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Pavloudi C, Zafeiropoulos H. Deciphering the community structure and the functional potential of a hypersaline marsh microbial mat community. FEMS Microbiol Ecol 2022; 98:6843573. [PMID: 36416806 DOI: 10.1093/femsec/fiac141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/31/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
Microbial mats are vertically stratified communities of microorganisms characterized by pronounced physiochemical gradients allowing for high species diversity and a wide range of metabolic capabilities. High Throughput Sequencing has the potential to reveal the biodiversity and function of such ecosystems in the cycling of elements. The present study combines 16S rRNA amplicon sequencing and shotgun metagenomics on a hypersaline marsh in Tristomo bay (Karpathos, Greece). Samples were collected in July 2018 and November 2019 from microbial mats, deeper sediment, aggregates observed in the water overlying the sediment, as well as sediment samples with no apparent layering. Metagenomic samples' coassembly and binning revealed 250 bacterial and 39 archaeal metagenome-assembled genomes, with completeness estimates higher than 70% and contamination less than 5%. All MAGs had KEGG Orthology terms related to osmoadaptation, with the 'salt in' strategy ones being prominent. Halobacteria and Bacteroidetes were the most abundant taxa in the mats. Photosynthesis was most likely performed by purple sulphur and nonsulphur bacteria. All samples had the capacity for sulphate reduction, dissimilatory arsenic reduction, and conversion of pyruvate to oxaloacetate. Overall, both sequencing methodologies resulted in similar taxonomic compositions and revealed that the formation of the microbial mat in this marsh exhibits seasonal variation.
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Affiliation(s)
- Christina Pavloudi
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), P.O. Box 2214, 71003, Heraklion, Crete, Greece.,Department of Biological Sciences, The George Washington University, 2029 G St NW, Bell Hall 302, Washington DC 20052, United States
| | - Haris Zafeiropoulos
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), P.O. Box 2214, 71003, Heraklion, Crete, Greece.,Department of Biology, University of Crete, Voutes University Campus, P.O. Box 2208, 70013, Heraklion, Crete, Greece.,Laboratory of Molecular Bacteriology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49, box 1028, 3000 Leuven, Belgium
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2
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Cheng X, Wang H, Zeng Z, Li L, Zhao R, Bodelier PLE, Wang Y, Liu X, Su C, Liu S. Niche differentiation of atmospheric methane-oxidizing bacteria and their community assembly in subsurface karst caves. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:886-896. [PMID: 35925016 DOI: 10.1111/1758-2229.13112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/05/2022] [Accepted: 07/17/2022] [Indexed: 06/17/2023]
Abstract
Karst caves are recently proposed as atmospheric methane sinks in terrestrial ecosystems. Despite of the detection of atmospheric methane-oxidizing bacteria (atmMOB) in caves, we still know little about their ecology and potential ability of methane oxidation in this ecosystem. To understand atmMOB ecology and their potential in methane consumption, we collected weathered rocks and sediments from three different caves in southwestern China. We determined the potential methane oxidization rates in the range of 1.25 ± 0.08 to 1.87 ± 0.41 ng CH4 g-1 DW h-1 , which are comparable to those reported in forest and grassland soils. Results showed that alkaline oligotrophic caves harbour high numbers of atmMOB, particularly upland soil cluster (USC), which significantly correlated with temperature, CH4 and CO2 concentrations. The absolute abundance of USCγ was higher than that of USCα. USCγ-OPS (open patch soil) and USCγ-SS (subsurface soil) dominated in most samples, whereas USCα-BFS (boreal forest soil) only predominated in the sediments near cave entrances, indicating niche differentiation of atmMOB in caves. Overwhelming dominance of homogenous selection in community assembly resulted in convergence of atmMOB communities. Collectively, our results demonstrated the niche differentiation of USC in subsurface alkaline caves and their non-negligible methane-oxidizing potential, providing brand-new knowledge about atmMOB ecology in subsurface biosphere.
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Affiliation(s)
- Xiaoyu Cheng
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Hongmei Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Zhilin Zeng
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Lu Li
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Yiheng Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Xiaoyan Liu
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Chuntian Su
- CAGS/Key Laboratory of Karst Dynamics, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, P. R. China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
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Changes in Soil Chemical Properties Due to Long-Term Compost Fertilization Regulate Methane Turnover Related Gene Abundances in Rice Paddy. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Maintaining rice yield, soil function, and fertility are essential components of long-term compost fertilization. However, paddy fields are major sources of anthropogenic methane emissions. The aim of the study is to evaluate the changes in soil chemical properties and their concurrent impact on the abundance of methanogenesis (mcrA) and methane oxidation (pmoA) related genes among compost (Com), NPK+Compost (NPKCom), and unfertilized (NF) fallow paddy fields under long-term compost fertilization. Results showed that compost and NPK+Compost fertilization altered the soil chemical properties of paddy fields with a significant increase in the functional gene abundance potentially associated with Methanobacteriaceae for mcrA (1.23 × 106 to 3.84 × 106 copy number g−1 dry soil) and methane oxidizing bacteria such as Methylomonas and Methylobacter for pmoA (1.65 × 106 to 4.3 × 106 copy number g−1 dry soil). Ordination plots visualized these changes, where treatments clustered distinctly indicating that Com and NPKCom treatments were characterized by paddy soils with elevated OM, TN, K and P content and higher abundances of methanogenesis and methane oxidation related genes. The study showed that long-term compost fertilization resulted in paddy fields with high nutrient content and high gene abundance, attributed to methanogens and methane oxidizing bacteria that responded well with compost fertilization. These results indicated the potential of these fallow paddy fields for methane emission and methane oxidation and that they are ‘primed’, potentially influencing subsequent paddy field responses to long-term compost application.
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Li Q, Peng C, Zhang J, Li Y, Song X. Nitrogen addition decreases methane uptake caused by methanotroph and methanogen imbalances in a Moso bamboo forest. Sci Rep 2021; 11:5578. [PMID: 33692387 PMCID: PMC7947007 DOI: 10.1038/s41598-021-84422-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 02/11/2021] [Indexed: 11/23/2022] Open
Abstract
Forest soils play an important role in controlling global warming by reducing atmospheric methane (CH4) concentrations. However, little attention has been paid to how nitrogen (N) deposition may alter microorganism communities that are related to the CH4 cycle or CH4 oxidation in subtropical forest soils. We investigated the effects of N addition (0, 30, 60, or 90 kg N ha−1 yr−1) on soil CH4 flux and methanotroph and methanogen abundance, diversity, and community structure in a Moso bamboo (Phyllostachys edulis) forest in subtropical China. N addition significantly increased methanogen abundance but reduced both methanotroph and methanogen diversity. Methanotroph and methanogen community structures under the N deposition treatments were significantly different from those of the control. In N deposition treatments, the relative abundance of Methanoculleus was significantly lower than that in the control. Soil pH was the key factor regulating the changes in methanotroph and methanogen diversity and community structure. The CH4 emission rate increased with N addition and was negatively correlated with both methanotroph and methanogen diversity but positively correlated with methanogen abundance. Overall, our results suggested that N deposition can suppress CH4 uptake by altering methanotroph and methanogen abundance, diversity, and community structure in subtropical Moso bamboo forest soils.
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Affiliation(s)
- Quan Li
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, 712100, China.,State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Changhui Peng
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, 712100, China. .,Department of Biology Sciences, Institute of Environment Sciences, University of Quebec at Montreal, Case Postale 8888, Succursale Centre-Ville, Montreal, H3C3P8, Canada.
| | - Junbo Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yongfu Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xinzhang Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China.
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Farhan Ul Haque M, Xu HJ, Murrell JC, Crombie A. Facultative methanotrophs - diversity, genetics, molecular ecology and biotechnological potential: a mini-review. MICROBIOLOGY (READING, ENGLAND) 2020; 166:894-908. [PMID: 33085587 PMCID: PMC7660913 DOI: 10.1099/mic.0.000977] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/20/2020] [Indexed: 12/18/2022]
Abstract
Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although Methylocella strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.
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Affiliation(s)
| | - Hui-Juan Xu
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andrew Crombie
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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Exploring the effect of plant substrates on bacterial community structure in termite fungus-combs. PLoS One 2020; 15:e0232329. [PMID: 32357167 PMCID: PMC7194444 DOI: 10.1371/journal.pone.0232329] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 04/14/2020] [Indexed: 11/19/2022] Open
Abstract
Fungus-cultivating termites are successful herbivores largely rely on the external symbiotic fungus-combs to decompose plant polysaccharides. The comb harbors both fungi and bacteria. However, the complementary roles and functions of the bacteria are out of the box. To this purpose, we look into different decomposition stages of fungus-combs using high-throughput sequencing of the 16S rRNA gene to examine bacterial community structure. We also explored the bacterial response to physicochemical indexes (such as moisture, ash content and organic matter) and plant substrates (leaves or branches or mix food). Some specific families such as Lachnospiraceae, Ruminococcaceae, and Peptostreptococcaceae may be involved in lignocellulose degradation, whereas Burkholderiaceae may be associated with aromatic compounds degradation. We observed that as the comb mature there is a shift of community composition which may be an adjustment of specific bacteria to deal with different lignocellulosic material. Our results indicated that threshold amount of physicochemical indexes are beneficial for bacterial diversity but too high moisture, low organic matter and high ash content may reduce their diversity. Furthermore, the average highest bacterial diversity was recorded from the comb built by branches followed by mix food and leaves. Besides, this study could help in the use of bacteria from the comb of fungus-cultivating termites in forestry and agricultural residues making them easier to digest as fodder.
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Wang PX, Yang YD, Wang XQ, Zhao J, Peixoto L, Zeng ZH, Zang HD. Manure amendment increased the abundance of methanogens and methanotrophs but suppressed the type I methanotrophs in rice paddies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:8016-8027. [PMID: 31889290 DOI: 10.1007/s11356-019-07464-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
Methane (CH4) emission is the consequence of CH4 production and consumption performed by methanogens and methanotrophs, respectively. Fertilization is an important factor that regulates the behavior of methanogens and methanotrophs; however, the effect of manure and rice straw addition combined with inorganic fertilizers on these communities is not well understood. This study aimed to explore how manure and rice straw amendments together with inorganic fertilizers influenced the methanogenic and methanotrophic communities in a 31-year fertilized rice paddy. Manure amendment significantly increased the abundance of mcrA and pmoA genes by 61.2% and 63.3% compared with the unfertilized control, whereas inorganic NPK fertilization alone or rice straw addition did not affect their abundances. Manure and rice straw amendments greatly decreased the Shannon index and ACE index of the methanogenic communities, whereas inorganic NPK fertilization alone increased the ACE index of the methanotrophic communities compared with the unfertilized control. Methanosarcinaceae and Methylococcaceae dominated at the family level, representing 23.1-35.0% and 48.7-67.2% of the total reads, for the methanogenic and methanotrophic communities, respectively. Application of manure together with inorganic fertilizers suppressed the Methanocellales methanogens and the type I methanotrophs (Methylococcus and Methylobacter). Fertilization greatly altered the community structure of methanogens and methanotrophs, and manure addition had more apparent effects than rice straw. Moreover, total nitrogen, soil organic carbon, available phosphorus, and available potassium correlated significantly to the abundance, composition, and community structure of methanogens and methanotrophs. In conclusion, our study revealed that long-term manure amendment in combination with inorganic fertilizers significantly increased the abundance of methanogens and methanotrophs, but suppressed the type I methanotrophs in rice paddies.
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Affiliation(s)
- Pei-Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Ya-Dong Yang
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Xi-Quan Wang
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Jie Zhao
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
| | - Leanne Peixoto
- Department of Agroecology, Aarhus University, Blichers Allé 20, 8830, Tjele, DK, Denmark
| | - Zhao-Hai Zeng
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China.
| | - Hua-Dong Zang
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
- Key Laboratory of Farming System, Ministry of Agriculture and Rural Affairs, Beijing, 100193, China
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Berkelmann D, Schneider D, Meryandini A, Daniel R. Unravelling the effects of tropical land use conversion on the soil microbiome. ENVIRONMENTAL MICROBIOME 2020; 15:5. [PMID: 33902736 PMCID: PMC8067294 DOI: 10.1186/s40793-020-0353-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/18/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND The consequences of deforestation and agricultural treatments are complex and affect all trophic levels. Changes of microbial community structure and composition associated with rainforest conversion to managed systems such as rubber and oil palm plantations have been shown by 16S rRNA gene analysis previously, but functional profile shifts have been rarely addressed. In this study, we analysed the effects of rainforest conversion to different converted land use systems, including agroforestry ("jungle rubber") and monoculture plantations comprising rubber and oil palm, on soilborne microbial communities by metagenomic shotgun sequencing in Sumatra, Indonesia. RESULTS The diversity of bacteria and archaea decreased whereas diversity of fungi increased in the converted land use systems. The soil microbiome was dominated by bacteria followed by fungi. We detected negative effects of land use conversion on the abundance of Proteobacteria (especially on Rhizobiales and Burkholderiales) and positive effects on the abundance of Acidobacteria and Actinobacteria. These abundance changes were mainly driven by pH, C:N ratio, and Fe, C and N content. With increasing land use intensity, the functional diversity decreased for bacteria, archaea and fungi. Gene abundances of specific metabolisms such as nitrogen metabolism and carbon fixation were affected by land use management practices. The abundance of genes related to denitrification and nitrogen fixation increased in plantations while abundance of genes involved in nitrification and methane oxidation showed no significant difference. Linking taxonomic and functional assignment per read indicated that nitrogen metabolism-related genes were mostly assigned to members of the Rhizobiales and Burkholderiales. Abundances of carbon fixation genes increased also with increasing land use intensity. Motility- and interaction-related genes, especially genes involved in flagellar assembly and chemotaxis genes, decreased towards managed land use systems. This indicated a shift in mobility and interspecific interactions in bacterial communities within these soils. CONCLUSIONS Rainforest conversion to managed land use systems drastically affects structure and functional potential of soil microbial communities. The decrease in motility- and interaction-related functions from rainforest to converted land use systems indicated not only a shift in nutrient cycling but also in community dynamics. Fertilizer application and correspondingly higher availability of nutrients in intensively managed plantations lead to an environment in which interspecific interactions are not favoured compared to rainforest soils. We could directly link effects of land management, microbial community structure and functional potential for several metabolic processes. As our study is the first study of this size and detail on soil microbial communities in tropical systems, we provide a basis for further analyses.
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Affiliation(s)
- Dirk Berkelmann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Anja Meryandini
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstr. 8, 37077, Göttingen, Germany.
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Erythritol as a single carbon source improves cultural isolation of Burkholderia pseudomallei from rice paddy soils. PLoS Negl Trop Dis 2019; 13:e0007821. [PMID: 31634353 PMCID: PMC6822774 DOI: 10.1371/journal.pntd.0007821] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/31/2019] [Accepted: 10/01/2019] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Isolation of the soil bacterium Burkholderia pseudomallei from tropical environments is important to generate a global risk map for man and animals to acquire the infectious disease melioidosis. There is increasing evidence, that the currently recommended soil culture protocol using threonine-basal salt solution with colistin (TBSS-C50) for enrichment of B. pseudomallei and Ashdown agar for subsequent subculture lacks sensitivity. We therefore investigated, if the otherwise rarely encountered erythritol catabolism of B. pseudomallei might be exploited to improve isolation of this bacterium from soil. METHODOLOGY/PRINCIPAL FINDINGS Based on TBSS-C50, we designed a new colistin-containing medium with erythritol as the single carbon source (EM). This medium was validated in various culture protocols by analyzing 80 soil samples from 16 different rice fields in Vietnam. B. pseudomallei enrichment was determined in all culture supernatants by a specific quantitative PCR (qPCR) targeting the type three secretion system 1. 51 out of 80 (63.8%) soil samples gave a positive qPCR signal in at least one of the culture conditions. We observed a significantly higher enrichment shown by lower median cycle threshold values for B. pseudomallei in a two-step culture with TBSS-C50 for 48 h followed by EM for 96h compared to single cultures in TBSS-C50 for either 48h or 144h (p<0.0001, respectively). Accordingly, B. pseudomallei could be isolated on Ashdown agar in 58.8% (30/51) of samples after subcultures from our novel two-step enrichment culture compared to only 9.8% (5/51) after standard enrichment with TBSS-C50 for 48h (p<0.0001) or 25.5% (13/51; p<0.01) after TBSS-C50 for 144h. CONCLUSIONS/SIGNIFICANCE In the present study, we show that specific exploitation of B. pseudomallei metabolic capabilities in enrichment protocols leads to a significantly improved isolation rate of this pathogen from soil compared to established standard procedures. Our new culture method might help to facilitate the creation of environmental risk maps for melioidosis in the future.
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Berkelmann D, Schneider D, Engelhaupt M, Heinemann M, Christel S, Wijayanti M, Meryandini A, Daniel R. How Rainforest Conversion to Agricultural Systems in Sumatra (Indonesia) Affects Active Soil Bacterial Communities. Front Microbiol 2018; 9:2381. [PMID: 30364106 PMCID: PMC6191527 DOI: 10.3389/fmicb.2018.02381] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
Palm oil production in Indonesia increased constantly over the last decades, which led to massive deforestation, especially on Sumatra island. The ongoing conversion of rainforest to agricultural systems results in high biodiversity loss. Here, we present the first RNA-based study on the effects of rainforest transformation to rubber and oil palm plantations in Indonesia for the active soil bacterial communities. For this purpose, bacterial communities of three different converted systems (jungle rubber, rubber plantation, and oil palm plantation) were studied in two landscapes with rainforest as reference by RT-PCR amplicon-based analysis of 16S rRNA gene transcripts. Active soil bacterial communities were dominated by Frankiales (Actinobacteria), subgroup 2 of the Acidobacteria and Alphaproteobacteria (mainly Rhizobiales and Rhodospirillales). Community composition differed significantly between the converted land use systems and rainforest reference sites. Alphaproteobacteria decreased significantly in oil palm samples compared to rainforest samples. In contrast, relative abundances of taxa within the Acidobacteria increased. Most important abiotic drivers for shaping soil bacterial communities were pH, calcium concentration, base saturation and C:N ratio. Indicator species analysis showed distinct association patterns for the analyzed land use systems. Nitrogen-fixing taxa including members of Rhizobiales and Rhodospirillales were associated with rainforest soils while nitrifiers and heat-resistant taxa including members of Actinobacteria were associated with oil palm soils. Predicted metabolic profiles revealed that the relative abundances of genes associated with fixation of nitrogen significantly decreased in plantation soils. Furthermore, predicted gene abundances regarding motility, competition or gene transfer ability indicated rainforest conversion-induced changes as well.
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Affiliation(s)
- Dirk Berkelmann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Martin Engelhaupt
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Melanie Heinemann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Stephan Christel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Marini Wijayanti
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Anja Meryandini
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
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Ueki A, Kaku N, Ueki K. Role of anaerobic bacteria in biological soil disinfestation for elimination of soil-borne plant pathogens in agriculture. Appl Microbiol Biotechnol 2018; 102:6309-6318. [DOI: 10.1007/s00253-018-9119-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/20/2018] [Accepted: 05/21/2018] [Indexed: 01/15/2023]
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Lv H, Sahin N, Tani A. Isolation and genomic characterization ofNovimethylophilus kurashikiensisgen. nov. sp. nov., a new lanthanide-dependent methylotrophic species ofMethylophilaceae. Environ Microbiol 2018; 20:1204-1223. [DOI: 10.1111/1462-2920.14062] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/17/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Haoxin Lv
- Institute of Plant Science and Resources, Okayama University; Okayama Japan
| | - Nurettin Sahin
- Egitim Fakultesi, Mugla Sitki Kocman University; 48170 Kotekli, Mugla Turkey
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University; Okayama Japan
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Jiang Y, van Groenigen KJ, Huang S, Hungate BA, van Kessel C, Hu S, Zhang J, Wu L, Yan X, Wang L, Chen J, Hang X, Zhang Y, Horwath WR, Ye R, Linquist BA, Song Z, Zheng C, Deng A, Zhang W. Higher yields and lower methane emissions with new rice cultivars. GLOBAL CHANGE BIOLOGY 2017; 23:4728-4738. [PMID: 28464384 DOI: 10.1111/gcb.13737] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/15/2017] [Accepted: 04/14/2017] [Indexed: 05/25/2023]
Abstract
Breeding high-yielding rice cultivars through increasing biomass is a key strategy to meet rising global food demands. Yet, increasing rice growth can stimulate methane (CH4 ) emissions, exacerbating global climate change, as rice cultivation is a major source of this powerful greenhouse gas. Here, we show in a series of experiments that high-yielding rice cultivars actually reduce CH4 emissions from typical paddy soils. Averaged across 33 rice cultivars, a biomass increase of 10% resulted in a 10.3% decrease in CH4 emissions in a soil with a high carbon (C) content. Compared to a low-yielding cultivar, a high-yielding cultivar significantly increased root porosity and the abundance of methane-consuming microorganisms, suggesting that the larger and more porous root systems of high-yielding cultivars facilitated CH4 oxidation by promoting O2 transport to soils. Our results were further supported by a meta-analysis, showing that high-yielding rice cultivars strongly decrease CH4 emissions from paddy soils with high organic C contents. Based on our results, increasing rice biomass by 10% could reduce annual CH4 emissions from Chinese rice agriculture by 7.1%. Our findings suggest that modern rice breeding strategies for high-yielding cultivars can substantially mitigate paddy CH4 emission in China and other rice growing regions.
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Affiliation(s)
- Yu Jiang
- Institute of Applied Ecology, Nanjing Agricultural University, Nanjing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing, China
| | - Kees Jan van Groenigen
- Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Shan Huang
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Chris van Kessel
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Shuijin Hu
- Institute of Applied Ecology, Nanjing Agricultural University, Nanjing, China
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Jun Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing, China
| | - Lianhai Wu
- Sustainable Soils and Grassland Systems Department, Rothamsted Research, Okehampton, UK
| | - Xiaojun Yan
- Institute of Applied Ecology, Nanjing Agricultural University, Nanjing, China
| | - Lili Wang
- Institute of Applied Ecology, Nanjing Agricultural University, Nanjing, China
| | - Jin Chen
- Soil and Fertilizer & Resources and Environmental Institute, Jiangxi Academy of Agricultural Science, Nanchang, China
| | - Xiaoning Hang
- Institute of Agricultural Resources and Environment, Chongqing Academy of Agricultural Science, Chongqing, China
| | - Yi Zhang
- Institute of Applied Ecology, Nanjing Agricultural University, Nanjing, China
| | - William R Horwath
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
| | - Rongzhong Ye
- Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Bruce A Linquist
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Zhenwei Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing, China
| | - Chengyan Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing, China
| | - Aixing Deng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing, China
| | - Weijian Zhang
- Institute of Applied Ecology, Nanjing Agricultural University, Nanjing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing, China
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14
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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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15
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Martínez-Porchas M, Vargas-Albores F. An efficient strategy using k-mers to analyse 16S rRNA sequences. Heliyon 2017; 3:e00370. [PMID: 28795166 PMCID: PMC5537200 DOI: 10.1016/j.heliyon.2017.e00370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/11/2017] [Accepted: 07/21/2017] [Indexed: 11/28/2022] Open
Abstract
The use of k-mers has been a successful strategy for improving metagenomics studies, including taxonomic classifications, or de novo assemblies, and can be used to obtain sequences of interest from the available databases. The aim of this manuscript was to propose a simple but efficient strategy to generate k-mers and to use them to obtain and analyse in silico 16S rRNA sequence fragments. A total of 513,309 bacterial sequences contained in the SILVA database were considered for the study, and homemade PHP scripts were used to search for specific nucleotide chains, recover fragments of bacterial sequences, make calculations and organize information. Consensus sequences matching conserved regions were constructed by aligning most of the primers used in the literature. Sequences of k nucleotides (9- to 15-mers) were extracted from the generated primer contigs. Frequency analysis revealed that k-mer size was inversely proportional to the occurrence of k-mers in the different conserved regions, suggesting a stringency relationship; high numbers of duplicate reactions were observed with short k-mers, and a lower proportion of sequences were obtained with large ones, with the best results obtained using 12-mers. Using 12-mers with the proposed method to obtain and study sequences was found to be a reliable approach for the analysis of 16S rRNA sequences and this strategy may probably be extended to other biomarkers. Furthermore, additional applications such as evaluating the degree of conservation and designing primers and other calculations are proposed as examples.
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Affiliation(s)
| | - Francisco Vargas-Albores
- Centro de Investigación en Alimentación y Desarrollo, A. C. Km 0.6 Carretera a La Victoria. Hermosillo, Sonora, México
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16
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Liu H, Wu X, Li Z, Wang Q, Liu D, Liu G. Responses of soil methanogens, methanotrophs, and methane fluxes to land-use conversion and fertilization in a hilly red soil region of southern China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:8731-8743. [PMID: 28213705 DOI: 10.1007/s11356-017-8628-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/10/2017] [Indexed: 06/06/2023]
Abstract
Changes in land-uses and fertilization are important factors regulating methane (CH4) emissions from paddy soils. However, the responses of soil CH4 emissions to these factors and the underlying mechanisms remain unclear. The objective of this study was to explore the effects of land-use conversion from paddies to orchards and fertilization on soil CH4 fluxes, and the abundance and community compositions of methanogens and methanotrophs. Soil CH4 fluxes were quantified by static chamber and gas chromatography technology. Abundance and community structures of methanogens and methanotrophs (based on mcrA and pmoA genes, respectively) were determined by quantitative real-time PCR (qPCR), and terminal restriction fragment length polymorphism (TRFLP), cloning and sequence analysis, respectively. Results showed that land-use conversion from paddies to orchards dramatically decreased soil CH4 fluxes, whereas fertilization did not distinctly affect soil CH4 fluxes. Furthermore, abundance of methanogens and methanotrophs were decreased after converting paddies to orchards. Fertilization decreased the abundance of these microorganisms, but the values were not statistically significant. Moreover, land-use conversion had fatal effects on some members of the methanogenic archaea (Methanoregula and Methanosaeta), increased type II methanotrophs (Methylocystis and Methylosinus), and decreased type I methanotrophs (Methylobacter and Methylococcus). However, fertilization could only significantly affect type I methanotrophs in the orchard plots. In addition, CH4 fluxes from paddy soils were positively correlated with soil dissolved organic carbon contents and methanogens abundance, whereas CH4 fluxes in orchard plots were negatively related to methanotroph abundance. Therefore, our results suggested that land-use conversion from paddies to orchards could change the abundance and community compositions of methanogens and methanotrophs, and ultimately alter the soil CH4 fluxes. Overall, our study shed insight on the underlying mechanisms of how land-use conversion from paddies to orchards decreased CH4 emissions.
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Affiliation(s)
- Huifeng Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Xing Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- Joint Center for Global Change Studies, Beijing, 100875, China.
| | - Zongshan Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Joint Center for Global Change Studies, Beijing, 100875, China
| | - Qing Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Dan Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Guohua Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- Joint Center for Global Change Studies, Beijing, 100875, China.
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17
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Martinez-Porchas M, Villalpando-Canchola E, Ortiz Suarez LE, Vargas-Albores F. How conserved are the conserved 16S-rRNA regions? PeerJ 2017; 5:e3036. [PMID: 28265511 PMCID: PMC5333541 DOI: 10.7717/peerj.3036] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/26/2017] [Indexed: 12/20/2022] Open
Abstract
The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123) were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers) were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%). Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker.
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18
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Butterfield CN, Li Z, Andeer PF, Spaulding S, Thomas BC, Singh A, Hettich RL, Suttle KB, Probst AJ, Tringe SG, Northen T, Pan C, Banfield JF. Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PeerJ 2016; 4:e2687. [PMID: 27843720 PMCID: PMC5103831 DOI: 10.7717/peerj.2687] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/14/2016] [Indexed: 01/03/2023] Open
Abstract
Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10–20 cm and 30–40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate. From ten samples, we reconstructed 198 metagenome-assembled genomes that represent all major phylotypes. We also quantified 6,835 proteins and 175 metabolites and showed that after the rain event the concentrations of many sugars and amino acids approach zero at the base of the soil profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that these abundant organisms contribute substantially to carbon turnover in the soil, given that methylotrophy proteins were among the most abundant proteins in the proteome. Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid degradation. Many of the other bacteria appear to breakdown other components of plant biomass, as evidenced by the prevalence of various sugar and amino acid transporters and corresponding hydrolyzing machinery in the proteome. Overall, our work provides organism-resolved insight into the spatial distribution of bacteria and archaea whose activities combine to degrade plant-derived organics, limiting the transport of methanol, amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously little known soil microbes, were made possible via the combination of metagenomics, proteomics, and metabolomics.
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Affiliation(s)
- Cristina N Butterfield
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Zhou Li
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN , Unites States
| | - Peter F Andeer
- Lawrence Berkeley National Laboratory , Berkeley , CA , United States
| | - Susan Spaulding
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Andrea Singh
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN , Unites States
| | - Kenwyn B Suttle
- Department of Ecology and Evolutionary Biology, University of California , Santa Cruz , CA , United States
| | - Alexander J Probst
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | | | - Trent Northen
- Lawrence Berkeley National Laboratory , Berkeley , CA , United States
| | - Chongle Pan
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN , Unites States
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, United States; Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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19
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Ali A, Ayesha, Hameed S, Imran A, Iqbal M, Iqbal J, Oresnik IJ. Functional characterization of a soybean growth stimulator Bradyrhizobium sp. strain SR-6 showing acylhomoserine lactone production. FEMS Microbiol Ecol 2016; 92:fiw115. [PMID: 27242370 DOI: 10.1093/femsec/fiw115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2016] [Indexed: 01/09/2023] Open
Abstract
A soybean nodule endophytic bacterium Bradyrhizobium sp. strain SR-6 was characterized for production of acyl homoserine lactones (AHLs) as quorum sensing molecules. Mass spectrometry analysis of AHLs revealed the presence of C6-HSL, 3OH-C6-HSL, C8-HSL, C10-HSL, 3oxoC10-HSL, 3oxo-C12-HSL and 3OH-C12-HSL which are significantly different from those reported earlier in soybean symbionts. Purified AHL extracts significantly improved wheat and soybean seedling growth and root hair development along with increased soybean nodulation under axenic conditions. A positive correlation was observed among in vivo nitrogenase and catalase enzyme activities of the strain SR-6. Transmission electron microscopic analysis showed the cytochemical localization of catalase activity within the bacteroids, specifically attached to the peribacteroidal membrane. Root and nodule colonization proved rhizosphere competence of SR-6. The inoculation of SR-6 resulted in increased shoot length (13%), plant dry matter (50%), grain weight (16%), seed yield (20%) and N-uptake (14%) as compared to non-inoculated soybean plants. The symbiotic bacterium SR-6 has potential to improve soybean growth and yield in sub-humid climate of Azad Jammu and Kashmir region of Pakistan. The production and mass spectrometric profiling of AHLs as well as in vivo cytochemical localization of catalase enzyme activity in soybean Bradyrhizobium sp. have never been reported earlier elsewhere before our these investigations.
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Affiliation(s)
- Amanat Ali
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, PO Box no. 577, Faisalabad 38000, Pakistan
| | - Ayesha
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, PO Box no. 577, Faisalabad 38000, Pakistan
| | - Sohail Hameed
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, PO Box no. 577, Faisalabad 38000, Pakistan
| | - Asma Imran
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, PO Box no. 577, Faisalabad 38000, Pakistan
| | - Mazhar Iqbal
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, PO Box no. 577, Faisalabad 38000, Pakistan
| | - Javed Iqbal
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, PO Box no. 577, Faisalabad 38000, Pakistan
| | - Ivan J Oresnik
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
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20
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Imhoff JF. New Dimensions in Microbial Ecology-Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment. Microorganisms 2016; 4:microorganisms4020019. [PMID: 27681913 PMCID: PMC5029485 DOI: 10.3390/microorganisms4020019] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 05/20/2016] [Accepted: 05/20/2016] [Indexed: 12/11/2022] Open
Abstract
During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5'phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane monooxygenase (pmoA) for methane oxidizing bacteria.
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Affiliation(s)
- Johannes F Imhoff
- GEOMAR Helmholtz-Zentrum für Ozeanforschung, Düsternbrooker Weg 20, D-24105 Kiel, Germany.
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21
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Breidenbach B, Pump J, Dumont MG. Microbial Community Structure in the Rhizosphere of Rice Plants. Front Microbiol 2016; 6:1537. [PMID: 26793175 PMCID: PMC4710755 DOI: 10.3389/fmicb.2015.01537] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/21/2015] [Indexed: 01/26/2023] Open
Abstract
The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth.
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Affiliation(s)
- Björn Breidenbach
- Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Judith Pump
- Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Marc G Dumont
- Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
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22
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Li H, Dietrich C, Zhu N, Mikaelyan A, Ma B, Pi R, Liu Y, Yang M, Brune A, Mo J. Age polyethism drives community structure of the bacterial gut microbiota in the fungus-cultivating termite Odontotermes formosanus. Environ Microbiol 2015; 18:1440-51. [PMID: 26346907 DOI: 10.1111/1462-2920.13046] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/30/2015] [Accepted: 09/02/2015] [Indexed: 11/28/2022]
Abstract
Fungus-cultivating termites (Macrotermitinae) possess an elaborate strategy of lignocellulose digestion. It involves a lignocellulose-degrading fungal symbiont (genus Termitomyces), a diverse gut microbiota and a characteristic labour division in food processing. In this study, using pyrotag sequencing and electron microscopy, we analysed the bacterial microbiota in the hindgut of Odontotermes formosanus and its fungus comb to investigate the spatial organization, establishment and temporal succession of the bacterial communities colonizing specific microhabitats. Our results document strong differences between the communities at the hindgut epithelium and the luminal fluid of newly moulted, young and old worker termites. The differences in community structure were consistent with the density, morphology and spatial distribution of bacterial cells and the pools of microbial metabolites in the hindgut compartment, underlining that both gut development and the age-specific changes in diet affect the composition and functional role of their gut microbiota. These findings provide strong support for the concept that changes in diet and gut environment are important determinants of community structure because they create new niches for microbial symbionts.
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Affiliation(s)
- Hongjie Li
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Carsten Dietrich
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Na Zhu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Aram Mikaelyan
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Bin Ma
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Ruoxi Pi
- Program in the Biological and Biomedical Sciences and Department of Microbial Pathogenesis, Yale University, New Haven, CT, USA
| | - Yu Liu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Mengyi Yang
- Xiaoshan Institute of Termite Control, Xiaoshan, Zhejiang, China
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jianchu Mo
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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23
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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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24
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Juottonen H, Kotiaho M, Robinson D, Merilä P, Fritze H, Tuittila ES. Microform-related community patterns of methane-cycling microbes in boreal Sphagnum bogs are site specific. FEMS Microbiol Ecol 2015. [PMID: 26220310 DOI: 10.1093/femsec/fiv094] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Vegetation and water table are important regulators of methane emission in peatlands. Microform variation encompasses these factors in small-scale topographic gradients of dry hummocks, intermediate lawns and wet hollows. We examined methane production and oxidization among microforms in four boreal bogs that showed more variation of vegetation within a bog with microform than between the bogs. Potential methane production was low and differed among bogs but not consistently with microform. Methane oxidation followed water table position with microform, showing higher rates closer to surface in lawns and hollows than in hummocks. Methanogen community, analysed by mcrA terminal restriction fragment length polymorphism and dominated by Methanoregulaceae or 'Methanoflorentaceae', varied strongly with bog. The extent of microform-related variation of methanogens depended on the bog. Methanotrophs identified as Methylocystis spp. in pmoA denaturing gradient gel electrophoresis similarly showed effect of bog, and microform patterns were stronger within individual bogs. Our results suggest that methane-cycling microbes in boreal Sphagnum bogs with seemingly uniform environmental conditions may show strong site-dependent variation. The bog-intrinsic factor may be related to carbon availability but contrary to expectations appears to be unrelated to current surface vegetation, calling attention to the origin of carbon substrates for microbes in bogs.
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Affiliation(s)
- Heli Juottonen
- Department of Biosciences, General Microbiology, University of Helsinki, FI-00014, Finland
| | - Mirkka Kotiaho
- Peatland Ecology Group, Department of Forest Sciences, University of Helsinki, FI-00014, Finland
| | - Devin Robinson
- Natural Resources Institute Finland, Vantaa Unit, FI-01370 Vantaa, Finland
| | - Päivi Merilä
- Natural Resources Institute Finland, Oulu Unit, University of Oulu, FI-90014, Finland
| | - Hannu Fritze
- Natural Resources Institute Finland, Vantaa Unit, FI-01370 Vantaa, Finland
| | - Eeva-Stiina Tuittila
- Peatland Ecology Group, Department of Forest Sciences, University of Helsinki, FI-00014, Finland
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25
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Meena KK, Kumar M, Mishra S, Ojha SK, Wakchaure GC, Sarkar B. Phylogenetic study of methanol oxidizers from chilika-lake sediments using genomic and metagenomic approaches. Indian J Microbiol 2015; 55:151-62. [PMID: 25805901 DOI: 10.1007/s12088-015-0510-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 01/03/2015] [Indexed: 01/13/2023] Open
Abstract
Group-wise diversity of sediment methylotrophs of Chilika lake (Lat. 19°28'-19°54'N; Long. 85°06'-85°35'E) Odisha, India at various identified sites was studied. Both the culturable and unculturable (metagenome) methylotrophs were investigated in the lake sediments employing both mxaF and 16S rRNA genes as markers. ARDRA profiling, 16S rRNA gene sequencing, PAGE profiling of HaeIII, EcoRI restricted mxaF gene and the mxaF gene sequences using culture-dependent approach revealed the relatedness of α-proteobacteria and Methylobacterium, Hyphomicrobium and Ancyclobacter sp. The total viable counts of the culturable aerobic methylotrophs were relatively higher in sediments near the sea mouth (S3; Panaspada), also demonstrated relatively high salinity (0.1 M NaCl) tolerance. Metagenomic DNA from the sediments, amplified using GC clamp mxaF primers and resolved through DGGE, revealed the diversity within the unculturable methylotrophic bacterium Methylobacterium organophilum, Ancyclobacter aquaticus, Burkholderiales and Hyphomicrobium sp. Culture-independent analyses revealed that up to 90 % of the methylotrophs were unculturable. The study enhances the general understandings of the metagenomic methylotrophs from such a special ecological niche.
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Affiliation(s)
- Kamlesh K Meena
- National Bureau of Agriculturally Important Microorganisms, Mau Nath Bhanjan, 275 101 UP India ; National Institute of Abiotic Stress Management, Malegaon, Baramati, Pune, Maharashtra India
| | - Manish Kumar
- National Bureau of Agriculturally Important Microorganisms, Mau Nath Bhanjan, 275 101 UP India
| | - Snehasish Mishra
- School of Biotechnology, KIIT University, Campus-11, Bhubaneswar, 751024 Odisha India
| | - Sanjay Kumar Ojha
- School of Biotechnology, KIIT University, Campus-11, Bhubaneswar, 751024 Odisha India
| | - Goraksha C Wakchaure
- National Institute of Abiotic Stress Management, Baramati, Pune, 413115 Maharashtra India
| | - Biplab Sarkar
- National Institute of Abiotic Stress Management, Baramati, Pune, 413115 Maharashtra India
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26
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Shan J, Huang W, Nguyen L, Yu Y, Zhang S, Li Y, Frenkel AI, Tao FF. Conversion of methane to methanol with a bent mono(μ-oxo)dinickel anchored on the internal surfaces of micropores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8558-8569. [PMID: 24896721 DOI: 10.1021/la501184b] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The oxidation of methane to methanol is a pathway to utilizing this relatively abundant, inexpensive energy resource. Here we report a new catalyst, bent mono(μ-oxo)dinickel anchored on an internal surface of micropores,which is active for direct oxidation. It is synthesized from the direct loading of a nickel precursor to the internal surface of micropores of ZSM5 following activation in O2. Ni 2p3/2 of this bent mono(μ-oxo)dinickel species formed on the internal surface of ZSM5 exhibits a unique photoemission feature, which distinguishes the mono(μ-oxo)dinickel from NiO nanoparticles. The formation of the mono(μ-oxo)dinickel species was confirmed with X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS). This mono(μ-oxo)dinickel species is active for the direct oxidation of methane to methanol under the mild condition of a temperature as low as 150 °C in CH4 at 1 bar. In-situ studies using UV-vis, XANES, and EXAFS suggest that this bent mono(μ-oxo)dinickel species is the active site for the direct oxidation of methane to methanol. The energy barrier of this direct oxidation of methane is 83.2 kJ/mol.
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Affiliation(s)
- Junjun Shan
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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27
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Radek R, Strassert JF, Krüger J, Meuser K, Scheffrahn RH, Brune A. Phylogeny and Ultrastructure of Oxymonas jouteli, a Rostellum-free Species, and Opisthomitus longiflagellatus sp. nov., Oxymonadid Flagellates from the Gut of Neotermes jouteli. Protist 2014; 165:384-99. [DOI: 10.1016/j.protis.2014.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 04/03/2014] [Accepted: 04/10/2014] [Indexed: 11/24/2022]
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28
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Liew EF, Tong D, Coleman NV, Holmes AJ. Mutagenesis of the hydrocarbon monooxygenase indicates a metal centre in subunit-C, and not subunit-B, is essential for copper-containing membrane monooxygenase activity. MICROBIOLOGY-SGM 2014; 160:1267-1277. [PMID: 24682027 DOI: 10.1099/mic.0.078584-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The hydrocarbon monooxygenase (HMO) of Mycobacterium NBB4 is a member of the copper-containing membrane monooxygenase (CuMMO) superfamily, which also contains particulate methane monooxygenases (pMMOs) and ammonia monooxygenases (AMOs). CuMMOs have broad applications due to their ability to catalyse the oxidation of difficult substrates of environmental and industrial relevance. Most of our understanding of CuMMO biochemistry is based on pMMOs and AMOs as models. All three available structures are from pMMOs. These share two metal sites: a dicopper centre coordinated by histidine residues in subunit-B and a 'variable-metal' site coordinated by carboxylate and histidine residues from subunit-C. The exact nature and role of these sites is strongly debated. Significant barriers to progress have been the physiologically specialized nature of methanotrophs and autotrophic ammonia-oxidizers, lack of a recombinant expression system for either enzyme and difficulty in purification of active protein. In this study we use the newly developed HMO model system to perform site-directed mutagenesis on the predicted metal-binding residues in the HmoB and HmoC of NBB4 HMO. All mutations of predicted HmoC metal centre ligands abolished enzyme activity. Mutation of a predicted copper-binding residue of HmoB (B-H155V) reduced activity by 81 %. Mutation of a site that shows conservation within physiologically defined subgroups of CuMMOs was shown to reduce relative HMO activity towards larger alkanes. The study demonstrates that the modelled dicopper site of subunit-B is not sufficient for HMO activity and that a metal centre predicted to be coordinated by residues in subunit-C is essential for activity.
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Affiliation(s)
- Elissa F Liew
- School of Molecular Bioscience, Building G08, University of Sydney, NSW 2006, Australia
| | - Daochen Tong
- School of Molecular Bioscience, Building G08, University of Sydney, NSW 2006, Australia
| | - Nicholas V Coleman
- School of Molecular Bioscience, Building G08, University of Sydney, NSW 2006, Australia
| | - Andrew J Holmes
- School of Molecular Bioscience, Building G08, University of Sydney, NSW 2006, Australia
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29
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Lee HJ, Kim SY, Kim PJ, Madsen EL, Jeon CO. Methane emission and dynamics of methanotrophic and methanogenic communities in a flooded rice field ecosystem. FEMS Microbiol Ecol 2014; 88:195-212. [DOI: 10.1111/1574-6941.12282] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 01/03/2014] [Accepted: 01/03/2014] [Indexed: 01/19/2023] Open
Affiliation(s)
- Hyo Jung Lee
- Department of Life Science; Chung-Ang University; Seoul Korea
| | - Sang Yoon Kim
- Division of Applied Life Science; Gyeongsang National University; Jinju Korea
| | - Pil Joo Kim
- Division of Applied Life Science; Gyeongsang National University; Jinju Korea
| | | | - Che Ok Jeon
- Department of Life Science; Chung-Ang University; Seoul Korea
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30
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Kizilova AK, Sukhacheva MV, Pimenov NV, Yurkov AM, Kravchenko IK. Methane oxidation activity and diversity of aerobic methanotrophs in pH-neutral and semi-neutral thermal springs of the Kunashir Island, Russian Far East. Extremophiles 2013; 18:207-18. [PMID: 24343375 DOI: 10.1007/s00792-013-0603-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 11/14/2013] [Indexed: 11/26/2022]
Abstract
Aerobic methane oxidation has been mostly studied in environments with moderate to low temperatures. However, the process also occurs in terrestrial thermal springs, where little research on the subject has been done to date. The potential activity of methane oxidation and diversity of aerobic methanotrophic bacteria were studied in sediments of thermal springs with various chemical and physical properties, sampled across the Kunashir Island, the Kuriles archipelago. Activity was measured by means of the radioisotope tracer technique utilizing (14)C-labeled methane. Biodiversity assessments were based on the particulate methane monooxygenase (pmoA) gene, which is found in all known thermophilic and thermotolerant methanotrophs. We demonstrated the possibility of methane oxidation in springs with temperature exceeding 74 °C, and the most intensive methane uptake was shown in springs with temperatures about 46 °C. PmoA was detected in 19 out of 30 springs investigated and the number of pmoA gene copies varied between 10(4) and 10(6) copies per ml of sediment. Phylogenetic analysis of PmoA sequences revealed the presence of methanotrophs from both the Alpha- and Gammaproteobacteria. Our results suggest that methanotrophs inhabiting thermal springs with temperature exceeding 50 °C may represent novel thermophilic and thermotolerant species of the genera Methylocystis and Methylothermus, as well as previously undescribed Gammaproteobacteria.
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Affiliation(s)
- A K Kizilova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, 117312, Moscow, Russia,
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31
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Ishida H, Golmen LG, West J, Krüger M, Coombs P, Berge JA, Fukuhara T, Magi M, Kita J. Effects of CO2 on benthic biota: an in situ benthic chamber experiment in Storfjorden (Norway). MARINE POLLUTION BULLETIN 2013; 73:443-451. [PMID: 23465619 DOI: 10.1016/j.marpolbul.2013.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 01/04/2013] [Accepted: 02/09/2013] [Indexed: 06/01/2023]
Abstract
Carbon capture and storage (CCS) methods, either sub-seabed or in ocean depths, introduces risk of CO2 leakage and subsequent interaction with the ecosystem. It is therefore important to obtain information on possible effects of CO2. In situ CO2 exposure experiments were carried out twice for 10 days during 2005 using a Benthic Chamber system at 400 m depth in Storfjorden, Norway. pCO2 in the water above the sediment in the chambers was controlled at approximately 500, 5000 and 20,000 μatm, respectively. This article describes the experiment and the results from measured the biological responses within the chamber sediments. The results show effects of elevated CO2 concentrations on biological processes such as increased nanobenthos density. Methane production and sulphate reduction was enhanced in the approximately 5000 μatm chamber.
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Affiliation(s)
- Hiroshi Ishida
- General Environmental Technos Co., Ltd., Tokyo 101-0042, Japan.
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32
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Foesel BU, Nägele V, Naether A, Wüst PK, Weinert J, Bonkowski M, Lohaus G, Polle A, Alt F, Oelmann Y, Fischer M, Friedrich MW, Overmann J. Determinants of Acidobacteria activity inferred from the relative abundances of 16S rRNA transcripts in German grassland and forest soils. Environ Microbiol 2013; 16:658-75. [PMID: 23802854 DOI: 10.1111/1462-2920.12162] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Accepted: 05/24/2013] [Indexed: 12/01/2022]
Abstract
16S rRNA genes and transcripts of Acidobacteria were investigated in 57 grassland and forest soils of three different geographic regions. Acidobacteria contributed 9-31% of bacterial 16S rRNA genes whereas the relative abundances of the respective transcripts were 4-16%. The specific cellular 16S rRNA content (determined as molar ratio of rRNA : rRNA genes) ranged between 3 and 80, indicating a low in situ growth rate. Correlations with flagellate numbers, vascular plant diversity and soil respiration suggest that biotic interactions are important determinants of Acidobacteria 16S rRNA transcript abundances in soils. While the phylogenetic composition of Acidobacteria differed significantly between grassland and forest soils, high throughput denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism fingerprinting detected 16S rRNA transcripts of most phylotypes in situ. Partial least squares regression suggested that chemical soil conditions such as pH, total nitrogen, C : N ratio, ammonia concentrations and total phosphorus affect the composition of this active fraction of Acidobacteria. Transcript abundance for individual Acidobacteria phylotypes was found to correlate with particular physicochemical (pH, temperature, nitrogen or phosphorus) and, most notably, biological parameters (respiration rates, abundances of ciliates or amoebae, vascular plant diversity), providing culture-independent evidence for a distinct niche specialization of different Acidobacteria even from the same subdivision.
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Affiliation(s)
- Bärbel U Foesel
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, 82152, Planegg- Martinsried, Germany; Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, 38124, Braunschweig, Germany
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33
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Saidi-Mehrabad A, He Z, Tamas I, Sharp CE, Brady AL, Rochman FF, Bodrossy L, Abell GC, Penner T, Dong X, Sensen CW, Dunfield PF. Methanotrophic bacteria in oilsands tailings ponds of northern Alberta. ISME JOURNAL 2012; 7:908-21. [PMID: 23254511 DOI: 10.1038/ismej.2012.163] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We investigated methanotrophic bacteria in slightly alkaline surface water (pH 7.4-8.7) of oilsands tailings ponds in Fort McMurray, Canada. These large lakes (up to 10 km(2)) contain water, silt, clay and residual hydrocarbons that are not recovered in oilsands mining. They are primarily anoxic and produce methane but have an aerobic surface layer. Aerobic methane oxidation was measured in the surface water at rates up to 152 nmol CH4 ml(-1) water d(-1). Microbial diversity was investigated via pyrotag sequencing of amplified 16S rRNA genes, as well as by analysis of methanotroph-specific pmoA genes using both pyrosequencing and microarray analysis. The predominantly detected methanotroph in surface waters at all sampling times was an uncultured species related to the gammaproteobacterial genus Methylocaldum, although a few other methanotrophs were also detected, including Methylomonas spp. Active species were identified via (13)CH4 stable isotope probing (SIP) of DNA, combined with pyrotag sequencing and shotgun metagenomic sequencing of heavy (13)C-DNA. The SIP-PCR results demonstrated that the Methylocaldum and Methylomonas spp. actively consumed methane in fresh tailings pond water. Metagenomic analysis of DNA from the heavy SIP fraction verified the PCR-based results and identified additional pmoA genes not detected via PCR. The metagenome indicated that the overall methylotrophic community possessed known pathways for formaldehyde oxidation, carbon fixation and detoxification of nitrogenous compounds but appeared to possess only particulate methane monooxygenase not soluble methane monooxygenase.
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Evidence for niche partitioning revealed by the distribution of sulfur oxidation genes collected from areas of a terrestrial sulfidic spring with differing geochemical conditions. Appl Environ Microbiol 2012; 79:1171-82. [PMID: 23220955 DOI: 10.1128/aem.02812-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The diversity and phylogenetic significance of bacterial genes in the environment has been well studied, but comparatively little attention has been devoted to understanding the functional significance of different variations of the same metabolic gene that occur in the same environment. We analyzed the geographic distribution of 16S rRNA pyrosequences and soxB genes along a geochemical gradient in a terrestrial sulfidic spring to identify how different taxonomic variations of the soxB gene were naturally distributed within the spring outflow channel and to identify possible evidence for altered SoxB enzyme function in nature. Distinct compositional differences between bacteria that utilize their SoxB enzyme in the Paracoccus sulfide oxidation pathway (e.g., Bradyrhizobium, Paracoccus, and Rhodovulum) and bacteria that utilize their SoxB enzyme in the branched pathway (e.g., Chlorobium, Thiothrix, Thiobacillus, Halothiobacillus, and Thiomonas) were identified. Different variations of the soxB genes were present at different locations within the spring outflow channel in a manner that significantly corresponded to geochemical conditions. The distribution of the different soxB gene sequence variations suggests that the enzymes encoded by these genes are functionally different and could be optimized to specific geochemical conditions that define niche space for bacteria capable of oxidizing reduced sulfur compounds.
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35
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Nam YD, Yi SH, Lim SI. Bacterial diversity of cheonggukjang, a traditional Korean fermented food, analyzed by barcoded pyrosequencing. Food Control 2012. [DOI: 10.1016/j.foodcont.2012.04.028] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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36
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Sizova MV, Panikov NS, Tourova TP, Flanagan PW. Isolation and characterization of oligotrophic acido-tolerant methanogenic consortia from a Sphagnum peat bog. FEMS Microbiol Ecol 2012; 45:301-15. [PMID: 19719599 DOI: 10.1016/s0168-6496(03)00165-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Two dense and highly enriched (up to 10(9) cells ml(-1), <10% of bacterial satellites) acido-tolerant (pH 4.0-6.5) methanogenic consortia, '26' and 'K', were isolated from the peat beneath a Sphagnum-Eriophorum-Carex community in West Siberia. Both consortia produced methane from CO2:H2 on chemically defined, diluted N-free media containing Ti(III)citrate as reducing agent. The phylogenetic analysis of 16S ribosomal DNA revealed three archaeal and nine bacterial sequence types. Consortium '26' contained single archaea Methanobacterium sp., represented by rods of 1.5-10x0.5-1.0 microm. In consortium 'K', there were two archaeal phylotypes, the respective methanogens were further differentiated morphologically with the fluorescence in situ hybridization technique: one less abundant (<2%) population of the long-curved rods (50-100x0.3-0.4 microm) fell into the order of Methanomicrobiales, while the dominant organism ( approximately 98%), represented by straight rods with abrupt rectangular ends (3-9x0.5 microm), was affiliated with earlier uncultured 'Rice cluster I'. The main bacterial satellite used citrate as a single carbon and energy source; it was similar in both consortia, and after isolation in pure culture, it was identified as a new member of the alpha-subclass of Proteobacteria. The other bacterial satellites were distributed among four taxonomic groups: the delta-subclass of Proteobacteria, the Flavobacterium-Bacteroides-Cytophaga line of descent, the Acidobacterium-Fibrobacter line of descent and the Green non-sulfur bacteria line of descent. At least 11 out of 12 components of acido-tolerant consortia are new to science at the species, genus and order levels; their existence until now was evident only from environmental gene retrievals. The Sphagnum wetlands, attracting attention only recently because of their global environmental role, are shown to be an especially valuable source of novel prokaryotic organisms.
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Affiliation(s)
- Maria V Sizova
- Chemistry and Chemical Biology Department, Stevens Institute of Technology, Castle Point on Hudson, Hoboken, NJ 07030, USA
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37
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Naether A, Foesel BU, Naegele V, Wüst PK, Weinert J, Bonkowski M, Alt F, Oelmann Y, Polle A, Lohaus G, Gockel S, Hemp A, Kalko EKV, Linsenmair KE, Pfeiffer S, Renner S, Schöning I, Weisser WW, Wells K, Fischer M, Overmann J, Friedrich MW. Environmental factors affect Acidobacterial communities below the subgroup level in grassland and forest soils. Appl Environ Microbiol 2012; 78:7398-406. [PMID: 22885760 PMCID: PMC3457104 DOI: 10.1128/aem.01325-12] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 08/04/2012] [Indexed: 11/20/2022] Open
Abstract
In soil, Acidobacteria constitute on average 20% of all bacteria, are highly diverse, and are physiologically active in situ. However, their individual functions and interactions with higher taxa in soil are still unknown. Here, potential effects of land use, soil properties, plant diversity, and soil nanofauna on acidobacterial community composition were studied by cultivation-independent methods in grassland and forest soils from three different regions in Germany. The analysis of 16S rRNA gene clone libraries representing all studied soils revealed that grassland soils were dominated by subgroup Gp6 and forest soils by subgroup Gp1 Acidobacteria. The analysis of a large number of sites (n = 57) by 16S rRNA gene fingerprinting methods (terminal restriction fragment length polymorphism [T-RFLP] and denaturing gradient gel electrophoresis [DGGE]) showed that Acidobacteria diversities differed between grassland and forest soils but also among the three different regions. Edaphic properties, such as pH, organic carbon, total nitrogen, C/N ratio, phosphorus, nitrate, ammonium, soil moisture, soil temperature, and soil respiration, had an impact on community composition as assessed by fingerprinting. However, interrelations with environmental parameters among subgroup terminal restriction fragments (T-RFs) differed significantly, e.g., different Gp1 T-RFs correlated positively or negatively with nitrogen content. Novel significant correlations of Acidobacteria subpopulations (i.e., individual populations within subgroups) with soil nanofauna and vascular plant diversity were revealed only by analysis of clone sequences. Thus, for detecting novel interrelations of environmental parameters with Acidobacteria, individual populations within subgroups have to be considered.
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Affiliation(s)
- Astrid Naether
- Abt. Mikrobielle Ökophysiologie, Biologie/Chemie, Universität Bremen, Bremen, Germany
- Max Planck Institut für terrestrische Mikrobiologie, Marburg, Germany
| | - Bärbel U. Foesel
- Mikrobiologie, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Leibniz-Institut DSMZ, Braunschweig, Germany
| | - Verena Naegele
- Mikrobiologie, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Pullacher Platz 7, Munich, Germany
| | - Pia K. Wüst
- Leibniz-Institut DSMZ, Braunschweig, Germany
| | - Jan Weinert
- Zoologisches Institut, Universität zu Köln, Cologne, Germany
| | | | - Fabian Alt
- Geoecology, University of Tübingen, Tübingen, Germany
| | | | - Andrea Polle
- Forstbotanik und Baumphysiologie, Universität Göttingen, Göttingen, Germany
| | - Gertrud Lohaus
- Forstbotanik und Baumphysiologie, Universität Göttingen, Göttingen, Germany
| | - Sonja Gockel
- Technische Universität München, Außenstelle Mülverstedt, Mülverstedt, Germany
| | - Andreas Hemp
- Biodiversitätsexploratorien, Biosphärenreservat Schorfheide-Chorin, Angermünde, Germany
| | | | | | - Simone Pfeiffer
- Institut für Biochemie und Biologie, Universität Potsdam, Potsdam, Germany
| | - Swen Renner
- Institut für Experimentelle Ökologie, Universität Ulm, Ulm, Germany
| | | | | | - Konstans Wells
- Biodiversitätsexploratorien, Biosphärenreservat Schorfheide-Chorin, Angermünde, Germany
| | - Markus Fischer
- Institut für Biochemie und Biologie, Universität Potsdam, Potsdam, Germany
- Universität Bern, Bern, Switzerland
| | - Jörg Overmann
- Mikrobiologie, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Leibniz-Institut DSMZ, Braunschweig, Germany
- Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael W. Friedrich
- Abt. Mikrobielle Ökophysiologie, Biologie/Chemie, Universität Bremen, Bremen, Germany
- Max Planck Institut für terrestrische Mikrobiologie, Marburg, Germany
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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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Gorra R, Webster G, Martin M, Celi L, Mapelli F, Weightman AJ. Dynamic microbial community associated with iron-arsenic co-precipitation products from a groundwater storage system in Bangladesh. MICROBIAL ECOLOGY 2012; 64:171-186. [PMID: 22349905 DOI: 10.1007/s00248-012-0014-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 01/19/2012] [Indexed: 05/31/2023]
Abstract
The prokaryotic community in Fe-As co-precipitation product from a groundwater storage tank in Bangladesh was investigated over a 5-year period to assess the diversity of the community and to infer biogeochemical mechanisms that may contribute to the formation and stabilisation of co-precipitation products and to Fe and As redox cycling. Partial 16S rRNA gene sequences from Bacteria and Archaea, functional markers (mcrA and dsrB) and iron-oxidising Gallionella-related 16S rRNA gene sequences were determined using denaturing gradient gel electrophoresis (DGGE). Additionally, a bacterial 16S rRNA gene library was also constructed from one representative sample. Biogeochemical characterization demonstrated that co-precipitation products consist of a mixture of inorganic minerals, mainly hydrous ferric oxides, intimately associated with organic matter of microbial origin that contribute to the chemical and physical stabilisation of a poorly ordered structure. DGGE analysis and polymerase chain reaction-cloning revealed that the diverse bacterial community structure in the co-precipitation product progressively stabilised with time resulting in a prevalence of methylotrophic Betaproteobacteria, while the archaeal community was less diverse and was dominated by members of the Euryarchaeota. Results show that Fe-As co-precipitation products provide a habitat characterised by anoxic/oxic niches that supports a phylogenetically and metabolically diverse group of prokaryotes involved in metal, sulphur and carbon cycling, supported by the presence of Gallionella-like iron-oxidizers, methanogens, methylotrophs, and sulphate reducers. However, no phylotypes known to be directly involved in As(V) respiration or As(III) oxidation were found.
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Affiliation(s)
- Roberta Gorra
- DIVAPRA, University of Turin, Grugliasco, TO, Italy.
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Köhler T, Dietrich C, Scheffrahn RH, Brune A. High-resolution analysis of gut environment and bacterial microbiota reveals functional compartmentation of the gut in wood-feeding higher termites (Nasutitermes spp.). Appl Environ Microbiol 2012; 78:4691-701. [PMID: 22544239 PMCID: PMC3370480 DOI: 10.1128/aem.00683-12] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 04/13/2012] [Indexed: 11/20/2022] Open
Abstract
Higher termites are characterized by a purely prokaryotic gut microbiota and an increased compartmentation of their intestinal tract. In soil-feeding species, each gut compartment has different physicochemical conditions and is colonized by a specific microbial community. Although considerable information has accumulated also for wood-feeding species of the genus Nasutitermes, including cellulase activities and metagenomic data, a comprehensive study linking physicochemical gut conditions with the structure of the microbial communities in the different gut compartments is lacking. In this study, we measured high-resolution profiles of H(2), O(2), pH, and redox potential in the gut of Nasutitermes corniger termites, determined the fermentation products accumulating in the individual gut compartments, and analyzed the bacterial communities in detail by pyrotag sequencing of the V3-V4 region of the 16S rRNA genes. The dilated hindgut paunch (P3 compartment) was the only anoxic gut region, showed the highest density of bacteria, and accumulated H(2) to high partial pressures (up to 12 kPa). Molecular hydrogen is apparently produced by a dense community of Spirochaetes and Fibrobacteres, which also dominate the gut of other Nasutitermes species. All other compartments, such as the alkaline P1 compartment (average pH, 10.0), showed high redox potentials and comprised small but distinct populations characteristic for each gut region. In the crop and the posterior hindgut compartments, the community was even more diverse than in the paunch. Similarities in the communities of the posterior hindgut and crop suggested that proctodeal trophallaxis or coprophagy also occurs in higher termites. The large sampling depths of pyrotag sequencing in combination with the determination of important physicochemical parameters allow cautious conclusions concerning the functions of particular bacterial lineages in the respective gut sections to be drawn.
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Affiliation(s)
- Tim Köhler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Carsten Dietrich
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Rudolf H. Scheffrahn
- Fort Lauderdale Research and Education Center, University of Florida, Davie, Florida, USA
| | - Andreas Brune
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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41
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Lu A, Li Y, Jin S, Wang X, Wu XL, Zeng C, Li Y, Ding H, Hao R, Lv M, Wang C, Tang Y, Dong H. Growth of non-phototrophic microorganisms using solar energy through mineral photocatalysis. Nat Commun 2012; 3:768. [DOI: 10.1038/ncomms1768] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 03/01/2012] [Indexed: 11/09/2022] Open
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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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Henneberger R, Lüke C, Mosberger L, Schroth MH. Structure and function of methanotrophic communities in a landfill-cover soil. FEMS Microbiol Ecol 2012; 81:52-65. [PMID: 22172054 DOI: 10.1111/j.1574-6941.2011.01278.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/23/2011] [Accepted: 12/05/2011] [Indexed: 11/30/2022] Open
Abstract
In landfill-cover soils, aerobic methane-oxidizing bacteria (MOB) convert CH(4) to CO(2), mitigating emissions of the greenhouse gas CH(4) to the atmosphere. We investigated overall MOB community structure and assessed spatial differences in MOB diversity, abundance and activity in a Swiss landfill-cover soil. Molecular cloning, terminal restriction-fragment length polymorphism (T-RFLP) and quantitative PCR of pmoA genes were applied to soil collected from 16 locations at three different depths to study MOB community structure, diversity and abundance; MOB activity was measured in the field using gas push-pull tests. The MOB community was highly diverse but dominated by Type Ia MOB, with novel pmoA sequences present. Type II MOB were detected mainly in deeper soil with lower nutrient and higher CH(4) concentrations. Substantial differences in MOB community structure were observed between one high- and one low-activity location. MOB abundance was highly variable across the site [4.0 × 10(4) to 1.1 × 10(7) (g soil dry weight)(-1)]. Potential CH(4) oxidation rates were high [1.8-58.2 mmol CH(4) (L soil air)(-1) day(-1) ] but showed significant lateral variation and were positively correlated with mean CH(4) concentrations (P < 0.01), MOB abundance (P < 0.05) and MOB diversity (weak correlation, P < 0.17). Our findings indicate that Methylosarcina and closely related MOB are key players and that MOB abundance and community structure are driving factors in CH(4) oxidation at this landfill.
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Affiliation(s)
- Ruth Henneberger
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zurich, Switzerland
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Tsutsumi M, Kojima H, Fukui M. Vertical profiles of abundance and potential activity of methane-oxidizing bacteria in sediment of Lake Biwa, Japan. Microbes Environ 2011; 27:67-71. [PMID: 22200642 PMCID: PMC4036029 DOI: 10.1264/jsme2.me11285] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Vertical profiles of the abundance, community composition, and potential activity of methane-oxidizing bacteria (MOB) were investigated in the sediment of Lake Biwa. Sediment samples were obtained from two sites at different water depths. The abundance of MOB was assessed as the copy number of the pmoA gene (encoding the alpha subunit of particulate methane monooxygenase), measured with quantitative real-time PCR. Abundance of the pmoA gene peaked in the 5–8 cm layer of the sediment from both sites. MOB community composition was investigated by denaturing gradient gel electrophoresis (DGGE) analysis of pmoA and 16S rRNA genes. The band patterns observed in DGGE did not significantly differ with sediment depths or sampling sites. Sequence analysis of the DGGE bands indicated the dominance of the genus Methylobacter. Potential activity, which was measured in the presence of sufficient amounts of methane and oxygen, decreased linearly from the sediment surface to deeper layers. These results suggest that the pmoA gene copy number cannot be regarded as an indicator of aerobic MOB that retain potential activity in sediments.
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Affiliation(s)
- Masazumi Tsutsumi
- The Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan
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Meena KK, Kumar M, Kalyuzhnaya MG, Yandigeri MS, Singh DP, Saxena AK, Arora DK. Epiphytic pink-pigmented methylotrophic bacteria enhance germination and seedling growth of wheat (Triticum aestivum) by producing phytohormone. Antonie van Leeuwenhoek 2011; 101:777-86. [PMID: 22200783 DOI: 10.1007/s10482-011-9692-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 12/15/2011] [Indexed: 10/14/2022]
Abstract
Methylotrophic bacteria were isolated from the phyllosphere of different crop plants such as sugarcane, pigeonpea, mustard, potato and radish. The methylotrophic isolates were differentiated based on growth characteristics and colony morphology on methanol supplemented ammonium mineral salts medium. Amplification of the mxaF gene helped in the identification of the methylotrophic isolates as belonging to the genus Methylobacterium. Cell-free culture filtrates of these strains enhanced seed germination of wheat (Triticum aestivum) with highest values of 98.3% observed using Methylobacterium sp. (NC4). Highest values of seedling length and vigour were recorded with Methylobacterium sp. (NC28). HPLC analysis of production by bacterial strains ranged from 1.09 to 9.89 μg ml(-1) of cytokinins in the culture filtrate. Such cytokinin producing beneficial methylotrophs can be useful in developing bio-inoculants through co-inoculation of pink-pigmented facultative methylotrophs with other compatible bacterial strains, for improving plant growth and productivity, in an environment-friendly manner.
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Affiliation(s)
- Kamlesh K Meena
- National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan, India.
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Bacteroidales ectosymbionts of gut flagellates shape the nitrogen-fixing community in dry-wood termites. ISME JOURNAL 2011; 6:1302-13. [PMID: 22189498 DOI: 10.1038/ismej.2011.194] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Although it is well documented that the lack of nitrogen in the diet of wood-feeding termites is compensated by the nitrogen-fixing capacity of their gut microbiota, the bacteria responsible for this activity are largely unknown. Here, we analyzed the diversity and expression of nitrogenase genes (homologs of nifH) in four species of dry-wood termites (Kalotermitidae), which thrive on a particularly nitrogen-poor resource. Although each species harbored a highly diverse suite of termite-specific homologs in their microliter-sized hindgut, only a core set related to nifH genes of Treponema and Azoarcus spp., 'Azobacteroides pseudotrichonymphae', the first member of the Bacteroidales identified as a diazotroph, and termite-gut-specific anfH genes of hitherto unknown origin were preferentially expressed. Transcription patterns corroborated that the populations of active diazotrophs differ fundamentally between termite genera. Capillary-picked suspensions of the flagellates Devescovina arta and Snyderella tabogae revealed that their bacterial ectosymbionts each possess two paralogs of nifH, which apparently have been acquired consecutively during evolution of Bacteroidales, but only one of them (anfH) is actively expressed. Transcription patterns correlated neither with the molybdenum content of the diet nor with intestinal hydrogen concentrations, measured with microsensors. We propose that the nitrogen-fixing community in different dry-wood termites is shaped by the symbionts of their specific flagellate populations. Our findings suggest that the diazotrophic nature of 'Armantifilum devescovinae' has an important role in the nitrogen metabolism of dry-wood termites and is the driving force of co-evolution with its flagellate host.
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Wellner S, Lodders N, Kämpfer P. Diversity and biogeography of selected phyllosphere bacteria with special emphasis on Methylobacterium spp. Syst Appl Microbiol 2011; 34:621-30. [PMID: 22000032 DOI: 10.1016/j.syapm.2011.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 08/17/2011] [Accepted: 08/23/2011] [Indexed: 11/26/2022]
Abstract
On the basis of cultivation-dependent (isolation on mineral salt medium supplemented with 0.5% methanol) and -independent (DGGE analysis) methods, we investigated the influence of the host plant species Trifolium repens and Cerastium holosteoides, three geographic locations and the land-use types meadow, mown pasture and pasture on the abundance and community composition of selected phyllosphere bacteria with emphasis on Methylobacterium species. Methylobacterium abundance was significantly higher on leaves of T. repens (mean value 2.0×10(7) CFU PPFM per g leaf) than on leaves of C. holosteoides (mean value 2.0×10(6) CFU per g leaf). Leaves from the sampling site Schorfheide-Chorin showed slightly lower Methylobacterium numbers than leaves of the other sampling sites. Land-use and sampling period had no consistent influence on Methylobacterium community size. Methylobacterium community composition was very similar over both sampling periods, all three sampling sites, all land-use types and both plant species. Moreover, no relationship between geographic and genetic distance was observed. Community composition of selected Proteobacteria was influenced by plant species, geographic location and land-use. Often, differences in community composition could be observed between meadows, mown pastures and pastures but not between different kinds of meadows (cutted once versus three times) and mown pastures (fertilized versus non-fertilized). The results also indicate, that whether there are differences between land-use types or not strongly depends on the investigated host plant species and ecosystem. Besides Methylobacterium, representatives of Methylophilus were detected. The results indicate that Methylobacterium species are generally abundant and stable members of the phyllosphere community whereas other genera occur more occasionally, and that Methylobacterium clearly dominates the methylotrophic phyllosphere community.
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Affiliation(s)
- S Wellner
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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48
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Dullius CH, Chen CY, Schink B. Nitrate-dependent degradation of acetone by Alicycliphilus and Paracoccus strains and comparison of acetone carboxylase enzymes. Appl Environ Microbiol 2011; 77:6821-5. [PMID: 21841031 PMCID: PMC3187103 DOI: 10.1128/aem.05385-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 08/02/2011] [Indexed: 11/20/2022] Open
Abstract
A novel acetone-degrading, nitrate-reducing bacterium, strain KN Bun08, was isolated from an enrichment culture with butanone and nitrate as the sole sources of carbon and energy. The cells were motile short rods, 0.5 to 1 by 1 to 2 μm in size, which gave Gram-positive staining results in the exponential growth phase and Gram-negative staining results in the stationary-growth phase. Based on 16S rRNA gene sequence analysis, the isolate was assigned to the genus Alicycliphilus. Besides butanone and acetone, the strain used numerous fatty acids as substrates. An ATP-dependent acetone-carboxylating enzyme was enriched from cell extracts of this bacterium and of Alicycliphilus denitrificans K601(T) by two subsequent DEAE Sepharose column procedures. For comparison, acetone carboxylases were enriched from two additional nitrate-reducing bacterial species, Paracoccus denitrificans and P. pantotrophus. The products of the carboxylase reaction were acetoacetate and AMP rather than ADP. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of cell extracts and of the various enzyme preparations revealed bands corresponding to molecular masses of 85, 78, and 20 kDa, suggesting similarities to the acetone carboxylase enzymes described in detail for the aerobic bacterium Xanthobacter autotrophicus strain Py2 (85.3, 78.3, and 19.6 kDa) and the phototrophic bacterium Rhodobacter capsulatus. Protein bands were excised and compared by mass spectrometry with those of acetone carboxylases of aerobic bacteria. The results document the finding that the nitrate-reducing bacteria studied here use acetone-carboxylating enzymes similar to those of aerobic and phototrophic bacteria.
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Affiliation(s)
| | | | - Bernhard Schink
- Fachbereich Biologie, University of Constance, D-78457 Constance, Germany
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Park SJ, Park BJ, Jung MY, Kim SJ, Chae JC, Roh Y, Forwick M, Yoon HI, Rhee SK. Influence of deglaciation on microbial communities in marine sediments off the coast of Svalbard, Arctic Circle. MICROBIAL ECOLOGY 2011; 62:537-548. [PMID: 21556884 DOI: 10.1007/s00248-011-9860-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 04/20/2011] [Indexed: 05/30/2023]
Abstract
Increases in global temperatures have been shown to enhance glacier melting in the Arctic region. Here, we have evaluated the effects of meltwater runoff on the microbial communities of coastal marine sediment located along a transect of Temelfjorden, in Svalbard. As close to the glacier front, the sediment properties were clearly influenced by deglaciation. Denaturing gradient gel electrophoresis profiles showed that the sediment microbial communities of the stations of glacier front (stations 188-178) were distinguishable from that of outer fjord region (station 176). Canonical correspondence analysis indicated that total carbon and calcium carbonate in sediment and chlorophyll a in bottom water were key factors driving the change of microbial communities. Analysis of 16S rRNA gene clone libraries suggested that microbial diversity was higher within the glacier-proximal zone (station 188) directly affected by the runoffs than in the outer fjord region. While the crenarchaeotal group I.1a dominated at station 176 (62%), Marine Benthic Group-B and other Crenarchaeota groups were proportionally abundant. With regard to the bacterial community, alpha-Proteobacteria and Flavobacteria lineages prevailed (60%) at station 188, whereas delta-Proteobacteria (largely sulfate-reducers) predominated (32%) at station 176. Considering no clone sequences related to sulfate-reducers, station 188 may be more oxic compared to station 176. The distance-wise compositional variation in the microbial communities is attributable to their adaptations to the sediment environments which are differentially affected by melting glaciers.
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Affiliation(s)
- Soo-Je Park
- Department of Microbiology, Chungbuk National University, Cheongju, 361-763 Chungbuk, Republic of Korea
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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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