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Lu Y, Liu Q, Fu L, Hu Y, Zhong L, Zhang S, Liu Q, Xie Q. The effect of modified biochar on methane emission and succession of methanogenic archaeal community in paddy soil. CHEMOSPHERE 2022; 304:135288. [PMID: 35691388 DOI: 10.1016/j.chemosphere.2022.135288] [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: 03/18/2022] [Revised: 05/24/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Modified biochars have been widely applied in ameliorating environmental problems. However, the effect of modified biochar on suppressing CH4 emission in rice paddy soil is not fully understood. In order to further study CH4 regulation in paddy soil via the modification of biochar and explore its influence on key archaeal communities, two modified biochars were generated with the pre-treatment of nitric acid (NBC) and hydrogen peroxide (OBC), respectively, and a control group was setup with water-washed biochar (WBC). Results showed that NBC significantly suppressed CH4 emission, followed by OBC and WBC, while NBC promoted the CO2 emission. Besides, the addition of biochars inhibited the accumulation of acetate and H2 in rice paddy soil, especially in the NBC treatment. 16S rRNA gene sequencing revealed that biochars amendment increased α-diversity of archaeal community and the modified biochars could mitigate the loss of α-diversity in the early stage of anaerobic incubation. Additionally, NBC amendment largely declined the relative abundance of methanogens (especially Methanosarcina) in archaeal community, while OBC and NBC promoted the relative abundance of Candidatus_Methanoperedens. Via Spearman's correlation coefficient analysis, NBC had positive correlations with Methanosaeta, and OBC showed a negative correlation with Methanocella. Overall, this study provided a practical way to regulate the CH4 emission and associated methanogenic archaea via the amendment of different modified biochars in rice paddy soil.
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Affiliation(s)
- Yue Lu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China.
| | - Qian Liu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Leiling Fu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Yingju Hu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Linrui Zhong
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Shoujuan Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Qi Liu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Qingqing Xie
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
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Effects of Water and Fertilizer Management Practices on Methane Emissions from Paddy Soils: Synthesis and Perspective. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19127324. [PMID: 35742575 PMCID: PMC9223590 DOI: 10.3390/ijerph19127324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 12/03/2022]
Abstract
Water and fertilizer management practices are considered to have great influence on soil methane (CH4) emissions from paddy fields. However, few studies have conducted a quantitative analysis of the effects of these management practices. Here, we selected 156 observations of water management from 34 articles and 288 observations of fertilizer management from 37 articles and conducted a global meta-analysis of the effects of water and fertilizer management practices on soil CH4 emissions in paddy fields. In general, compared with traditional irrigation (long-term flooding irrigation), water-saving irrigation significantly decreased soil CH4 emissions but increased rice yield. Among the different practices, intermittent irrigation had the fewest reductions in CH4 emissions but the greatest increase in rice yield. In addition, fertilization management practices such as manure, mixed fertilizer (mixture), and straw significantly enhanced CH4 emissions. Rice yields were increased under fertilization with a mixture, traditional fertilizer, and controlled release fertilizer. Our results highlight that suitable agricultural water and fertilizer management practices are needed to effectively reduce CH4 emissions while maintaining rice yields. We also put forward some prospects for mitigating soil CH4 emissions from paddy fields in the context of global warming in the future.
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3
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Furtak K, Grządziel J, Gałązka A. Can Model Experiments Give Insight into the Response of the Soil Environment to Flooding? A Comparison of Microcosm and Natural Event. BIOLOGY 2022; 11:biology11030386. [PMID: 35336760 PMCID: PMC8945539 DOI: 10.3390/biology11030386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/21/2022] [Accepted: 02/26/2022] [Indexed: 11/16/2022]
Abstract
Studies using soil microcosms are very common, but few involve flooded soils, and comparing the results from such an experiment with natural conditions is unheard of. In the present study, we investigated the biological activity of soil (pH value, dehydrogenases and phosphatase activities) and the metabolic potential (EcoPlate™ Biolog®) of soil microorganisms in three fluvisol subjected to flooding under laboratory and natural conditions. The results indicate that soil flooding under both natural and laboratory conditions affected soil pH, enzymatic activity and metabolic potential (AWCD, average well colour development) of soil microorganisms. Changes in these parameters are more pronounced in the microcosmic experiment than in the field conditions. Furthermore, depending on the characteristics of the soil (i.e., its type, structure, vegetation) some of the soil quality parameters may return to their preflood state. Microcosm studies are needed in environmental ecology and microbiology to predict changes due to various factors, but their scale and course must be carefully planned.
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Rani V, Bhatia A, Kaushik R. Inoculation of plant growth promoting-methane utilizing bacteria in different N-fertilizer regime influences methane emission and crop growth of flooded paddy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 775:145826. [PMID: 33631576 DOI: 10.1016/j.scitotenv.2021.145826] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Methane (CH4) emission in rice fields is greatly influenced by the type and quantity of nitrogenous fertilizer used. The net methane emission from paddy fields is also influenced by the activity of methane utilizing bacteria, which inhabit the flooded paddy ecosystem. Efficient methane utilizing and plant growth promoting bacteria Methylobacterium oryzae MNL7 and Paenibacillus polymyxa MaAL70, respectively were co-inoculated along with different nitrogenous fertilizer combinations in flooded paddy to assess their impact on cumulative methane emission and crop growth promotion. Co-inoculation significantly influenced the plant growth parameters of paddy, resulting in an increase in grain yield by 14.04, 11.08, and 12.38% in treatments receiving Urea, Di-ammonium Phosphate (DAP) + Urea, or farm yard manure (FYM), over their respective un-inoculated plots. Significant improvement in the rice grain nutrient quality in term of crude protein, Fe and Zn content was observed as a result of bacterial co-inoculation in FYM fertilized plots as compared to Urea and DAP+ Urea fertilized plots. Significantly higher cumulative methane emission of 63.39 kg ha-1 was observed in uninoculated plots fertilized with FYM treatment as compared to Urea (33.83 kg ha-1) and DAP+Urea (31.66 kg ha-1) treatments. Bacterial co-inoculation significantly reduced the cumulative methane emission by 12.03, 11.47 and 6.92% in Urea, DAP+Urea, and FYM fertilized plots over their respective uninoculated treatments. Among the different fertilizer treatments, bacterial co-inoculation with urea application performed significantly better in reducing cumulative methane emission. These findings suggest that methane utilizing bacteria which also possess plant growth promoting trait can be explored for developing a novel biofertilizer for flooded paddies, as they can aid in managing both the overall methane emission and enhancing crop yield.
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Affiliation(s)
- Vijaya Rani
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Arti Bhatia
- Center for Environemtal Sciences and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rajeev Kaushik
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
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Gontijo JB, Paula FS, Venturini AM, Yoshiura CA, Borges CD, Moura JMS, Bohannan BJM, Nüsslein K, Rodrigues JLM, Tsai SM. Not just a methane source: Amazonian floodplain sediments harbour a high diversity of methanotrophs with different metabolic capabilities. Mol Ecol 2021; 30:2560-2572. [PMID: 33817881 DOI: 10.1111/mec.15912] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 01/03/2023]
Abstract
The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and function as a significant CH4 source contributing to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH4 emissions across floodplain areas. Here, we report the in situ composition of CH4 cycling microbial communities in Amazonian floodplain sediments. We considered how abiotic factors may affect the microbial community composition and, more specifically, CH4 cycling groups. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the presence of methanogenic (mcrA) and methanotrophic (pmoA) microorganisms. Methanogens were found to be present in high abundance in floodplain sediments, and they seem to resist the dramatic environmental changes between flooded and nonflooded conditions. Methanotrophs known to use different pathways to oxidise CH4 were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry but also the composition of the microbial communities. These environmental changes seem also to affect the pools of methanotrophs occupying distinct niches. Understanding these shifts in the methanotrophic communities could improve our comprehension of the CH4 emissions in the region.
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Affiliation(s)
- Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Fabiana S Paula
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil.,Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, Brazil
| | - Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Caio A Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Clovis D Borges
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - José Mauro S Moura
- Center for Interdisciplinary Formation, Federal University of Western Pará, Santarém, Brazil
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Jorge L Mazza Rodrigues
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
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Fernandez M, Paisio CE, Perotti R, Pereira PP, Agostini E, González PS. Laboratory and field microcosms as useful experimental systems to study the bioaugmentation treatment of tannery effluents. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 234:503-511. [PMID: 30648649 DOI: 10.1016/j.jenvman.2019.01.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 01/02/2019] [Accepted: 01/06/2019] [Indexed: 06/09/2023]
Abstract
Tannery effluents require effective treatment prior to their final disposal, and the use of native bacterial consortia could be an appropriate strategy for this purpose. In the present work, consortium SFC 500-1 was found to be highly tolerant to different metals, metalloids and aromatic compounds like phenols. It was also able to remove the black dye commonly used in tanneries. Moreover, it promoted a significant reduction in chemical oxygen demand and exhibited high capability for the simultaneous removal of Cr(VI) and phenol. However, the effectiveness of the remediation processes markedly varied from one experimental system (Erlenmeyer flasks) to another (field microcosm system), highlighting the importance of moving from a small-scale study system to one involving more realistic environmental scenarios. In addition, we found a decrease in the toxicity of the effluent treated with consortium SFC 500-1. Taken together, our results indicate that this consortium possesses great potential for the treatment of tannery effluents. We conclude that for the development of a bioremediation strategy, it is necessary to develop experiments at a larger scale under conditions similar to those of the original system, in order to complete the scenario first created by in vitro approaches.
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Affiliation(s)
- Marilina Fernandez
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto, 5800 Río Cuarto, Córdoba, Argentina.
| | - Cintia E Paisio
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto, 5800 Río Cuarto, Córdoba, Argentina.
| | - Romina Perotti
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto, 5800 Río Cuarto, Córdoba, Argentina.
| | - Paola P Pereira
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto, 5800 Río Cuarto, Córdoba, Argentina.
| | - Elizabeth Agostini
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto, 5800 Río Cuarto, Córdoba, Argentina.
| | - Paola S González
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto, 5800 Río Cuarto, Córdoba, Argentina.
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7
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Lupatini M, Suleiman AKA, Jacques RJS, Lemos LN, Pylro VS, Van Veen JA, Kuramae EE, Roesch LFW. Moisture Is More Important than Temperature for Assembly of Both Potentially Active and Whole Prokaryotic Communities in Subtropical Grassland. MICROBIAL ECOLOGY 2019; 77:460-470. [PMID: 30607437 DOI: 10.1007/s00248-018-1310-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Moisture and temperature play important roles in the assembly and functioning of prokaryotic communities in soil. However, how moisture and temperature regulate the function of niche- versus neutral-based processes during the assembly of these communities has not been examined considering both the total microbial community and the sole active portion with potential for growth in native subtropical grassland. We set up a well-controlled microcosm-based experiment to investigate the individual and combined effects of moisture and temperature on soil prokaryotic communities by simulating subtropical seasons in grassland. The prokaryotic populations with potential for growth and the total prokaryotic community were assessed by 16S rRNA transcript and 16S rRNA gene analyses, respectively. Moisture was the major factor influencing community diversity and structure, with a considerable effect of this factor on the total community. The prokaryotic populations with potential for growth and the total communities were influenced by the same assembly rules, with the niche-based mechanism being more influential in communities under dry condition. Our results provide new information regarding moisture and temperature in microbial communities of soil and elucidate how coexisting prokaryotic populations, under different physiological statuses, are shaped in native subtropical grassland soil.
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Affiliation(s)
- Manoeli Lupatini
- Departamento de Solos, Programa de Pós-graduação em Ciência do Solo, Universidade Federal de Santa Maria, Roraima, 1000, Santa Maria, 97105-900, Brazil
| | - Afnan K A Suleiman
- Departamento de Solos, Programa de Pós-graduação em Ciência do Solo, Universidade Federal de Santa Maria, Roraima, 1000, Santa Maria, 97105-900, Brazil
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Rodrigo J S Jacques
- Departamento de Solos, Programa de Pós-graduação em Ciência do Solo, Universidade Federal de Santa Maria, Roraima, 1000, Santa Maria, 97105-900, Brazil
| | - Leandro N Lemos
- Laboratório de Biologia Molecular e Celular, Centro de Energia Nuclear na Agricultura CENA, Universidade de São Paulo USP, Piracicaba, SP, Brazil
| | - Victor S Pylro
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil
| | - Johannes A Van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Luiz F W Roesch
- Centro Interdisciplinar de Pesquisas em Biotecnologia - CIP-Biotec, Universidade Federal do Pampa, Campus São Gabriel, Avenida Antonio Trilha, 1847, São Gabriel, 97300-000, Brazil.
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Methanobactin from Methylosinus trichosporium OB3b inhibits N 2O reduction in denitrifiers. ISME JOURNAL 2018; 12:2086-2089. [PMID: 29330532 DOI: 10.1038/s41396-017-0022-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/09/2017] [Accepted: 11/17/2017] [Indexed: 11/09/2022]
Abstract
Methanotrophs synthesize methanobactin, a secondary metabolite that binds copper with an unprecedentedly high affinity. Such a strategy may provide methanotrophs a "copper monopoly" that can inhibit the activity of copper-containing enzymes of other microbes, e.g., copper-dependent N2O reductases. Here, we show that methanobactin from Methylosinus trichosporium OB3b inhibited N2O reduction in denitrifiers. When Pseudomonas stutzeri DCP-Ps1 was incubated in cocultures with M. trichosporium OB3b or with purified methanobactin from M. trichosporium OB3b, stoichiometric N2O production was observed from NO3- reduction, whereas no significant N2O accumulation was observed in cocultures with a mutant defective in methanobactin production. Copper uptake by P. stutzeri DCP-Ps1 was inhibited by the presence of purified methanobactin, leading to a significant downregulation of nosZ transcription. Similar findings were observed with three other denitrifier strains. These results suggest that in situ stimulation of methanotrophs can inadvertently increase N2O emissions, with the potential for increasing net greenhouse gas emissions.
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Liu Y, Liu X, Cheng K, Li L, Zhang X, Zheng J, Zheng J, Pan G. Responses of Methanogenic and Methanotrophic Communities to Elevated Atmospheric CO 2 and Temperature in a Paddy Field. Front Microbiol 2016; 7:1895. [PMID: 27933055 PMCID: PMC5121223 DOI: 10.3389/fmicb.2016.01895] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/11/2016] [Indexed: 11/13/2022] Open
Abstract
Although climate change is predicted to affect methane (CH4) emissions in paddy soil, the dynamics of methanogens and methanotrophs in paddy fields under climate change have not yet been fully investigated. To address this issue, a multifactor climate change experiment was conducted in a Chinese paddy field using the following experimental treatments: (1) enrichment of atmospheric CO2 concentrations (500 ppm, CE), (2) canopy air warming (2°C above the ambient, WA), (3) combined CO2 enrichment and warming (CW), and (4) ambient conditions (CK). We analyzed the abundance of methanogens and methanotrophs, community structures, CH4 production and oxidation potentials, in situ CH4 emissions using real-time PCR, T-RFLP, and clone library techniques, as well as biochemical assays. Compared to the control under CE and CW treatments, CH4 production potential, methanogenic gene abundance and soil microbial biomass carbon significantly increased; the methanogenic community, however, remained stable. The canopy air warming treatment only had an effect on CH4 oxidation potential at the ripening stage. Phylogenic analysis indicated that methanogens in the rhizosphere were dominated by Methanosarcina, Methanocellales, Methanobacteriales, and Methanomicrobiales, while methanotrophic sequences were classified as Methylococcus, Methylocaldum, Methylomonas, Methylosarcina (Type I) and Methylocystis (Type II). However, the relative abundance of Methylococcus (Type I) decreased under CE and CW treatments and the relative abundance of Methylocystis (Type II) increased. The in situ CH4 fluxes indicated similar seasonal patterns between treatments; both CE and CW increased CH4 emissions. In conclusion results suggest that methanogens and methanotrophs respond differently to elevated atmospheric CO2 concentrations and warming, thus adding insights into the effects of simulated global climate change on CH4 emissions in paddy fields.
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Affiliation(s)
- Yuan Liu
- Department of Bioengineering, College of Life Science, Huaibei Normal University Huaibei, China
| | - Xiaoyu Liu
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Kun Cheng
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Lianqing Li
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Xuhui Zhang
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Jufeng Zheng
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Jinwei Zheng
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Genxing Pan
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural UniversityNanjing, China; Zhejiang Provincial Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration, School of Environmental and Resource Sciences, Zhejiang A & F University, Lin'anHangzhou, China
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Draft Genome Sequence of Methylosinus sp. Strain 3S-1, an Isolate from Rice Root in a Low-Nitrogen Paddy Field. GENOME ANNOUNCEMENTS 2016; 4:4/5/e00932-16. [PMID: 27587832 PMCID: PMC5009989 DOI: 10.1128/genomea.00932-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
N2-fixing methanotrophs play an important role in the methane-nitrogen cycle in rice paddies. We report here the draft genome sequence of Methylosinus sp. strain 3S-1 isolated from rice root in a paddy field without N fertilizer input.
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11
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Pandit PS, Rahalkar MC, Dhakephalkar PK, Ranade DR, Pore S, Arora P, Kapse N. Deciphering Community Structure of Methanotrophs Dwelling in Rice Rhizospheres of an Indian Rice Field Using Cultivation and Cultivation-Independent Approaches. MICROBIAL ECOLOGY 2016; 71:634-644. [PMID: 26547567 DOI: 10.1007/s00248-015-0697-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/26/2015] [Indexed: 06/05/2023]
Abstract
Methanotrophs play a crucial role in filtering out methane from habitats, such as flooded rice fields. India has the largest area under rice cultivation in the world; however, to the best of our knowledge, methanotrophs have not been isolated and characterized from Indian rice fields. A cultivation strategy composing of a modified medium, longer incubation time, and serial dilutions in microtiter plates was used to cultivate methanotrophs from a rice rhizosphere sample from a flooded rice field in Western India. We compared the cultured members with the uncultured community as revealed by three culture-independent methods. A novel type Ia methanotroph (Sn10-6), at the rank of a genus, and a putative novel species of a type II methanotroph (Sn-Cys) were cultivated from the terminal positive dilution (10(-6)). From lower dilution (10(-4)), a strain of Methylomonas spp. was cultivated. All the three culture-independent analyses, i.e., pmoA clone library, terminal restriction fragment length polymorphism (T-RFLP), and metagenomics approach, revealed the dominance of type I methanotrophs. Only metagenomic analysis showed significant presence of type II methanotrophs, albeit in lower proportion (37 %). All the three isolates showed relevance to the methanotrophic community as depicted by uncultured methods; however, the cultivated members might not be the most dominant ones. In conclusion, a combined cultivation and cultivation-independent strategy yielded us a broader picture of the methanotrophic community from rice rhizospheres of a flooded rice field in India.
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Affiliation(s)
- Pranitha S Pandit
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
| | - Monali C Rahalkar
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.
| | | | - Dilip R Ranade
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
- Microbial Culture Collection, NCCS, Sai-Trinity Building Garware Circle, Pashan, Pune, Maharashtra, 411021, India
| | - Soham Pore
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
| | - Preeti Arora
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
| | - Neelam Kapse
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
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12
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Sherry A, Osborne KA, Sidgwick FR, Gray ND, Talbot HM. A temperate river estuary is a sink for methanotrophs adapted to extremes of pH, temperature and salinity. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:122-31. [PMID: 26617278 PMCID: PMC4959530 DOI: 10.1111/1758-2229.12359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 11/19/2015] [Indexed: 05/08/2023]
Abstract
River Tyne (UK) estuarine sediments harbour a genetically and functionally diverse community of methane-oxidizing bacteria (methanotrophs), the composition and activity of which were directly influenced by imposed environmental conditions (pH, salinity, temperature) that extended far beyond those found in situ. In aerobic sediment slurries methane oxidation rates were monitored together with the diversity of a functional gene marker for methanotrophs (pmoA). Under near in situ conditions (4-30°C, pH 6-8, 1-15 g l(-1) NaCl), communities were enriched by sequences affiliated with Methylobacter and Methylomonas spp. and specifically a Methylobacter psychrophilus-related species at 4-21°C. More extreme conditions, namely high temperatures ≥ 40°C, high ≥ 9 and low ≤ 5 pH, and high salinities ≥ 35 g l(-1) selected for putative thermophiles (Methylocaldum), acidophiles (Methylosoma) and haloalkaliphiles (Methylomicrobium). The presence of these extreme methanotrophs (unlikely to be part of the active community in situ) indicates passive dispersal from surrounding environments into the estuary.
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Affiliation(s)
- Angela Sherry
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kate A Osborne
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Frances R Sidgwick
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Neil D Gray
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Helen M Talbot
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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13
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Single gene locus changes perturb complex microbial communities as much as apex predator loss. Nat Commun 2015; 6:8235. [PMID: 26354365 PMCID: PMC4579780 DOI: 10.1038/ncomms9235] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 07/30/2015] [Indexed: 02/08/2023] Open
Abstract
Many bacterial species are highly social, adaptively shaping their local environment through the production of secreted molecules. This can, in turn, alter interaction strengths among species and modify community composition. However, the relative importance of such behaviours in determining the structure of complex communities is unknown. Here we show that single-locus changes affecting biofilm formation phenotypes in Bacillus subtilis modify community structure to the same extent as loss of an apex predator and even to a greater extent than loss of B. subtilis itself. These results, from experimentally manipulated multitrophic microcosm assemblages, demonstrate that bacterial social traits are key modulators of the structure of their communities. Moreover, they show that intraspecific genetic variability can be as important as strong trophic interactions in determining community dynamics. Microevolution may therefore be as important as species extinctions in shaping the response of microbial communities to environmental change. Some species of social bacteria can chemically modify their nutrient environments, which may influence community interactions. Here, McClean et al. show that changes at a single gene locus in a biofilm-forming bacteria can perturb community structure to the same extent as the loss of an apex predator.
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14
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Leng L, Chang J, Geng K, Lu Y, Ma K. Uncultivated Methylocystis Species in Paddy Soil Include Facultative Methanotrophs that Utilize Acetate. MICROBIAL ECOLOGY 2015; 70:88-96. [PMID: 25475784 DOI: 10.1007/s00248-014-0540-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 11/21/2014] [Indexed: 06/04/2023]
Abstract
Methanotrophs are crucial in regulating methane emission from rice field systems. Type II methanotrophs in particular are often observed in high abundance in paddy soil. Some cultivated species of Methylocystis are able to grow on acetate in the absence of methane. We hypothesize that the dominant type II methanotrophs in paddy soil might facultatively utilize acetate for growth, which we evaluate in the present study. The measurement of methane oxidation rates showed that the methanotrophic activity in paddy soil was inhibited by the addition of acetate compared to the continuous supplementation of methane, but the paddy soil maintained the methane oxidation capacity and recovered following methane supplementation. Terminal restriction fragment length polymorphism analysis (T-RFLP) combined with cloning and sequencing of pmoA genes showed that Methylocystis was enriched after incubation with added acetate, while the type I methanotrophs Methylocaldum/Methylococcus and Methylobacter were enriched by methane supplementation. A comparison of pmoA sequences obtained in this study with those in the public database indicated that they were globally widespread in paddy soils or in associated with rice roots. Furthermore, we performed stable isotope probing (SIP) of pmoA messenger RNA (mRNA) to investigate the assimilation of (13)C-acetate by paddy soil methanotrophs. RNA-SIP revealed that Methylocystis-related methanotrophs which shared the same genotype of the above enriched species were significantly labelled. It indicates that these methanotrophs actively assimilated the labelled acetate in paddy soil. Altogether, these results suggested that uncultivated Methylocystis species are facultative methanotrophs utilizing acetate as a secondary carbon source in paddy soil.
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Affiliation(s)
- Lingqin Leng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
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15
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Lee HJ, Jeong SE, Kim PJ, Madsen EL, Jeon CO. High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy. Front Microbiol 2015; 6:639. [PMID: 26161079 PMCID: PMC4479796 DOI: 10.3389/fmicb.2015.00639] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/12/2015] [Indexed: 11/24/2022] Open
Abstract
The communities and abundances of methanotrophs and methanogens, along with the oxygen, methane, and total organic carbon (TOC) concentrations, were investigated along a depth gradient in a flooded rice paddy. Broad patterns in vertical profiles of oxygen, methane, TOC, and microbial abundances were similar in the bulk and rhizosphere soils, though methane and TOC concentrations and 16S rRNA gene copies were clearly higher in the rhizosphere soil than in the bulk soil. Oxygen concentrations decreased sharply to below detection limits at 8 mm depth. Pyrosequencing of 16S rRNA genes showed that bacterial and archaeal communities varied according to the oxic, oxic-anoxic, and anoxic zones, indicating that oxygen is a determining factor for the distribution of bacterial and archaeal communities. Aerobic methanotrophs were maximally observed near the oxic-anoxic interface, while methane, TOC, and methanogens were highest in the rhizosphere soil at 30–200 mm depth, suggesting that methane is produced mainly from organic carbon derived from rice plants and is metabolized aerobically. The relative abundances of type I methanotrophs such as Methylococcus, Methylomonas, and Methylocaldum decreased more drastically than those of type II methanotrophs (such as Methylocystis and Methylosinus) with increasing depth. Methanosaeta and Methanoregula were predominant methanogens at all depths, and the relative abundances of Methanosaeta, Methanoregula, and Methanosphaerula, and GOM_Arc_I increased with increasing depth. Based on contrasts between absolute abundances of methanogens and methanotrophs at depths sampled across rhizosphere and bulk soils (especially millimeter-scale slices at the surface), we have identified populations of methanogens (Methanosaeta, Methanoregula, Methanocella, Methanobacterium, and Methanosphaerula), and methanotrophs (Methylosarcina, Methylococcus, Methylosinus, and unclassified Methylocystaceae) that are likely physiologically active in situ.
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Affiliation(s)
- Hyo Jung Lee
- Department of Life Science, Chung-Ang University Seoul, South Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University Seoul, South Korea
| | - Pil Joo Kim
- Division of Applied Life Science, Gyeongsang National University Jinju, South Korea
| | - Eugene L Madsen
- Department of Microbiology, Cornell University Ithaca, NY, USA
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University Seoul, South Korea
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16
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Kerckhof FM, Courtens ENP, Geirnaert A, Hoefman S, Ho A, Vilchez-Vargas R, Pieper DH, Jauregui R, Vlaeminck SE, Van de Wiele T, Vandamme P, Heylen K, Boon N. Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity. PLoS One 2014; 9:e99517. [PMID: 24937032 PMCID: PMC4061060 DOI: 10.1371/journal.pone.0099517] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 05/15/2014] [Indexed: 12/26/2022] Open
Abstract
The use of mixed microbial communities (microbiomes) for biotechnological applications has steadily increased over the past decades. However, these microbiomes are not readily available from public culture collections, hampering their potential for widespread use. The main reason for this lack of availability is the lack of an effective cryopreservation protocol. Due to this critical need, we evaluated the functionality as well as the community structure of three different types of microbiomes before and after cryopreservation with two cryoprotective agents (CPA). Microbiomes were selected based upon relevance towards applications: (1) a methanotrophic co-culture (MOB), with potential for mitigation of greenhouse gas emissions, environmental pollutants removal and bioplastics production; (2) an oxygen limited autotrophic nitrification/denitrification (OLAND) biofilm, with enhanced economic and ecological benefits for wastewater treatment, and (3) fecal material from a human donor, with potential applications for fecal transplants and pre/probiotics research. After three months of cryopreservation at −80°C, we found that metabolic activity, in terms of the specific activity recovery of MOB, aerobic ammonium oxidizing bacteria (AerAOB) and anaerobic AOB (AnAOB, anammox) in the OLAND mixed culture, resumes sooner when one of our selected CPA [dimethyl sulfoxide (DMSO) and DMSO plus trehalose and tryptic soy broth (DMSO+TT)] was added. However, the activity of the fecal community was not influenced by the CPA addition, although the preservation of the community structure (as determined by 16S rRNA gene sequencing) was enhanced by addition of CPA. In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. This will allow individual laboratories and culture collections to boost the use of microbiomes in biotechnological applications.
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Affiliation(s)
- Frederiek-Maarten Kerckhof
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Emilie N. P. Courtens
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Annelies Geirnaert
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Sven Hoefman
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Gent, Belgium
| | - Adrian Ho
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Ramiro Vilchez-Vargas
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Siegfried E. Vlaeminck
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Tom Van de Wiele
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Gent, Belgium
| | - Kim Heylen
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Gent, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
- * E-mail:
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17
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Bao Z, Watanabe A, Sasaki K, Okubo T, Tokida T, Liu D, Ikeda S, Imaizumi-Anraku H, Asakawa S, Sato T, Mitsui H, Minamisawa K. A rice gene for microbial symbiosis, Oryza sativa CCaMK, reduces CH4 flux in a paddy field with low nitrogen input. Appl Environ Microbiol 2014; 80:1995-2003. [PMID: 24441161 PMCID: PMC3957643 DOI: 10.1128/aem.03646-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/10/2014] [Indexed: 11/20/2022] Open
Abstract
Plants have mutualistic symbiotic relationships with rhizobia and fungi by the common symbiosis pathway, of which Ca(2+)/calmodulin-dependent protein kinase (encoded by CCaMK) is a central component. Although Oryza sativa CCaMK (OsCCaMK) is required for fungal accommodation in rice roots, little is known about the role of OsCCaMK in rice symbiosis with bacteria. Here, we report the effect of a Tos17-induced OsCCaMK mutant (NE1115) on CH4 flux in low-nitrogen (LN) and standard-nitrogen (SN) paddy fields compared with wild-type (WT) Nipponbare. The growth of NE1115 was significantly decreased compared with that of the WT, especially in the LN field. The CH4 flux of NE1115 in the LN field was significantly greater (156 to 407% in 2011 and 170 to 816% in 2012) than that of the WT, although no difference was observed in the SN field. The copy number of pmoA (encodes methane monooxygenase in methanotrophs) was significantly higher in the roots and rhizosphere soil of the WT than in those of NE1115. However, the mcrA (encodes methyl coenzyme M reductase in methanogens) copy number did not differ between the WT and NE1115. These results were supported by a (13)C-labeled CH4-feeding experiment. In addition, the natural abundance of (15)N in WT shoots (3.05‰) was significantly lower than in NE1115 shoots (3.45‰), suggesting greater N2 fixation in the WT because of dilution with atmospheric N2 (0.00‰). Thus, CH4 oxidation and N2 fixation were simultaneously activated in the root zone of WT rice in the LN field and both processes are likely controlled by OsCCaMK.
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Affiliation(s)
- Zhihua Bao
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
| | - Aya Watanabe
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
| | - Kazuhiro Sasaki
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
| | - Takashi Okubo
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
| | - Takeshi Tokida
- National Institute for Agro-Environmental Sciences, Tsukuba, Japan
| | - Dongyan Liu
- Graduate School of Agricultural Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Japan
| | - Seishi Ikeda
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
- Memuro Research Station, National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro-cho, Kasaigun, Hokkaido, Japan
| | - Haruko Imaizumi-Anraku
- Department of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Susumu Asakawa
- Graduate School of Agricultural Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Japan
| | - Tadashi Sato
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
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18
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Lüke C, Frenzel P, Ho A, Fiantis D, Schad P, Schneider B, Schwark L, Utami SR. Macroecology of methane-oxidizing bacteria: the β-diversity ofpmoAgenotypes in tropical and subtropical rice paddies. Environ Microbiol 2013; 16:72-83. [DOI: 10.1111/1462-2920.12190] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Claudia Lüke
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
- Radboud University Nijmegen; Heyendaalsweg 135 Nijmegen 6525 AJ The Netherlands
| | - Peter Frenzel
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
| | - Adrian Ho
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
- Laboratory for Microbial Ecology and Technology (LabMET); Faculty of Bioscience Engineering; Coupure Links 653 Ghent 9000 Belgium
| | - Dian Fiantis
- Department of Soil Science; Faculty of Agriculture; Andalas University; Kampus Unand Limau Manis Padang 25163 Indonesia
| | - Peter Schad
- Department Ecology and Ecosystem Management; Center of Life and Food Sciences Weihenstephan; Technische Universität München; Lehrstuhl für Bodenkunde Freising-Weihenstephan D-85350 Germany
| | - Bellinda Schneider
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
| | - Lorenz Schwark
- Institute of Geosciences; University Kiel; Ludewig-Meyn-Straße 10 Kiel 24118 Germany
- WA-OIGC; Curtin University; Perth WA 6845 Australia
| | - Sri Rahayu Utami
- Department of Soil Science; Faculty of Agriculture; Brawijaya University; Jalan Veteran Malang 65145 East Java Indonesia
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Dry/Wet cycles change the activity and population dynamics of methanotrophs in rice field soil. Appl Environ Microbiol 2013; 79:4932-9. [PMID: 23770899 DOI: 10.1128/aem.00850-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The methanotrophs in rice field soil are crucial in regulating the emission of methane. Drainage substantially reduces methane emission from rice fields. However, it is poorly understood how drainage affects microbial methane oxidation. Therefore, we analyzed the dynamics of methane oxidation rates, composition (using terminal restriction fragment length polymorphism [T-RFLP]), and abundance (using quantitative PCR [qPCR]) of methanotroph pmoA genes (encoding a subunit of particulate methane monooxygenase) and their transcripts over the season and in response to alternate dry/wet cycles in planted paddy field microcosms. In situ methane oxidation accounted for less than 15% of total methane production but was enhanced by intermittent drainage. The dry/wet alternations resulted in distinct effects on the methanotrophic communities in different soil compartments (bulk soil, rhizosphere soil, surface soil). The methanotrophic communities of the different soil compartments also showed distinct seasonal dynamics. In bulk soil, potential methanotrophic activity and transcription of pmoA were relatively low but were significantly stimulated by drainage. In contrast, however, in the rhizosphere and surface soils, potential methanotrophic activity and pmoA transcription were relatively high but decreased after drainage events and resumed after reflooding. While type II methanotrophs dominated the communities in the bulk soil and rhizosphere soil compartments (and to a lesser extent also in the surface soil), it was the pmoA of type I methanotrophs that was mainly transcribed under flooded conditions. Drainage affected the composition of the methanotrophic community only minimally but strongly affected metabolically active methanotrophs. Our study revealed dramatic dynamics in the abundance, composition, and activity of the various type I and type II methanotrophs on both a seasonal and a spatial scale and showed strong effects of dry/wet alternation cycles, which enhanced the attenuation of methane flux into the atmosphere.
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20
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Ho A, Kerckhof FM, Luke C, Reim A, Krause S, Boon N, Bodelier PLE. Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:335-45. [PMID: 23754714 DOI: 10.1111/j.1758-2229.2012.00370.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/06/2012] [Accepted: 07/15/2012] [Indexed: 05/11/2023]
Abstract
Methane-oxidizing bacteria (MOB) possess the ability to use methane for energy generation and growth, thereby, providing a key ecosystem service that is highly relevant to the regulation of the global climate. MOB subgroups have different responses to key environmental controls, reflecting on their functional traits. Their unique features (C1-metabolism, unique lipids and congruence between the 16S rRNA and pmoA gene phylogeny) have facilitated numerous environmental studies, which in combination with the availability of cultured representatives, yield the most comprehensive ecological picture of any known microbial functional guild. Here, we focus on the broad MOB subgroups (type I and type II MOB), and aim to conceptualize MOB functional traits and observational characteristics derived primarily from these environmental studies to be interpreted as microbial life strategies. We focus on the functional traits, and the conditions under which these traits will render different MOB subgroups a selective advantage. We hypothesize that type I and type II MOB generally have distinct life strategies, enabling them to predominate under different conditions and maintain functionality. The ecological characteristics implicated in their adopted life strategies are discussed, and incorporated into the Competitor-Stress tolerator-Ruderal functional classification framework as put forward for plant communities. In this context, type I MOB can broadly be classified as competitor-ruderal while type II MOB fit more within the stress tolerator categories. Finally, we provide an outlook on MOB applications by exemplifying two approaches where their inferred life strategies could be exploited thereby, putting MOB into the context of microbial resource management.
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Affiliation(s)
- Adrian Ho
- Laboratory of Microbial Ecology and Technology (LabMET), Faculty of Bioscience Engineering, Coupure Links 653, B-9000 Ghent, Belgium
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21
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One millimetre makes the difference: high-resolution analysis of methane-oxidizing bacteria and their specific activity at the oxic-anoxic interface in a flooded paddy soil. ISME JOURNAL 2012; 6:2128-39. [PMID: 22695859 DOI: 10.1038/ismej.2012.57] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Aerobic methane-oxidizing bacteria (MOB) use a restricted substrate range, yet >30 species-equivalent operational taxonomical units (OTUs) are found in one paddy soil. How these OTUs physically share their microhabitat is unknown. Here we highly resolved the vertical distribution of MOB and their activity. Using microcosms and cryosectioning, we sub-sampled the top 3-mm of a water-saturated soil at near in situ conditions in 100-μm steps. We assessed the community structure and activity using the particulate methane monooxygenase gene pmoA as a functional and phylogenetic marker by terminal restriction fragment length polymorphism (t-RFLP), a pmoA-specific diagnostic microarray, and cloning and sequencing. pmoA genes and transcripts were quantified using competitive reverse transcriptase PCR combined with t-RFLP. Only a subset of the methanotroph community was active. Oxygen microprofiles showed that 89% of total respiration was confined to a 0.67-mm-thick zone immediately above the oxic-anoxic interface, most probably driven by methane oxidation. In this zone, a Methylobacter-affiliated OTU was highly active with up to 18 pmoA transcripts per cell and seemed to be adapted to oxygen and methane concentrations in the micromolar range. Analysis of transcripts with a pmoA-specific microarray found a Methylosarcina-affiliated OTU associated with the surface zone. High oxygen but only nanomolar methane concentrations at the surface suggested an adaptation of this OTU to oligotrophic conditions. No transcripts of type II methanotrophs (Methylosinus, Methylocystis) were found, which indicated that this group was represented by resting stages only. Hence, different OTUs within a single guild shared the same microenvironment and exploited different niches.
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22
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Krause S, Lüke C, Frenzel P. Methane source strength and energy flow shape methanotrophic communities in oxygen-methane counter-gradients. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:203-8. [PMID: 23757274 DOI: 10.1111/j.1758-2229.2011.00322.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The role of microbial diversity for ecosystem functioning has become an important subject in microbial ecology. Recent work indicates that microbial communities and microbial processes can be very sensitive to anthropogenic disturbances. However, to what extent microbial communities may change upon, resist to, or overcome disturbances might differ depending on substrate availability. We used soil from an Italian rice field in gradient microcosms, and analysed the response of methanotrophic communities to an NH4 (+) pulse as a potential disturbance under two different CH4 source strengths. We found a significant influence of source strength, i.e. the energy flow through the methanotrophic community, while NH4 (+) had no effect. Our data suggest that historical contingencies, i.e. nitrogen fertilization, led to an ammonium-tolerant MOB community. Methanotrophs were able to oxidize virtually all CH4 diffusing into the oxic-anoxic boundary layer regardless of NH4 (+) addition. Total and active methanotrophic communities were assessed by a pmoA-specific microarray. From the reservoir of dormant methanotrophs, different species became active with Methylobacter and an environmental cluster affiliated with paddy soils being indicative for high CH4 source strength. Thus, a microbial seed bank is an important prerequisite to maintain functioning in a fluctuating environment.
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Affiliation(s)
- Sascha Krause
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, 6708 AB Wageningen, The Netherlands
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23
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Dianou D, Ueno C, Ogiso T, Kimura M, Asakawa S. Diversity of cultivable methane-oxidizing bacteria in microsites of a rice paddy field: investigation by cultivation method and fluorescence in situ hybridization (FISH). Microbes Environ 2012; 27:278-87. [PMID: 22446309 PMCID: PMC4036049 DOI: 10.1264/jsme2.me11327] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The diversity of cultivable methane-oxidizing bacteria (MOB) in the rice paddy field ecosystem was investigated by combined culture-dependent and fluorescence in situ hybridization (FISH) techniques. Seven microsites of a Japanese rice paddy field were the focus of the study: floodwater, surface soil, bulk soil, rhizosphere soil, root, basal stem of rice plant, and rice stumps of previous harvest. Based on pmoA gene analysis and transmission electron microscopy (TEM), four type I, and nine type II MOB isolates were obtained from the highest dilution series of enrichment cultures. The type I MOB isolates included a novel species in the genus Methylomonas from floodwater and this is the first type I MOB strain isolated from floodwater of a rice paddy field. In the type I MOB, two isolates from stumps were closely related to Methylomonas spp.; one isolate obtained from rhizosphere soil was most related to Methyloccocus-Methylocaldum-Methylogaea clade. Almost all the type II MOB isolates were related to Methylocystis methanotrophs. FISH confirmed the presence of both types I and II MOB in all the microsites and in the related enrichment cultures. The study reported, for the first time, the diversity of cultivable methanotrophs including a novel species of type I MOB in rice paddy field compartments. Refining growth media and culture conditions, in combination with molecular approaches, will allow us to broaden our knowledge on the MOB community in the rice paddy field ecosystem and consequently to implement strategies for mitigating CH4 emission from this ecosystem.
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Affiliation(s)
- Dayéri Dianou
- Centre National de la Recherche Scientifique et Technologique, 03BP7192 Ouagadougou, Burkina Faso
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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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25
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Mayumi D, Yoshimoto T, Uchiyama H, Nomura N, Nakajima-Kambe T. Seasonal change in methanotrophic diversity and populations in a rice field soil assessed by DNA-stable isotope probing and quantitative real-time PCR. Microbes Environ 2011; 25:156-63. [PMID: 21576868 DOI: 10.1264/jsme2.me10120] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The community structure of methane-oxidizing bacteria (methanotrophs) is affected by concentrations of methane and oxygen. In rice fields, concentrations of both gases differ significantly between the flooded and drained seasons. We investigated the active methanotrophic community structures in flooded and drained soils by DNA-based stable isotope probing. Active methanotrophic diversity was assessed with clone library-based analyses of the 16S rRNA gene and the particulate methane monooxygenase gene (pmoA). The active methanotrophic populations were also estimated by group-specific quantitative real-time PCR assays targeting the 16S rRNA gene and the pmoA gene in (13)C-labeled DNA. These molecular biological analyses showed that the flooded rice field soil was dominated by Type II methanotrophs closely related to the genera Methylocystis and Methylosinus, whereas the drained rice field soil was dominated by Type I methanotrophs closely related to the genera Methylomonas, Methylosarcina, and Methylomicrobium. The alternating conditions in a rice field select for methanotrophs adapted to each environment, resulting in a dramatic change in methanotrophic community structure from one season to another.
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Affiliation(s)
- Daisuke Mayumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8572, Japan
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26
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Lee EH, Park H, Cho KS. Characterization of methane, benzene and toluene-oxidizing consortia enriched from landfill and riparian wetland soils. JOURNAL OF HAZARDOUS MATERIALS 2010; 184:313-320. [PMID: 20832163 DOI: 10.1016/j.jhazmat.2010.08.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 07/14/2010] [Accepted: 08/11/2010] [Indexed: 05/29/2023]
Abstract
The microbial oxidations of methane (M) and volatile organic compounds (VOCs) were compared with those of M and VOCs alone after enriching soil samples with M and/or VOCs. Landfill cover and riparian wetland soils from which M and VOCs were simultaneously emitted were selected as representative samples. Benzene (B) and toluene (T) were employed as the model VOCs. With the landfill soil consortia, the rate of M oxidation decreased from 4.15-5.56 to 2.26-3.42 μmol g-dry soil(-1)h(-1) in the presence of both B and T, but with the wetland soil consortia the rate of M oxidation (3.09 μmol g-dry soil(-1)h(-1)) in the mixture of M as well as both B and T was similar to that of M alone (3.04 μmol g-dry soil(-1)h(-1)). Compared with the methanotrophic community with M alone, the portion of type II methanotrophs was greater in the landfill consortia; whereas, the proportion in wetland consortia was less in the presence of both B and T. The oxidations of B and T were stimulated by the presence of M with both the landfill and wetland consortia. There were no correlations between the oxidation rate of M and those of B and T with the gene copy numbers of pmoA and tmoA responsible for the oxidations.
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Affiliation(s)
- Eun-Hee Lee
- Department of Environmental Science and Engineering, Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-gu, Seoul 120-750, Republic of Korea
| | - Hyunjung Park
- Department of Environmental Science and Engineering, Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-gu, Seoul 120-750, Republic of Korea
| | - Kyung-Suk Cho
- Department of Environmental Science and Engineering, Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-gu, Seoul 120-750, Republic of Korea.
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27
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Recovery of methanotrophs from disturbance: population dynamics, evenness and functioning. ISME JOURNAL 2010; 5:750-8. [PMID: 20981115 DOI: 10.1038/ismej.2010.163] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biodiversity is claimed to be essential for ecosystem functioning, but is threatened by anthropogenic disturbances. Prokaryotes have been assumed to be functionally redundant and virtually inextinguishable. However, recent work indicates that microbes may well be sensitive to environmental disturbance. Focusing on methane-oxidizing bacteria as model organisms, we simulated disturbance-induced mortality by mixing native with sterilized paddy soil in two ratios, 1:4 and 1:40, representing moderate and severe die-offs. Disturbed microcosms were compared with an untreated control. Recovery of activity and populations was followed over 4 months by methane uptake measurements, pmoA-qPCR, pmoA-based terminal restriction fragment length polymorphism and a pmoA-based diagnostic microarray. Diversity and evenness of methanotrophs decreased in disturbed microcosms, but functioning was not compromised. We consistently observed distinctive temporal shifts between type I and type II methanotrophs, and a rapid population growth leading to even higher cell numbers comparing disturbed microcosms with the control. Overcompensating mortality suggested that population size in the control was limited by competition with other bacteria. Overall, methanotrophs showed a remarkable ability to compensate for die-offs.
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28
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Succession of methanotrophs in oxygen-methane counter-gradients of flooded rice paddies. ISME JOURNAL 2010; 4:1603-7. [PMID: 20574459 DOI: 10.1038/ismej.2010.82] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Little is known about population dynamics and contribution of specific taxa to methane oxidation in flooded rice paddies. In this article we investigate the succession of methanotrophs in oxygen-methane counter-gradients. We used a gradient microcosm system that simulates oxic-anoxic interfaces of a water-saturated paddy soils, and measured pmoA-based (gene encoding particulate methane monooxygenase) terminal restriction fragment length polymorphism (T-RFLP) profiles at both the transcription (mRNA) and the population (DNA) levels. The DNA T-RFLP profiles indicated that the methanotrophic community present clearly differed from the active methanotrophic community. We observed a succession of the methanotrophic community over time without any direct effect of pore water chemistry on the community structure. Both the total population and the active subpopulation changed with time, whereas methane oxidation rates remained nearly constant. Hence, we suggest that a diverse microbial seed bank of methanotrophs is important in maintaining the function in a dynamic ecosystem.
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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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Longa CMO, Pertot I. An intact soil-core microcosm method to evaluate the survival and vertical dispersal ofTrichoderma atrovirideSC1. Lett Appl Microbiol 2009; 49:609-14. [PMID: 19780964 DOI: 10.1111/j.1472-765x.2009.02715.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- C M O Longa
- IASMA Research and Innovation Center, Fondazione Edmund Mach, 38010 S. Michele all'Adige (TN), Italy.
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31
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Conrad R, Klose M, Noll M. Functional and structural response of the methanogenic microbial community in rice field soil to temperature change. Environ Microbiol 2009; 11:1844-53. [PMID: 19508556 DOI: 10.1111/j.1462-2920.2009.01909.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microbial community in anoxic rice field soil produces CH(4) over a wide temperature range up to 55°C. However, at temperatures higher than about 40°C, the methanogenic path changes from CH(4) production by hydrogenotrophic plus acetoclastic methanogenesis to exclusively hydrogenotrophic methanogenesis and simultaneously, the methanogenic community consisting of Methanosarcinaceae, Methanoseataceae, Methanomicrobiales, Methanobacteriales and Rice Cluster I (RC-1) changes to almost complete dominance of RC-1. We studied changes in structure and function of the methanogenic community with temperature to see whether microbial members of the community were lost or their function impaired by exposure to high temperature. We characterized the function of the community by the path of CH(4) production measuring δ(13)C in CH(4) and CO(2) and calculating the apparent fractionation factor (α(app)) and the structure of the community by analysis of the terminal restriction fragment length polymorphism (T-RFLP) of the microbial 16S rRNA genes. Shift of the temperature from 45°C to 35°C resulted in a corresponding shift of function and structure, especially when some 35°C soil was added to the 45°C soil. The bacterial community (T-RFLP patterns), which was much more diverse than the archaeal community, changed in a similar manner upon temperature shift. Incubation of a mixture of 35°C and 50°C pre-incubated methanogenic rice field soil at different temperatures resulted in functionally and structurally well-defined communities. Although function changed from a mixture of acetoclastic and hydrogenotrophic methanogenesis to exclusively hydrogenotrophic methanogenesis over a rather narrow temperature range of 42-46°C, each of these temperatures also resulted in only one characteristic function and structure. Our study showed that temperature conditions defined structure and function of the methanogenic microbial community.
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Affiliation(s)
- Ralf Conrad
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str., 35043 Marburg, Germany.
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32
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Ferrando L, Tarlera S. Activity and diversity of methanotrophs in the soil-water interface and rhizospheric soil from a flooded temperate rice field. J Appl Microbiol 2009; 106:306-16. [DOI: 10.1111/j.1365-2672.2008.04004.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Applying stable isotope probing of phospholipid fatty acids and rRNA in a Chinese rice field to study activity and composition of the methanotrophic bacterial communities in situ. ISME JOURNAL 2008; 2:602-14. [DOI: 10.1038/ismej.2008.34] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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34
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Shrestha M, Abraham WR, Shrestha PM, Noll M, Conrad R. Activity and composition of methanotrophic bacterial communities in planted rice soil studied by flux measurements, analyses of pmoA gene and stable isotope probing of phospholipid fatty acids. Environ Microbiol 2008; 10:400-12. [DOI: 10.1111/j.1462-2920.2007.01462.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Liebner S, Wagner D. Abundance, distribution and potential activity of methane oxidizing bacteria in permafrost soils from the Lena Delta, Siberia. Environ Microbiol 2007; 9:107-17. [PMID: 17227416 DOI: 10.1111/j.1462-2920.2006.01120.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The methane oxidation potential of active layer profiles of permafrost soils from the Lena Delta, Siberia, was studied with regard to its respond to temperature, and abundance and distribution of type I and type II methanotrophs. Our results indicate vertical shifts within the optimal methane oxidation temperature and within the distribution of type I and type II methanotrophs. In the upper active layer, maximum methane oxidation potentials were detected at 21 degrees C. Deep active layer zones that are constantly exposed to temperatures below 2 degrees C showed a maximum potential to oxidize methane at 4 degrees C. Our results indicate a dominance of psychrophilic methanotrophs close to the permafrost table. Type I methanotrophs dominated throughout the active layer profiles but their number strongly fluctuated with depth. In contrast, type II methanotrophs were constantly abundant through the whole active layer and displaced type I methanotrophs close to the permafrost table. No correlation between in situ temperatures and the distribution of type I and type II methanotrophs was found. However, the distribution of type I and type II methanotrophs correlated significantly with in situ methane concentrations. Beside vertical fluctuations, the abundance of methane oxidizers also fluctuated according to different geomorphic units. Similar methanotroph cell counts were detected in samples of a flood plain and a polygon rim, whereas cell counts in samples of a polygon centre were up to 100 times lower.
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Affiliation(s)
- Susanne Liebner
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Telegrafenberg A43, 14473 Potsdam, Germany.
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36
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Lim JM, Jeon CO, Lee GS, Park DJ, Kang UG, Park CY, Kim CJ. Leeia oryzae gen. nov., sp. nov., isolated from a rice field in Korea. Int J Syst Evol Microbiol 2007; 57:1204-1208. [PMID: 17551030 DOI: 10.1099/ijs.0.64582-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly aerobic, non-spore-forming, Gram-negative bacterium, designated strain HW7T, was isolated from a rice field in Korea. Cells of strain HW7T were short rod-shaped and motile with single polar flagella. The major cellular fatty acids of strain HW7T were C16 : 0 and summed feature 3 (C16 : 1
ω7c and/or iso-C15 : 0 2-OH). The genomic DNA G+C content was 56 mol% and the major isoprenoid quinone was Q-8. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HW7T forms a distinct lineage with respect to closely related genera within the class Betaproteobacteria and that the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93 %. On the basis of the physiological and phylogenetic data, strain HW7T represents a novel genus and species of the Betaproteobacteria, for which the name Leeia oryzae gen. nov., sp. nov. is proposed. The type strain is HW7T (=KCTC 12585T=DSM 17879T).
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MESH Headings
- Aerobiosis
- Base Composition
- Betaproteobacteria/classification
- Betaproteobacteria/genetics
- Betaproteobacteria/isolation & purification
- Betaproteobacteria/physiology
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Genes, rRNA
- Korea
- Locomotion
- Molecular Sequence Data
- Oryza
- Phylogeny
- Quinones/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
- Spores, Bacterial
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Affiliation(s)
- Jee-Min Lim
- Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Yusong, Daejeon 305-333, Republic of Korea
| | - Che Ok Jeon
- Division of Applied Life Science, EB-NCRC, PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Gye Suk Lee
- Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Yusong, Daejeon 305-333, Republic of Korea
| | - Dong-Jin Park
- Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Yusong, Daejeon 305-333, Republic of Korea
| | - Ui-Gum Kang
- Yeongnam Agricultural Research Institute, 1085 Neidong, Milyang 627-803, Republic of Korea
| | - Chang-Young Park
- Yeongnam Agricultural Research Institute, 1085 Neidong, Milyang 627-803, Republic of Korea
| | - Chang-Jin Kim
- Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Yusong, Daejeon 305-333, Republic of Korea
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Saito A, Ikeda S, Ezura H, Minamisawa K. Microbial Community Analysis of the Phytosphere Using Culture-Independent Methodologies. Microbes Environ 2007. [DOI: 10.1264/jsme2.22.93] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Asami Saito
- Graduate School of Life Sciences, Tohoku University
| | - Seishi Ikeda
- Graduate School of Life Sciences, Tohoku University
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Murase J, Noll M, Frenzel P. Impact of protists on the activity and structure of the bacterial community in a rice field soil. Appl Environ Microbiol 2006; 72:5436-44. [PMID: 16885296 PMCID: PMC1538762 DOI: 10.1128/aem.00207-06] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 05/31/2006] [Indexed: 11/20/2022] Open
Abstract
Flooded rice fields have become a model system for the study of soil microbial ecology. In Italian rice fields, in particular, aspects from biogeochemistry to molecular ecology have been studied, but the impact of protistan grazing on the structure and function of the prokaryotic community has not been examined yet. We compared an untreated control soil with a gamma-radiation-sterilized soil that had been reinoculated with a natural bacterial assemblage. In order to verify that the observed effects were due to protistan grazing and did not result from sterilization, we set up a third set of microcosms containing sterilized soil that had been reinoculated with natural assemblage bacteria plus protists. The spatial and temporal changes in the protistan and prokaryotic communities were examined by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analysis, respectively, both based on the small-subunit gene. Sequences retrieved from DGGE bands were preferentially affiliated with Cercozoa and other bacteriovorous flagellates. Without protists, the level of total DNA increased with incubation time, indicating that the level of the microbial biomass was elevated. Betaproteobacteria were preferentially preyed upon, while low-G + C-content gram-positive bacteria became more dominant under grazing pressure. The bacterial diversity detectable by T-RFLP analysis was greater in the presence of protists. The level of extractable NH4+ was lower and the level of extractable SO4(2-) was higher without protists, indicating that nitrogen mineralization and SO4(2-) reduction were stimulated by protists. Most of these effects were more obvious in the partially oxic surface layer (0 to 3 mm), but they could also be detected in the anoxic subsurface layer (10 to 13 mm). Our observations fit well into the overall framework developed for protistan grazing, but with some modifications pertinent to the wetland situation: O2 was a major control, and O2 availability may have limited directly and indirectly the development of protists. Although detectable in the lower anoxic layer, grazing effects were much more obvious in the partially oxic surface layer.
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Affiliation(s)
- Jun Murase
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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39
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Eller G, Deines P, Grey J, Richnow HH, Krüger M. Methane cycling in lake sediments and its influence on chironomid larval delta13C. FEMS Microbiol Ecol 2006; 54:339-50. [PMID: 16332332 DOI: 10.1016/j.femsec.2005.04.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2005] [Revised: 04/19/2005] [Accepted: 04/20/2005] [Indexed: 11/29/2022] Open
Abstract
Stable carbon isotope analysis of chironomid larvae gave rise to the hypothesis that methane-oxidizing bacteria can provide an important food source for higher trophic levels in lakes. To investigate the importance of the methane cycle for the larval stable carbon signatures, isotope analysis and microbiological and biogeochemical investigations were combined. The study was based on comparison of a dimictic lake (Holzsee) and a polymictic, shallow lake (Grosser Binnensee), both located in northern Germany. Both lakes are inhabited by Chironomus plumosus larvae, which exhibited a stronger (13)C-depletion in Holzsee than in Grosser Binnensee, indicating a greater contribution of methane-carbon in the former. Indeed, the processes involved in the microbial methane cycle were found to be more active in Holzsee, showing higher potential methane production and methane oxidation rates. Consistently, cell numbers of methane-oxidizing bacteria were with 0.5 - 1.7 x 10(6) cells g(dw)(-1) about one order of magnitude higher in Holzsee than in Grosser Binnensee. Molecular analysis of the microbial community structure revealed no differences in the methanotrophic community between the two lakes, with a clear dominance of type I methanotrophs. The methanogenic population seemed to be adapted to the prevailing substrate in the respective lake (H(2)/CO(2) in Holzsee and acetate in Grosser Binnensee), even though differences were minor. In conclusion, the stronger larval (13)C-depletion in Holzsee was not reflected in differences in the microbial community structure, but in the activity and size of the methanogenic and methanotrophic populations in the lake sediment.
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Affiliation(s)
- Gundula Eller
- Max Planck Institute for Limnology, August-Thienemann-Strasse 2, 24306 Plön, Germany.
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40
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Mohanty SR, Bodelier PLE, Floris V, Conrad R. Differential effects of nitrogenous fertilizers on methane-consuming microbes in rice field and forest soils. Appl Environ Microbiol 2006; 72:1346-54. [PMID: 16461686 PMCID: PMC1392950 DOI: 10.1128/aem.72.2.1346-1354.2006] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The impact of environmental perturbation (e.g., nitrogenous fertilizers) on the dynamics of methane fluxes from soils and wetland systems is poorly understood. Results of fertilizer studies are often contradictory, even within similar ecosystems. In the present study the hypothesis of whether these contradictory results may be explained by the composition of the methane-consuming microbial community and hence whether methanotrophic diversity affects methane fluxes was investigated. To this end, rice field and forest soils were incubated in microcosms and supplemented with different nitrogenous fertilizers and methane concentrations. By labeling the methane with 13C, diversity and function could be coupled by analyses of phospholipid-derived fatty acids (PLFA) extracted from the soils at different time points during incubation. In both rice field and forest soils, the activity as well as the growth rate of methane-consuming bacteria was affected differentially. For type I methanotrophs, fertilizer application stimulated the consumption of methane and the subsequent growth, while type II methanotrophs were generally inhibited. Terminal restriction fragment length polymorphism analyses of the pmoA gene supported the PLFA results. Multivariate analyses of stable-isotope-probing PLFA profiles indicated that in forest and rice field soils, Methylocystis (type II) species were affected by fertilization. The type I methanotrophs active in forest soils (Methylomicrobium/Methylosarcina related) differed from the active species in rice field soils (Methylobacter/Methylomonas related). Our results provide a case example showing that microbial community structure indeed matters, especially when assessing and predicting the impact of environmental change on biodiversity loss and ecosystem functioning.
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Affiliation(s)
- Santosh R Mohanty
- Max Planck Institute for Terrestrial Microbiology, Department of Biogeochemistry, Karl-von-Frisch-Str., 35043 Marburg, Germany
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