smaller than those normally measured.
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Affiliation(s)
- Sascha Krause
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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Bodelier PLE, Bär-Gilissen MJ, Meima-Franke M, Hordijk K. Structural and functional response of methane-consuming microbial communities to different flooding regimes in riparian soils. Ecol Evol 2012; 2:106-27. [PMID: 22408730 PMCID: PMC3297182 DOI: 10.1002/ece3.34] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 08/12/2011] [Accepted: 08/17/2011] [Indexed: 02/02/2023] Open
Abstract
Climate change will lead to more extreme precipitation and associated increase of flooding events of soils. This can turn these soils from a sink into a source of atmospheric methane. The latter will depend on the balance of microbial methane production and oxidation. In the present study, the structural and functional response of methane oxidizing microbial communities was investigated in a riparian flooding gradient. Four sites differing in flooding frequency were sampled and soil-physico-chemistry as well as methane oxidizing activities, numbers and community composition were assessed. Next to this, the active community members were determined by stable isotope probing of lipids. Methane consumption as well as population size distinctly increased with flooding frequency. All methane consumption parameters (activity, numbers, lipids) correlated with soil moisture, organic matter content, and conductivity. Methane oxidizing bacteria were present and activated quickly even in seldom flooded soils. However, the active species comprised only a few representatives belonging to the genera Methylobacter, Methylosarcina, and Methylocystis, the latter being active only in permanently or regularly flooded soils. This study demonstrates that soils exposed to irregular flooding harbor a very responsive methane oxidizing community that has the potential to mitigate methane produced in these soils. The number of active species is limited and dominated by one methane oxidizing lineage. Knowledge on the characteristics of these microbes is necessary to assess the effects of flooding of soils and subsequent methane cycling therein.
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Affiliation(s)
- Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Droevendaalsesteeg 10, 6708PB Wageningen, The Netherlands
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12
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Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME JOURNAL 2011; 6:1378-90. [PMID: 22189496 DOI: 10.1038/ismej.2011.192] [Citation(s) in RCA: 362] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The above- and below-ground parts of rice plants create specific habitats for various microorganisms. In this study, we characterized the phyllosphere and rhizosphere microbiota of rice cultivars using a metaproteogenomic approach to get insight into the physiology of the bacteria and archaea that live in association with rice. The metaproteomic datasets gave rise to a total of about 4600 identified proteins and indicated the presence of one-carbon conversion processes in the rhizosphere as well as in the phyllosphere. Proteins involved in methanogenesis and methanotrophy were found in the rhizosphere, whereas methanol-based methylotrophy linked to the genus Methylobacterium dominated within the protein repertoire of the phyllosphere microbiota. Further, physiological traits of differential importance in phyllosphere versus rhizosphere bacteria included transport processes and stress responses, which were more conspicuous in the phyllosphere samples. In contrast, dinitrogenase reductase was exclusively identified in the rhizosphere, despite the presence of nifH genes also in diverse phyllosphere bacteria.
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Ho A, Lüke C, Cao Z, Frenzel P. Ageing well: methane oxidation and methane oxidizing bacteria along a chronosequence of 2000 years. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:738-43. [PMID: 23761364 DOI: 10.1111/j.1758-2229.2011.00292.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Rice is the staple food for more than half of the world's growing population. While the area planted to wetland rice is expected to increase further, virtually nothing is known about the long-term development of the respective microbial communities, and how these might influence biogeochemistry. Focusing on methane oxidizing bacteria, we studied a chronosequence of paddy fields in China aged 50-2000 years. Potential methanotrophic activity increased substantially with age of soil. Community composition was relatively similar in all fields. However, growth and activity of one particular subgroup of methanotrophs correlated to soil age suggesting an intricate abiotic control on methanotrophs evolving with time. Our results demonstrate that continuous rice agriculture does not only shape the microbial community, but also modifies the micro-environment in a way enabling faster growth and higher activity of selected populations.
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Affiliation(s)
- Adrian Ho
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany. Institute of Soil Science, Chinese Academy of Sciences, 210008 Nanjing, China
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14
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Lüke C, Krause S, Cavigiolo S, Greppi D, Lupotto E, Frenzel P. Biogeography of wetland rice methanotrophs. Environ Microbiol 2009; 12:862-72. [DOI: 10.1111/j.1462-2920.2009.02131.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Conrad R. The global methane cycle: recent advances in understanding the microbial processes involved. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:285-292. [PMID: 23765881 DOI: 10.1111/j.1758-2229.2009.00038.x] [Citation(s) in RCA: 406] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The global budget of atmospheric CH4 , which is on the order of 500-600 Tg CH4 per year, is mainly the result of environmental microbial processes, such as archaeal methanogenesis in wetlands, rice fields, ruminant and termite digestive systems and of microbial methane oxidation under anoxic and oxic conditions. This review highlights recent progress in the research of anaerobic CH4 oxidation, of CH4 production in the plant rhizosphere, of CH4 serving as substrate for the aquatic trophic food chain and the discovery of novel aerobic methanotrophs. It also emphasizes progress and deficiencies in our knowledge of microbial utilization of low atmospheric CH4 concentrations in soil, CH4 production in the plant canopy, intestinal methanogenesis and CH4 production in pelagic water.
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Affiliation(s)
- Ralf Conrad
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str.8, 35043 Marburg, Germany
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16
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Bodelier PLE, Gillisen MJB, Hordijk K, Damsté JSS, Rijpstra WIC, Geenevasen JAJ, Dunfield PF. A reanalysis of phospholipid fatty acids as ecological biomarkers for methanotrophic bacteria. ISME JOURNAL 2009; 3:606-17. [PMID: 19194481 DOI: 10.1038/ismej.2009.6] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Aerobic methane-oxidizing bacteria (MB) are the primary terrestrial sinks for the greenhouse gas methane. A distinct characteristic of MB is the presence of specific phospholipid ester-linked fatty acids (PLFA) in their membranes that differentiate them from each other and also from all other organisms. These distinct PLFA patterns facilitate microbial ecology studies. For example, the assimilation of C from methane into PLFA can be traced in environmental samples using stable isotope ((13)C) probing (SIP), which links the activity of MB to their community composition in situ. However, the phylogenetic resolution of this method is low because of a lack of PLFA profiles from cultured MB species. In this study, PLFA profiles of 22 alphaproteobacterial (type II) MB were analysed after growth on methane, methanol or both substrates together. Growth on different substrates did not affect the PLFA profiles of the investigated strains. A number of Methylocystis strains contained novel C18:2 fatty acids (omega 7c,12c and omega 6c,12c) that can be used as diagnostic biomarkers. The detection of these novel PLFA, combined with the analyses of multiple type II strains, increased the phylogenetic resolution of PLFA analysis substantially. Multivariate analysis of the expanded MB PLFA database identified species groups that closely reflected phylogenies based on 16S rRNA and pmoA gene sequences. The PLFA database therefore provides a robust framework for linking identity to activity in MB communities with a higher resolution than was previously possible.
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Affiliation(s)
- Paul L E Bodelier
- Department of Microbial Wetland Ecology, Centre for Limnology, Netherlands Institute of Ecology (NIOO-KNAW), Maarssen, The Netherlands.
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17
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Mohanty SR, Bharati K, Rao VR, Adhya TK. Dynamics of changes in methanogenesis and associated microflora in a flooded alluvial soil following repeated application of dicyandiamide, a nitrification inhibitor. Microbiol Res 2009; 164:71-80. [PMID: 17207983 DOI: 10.1016/j.micres.2006.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2006] [Indexed: 10/23/2022]
Abstract
Influence of repeated application of the nitrification inhibitor dicyandiamide (DCD), on CH(4) production and associated microflora in a flooded alluvial soil, was investigated in a laboratory incubation study. Application of DCD at the time of soil incubation resulted in a substantial reduction in CH(4) production (31% over that of untreated control). Second repeat application of DCD, on the contrary, annulled the inhibitory effect on CH(4) production, restoring it to the level of unamended soil. Application of the third dose of DCD maintained CH(4) production almost to the same extent as that of second application. The alleviation of the initial inhibitory effect of DCD on CH(4) production was linked to the enhanced degradation of DCD following its repeated application to the flooded soil. Admittedly, abatement of the initial inhibitory effect of DCD on CH(4) production in soil repeatedly amended with DCD was also related to the inhibition of CH(4)-oxidizing bacterial population and noticeable stimulation of heterotrophic bacterial population. Results suggest that repeat application of DCD with fertilizer-N to flooded rice soils might not be effective in controlling CH(4) production under field condition.
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Affiliation(s)
- S R Mohanty
- Laboratory of Soil Microbiology, Division of Soil Science and Microbiology, Central Rice Research Institute, Cuttack 753006, Orissa, India
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18
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Noll M, Frenzel P, Conrad R. Selective stimulation of type I methanotrophs in a rice paddy soil by urea fertilization revealed by RNA-based stable isotope probing. FEMS Microbiol Ecol 2008; 65:125-32. [PMID: 18544098 DOI: 10.1111/j.1574-6941.2008.00497.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Methane-oxidizing bacteria (MOB) in soil are not only controlled by their main substrates, methane and oxygen, but also by nitrogen availability. We compared an unfertilized control with a urea-fertilized treatment and applied RNA-stable-isotope-probing to follow activity changes upon fertilization as closely as possible. Nitrogen fertilization of an Italian rice field soil increased the CH4 oxidation rates sevenfold. In the fertilized treatment, isopycnic separation of 13C-enriched RNA became possible after 7 days when 300 micromol 13CH4 g(dry soil)(-1) had been consumed. Terminal-restriction fragment length polymorphism (T-RFLP) fingerprints and clone libraries documented that the type I methanotrophic genera Methylomicrobium and Methylocaldum assimilated 13CH4 nearly exclusively. Although previous studies had shown that the same soil contains a much larger diversity of MOB, including both type I and type II, nitrogen fertilization apparently activated only a small subset of the overall diversity of MOB, type I MOB in particular.
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Affiliation(s)
- Matthias Noll
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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19
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Mohanty SR, Nayak DR, Babu YJ, Adhya TK. Butachlor inhibits production and oxidation of methane in tropical rice soils under flooded condition. Microbiol Res 2004; 159:193-201. [PMID: 15462519 DOI: 10.1016/j.micres.2004.03.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In laboratory incubation experiments, application of a commercial formulation of the herbicide butachlor (N-butoxymethyl-2-chloro-2',6'-diethyl acetanilide) to three tropical rice soils, widely differing in their physicochemical characteristics, under flooded condition inhibited methane (CH4) production. The inhibitory effect was concentration dependent and most remarkable in the alluvial soil. Thus, following application of butachlor at 5, 10, 50 and 100 microg g(-1) soil, respectively, cumulative CH4 production in the alluvial soil was inhibited by 15%, 31%, 91% and 98% over unamended control. Since CH4 production was less pronounced in the sandy loam and acid sulfate soil, the impact of amendment with butchalor, albeit inhibitory, was less extensive than the alluvial soil. Inhibition of CH4 production in butachlor-amended alluvial soil was related to the prevention in the drop in redox potential as well as low methanogenic bacterial population especially at high concentrations of butachlor. CH4 oxidation was also inhibited in butachlor-amended alluvial soil with the inhibitory effect being more prevalent under flooded condition. Inhibition in CH4 oxidation was related to a reduction in the population of soluble methane monooxygenase producing methanotrophs. Results demonstrate that butachlor, a commonly used herbicide in rice cultivation, even at very low concentrations can affect CH4 production and its oxidation, thereby influencing the biogeochemical cycle of CH4 in flooded rice soils.
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Affiliation(s)
- S R Mohanty
- Laboratory of Soil Microbiology, Division of Soil Science and Microbiology, Central Rice Research Institute, Cuttack 753006, Orissa, India
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20
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Bodelier PLE. Interactions Between Oxygen-Releasing Roots and Microbial Processes in Flooded Soils and Sediments. ROOT ECOLOGY 2003. [DOI: 10.1007/978-3-662-09784-7_13] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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21
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Affiliation(s)
- Russell K. Monson
- Department of Environmental, Population and Organismic Biology and the Cooperative Institute for Research in Environmental Science, University of Colorado, Boulder, Colorado; e-mail:
- Max-Planck Institute for Biogeochemistry, Jena, Germany
| | - Elisabeth A. Holland
- Department of Environmental, Population and Organismic Biology and the Cooperative Institute for Research in Environmental Science, University of Colorado, Boulder, Colorado; e-mail:
- Max-Planck Institute for Biogeochemistry, Jena, Germany
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22
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Horz HP, Yimga MT, Liesack W. Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA, mmoX, mxaF, and 16S rRNA and ribosomal DNA, including pmoA-based terminal restriction fragment length polymorphism profiling. Appl Environ Microbiol 2001; 67:4177-85. [PMID: 11526021 PMCID: PMC93145 DOI: 10.1128/aem.67.9.4177-4185.2001] [Citation(s) in RCA: 172] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diversity of methanotrophic bacteria associated with roots of submerged rice plants was assessed using cultivation-independent techniques. The research focused mainly on the retrieval of pmoA, which encodes the alpha subunit of the particulate methane monooxygenase. A novel methanotroph-specific community-profiling method was established using the terminal restriction fragment length polymorphism (T-RFLP) technique. The T-RFLP profiles clearly revealed a more complex root-associated methanotrophic community than did banding patterns obtained by pmoA-based denaturing gradient gel electrophoresis. The comparison of pmoA-based T-RFLP profiles obtained from rice roots and bulk soil of flooded rice microcosms suggested that there was a substantially higher abundance of type I methanotrophs on rice roots than in the bulk soil. These were affiliated to the genera Methylomonas, Methylobacter, Methylococcus, and to a novel type I methanotroph sublineage. By contrast, type II methanotrophs of the Methylocystis-Methylosinus group could be detected with high relative signal intensity in both soil and root compartments. Phylogenetic treeing analyses and a set of substrate-diagnostic amino acid residues provided evidence that a novel pmoA lineage was detected. This branched distinctly from all currently known methanotrophs. To examine whether the retrieval of pmoA provided a complete view of root-associated methanotroph diversity, we also assessed the diversity detectable by recovery of genes coding for subunits of soluble methane monooxygenase (mmoX) and methanol dehydrogenase (mxaF). In addition, both 16S rRNA and 16S ribosomal DNA (rDNA) were retrieved using a PCR primer set specific to type I methanotrophs. The overall methanotroph diversity detected by recovery of mmoX, mxaF, and 16S rRNA and 16S rDNA corresponded well to the diversity detectable by retrieval of pmoA.
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Affiliation(s)
- H P Horz
- Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany
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