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Garg D, Patel N, Rawat A, Rosado AS. Cutting edge tools in the field of soil microbiology. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100226. [PMID: 38425506 PMCID: PMC10904168 DOI: 10.1016/j.crmicr.2024.100226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
The study of the whole of the genetic material contained within the microbial populations found in a certain environment is made possible by metagenomics. This technique enables a thorough knowledge of the variety, function, and interactions of microbial communities that are notoriously difficult to research. Due to the limitations of conventional techniques such as culturing and PCR-based methodologies, soil microbiology is a particularly challenging field. Metagenomics has emerged as an effective technique for overcoming these obstacles and shedding light on the dynamic nature of the microbial communities in soil. This review focuses on the principle of metagenomics techniques, their potential applications and limitations in soil microbial diversity analysis. The effectiveness of target-based metagenomics in determining the function of individual genes and microorganisms in soil ecosystems is also highlighted. Targeted metagenomics, including high-throughput sequencing and stable-isotope probing, is essential for studying microbial taxa and genes in complex ecosystems. Shotgun metagenomics may reveal the diversity of soil bacteria, composition, and function impacted by land use and soil management. Sanger, Next Generation Sequencing, Illumina, and Ion Torrent sequencing revolutionise soil microbiome research. Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)'s third and fourth generation sequencing systems revolutionise long-read technology. GeoChip, clone libraries, metagenomics, and metabarcoding help comprehend soil microbial communities. The article indicates that metagenomics may improve environmental management and agriculture despite existing limitations.Metagenomics has revolutionised soil microbiology research by revealing the complete diversity, function, and interactions of microorganisms in soil. Metagenomics is anticipated to continue defining the future of soil microbiology research despite some limitations, such as the difficulty of locating the appropriate sequencing method for specific genes.
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Affiliation(s)
- Diksha Garg
- Department of Microbiology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Niketan Patel
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
- Computational Bioscience Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
| | - Anamika Rawat
- Center of Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
| | - Alexandre Soares Rosado
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
- Computational Bioscience Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
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Cheng M, Luo S, Zhang P, Xiong G, Chen K, Jiang C, Yang F, Huang H, Yang P, Liu G, Zhang Y, Ba S, Yin P, Xiong J, Miao W, Ning K. A genome and gene catalog of the aquatic microbiomes of the Tibetan Plateau. Nat Commun 2024; 15:1438. [PMID: 38365793 PMCID: PMC10873407 DOI: 10.1038/s41467-024-45895-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/07/2024] [Indexed: 02/18/2024] Open
Abstract
The Tibetan Plateau supplies water to nearly 2 billion people in Asia, but climate change poses threats to its aquatic microbial resources. Here, we construct the Tibetan Plateau Microbial Catalog by sequencing 498 metagenomes from six water ecosystems (saline lakes, freshwater lakes, rivers, hot springs, wetlands and glaciers). Our catalog expands knowledge of regional genomic diversity by presenting 32,355 metagenome-assembled genomes that de-replicated into 10,723 representative genome-based species, of which 88% were unannotated. The catalog contains nearly 300 million non-redundant gene clusters, of which 15% novel, and 73,864 biosynthetic gene clusters, of which 50% novel, thus expanding known functional diversity. Using these data, we investigate the Tibetan Plateau aquatic microbiome's biogeography along a distance of 2,500 km and >5 km in altitude. Microbial compositional similarity and the shared gene count with the Tibetan Plateau microbiome decline along with distance and altitude difference, suggesting a dispersal pattern. The Tibetan Plateau Microbial Catalog stands as a substantial repository for high-altitude aquatic microbiome resources, providing potential for discovering novel lineages and functions, and bridging knowledge gaps in microbiome biogeography.
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Affiliation(s)
- Mingyue Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Shuai Luo
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Peng Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- Laboratory of Tibetan Plateau Wetland and Watershed Ecosystem, College of Science, Tibet University, Lhasa, China
| | - Guangzhou Xiong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chuanqi Jiang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Fangdian Yang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- Laboratory of Tibetan Plateau Wetland and Watershed Ecosystem, College of Science, Tibet University, Lhasa, China
| | - Hanhui Huang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guanxi Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yuhao Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Sang Ba
- Laboratory of Tibetan Plateau Wetland and Watershed Ecosystem, College of Science, Tibet University, Lhasa, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jie Xiong
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China.
| | - Wei Miao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
- Laboratory of Tibetan Plateau Wetland and Watershed Ecosystem, College of Science, Tibet University, Lhasa, China.
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China.
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center of Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
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Wang Y, Xue K. Cold-adaptative methanogens and methanotrophs drive ecosystem feedback. Sci Bull (Beijing) 2023; 68:1359-1360. [PMID: 37321870 DOI: 10.1016/j.scib.2023.05.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing 101408, China; State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Beijing 100101, China.
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing 101408, China
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Yang WT, Shen LD, Bai YN. Role and regulation of anaerobic methane oxidation catalyzed by NC10 bacteria and ANME-2d archaea in various ecosystems. ENVIRONMENTAL RESEARCH 2023; 219:115174. [PMID: 36584837 DOI: 10.1016/j.envres.2022.115174] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/07/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands are recognized as important sources of atmospheric methane (CH4). Currently, increasing evidence shows the potential importance of the anaerobic oxidation of methane (AOM) mediated by NC10 bacteria and a novel cluster of anaerobic methanotrophic archaea (ANME)-ANME-2d in mitigating CH4 emissions from different ecosystems. To better understand the role of NC10 bacteria and ANME-2d archaea in CH4 emission reduction, the current review systematically summarizes different AOM processes and the functional microorganisms involved in freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands. NC10 bacteria are widely present in these ecosystems, and the nitrite-dependent AOM is identified as an important CH4 sink and induces nitrogen loss. Nitrite- and nitrate-dependent AOM co-occur in the environment, and they are mainly affected by soil/sediment inorganic nitrogen and organic carbon contents. Furthermore, salinity is another key factor regulating the two AOM processes in coastal wetlands. In addition, ANME-2d archaea have the great potential to couple AOM to the reduction of iron (III), manganese (IV), sulfate, and even humics in different ecosystems. However, the study on the environmental distribution of ANME-2d archaea and their role in CH4 mitigation in environments is insufficient. In this study, we propose several directions for future research on the different AOM processes and respective functional microorganisms.
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Affiliation(s)
- Wang-Ting Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Li-Dong Shen
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Ya-Nan Bai
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
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Li J, Liu YX, Lü PP, Wang YL, Li ZF, Zhang Y, Gan HY, Li XC, Mandal D, Cai J, Guo ZX, Yao H, Guo LD. Community Assembly of Fungi and Bacteria along Soil-Plant Continuum Differs in a Zoige Wetland. Microbiol Spectr 2022; 10:e0226022. [PMID: 36135597 PMCID: PMC9604091 DOI: 10.1128/spectrum.02260-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/28/2022] [Indexed: 01/04/2023] Open
Abstract
Distinct plant associated microbiomes live in rhizosphere soil, roots, and leaves. However, the differences in community assembly of fungi and bacteria along soil-plant continuum are less documented in ecosystems. We examined fungal and bacterial communities associated with leaves, roots, and rhizosphere soil of the dominant arbuscular mycorrhizal (AM) plants Taraxacum mongolicum and Elymus nutans and non-AM plant Carex enervis in the Zoige Wetland by using high throughput sequencing techniques. The operational taxonomic unit (OTU) richness of fungi and bacteria was significantly higher in rhizosphere soil than in roots and leaves, and their community compositions were significantly different in the rhizosphere soil, roots, and leaves in each plant species. The co-occurrence network analysis revealed that the sensitive fungal and bacterial OTUs with various taxonomic positions were mainly clustered into different modules according to rhizosphere soil, roots, and leaves in each plant species. Along the soil-plant continuum, the rhizosphere soil pool contributed more source on bacterial than on fungal communities in roots and leaves of the three plant species, and more source on bacterial and fungal communities in leaves of T. mongolicum and E. nutans compared with C. enervis. Furthermore, the root pool contributed more source on bacterial than on fungal communities in leaves of T. mongolicum and E. nutans but not that of C. enervis. This study highlights that the host plant selection intensity is higher in fungal than in bacterial communities in roots and leaves from rhizosphere soil in each plant species, and differs in fungal and bacterial communities along the soil-plant continuum in AM plants T. mongolicum and E. nutans and non-AM plant C. enervis in the Zoige Wetland. IMPORTANCE Elucidating the community microbiome assemblage alone the soil-plant continuum will help to better understand the biodiversity maintenance and ecosystem functioning. Here, we examined the fungal and bacterial communities in rhizosphere soil, roots, and leaves of two dominant AM plants and a non-AM plant in Zoige Wetland. We found that along the soil - plant continuum, host plant selection intensity is higher in fungal than in bacterial communities in roots and leaves from rhizosphere soil in each plant species, and differs in fungal and bacterial communities in the AM- and non-AM plants. This is the first report provides evidence of different assembly patterns of fungal and bacterial communities along the soil-plant continuum in the AM- and non-AM plants in the Zoige Wetland.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yu-Xuan Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peng-Peng Lü
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Yong-Long Wang
- Faculty of Biological Science and Technology, Baotou Teacher's College, Baotou, China
| | - Zhong-Feng Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Yue Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hui-Yun Gan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xing-Chun Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dipa Mandal
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Xuan Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hui Yao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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Yang Y, Shen L, Bai Y, Zhao X, Wang S, Liu J, Liu X, Tian M, Yang W, Jin J, Huang H, Wu H. Response of potential activity, abundance and community composition of nitrite-dependent anaerobic methanotrophs to long-term fertilization in paddy soils. Environ Microbiol 2022; 24:5005-5018. [PMID: 35799420 DOI: 10.1111/1462-2920.16102] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/12/2022] [Indexed: 11/29/2022]
Abstract
The process of nitrite-dependent anaerobic methane oxidation (n-damo) catalysed by Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria is a novel pathway in regulating methane (CH4 ) emissions from paddy fields. Nitrogen fertilization is essential to improve rice yields and soil fertility; however, its effect on the n-damo process is largely unknown. Here, the potential n-damo activity, abundance and community composition of M. oxyfera-like bacteria were investigated in paddy fields under three long-term (32 years) fertilization treatments, i.e. unfertilized control (CK), chemical fertilization (NPK) and straw incorporation with chemical fertilization (SNPK). Relative to the CK, both NPK and SNPK treatments significantly (p < 0.05) increased the potential n-damo activity (88%-110%) and the abundance (52%-105%) of M. oxyfera-like bacteria. The variation of soil organic carbon (OrgC) content and inorganic nitrogen content caused by the input of chemical fertilizers and straw returning were identified as the key factors affecting the potential n-damo activity and the abundance of M. oxyfera-like bacteria. However, the community composition and diversity of M. oxyfera-like bacteria did not change significantly by the input of fertilizers. Overall, our results provide the first evidence that long-term fertilization greatly stimulates the n-damo process, indicating its active role in controlling CH4 emissions from paddy fields.
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Affiliation(s)
- Yuling Yang
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Lidong Shen
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Yanan Bai
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Xu Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Shuwei Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jiaqi Liu
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Xin Liu
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Maohui Tian
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Wangting Yang
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Jinghao Jin
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Hechen Huang
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Hongsheng Wu
- Department of Agricultural Resources and Environment, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
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