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Dindhoria K, Kumar R, Bhargava B, Kumar R. Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils. mSystems 2024; 9:e0105023. [PMID: 38377278 PMCID: PMC10949518 DOI: 10.1128/msystems.01050-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/19/2024] [Indexed: 02/22/2024] Open
Abstract
Climate change is causing unpredictable seasonal variations globally. Due to the continuously increasing earth's surface temperature, the rate of water evaporation is enhanced, conceiving a problem of soil salinization, especially in arid and semi-arid regions. The accumulation of salt degrades soil quality, impairs plant growth, and reduces agricultural yields. Salt-tolerant, plant-growth-promoting microorganisms may offer a solution, enhancing crop productivity and soil fertility in salinized areas. In the current study, genome-resolved metagenomic analysis has been performed to investigate the salt-tolerating and plant growth-promoting potential of two hypersaline ecosystems, Sambhar Lake and Drang Mine. The samples were co-assembled independently by Megahit, MetaSpades, and IDBA-UD tools. A total of 67 metagenomic assembled genomes (MAGs) were reconstructed following the binning process, including 15 from Megahit, 26 from MetaSpades, and 26 from IDBA_UD assembly tools. As compared to other assemblers, the MAGs obtained by MetaSpades were of superior quality, with a completeness range of 12.95%-96.56% and a contamination range of 0%-8.65%. The medium and high-quality MAGs from MetaSpades, upon functional annotation, revealed properties such as salt tolerance (91.3%), heavy metal tolerance (95.6%), exopolysaccharide (95.6%), and antioxidant (60.86%) biosynthesis. Several plant growth-promoting attributes, including phosphate solubilization and indole-3-acetic acid (IAA) production, were consistently identified across all obtained MAGs. Conversely, characteristics such as iron acquisition and potassium solubilization were observed in a substantial majority, specifically 91.3%, of the MAGs. The present study indicates that hypersaline microflora can be used as bio-fertilizing agents for agricultural practices in salinized areas by alleviating prevalent stresses. IMPORTANCE The strategic implementation of metagenomic assembled genomes (MAGs) in exploring the properties and harnessing microorganisms from ecosystems like hypersaline niches has transformative potential in agriculture. This approach promises to redefine our comprehension of microbial diversity and its ecosystem roles. Recovery and decoding of MAGs unlock genetic resources, enabling the development of new solutions for agricultural challenges. Enhanced understanding of these microbial communities can lead to more efficient nutrient cycling, pest control, and soil health maintenance. Consequently, traditional agricultural practices can be improved, resulting in increased yields, reduced environmental impacts, and heightened sustainability. MAGs offer a promising avenue for sustainable agriculture, bridging the gap between cutting-edge genomics and practical field applications.
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Affiliation(s)
- Kiran Dindhoria
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Raghawendra Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Bhavya Bhargava
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Xing T, Liu K, Ji M, Chen Y, Liu Y. Bacterial diversity in a continuum from supraglacial habitats to a proglacial lake on the Tibetan Plateau. FEMS Microbiol Lett 2024; 371:fnae021. [PMID: 38521984 DOI: 10.1093/femsle/fnae021] [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: 08/23/2023] [Revised: 01/14/2024] [Accepted: 03/22/2024] [Indexed: 03/25/2024] Open
Abstract
Mountain glaciers are frequently assessed for their hydrological connectivity from glaciers to proglacial lakes. Ecological process on glacier surfaces and downstream ecosystems have often been investigated separately, but few studies have focused on the connectivity between the different glacial habitats. Therefore, it remains a limited understanding of bacterial community assembly across different habitats along the glacier hydrological continuum. In this study, we sampled along a glacial catchment from supraglacial snow, cryoconite holes, supraglacial runoff, ice-marginal moraine and proglacial lake on the Tibetan Plateau. The bacterial communities in these habitats were analyzed using high-throughput DNA sequencing of the 16S rRNA gene to determine the bacterial composition and assembly. Our results showed that each habitat hosted unique bacterial communities, with higher bacterial α-diversity in transitional habitats (e.g. runoff and ice-marginal moraine). Null model analysis indicated that deterministic processes predominantly shaped bacterial assembly in snow, cryoconite holes and lake, while stochastic process dominantly governed bacterial community in transitional habitats. Collectively, our findings suggest that local environment play a critical role in filtering bacterial community composition within glacier habitats. This study enhances our understanding of microbial assembly process in glacier environments and provides valuable insights into the factors governing bacterial community compositions across different habitats along the glacial hydrological continuum.
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Affiliation(s)
- Tingting Xing
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Yuying Chen
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
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Microbial community structure analysis of hypersaline niches and elucidation of their role in the biogeochemical cycling of nitrogen, sulphur and methane. ECOL INFORM 2023. [DOI: 10.1016/j.ecoinf.2023.102023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Li J, Zhai Y, Ge G, Xu Y, Wang C, Hu A, Han Y, Shan N, Liu B, Chen J, Wang W. Bacterial Community Composition and Function of Tropical River Ecosystem along the Nandu River on Hainan Island, China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 20:382. [PMID: 36612703 PMCID: PMC9819888 DOI: 10.3390/ijerph20010382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Microorganisms play a pivotal role in nutrient cycling in aquatic ecosystems. Understanding bacterial diversity and its functional composition are crucial for aquatic ecology and protection. We investigated the bacterial community structure using 16S rRNA gene amplicons high-throughput sequencing in this study. Results showed that 105 amplicon sequence variants (ASVs) account for 43.8% of the total sequences shared by the Nandu River's lower, middle, and upper reach and the Songtao Reservoir. The dominant bacterial phylum in the Nandu River and its connected Songtao Reservoir were Proteobacteria and Actinobacteriota, respectively. The highest Chao1 and Shannon index values were found in the lower reach of the Nandu River. Beta diversity analysis showed the divergence in bacterial communities in the Nandu River and Songtao Reservoir, but not in different reaches. Among the water properties, based on the Mantel test, dissolved oxygen, total nitrogen, and nitrite significantly affected the bacterial communities. The functional profiles predicted by Tax4Fun2 showed that metabolism was the most abundant function group. The relative abundance of genetic information processing was significantly higher in the Songtao Reservoir than in the Nandu River, while the relative abundance of human diseases was significantly lower in the Songtao Reservoir than in the Nandu River. The appearance of the xenobiotics biodegradation and metabolism function group requires us to pay more attention to possible water pollution, especially at the upper reach of the Nandu River.
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Affiliation(s)
- Jinbiao Li
- School of Geographic Science, Nantong University, Nantong 226019, China
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China
- State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Lake Hulun Wetland, Hulunbuir 021000, China
| | - Yangni Zhai
- School of Geographic Science, Nantong University, Nantong 226019, China
- State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Lake Hulun Wetland, Hulunbuir 021000, China
| | - Guojian Ge
- School of Geographic Science, Nantong University, Nantong 226019, China
- State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Lake Hulun Wetland, Hulunbuir 021000, China
| | - Yang Xu
- School of Geographic Science, Nantong University, Nantong 226019, China
- State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Lake Hulun Wetland, Hulunbuir 021000, China
| | - Can Wang
- School of Geographic Science, Nantong University, Nantong 226019, China
- State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Lake Hulun Wetland, Hulunbuir 021000, China
| | - Anyong Hu
- School of Geographic Science, Nantong University, Nantong 226019, China
- State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Lake Hulun Wetland, Hulunbuir 021000, China
| | - Yujie Han
- School of Geographic Science, Nantong University, Nantong 226019, China
- State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Lake Hulun Wetland, Hulunbuir 021000, China
| | - Nan Shan
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China
- State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Lake Hulun Wetland, Hulunbuir 021000, China
| | - Bo Liu
- School of Geographic Science, Nantong University, Nantong 226019, China
- State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Lake Hulun Wetland, Hulunbuir 021000, China
| | - Jinlin Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wenlin Wang
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China
- State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Lake Hulun Wetland, Hulunbuir 021000, China
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Suyal DC, Joshi D, Kumar S, Bhatt P, Narayan A, Giri K, Singh M, Soni R, Kumar R, Yadav A, Devi R, Kaur T, Kour D, Yadav AN. Himalayan Microbiomes for Agro-environmental Sustainability: Current Perspectives and Future Challenges. MICROBIAL ECOLOGY 2022; 84:643-675. [PMID: 34647148 DOI: 10.1007/s00248-021-01849-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
The Himalayas are one of the most mystical, yet least studied terrains of the world. One of Earth's greatest multifaceted and diverse montane ecosystems is also one of the thirty-four global biodiversity hotspots of the world. These are supposed to have been uplifted about 60-70 million years ago and support, distinct environments, physiography, a variety of orogeny, and great biological diversity (plants, animals, and microbes). Microbes are the pioneer colonizer of the Himalayas that are involved in various bio-geological cycles and play various significant roles. The applications of Himalayan microbiomes inhabiting in lesser to greater Himalayas have been recognized. The researchers explored the applications of indigenous microbiomes in both agricultural and environmental sectors. In agriculture, microbiomes from Himalayan regions have been suggested as better biofertilizers and biopesticides for the crops growing at low temperature and mountainous areas as they help in the alleviation of cold stress and other biotic stresses. Along with alleviation of low temperature, Himalayan microbes also have the capability to enhance plant growth by availing the soluble form of nutrients like nitrogen, phosphorus, potassium, zinc, and iron. These microbes have been recognized for producing plant growth regulators (abscisic acid, auxin, cytokinin, ethylene, and gibberellins). These microbes have been reported for bioremediating the diverse pollutants (pesticides, heavy metals, and xenobiotics) for environmental sustainability. In the current perspectives, present review provides a detailed discussion on the ecology, biodiversity, and adaptive features of the native Himalayan microbiomes in view to achieve agro-environmental sustainability.
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Affiliation(s)
- Deep Chandra Suyal
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Sirmaur, Himachal Pradesh, India
| | - Divya Joshi
- Uttarakhand Pollution Control Board, Regional Office, Kashipur, Uttarakhand, India
| | - Saurabh Kumar
- Division of Crop Research, Research Complex for Eastern Region, Patna, Bihar, India
| | - Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Arun Narayan
- Forest Research Institute, Dehradun, 2480 06, India
| | - Krishna Giri
- Rain Forest Research Institute, Jorhat, 785 010, India
| | - Manali Singh
- Department of Biotechnology, Invertis Institute of Engineering and Technology (IIET), Invertis University, Bareilly, 243123, Uttar Pradesh, India
| | - Ravindra Soni
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwa Vidyalaya, Raipur, Chhattisgarh, India
| | - Rakshak Kumar
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Ashok Yadav
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Rubee Devi
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Tanvir Kaur
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Divjot Kour
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Ajar Nath Yadav
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India.
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Kohler TJ, Fodelianakis S, Michoud G, Ezzat L, Bourquin M, Peter H, Busi SB, Pramateftaki P, Deluigi N, Styllas M, Tolosano M, de Staercke V, Schön M, Brandani J, Marasco R, Daffonchio D, Wilmes P, Battin TJ. Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function. GLOBAL CHANGE BIOLOGY 2022; 28:3846-3859. [PMID: 35320603 PMCID: PMC9323552 DOI: 10.1111/gcb.16169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/06/2022] [Indexed: 05/22/2023]
Abstract
The shrinking of glaciers is among the most iconic consequences of climate change. Despite this, the downstream consequences for ecosystem processes and related microbiome structure and function remain poorly understood. Here, using a space-for-time substitution approach across 101 glacier-fed streams (GFSs) from six major regions worldwide, we investigated how glacier shrinkage is likely to impact the organic matter (OM) decomposition rates of benthic biofilms. To do this, we measured the activities of five common extracellular enzymes and estimated decomposition rates by using enzyme allocation equations based on stoichiometry. We found decomposition rates to average 0.0129 (% d-1 ), and that decreases in glacier influence (estimated by percent glacier catchment coverage, turbidity, and a glacier index) accelerates decomposition rates. To explore mechanisms behind these relationships, we further compared decomposition rates with biofilm and stream water characteristics. We found that chlorophyll-a, temperature, and stream water N:P together explained 61% of the variability in decomposition. Algal biomass, which is also increasing with glacier shrinkage, showed a particularly strong relationship with decomposition, likely indicating their importance in contributing labile organic compounds to these carbon-poor habitats. We also found high relative abundances of chytrid fungi in GFS sediments, which putatively parasitize these algae, promoting decomposition through a fungal shunt. Exploring the biofilm microbiome, we then sought to identify bacterial phylogenetic clades significantly associated with decomposition, and found numerous positively (e.g., Saprospiraceae) and negatively (e.g., Nitrospira) related clades. Lastly, using metagenomics, we found evidence of different bacterial classes possessing different proportions of EEA-encoding genes, potentially informing some of the microbial associations with decomposition rates. Our results, therefore, present new mechanistic insights into OM decomposition in GFSs by demonstrating that an algal-based "green food web" is likely to increase in importance in the future and will promote important biogeochemical shifts in these streams as glaciers vanish.
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Affiliation(s)
- Tyler J. Kohler
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Stilianos Fodelianakis
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Grégoire Michoud
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Leïla Ezzat
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Massimo Bourquin
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Hannes Peter
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Susheel Bhanu Busi
- Systems Ecology Research GroupLuxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Paraskevi Pramateftaki
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Nicola Deluigi
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Michail Styllas
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Matteo Tolosano
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Vincent de Staercke
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Martina Schön
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Jade Brandani
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Paul Wilmes
- Systems Ecology Research GroupLuxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Tom J. Battin
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
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