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Jiang H, Okoye CO, Chen X, Zhang F, Jiang J. High-throughput 16S rRNA gene-based amplicon sequencing reveals the functional divergence of halophilic bacterial communities in the Suaeda salsa root compartments on the eastern coast of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 942:173775. [PMID: 38844238 DOI: 10.1016/j.scitotenv.2024.173775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/13/2024]
Abstract
The rhizosphere environment of plants, which harbors halophilic bacterial communities, faces significant challenges in coping with environmental stressors, particularly saline soil properties. This study utilizes a high-throughput 16S rRNA gene-based amplicon sequencing to investigate the variations in bacterial community dynamics in rhizosphere soil (RH), root surface soil (RS), root endophytic bacteria (PE) compartments of Suaeda salsa roots, and adjoining soils (CK) across six locations along the eastern coast of China: Nantong (NT), Yancheng (YC), Dalian (DL), Tianjin (TJ), Dongying (DY), and Qingdao (QD), all characterized by chloride-type saline soil. Variations in the physicochemical properties of the RH compartment were also evaluated. The results revealed significant changes in pH, electrical conductivity, total salt content, and ion concentrations in RH samples from different locations. Notably, the NT location exhibited the highest alkalinity and nitrogen availability. The pH variations were linked to HCO3- accumulation in S. salsa roots, while salinity stress influenced soil pH through H+ discharge. Despite salinity stress, enzymatic activities such as catalase and urease were higher in soils from various locations. The diversity and richness of bacterial communities were higher in specific locations, with Proteobacteria dominating PE samples from the DL location. Additionally, Vibrio and Marinobacter were prevalent in RH samples. Significant correlations were found between soil pH, salinity, nutrient content, and the abundance and diversity of bacterial taxa in RH samples. Bioinformatics analysis revealed the prevalence of halophilic bacteria, such as Bacillus, Halomonas, and Streptomyces, with diverse metabolic functions, including amino acid and carbohydrate metabolisms. Essential genes, such as auxin response factor (ARF) and GTPase-encoding genes, were abundant in RH samples, suggesting adaptive strategies for harsh environments. Likewise, proline/betaine transport protein genes were enriched, indicating potential bioremediation mechanisms against high salt stress. These findings provide insight into the metabolic adaptations facilitating resilience in saline ecosystems and contribute to understanding the complex interplay between soil conditions, bacterial communities, and plant adaptation.
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Affiliation(s)
- Huifang Jiang
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Charles Obinwanne Okoye
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China; School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; Department of Zoology & Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria
| | - Xunfeng Chen
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Fusheng Zhang
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jianxiong Jiang
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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Jagadesh M, Dash M, Kumari A, Singh SK, Verma KK, Kumar P, Bhatt R, Sharma SK. Revealing the hidden world of soil microbes: Metagenomic insights into plant, bacteria, and fungi interactions for sustainable agriculture and ecosystem restoration. Microbiol Res 2024; 285:127764. [PMID: 38805978 DOI: 10.1016/j.micres.2024.127764] [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: 11/30/2023] [Revised: 03/10/2024] [Accepted: 05/11/2024] [Indexed: 05/30/2024]
Abstract
The future of agriculture is questionable under the current climate change scenario. Climate change and climate-related calamities directly influence biotic and abiotic factors that control agroecosystems, endangering the safety of the world's food supply. The intricate interactions between soil microorganisms, including plants, bacteria, and fungi, play a pivotal role in promoting sustainable agriculture and ecosystem restoration. Soil microbes play a major part in nutrient cycling, including soil organic carbon (SOC), and play a pivotal function in the emission and depletion of greenhouse gases, including CH4, CO2, and N2O, which can impact the climate. At this juncture, developing a triumphant metagenomics approach has greatly increased our knowledge of the makeup, functionality, and dynamics of the soil microbiome. Currently, the involvement of plants in climate change indicates that they can interact with the microbial communities in their environment to relieve various stresses through the innate microbiome assortment of focused strains, a phenomenon dubbed "Cry for Help." The metagenomics method has lately appeared as a new platform to adjust and encourage beneficial communications between plants and microbes and improve plant fitness. The metagenomics of soil microbes can provide a powerful tool for designing and evaluating ecosystem restoration strategies that promote sustainable agriculture under a changing climate. By identifying the specific functions and activities of soil microbes, we can develop restoration programs that support these critical components of healthy ecosystems while providing economic benefits through ecosystem services. In the current review, we highlight the innate functions of microbiomes to maintain the sustainability of agriculture and ecosystem restoration. Through this insight study of soil microbe metagenomics, we pave the way for innovative strategies to address the pressing challenges of food security and environmental conservation. The present article elucidates the mechanisms through which plants and microbes communicate to enhance plant resilience and ecosystem restoration and to leverage metagenomics to identify and promote beneficial plant-microbe interactions. Key findings reveal that soil microbes are pivotal in nutrient cycling, greenhouse gas modulation, and overall ecosystem health, offering novel insights into designing ecosystem restoration strategies that bolster sustainable agriculture. As this is a topic many are grappling with, hope these musings will provide people alike with some food for thought.
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Affiliation(s)
- M Jagadesh
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Munmun Dash
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Aradhna Kumari
- College of Agriculture, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Ganj Basoda, Vidisha, Madhya Pradesh, India.
| | - Santosh Kumar Singh
- Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, India.
| | - Krishan K Verma
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi 530007, China.
| | - Prasann Kumar
- Department of Agronomy, School of Agriculture, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Rajan Bhatt
- Krishi Vigyan Kendra, Amritsar, Punjab Agricultural University (PAU), Ludhiana, Punjab 144601, India
| | - Satish Kumar Sharma
- College of Agriculture, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Ganj Basoda, Vidisha, Madhya Pradesh, India
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Cao YH, Zhao XW, Nie G, Wang ZY, Song X, Zhang MX, Hu JP, Zhao Q, Jiang Y, Zhang JL. The salt-tolerance of perennial ryegrass is linked with root exudate profiles and microflora recruitment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170205. [PMID: 38272075 DOI: 10.1016/j.scitotenv.2024.170205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/14/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024]
Abstract
Salinity poses a significant threat to plant growth and development. The root microbiota plays a key role in plant adaptation to saline environments. Nevertheless, it remains poorly understood whether and how perennial grass plants accumulate specific root-derived bacteria when exposed to salinity. Here, we systematically analyzed the composition and variation of rhizosphere and endophytic bacteria, as well as root exudates in perennial ryegrass differing in salt tolerance grown in unsterilized soils with and without salt. Both salt-sensitive (P1) and salt-tolerant (P2) perennial ryegrass genotypes grew better in unsterilized soils compared to sterilized soils under salt stress. The rhizosphere and endophytic bacteria of both P1 and P2 had lower alpha-diversity under salt treatment compared to control. The reduction of alpha-diversity was more pronounced for P1 than for P2. The specific root-derived bacteria, particularly the genus Pseudomonas, were enriched in rhizosphere and endophytic bacteria under salt stress. Changes in bacterial functionality induced by salt stress differed in P1 and P2. Additionally, more root exudates were altered under salt stress in P2 than in P1. The content of important root exudates, mainly including phenylpropanoids, benzenoids, organic acids, had a significantly positive correlation with the abundance of rhizosphere and endophytic bacteria under salt stress. The results indicate that the interactions between root-derived bacteria and root exudates are crucial for the salt tolerance of perennial ryegrass, which provides a potential strategy to manipulate root microbiome for improved stress tolerance of perennial grass species.
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Affiliation(s)
- Yan-Hua Cao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, PR China
| | - Xiong-Wei Zhao
- College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, PR China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Zhi-Yong Wang
- Sanya Institute of Breeding and Multiplication, School of Tropical Agricultural and Forestry, Hainan University, Sanya 572025, PR China
| | - Xin Song
- College of Life Science and Resources and Environment, Yichun University, Yichun 336000, PR China
| | - Ming-Xu Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, PR China
| | - Jin-Peng Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, PR China
| | - Qi Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, PR China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA.
| | - Jin-Lin Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, PR China; Sanya Institute of Breeding and Multiplication, School of Tropical Agricultural and Forestry, Hainan University, Sanya 572025, PR China.
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Tang H, Zhong Z, Hou J, You L, Zhao Z, Kwok LY, Bilige M. Metagenomic analysis revealed the potential of lactic acid bacteria in improving natural saline-alkali land. Int Microbiol 2024; 27:311-324. [PMID: 37386210 DOI: 10.1007/s10123-023-00388-4] [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: 02/01/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 07/01/2023]
Abstract
Management and improving saline-alkali land is necessary for sustainable agricultural development. We conducted a field experiment to investigate the effects of spraying lactic acid bacteria (LAB) on the cucumber and tomato plant soils. Three treatments were designed, including spraying of water, viable or sterilized LAB preparations to the soils of cucumber and tomato plants every 20 days. Spraying sterilized or viable LAB could reduce the soil pH, with a more obvious effect by using viable LAB, particularly after multiple applications. Metagenomic sequencing revealed that the soil microbiota in LAB-treated groups had higher alpha-diversity and more nitrogen-fixing bacteria compared with the water-treated groups. Both viable and sterilized LAB, but not water application, increased the complexity of the soil microbiota interactive network. The LAB-treated subgroups were enriched in some KEGG pathways compared with water or sterilized LAB subgroups, such as environmental information processing-related pathways in cucumber plant; and metabolism-related pathways in tomato plant, respectively. Redundancy analysis revealed association between some soil physico-chemical parameters (namely soil pH and total nitrogen) and bacterial biomarkers (namely Rhodocyclaceae, Pseudomonadaceae, Gemmatimonadaceae, and Nitrosomonadales). Our study demonstrated that LAB is a suitable strategy for decreasing soil pH and improving the microbial communities in saline-alkali land.
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Affiliation(s)
- Hai Tang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Scientific Observation and Experiment Station of Utilization of Agricultural Microbial Resources in Northeast Region, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Zhi Zhong
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Scientific Observation and Experiment Station of Utilization of Agricultural Microbial Resources in Northeast Region, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Jingqing Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Scientific Observation and Experiment Station of Utilization of Agricultural Microbial Resources in Northeast Region, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Lijun You
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Scientific Observation and Experiment Station of Utilization of Agricultural Microbial Resources in Northeast Region, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Zhixin Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Scientific Observation and Experiment Station of Utilization of Agricultural Microbial Resources in Northeast Region, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
- Key Laboratory of Dairy Products Processing, Scientific Observation and Experiment Station of Utilization of Agricultural Microbial Resources in Northeast Region, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China
| | - Menghe Bilige
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China.
- Key Laboratory of Dairy Products Processing, Scientific Observation and Experiment Station of Utilization of Agricultural Microbial Resources in Northeast Region, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China.
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5
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Jansson JK, McClure R, Egbert RG. Soil microbiome engineering for sustainability in a changing environment. Nat Biotechnol 2023; 41:1716-1728. [PMID: 37903921 DOI: 10.1038/s41587-023-01932-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/01/2023] [Indexed: 11/01/2023]
Abstract
Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth's soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.
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Affiliation(s)
- Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Ryan McClure
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert G Egbert
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
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6
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Ngamcharungchit C, Chaimusik N, Panbangred W, Euanorasetr J, Intra B. Bioactive Metabolites from Terrestrial and Marine Actinomycetes. Molecules 2023; 28:5915. [PMID: 37570885 PMCID: PMC10421486 DOI: 10.3390/molecules28155915] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Actinomycetes inhabit both terrestrial and marine ecosystems and are highly proficient in producing a wide range of natural products with diverse biological functions, including antitumor, immunosuppressive, antimicrobial, and antiviral activities. In this review, we delve into the life cycle, ecology, taxonomy, and classification of actinomycetes, as well as their varied bioactive metabolites recently discovered between 2015 and 2023. Additionally, we explore promising strategies to unveil and investigate new bioactive metabolites, encompassing genome mining, activation of silent genes through signal molecules, and co-cultivation approaches. By presenting this comprehensive and up-to-date review, we hope to offer a potential solution to uncover novel bioactive compounds with essential activities.
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Affiliation(s)
- Chananan Ngamcharungchit
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Mahidol University and Osaka University Collaborative Research Center on Bioscience and Biotechnology, Bangkok 10400, Thailand
| | - Nutsuda Chaimusik
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Mahidol University and Osaka University Collaborative Research Center on Bioscience and Biotechnology, Bangkok 10400, Thailand
| | - Watanalai Panbangred
- Research, Innovation and Partnerships Office, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
| | - Jirayut Euanorasetr
- Department of Microbiology, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
- Laboratory of Biotechnological Research for Energy and Bioactive Compounds, Department of Microbiology, Faculty of Science, King Mongkut’s University of Technology Thonburi, Khet Thung Khru, Bangkok 10140, Thailand
| | - Bungonsiri Intra
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Mahidol University and Osaka University Collaborative Research Center on Bioscience and Biotechnology, Bangkok 10400, Thailand
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7
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Wang Y, Wang Y, Zhang Q, Fan H, Wang X, Wang J, Zhou Y, Chen Z, Sun F, Cui X. Saline-Alkali Soil Property Improved by the Synergistic Effects of Priestia aryabhattai JL-5, Staphylococcus pseudoxylosus XW-4, Leymus chinensis and Soil Microbiota. Int J Mol Sci 2023; 24:ijms24097737. [PMID: 37175442 PMCID: PMC10178608 DOI: 10.3390/ijms24097737] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Two saline-alkali-tolerant bacterial strains, Priestia aryabhattai JL-5 and Staphylococcus pseudoxylosus XW-4, were isolated, with high capabilities of hydrolyzing phosphate and producing cellulase, respectively. The molecular mechanisms regulating the saline-alkali tolerance in the strain JL-5 were further investigated using transcriptome analysis. The contents of lactic acid and proline and the enzymatic activity of glutamine synthetase in the strain JL-5 were significantly increased. The properties of saline-alkali soils were significantly improved by the enhanced growth of the indicator plant Leymus chinensis under the combined applications of the strains JL-5 and XW-4 mixed with corn straw. The contents of catalase, peroxidase, superoxide dismutase and proline of L. chinensis were significantly increased, and the content of malondialdehyde was significantly decreased in the combined treatment of both bacterial strains. The contents of available nitrogen, phosphorus and potassium and organic matters in the soil treated with both strains were significantly increased, as well as the diversity and abundance of the soil microbiota. Our study evidently demonstrated the synergistic effects of the strains JL-5 and XW-4, indicator plants and the local microbiota in terms of improving the saline-alkali soil properties, providing strong experimental evidence to support the commercial development of the combined application of both strains to improve the properties of saline-alkali soils.
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Affiliation(s)
- Yujue Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Yan Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Qian Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Hangzhe Fan
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Xinyu Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Jianan Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Ying Zhou
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Zhanyu Chen
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Fengjie Sun
- Department of Biological Sciences, School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA
| | - Xiyan Cui
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
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Viral Community Structure and Potential Functions in the Dried-Out Aral Sea Basin Change along a Desiccation Gradient. mSystems 2023; 8:e0099422. [PMID: 36625585 PMCID: PMC9948696 DOI: 10.1128/msystems.00994-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The dried-out Aral Sea basin represents an extreme environment due to a man-made ecological disaster. Studies conducted in this unique environment revealed high levels of pollution and a specifically adapted microbiota; however, viral populations remained entirely unexplored. By employing an in-depth analysis based on the sequencing of metagenomic DNA recovered from rhizosphere samples of Suaeda acuminata (C. A. Mey.) Moq. along a desiccation gradient of 5, 10, and 40 years, we detected a diverse viral community comprising 674 viral populations (viral operational taxonomic units [vOTUs]) dominated by Caudovirales. Targeted analyses highlighted that viral populations in this habitat are subjected to certain dynamics that are driven mainly by the gradient of desiccation, the corresponding salinity, and the rhizosphere bacterial populations. In silico predictions linked the viruses to dominant prokaryotic taxa in the Aral Sea basin, such as Gammaproteobacteria, Actinomycetia, and Bacilli. The lysogenic lifestyle was predicted to be predominant in areas that dried out 5 years ago, representing the early revegetation phase. Metabolic prediction of viral auxiliary metabolic genes (AMGs) suggests that viruses may play a role in the biogeochemical cycles, stress resilience, and competitiveness of their hosts due to the presence of genes that are involved in biofilm formation. Overall, our study provides important insights into viral ecology in an extreme environment and expands our knowledge related to virus occurrence in terrestrial systems. IMPORTANCE Environmental viruses have added a wealth of knowledge to ecological studies with the emergence of metagenomic technology and approaches. They are also becoming recognized as important genetic repositories that underpin the functioning of terrestrial ecosystems but have remain moslty unexplored. Using shotgun metagenome sequencing and bioinformatic tools, we found that the viral community structure was affected during natural revegetation in the dried-up Aral Sea area, a model habitat for investigating natural ecological restoration but still understudied. In this study, we highlight the importance of viruses, elements that are overlooked, for their potential contribution to terrestrial ecosystems, i.e., nutrient cycles, stress resilience, and host competitiveness, during natural revegetation.
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Li B, Zhao L, Liu D, Zhang Y, Wang W, Miao Y, Han L. Bacillus subtilis Promotes Cucumber Growth and Quality under Higher Nutrient Solution by Altering the Rhizospheric Microbial Community. PLANTS (BASEL, SWITZERLAND) 2023; 12:298. [PMID: 36679013 PMCID: PMC9862796 DOI: 10.3390/plants12020298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Bacillus subtilis was applied in peat-based soilless cultivation systems containing a mixed substrate (peat:vermiculite:perlite = 2:1:1, v/v/v) and irrigated by one-strength or four-strength Hoagland's nutrient solution to explore whether it can alleviate inhibition by higher-nutrient solutions (four-strength) and bring benefits to improvements of quality. The results showed that higher-nutrient solutions improved the flavor quality of cucumber fruit; especially, the contents of (E,Z)-2,6-nonadienal and (E)-2-Nonenal were effectively increased, which are the special flavor substances of cucumber. B. subtilis K424 effectively improved growth performance, photosynthetic capacity, vitamin C content, soluble sugars, soluble protein, and total pectin in cucumber under higher nutrition solution conditions. Compared with the higher solution treatment, the bacterial diversity significantly increased, whereas the presence of fungi had no significant difference following the B. subtilis K424 application. Moreover, B. subtilis K424 reduced the relative abundance of Actinomadura and promoted that of the Rhodanobacter, Bacillus, Pseudomonas, Devosiaceae, and Blastobotrys genera. Redundancy analysis showed that Bacillus, Rhodanobacter, and Blastobotrys were positively correlated with the substrate enzyme of sucrase, catalase, and urease. This study provides insight that B. subtilis K424 mitigated the deleterious effects of high levels of nutrition solution on cucumber growth and quality by improving the substrate enzyme, regulating the microbial community structure, and enhancing the photosynthetic capacity.
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Affiliation(s)
- Bin Li
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China
- Quwo Fruit and Vegetable Research Institute, Shanxi Agricultural University, Linfen 043400, China
| | - Lixiang Zhao
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China
| | - Dongxu Liu
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China
| | - Yi Zhang
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China
- Quwo Fruit and Vegetable Research Institute, Shanxi Agricultural University, Linfen 043400, China
| | - Wenjiao Wang
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China
- Quwo Fruit and Vegetable Research Institute, Shanxi Agricultural University, Linfen 043400, China
| | - Yanxiu Miao
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China
- Quwo Fruit and Vegetable Research Institute, Shanxi Agricultural University, Linfen 043400, China
| | - Lingjuan Han
- College of Grassland Science, Shanxi Agricultural University, Jinzhong 030801, China
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Zamanzadeh-Nasrabadi SM, Mohammadiapanah F, Hosseini-Mazinani M, Sarikhan S. Salinity stress endurance of the plants with the aid of bacterial genes. Front Genet 2023; 14:1049608. [PMID: 37139239 PMCID: PMC10149814 DOI: 10.3389/fgene.2023.1049608] [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] [Received: 09/20/2022] [Accepted: 03/23/2023] [Indexed: 05/05/2023] Open
Abstract
The application of plant growth-promoting bacteria (PGPB) is vital for sustainable agriculture with continuous world population growth and an increase in soil salinity. Salinity is one of the severe abiotic stresses which lessens the productivity of agricultural lands. Plant growth-promoting bacteria are key players in solving this problem and can mitigate salinity stress. The highest of reported halotolerant Plant growth-promoting bacteria belonged to Firmicutes (approximately 50%), Proteobacteria (40%), and Actinobacteria (10%), respectively. The most dominant genera of halotolerant plant growth-promoting bacteria are Bacillus and Pseudomonas. Currently, the identification of new plant growth-promoting bacteria with special beneficial properties is increasingly needed. Moreover, for the effective use of plant growth-promoting bacteria in agriculture, the unknown molecular aspects of their function and interaction with plants must be defined. Omics and meta-omics studies can unreveal these unknown genes and pathways. However, more accurate omics studies need a detailed understanding of so far known molecular mechanisms of plant stress protection by plant growth-promoting bacteria. In this review, the molecular basis of salinity stress mitigation by plant growth-promoting bacteria is presented, the identified genes in the genomes of 20 halotolerant plant growth-promoting bacteria are assessed, and the prevalence of their involved genes is highlighted. The genes related to the synthesis of indole acetic acid (IAA) (70%), siderophores (60%), osmoprotectants (80%), chaperons (40%), 1-aminocyclopropane-1-carboxylate (ACC) deaminase (50%), and antioxidants (50%), phosphate solubilization (60%), and ion homeostasis (80%) were the most common detected genes in the genomes of evaluated halotolerant plant growth-promoting and salinity stress-alleviating bacteria. The most prevalent genes can be applied as candidates for designing molecular markers for screening of new halotolerant plant growth-promoting bacteria.
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Affiliation(s)
- Seyyedeh Maryam Zamanzadeh-Nasrabadi
- Pharmaceutial Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Fatemeh Mohammadiapanah
- Pharmaceutial Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
- *Correspondence: Fatemeh Mohammadiapanah,
| | | | - Sajjad Sarikhan
- Molecular Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
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11
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Rai S, Omar AF, Rehan M, Al-Turki A, Sagar A, Ilyas N, Sayyed RZ, Hasanuzzaman M. Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture. PLANTA 2022; 257:27. [PMID: 36583789 DOI: 10.1007/s00425-022-04052-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
This review is an effort to provide in-depth knowledge of microbe's interaction and its role in crop microbiome using combination of advanced molecular and OMICS technology to translate this information for the sustenance of agriculture. Increasing population, climate change and exhaustive agricultural practices either influenced nutrient inputs of soil or generating biological and physico-chemical deterioration of the soils and affecting the agricultural productivity and agro-ecosystems. Alarming concerns toward food security and crop production claim for renewed attention in microbe-based farming practices. Microbes are omnipresent (soil, water, and air) and their close association with plants would help to accomplish sustainable agriculture goals. In the last few decades, the search for beneficial microbes in crop production, soil fertilization, disease management, and plant growth promotion is the thirst for eco-friendly agriculture. The crop microbiome opens new paths to utilize beneficial microbes and manage pathogenic microbes through integrated advanced biotechnology. The crop microbiome helps plants acquire nutrients, growth, resilience against phytopathogens, and tolerance to abiotic stresses, such as heat, drought, and salinity. Despite the emergent functionality of the crop microbiome as a complicated constituent of the plant fitness, our understanding of how the functionality of microbiome influenced by numerous factors including genotype of host, climatic conditions, mobilization of minerals, soil composition, nutrient availability, interaction between nexus of microbes, and interactions with other external microbiomes is partially understood. However, the structure, composition, dynamics, and functional contribution of such cultured and uncultured crop microbiome are least explored. The advanced biotechnological approaches are efficient tools for acquiring the information required to investigate the microbiome and extract data to develop high yield producing and resistant variety crops. This knowledge fills the fundamental gap between the theoretical concepts and the operational use of these advanced tools in crop microbiome studies. Here, we review (1) structure and composition of crop microbiome, (2) microbiome-mediated role associated with crops fitness, (3) Molecular and -omics techniques for exploration of crop microbiome, and (4) current approaches and future prospectives of crop microbiome and its exploitation for sustainable agriculture. Recent -omic approaches are influential tool for mapping, monitoring, modeling, and management of crops microbiome. Identification of crop microbiome, using system biology and rhizho-engineering, can help to develop future bioformulations for disease management, reclamation of stressed agro-ecosystems, and improved productivity of crops. Nano-system approaches combined with triggering molecules of crop microbiome can help in designing of nano-biofertilizers and nano-biopesticides. This combination has numerous merits over the traditional bioinoculants. They stimulate various defense mechanisms in plants facing stress conditions; provide bioavailability of nutrients in the soil, helps mitigate stress conditions; and enhance chances of crops establishment.
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Affiliation(s)
- Shalini Rai
- Department of Biotechnology, SHEPA, Varanasi, India.
| | - Ayman F Omar
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, 51452, Saudi Arabia.
- Department of Plant Pathology, Plant Pathology and Biotechnology Laboratory and EPCRS Excellence Center, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, 33516, Egypt.
| | - Medhat Rehan
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, 51452, Saudi Arabia
- Department of Genetics, College of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, 33516, Egypt
| | - Ahmad Al-Turki
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, 51452, Saudi Arabia
| | - Alka Sagar
- Department of Microbiology, MIET, Meerut, India
| | - Noshin Ilyas
- Department of Botany, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
| | - R Z Sayyed
- Asian PGPR Society, Auburn Venture, Auburn, AL, USA.
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-E-Bangla Agricultural University (SAU), Sher-E-Bangla Nagar, Dhaka, 1207, Bangladesh
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12
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Cao TND, Bui XT, Le LT, Dang BT, Tran DPH, Vo TKQ, Tran HT, Nguyen TB, Mukhtar H, Pan SY, Varjani S, Ngo HH, Vo TDH. An overview of deploying membrane bioreactors in saline wastewater treatment from perspectives of microbial and treatment performance. BIORESOURCE TECHNOLOGY 2022; 363:127831. [PMID: 36029979 DOI: 10.1016/j.biortech.2022.127831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
The discharged saline wastewater has severely influenced the aquatic environment as the treatment performance of many wastewater treatment techniques is limited. In addition, the sources of saline wastewater are also plentiful from agricultural and various industrial fields such as food processing, tannery, pharmaceutical, etc. Although high salinity levels negatively impact the performance of both physicochemical and biological processes, membrane bioreactor (MBR) processes are considered as a potential technology to treat saline wastewater under different salinity levels depending on the adaption of the microbial community. Therefore, this study aims to systematically review the application of MBR widely used in the saline wastewater treatment from the perspectives of microbial structure and treatment efficiencies. At last, the concept of carbon dioxide capture and storage will be proposed for the MBR-treating saline wastewater technologies and considered toward the circular economy with the target of zero emission.
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Affiliation(s)
- Thanh Ngoc-Dan Cao
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan ROC
| | - Xuan-Thanh Bui
- Key Laboratory of Advanced Waste Treatment Technology & Faculty of Environment and Natural Resources, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, district 10, Ho Chi Minh City 700000, Viet Nam; Vietnam National University Ho Chi Minh (VNU-HCM), Linh Trung ward, Ho Chi Minh City 700000, Viet Nam.
| | - Linh-Thy Le
- Key Laboratory of Advanced Waste Treatment Technology & Faculty of Environment and Natural Resources, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, district 10, Ho Chi Minh City 700000, Viet Nam; Faculty of Public Health, University of Medicine and Pharmacy at Ho Chi Minh City (UMP), Ward 11, District 5, Ho Chi Minh City 72714, Viet Nam
| | - Bao-Trong Dang
- Vietnam National University Ho Chi Minh (VNU-HCM), Linh Trung ward, Ho Chi Minh City 700000, Viet Nam; Faculty of Chemical Engineering, Ho Chi Minh University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City 700000, Viet Nam
| | - Duyen Phuc-Hanh Tran
- Key Laboratory of Advanced Waste Treatment Technology & Faculty of Environment and Natural Resources, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, district 10, Ho Chi Minh City 700000, Viet Nam; Vietnam National University Ho Chi Minh (VNU-HCM), Linh Trung ward, Ho Chi Minh City 700000, Viet Nam
| | - Thi-Kim-Quyen Vo
- Faculty of Biology and Environment, Ho Chi Minh City University of Food Industry (HUFI), 140 Le Trong Tan street, Tay Thanh ward, Tan Phu district, Ho Chi Minh City 700000, Viet Nam
| | - Huu-Tuan Tran
- Department of Civil, Environmental & Architectural Engineering, The University of Kansas, Lawrence, KS 66045, United States
| | - Thanh-Binh Nguyen
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Hussnain Mukhtar
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan ROC
| | - Shu-Yuan Pan
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan ROC
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar 382010, Gujarat, India
| | - Huu Hao Ngo
- School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NWS 2007, Australia
| | - Thi-Dieu-Hien Vo
- Faculty of Environmental and Food Engineering, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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Xin Y, Ji L, Wang Z, Li K, Xu X, Guo D. Functional Diversity and CO 2 Emission Characteristics of Soil Bacteria during the Succession of Halophyte Vegetation in the Yellow River Delta. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:12919. [PMID: 36232219 PMCID: PMC9564505 DOI: 10.3390/ijerph191912919] [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: 08/15/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 06/17/2023]
Abstract
Carbon dioxide (CO2) is the most important greenhouse gas in the atmosphere, which is mainly derived from microbial respiration in soil. Soil bacteria are an important part of the soil ecosystem and play an important role in the process of plant growth, mineralization, and decomposition of organic matter. In this paper, we discuss a laboratory incubation experiment that we conducted to investigate the CO2 emissions and the underlying bacterial communities under the natural succession of halophyte vegetation in the Yellow River Delta by using high-throughput sequencing technology and PICRUSt functional prediction. The results showed that the bacterial abundance and diversity increased significantly along with the succession of halophyte vegetation. Metabolic function is the dominant function of soil bacteria in the study area. With the succession of halophyte vegetation, the rate of CO2 emissions gradually increased, and were significantly higher in soil covered with vegetation than that of the bare land without vegetation coverage. These results helped to better understand the relationships of soil bacterial communities under the background of halophyte vegetation succession, which can help to make efficient strategies to mitigate CO2 emissions and enhance carbon sequestration.
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14
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Wang Y, Wang J, Zou X, Qu M, Li J. Groundwater depth regulates assembly processes of abundant and rare bacterial communities across arid inland river basin. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 319:115767. [PMID: 35982567 DOI: 10.1016/j.jenvman.2022.115767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/18/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Although numerous studies on bacterial biogeographic patterns in dryland have been conducted, bacterial community assembly across arid inland river basins is unclear. Here, we assessed the ecological drivers that regulate the assembly processes of abundant (ABS) and rare (RBS) bacterial subcommunities based on 162 soil samples collected in an arid inland river basin of China. The results showed that: (1) ABS exhibited a steeper distance-decay slope, and were more strongly affected by dispersal limitation (75.5% and 84.5%), than RBS in surface and subsurface soil. RBS were predominantly controlled by variable selection (54.6% and 50.2%). (2) Soil electric conductivity played a decisive role in mediating the balance between deterministic and stochastic processes of ABS and RBS in surface soil, increasing soil electric conductivity increased the importance of deterministic process. For subsurface soil, soil available phosphorus (SAP) and soil pH drove the balance in the assembly processes of ABS and RBS, respectively. The RBS shifted from determinism to stochasticity with decreased pH, while the dominance of deterministic processes was higher in low-SAP sites. (3) Groundwater depth seasonality had substantial effects on the assembly processes of ABS and RBS, but groundwater depth seasonality affected them indirectly mainly by regulating soil properties. Collectively, our study provides robust evidence that groundwater-driven variations in soil properties mediates the community assembly process of soil bacteria in arid inland river basins. This finding is of importance for forecasting the dynamics of soil microbial community and soil process in response to current and future depleted groundwater.
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Affiliation(s)
- Yin Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083, China.
| | - Jianming Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083, China.
| | - Xuge Zou
- School of Ecology and Nature Conservation, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083, China.
| | - Mengjun Qu
- School of Ecology and Nature Conservation, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083, China.
| | - Jingwen Li
- School of Ecology and Nature Conservation, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083, China.
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15
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Cui MH, Chen XY, Yin FX, Xia GM, Yi Y, Zhang YB, Liu SW, Li F. Hybridization affects the structure and function of root microbiome by altering gene expression in roots of wheat introgression line under saline-alkali stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155467. [PMID: 35489489 DOI: 10.1016/j.scitotenv.2022.155467] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
The mutually beneficial relationship between plants and their root microbiota is essential for plants to adapt to unfavorable environments. However, the molecular mechanism of wheat regulating the structure of root microbiome and the influence of distant hybridization on this process are poorly understood. In this study, we systematically compared the root transcriptome and microbiome between a saline-alkali tolerant wheat introgression line SR4 (derived from somatic hybridization between wheat and tall wheatgrass) and its parent wheat variety JN177. The results indicated that root microorganisms were key factor maintaining better homeostasis of the sodium and potassium ion contents in SR4 than in JN177 under saline-alkali stress. Through systematic comparisons, we identified SR4-specific root bacterial and fungal taxa under saline-alkali stress. Through a weighted gene correlation network analysis (WGCNA) combining microbiome and transcriptome data, key functional genes and pathways, which were strongly related to root bacteria and fungi with differential abundance between JN177 and SR4, were identified. These results suggest that somatic hybridization has altered the key genes regulating root microbiome in wheat, further improving the saline-alkali tolerance of wheat introgression line. These findings provide the key bacterial and fungal taxa and functional target genes for wheat root microbiome engineering under saline-alkali stress.
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Affiliation(s)
- Ming-Han Cui
- Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, 116 Baoshan Road (N), Guiyang, Guizhou 550001, China; Key Laboratory of Plant Development and and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Xiang-Yu Chen
- Key Laboratory of Plant Development and and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Feng-Xiang Yin
- Key Laboratory of Plant Development and and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Guang-Min Xia
- Key Laboratory of Plant Development and and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Yin Yi
- Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, 116 Baoshan Road (N), Guiyang, Guizhou 550001, China
| | - Yu-Bin Zhang
- Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, 116 Baoshan Road (N), Guiyang, Guizhou 550001, China
| | - Shu-Wei Liu
- Key Laboratory of Plant Development and and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China.
| | - Fei Li
- Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, 116 Baoshan Road (N), Guiyang, Guizhou 550001, China.
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16
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Salt flat microbial diversity and dynamics across salinity gradient. Sci Rep 2022; 12:11293. [PMID: 35788147 PMCID: PMC9253026 DOI: 10.1038/s41598-022-15347-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/22/2022] [Indexed: 11/19/2022] Open
Abstract
Sabkhas are hypersaline, mineral-rich, supratidal mudflats that harbor microbes that are adapted to high salt concentration. Sabkha microbial diversity is generally studied for their community composition, but less is known about their genetic structure and heterogeneity. In this study, we analyzed a coastal sabkha for its microbial composition using 16S rDNA and whole metagenome, as well as for its population genetic structure. Our 16S rDNA analysis show high alpha diversity in both inner and edge sabkha than outer sabkha. Beta diversity result showed similar kind of microbial composition between inner and edge sabkha, while outer sabkha samples show different microbial composition. At phylum level, Bacteroidetes (~ 22 to 34%), Euryarchaeota (~ 18 to ~ 30%), unclassified bacteria (~ 24 to ~ 35%), Actinobacteria (~ 0.01 to ~ 11%) and Cyanobacteria (less than 1%) are predominantly found in both inside and edge sabkha regions, whereas Proteobacteria (~ 92 to ~ 97%) and Parcubacteria (~ 1 to ~ 2%) are predominately found in outer sabkha. Our 225 metagenomes assembly from this study showed similar bacterial community profile as observed in 16S rDNA-based analysis. From the assembled genomes, we found important genes that are involved in biogeochemical cycles and secondary metabolite biosynthesis. We observed a dynamic, thriving ecosystem that engages in metabolic activity that shapes biogeochemical structure via carbon fixation, nitrogen, and sulfur cycling. Our results show varying degrees of horizontal gene transfers (HGT) and homologous recombination, which correlates with the observed high diversity for these populations. Moreover, our pairwise population differentiation (Fst) for the abundance of species across the salinity gradient of sabkhas identified genes with strong allelic differentiation, lower diversity and elevated nonsynonymous to synonymous ratio of variants, which suggest selective sweeps for those gene variants. We conclude that the process of HGT, combined with recombination and gene specific selection, constitute the driver of genetic variation in bacterial population along a salinity gradient in the unique sabkha ecosystem.
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Nwachukwu BC, Babalola OO. Metagenomics: A Tool for Exploring Key Microbiome With the Potentials for Improving Sustainable Agriculture. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.886987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microorganisms are immense in nature and exist in every imaginable ecological niche, performing a wide range of metabolic processes. Unfortunately, using traditional microbiological methods, most microorganisms remain unculturable. The emergence of metagenomics has resolved the challenge of capturing the entire microbial community in an environmental sample by enabling the analysis of whole genomes without requiring culturing. Metagenomics as a non-culture approach encompasses a greater amount of genetic information than traditional approaches. The plant root-associated microbial community is essential for plant growth and development, hence the interactions between microorganisms, soil, and plants is essential to understand and improve crop yields in rural and urban agriculture. Although some of these microorganisms are currently unculturable in the laboratory, metagenomic techniques may nevertheless be used to identify the microorganisms and their functional traits. A detailed understanding of these organisms and their interactions should facilitate an improvement of plant growth and sustainable crop production in soil and soilless agriculture. Therefore, the objective of this review is to provide insights into metagenomic techniques to study plant root-associated microbiota and microbial ecology. In addition, the different DNA-based techniques and their role in elaborating plant microbiomes are discussed. As an understanding of these microorganisms and their biotechnological potentials are unlocked through metagenomics, they can be used to develop new, useful and unique bio-fertilizers and bio-pesticides that are not harmful to the environment.
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Mujakić I, Piwosz K, Koblížek M. Phylum Gemmatimonadota and Its Role in the Environment. Microorganisms 2022; 10:microorganisms10010151. [PMID: 35056600 PMCID: PMC8779627 DOI: 10.3390/microorganisms10010151] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/06/2023] Open
Abstract
Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.
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Affiliation(s)
- Izabela Mujakić
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237, 379 81 Třeboň, Czech Republic; (I.M.); (K.P.)
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
| | - Kasia Piwosz
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237, 379 81 Třeboň, Czech Republic; (I.M.); (K.P.)
- National Marine Fisheries Research Institute, Kołłątaja 1, 81-332 Gdynia, Poland
| | - Michal Koblížek
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237, 379 81 Třeboň, Czech Republic; (I.M.); (K.P.)
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
- Correspondence:
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Bonomo MG, Calabrone L, Scrano L, Bufo SA, Di Tomaso K, Buongarzone E, Salzano G. Metagenomic monitoring of soil bacterial community after the construction of a crude oil flowline. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:48. [PMID: 34978609 PMCID: PMC8724107 DOI: 10.1007/s10661-021-09637-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/20/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to assess the metagenomic changes of soil bacterial community after constructing a crude oil flowline in Basilicata region, Italy. Soils identified a total of 56 taxa at the phylum level and 485 at the family level, with a different taxa distribution, especially in samples collected on 2014. Since microbiological diversity occurred in the soils collected after 2013 (the reference year), we performed a differential abundance analysis using DESeq2 by GAIA pipeline. In the forest area, 14 phyla and 126 families were differentially abundant (- 6.06 < logFC > 7.88) in 2014 compared to 2013. Nine families were differentially abundant in 2015, with logFC between - 3.16 and 4.66, while 20 families were significantly more abundant and 16 less abundant in 2016, with logFC between - 6.48 and 6.45. In the cultivated area, 33 phyla and 260 families showed differential abundance in 2014. In the next year (2015), 14 phyla were significantly more abundant and 19 less abundant, while 29 families were substantially more abundant and 139 less abundant, with fold changes ranging between - 5.67 and 4.01. In 2016, 33 phyla showed a significantly different abundance, as 14 were more abundant and 19 decreased, and 81 families showed a significantly increased amount with logFC between - 5.31 and 5.38. These results hypothesise that the analysed site is an altered soil where the development of particular bacterial groups attends to bioremediation processes, naturally occurring to restore optimal conditions.
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Affiliation(s)
| | - Luana Calabrone
- Department of Sciences, University of Basilicata, Potenza, Italy
| | - Laura Scrano
- Department of European Cultures, University of Basilicata, Potenza, Italy
| | - Sabino Aurelio Bufo
- Department of Sciences, University of Basilicata, Potenza, Italy
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Johannesburg, South Africa
| | - Katia Di Tomaso
- Department of Sciences, University of Basilicata, Potenza, Italy
| | | | - Giovanni Salzano
- Department of Sciences, University of Basilicata, Potenza, Italy
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Tripathi S, Purchase D, Al-Rashed S, Chandra R. Microbial community dynamics and their relationships with organic and metal pollutants of sugarcane molasses-based distillery wastewater sludge. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118267. [PMID: 34601036 DOI: 10.1016/j.envpol.2021.118267] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
Distillery sludge is a major source of aquatic pollution, but little is known about their microbial community and their association with the organic and metal pollutants. Sugarcane molasses-based distillery is an important industry in India, although the waste is usually treated prior to disposal, the treatment is often inadequate. The adverse effects of the organic and metal pollutants in sugarcane molasses-based distillery sludge on the microbial biodiversity and abundance in the disposal site have not been elucidated. This study aims to address this gap of knowledge. Samples were collected from the discharge point, 1 and 2 km downstream (D1, D2, and D3, respectively) of a sugarcane distillery in Uttar Pradesh, India, and their physico-chemical properties characterised. Using QIIME, taxonomic assignment for the V3 and V4 hypervariable regions of 16 S rRNA was performed. The phyla Proteobacteria (28-39%), Firmicutes (20-28%), Bacteriodetes (9-10%), Actinobacteria (5-10%), Tenericutes (1-9%) and Patescibacteria (2%) were the predominant bacteria in all three sites. Euryechaeota, were detected in sites D1 and D2 (1-2%) but absent in D3. Spirochaetes (5%), Sinergistetes (2%) and Cloacimonetes (1%) were only detected in samples from site D1. Shannon, Simpson, Chao1, and Observed-species indices indicated that site D1 (10.18, 0.0013, 36706.55 and 45653.84, respectively) has higher bacterial diversity and richness than D2 (6.66, 0.0001, 25987.71 and 49655.89, respectively) and D3 (8.31, 0.002, 30345.53 and 30654.88, respectively), suggesting the organic and metal pollutants provided the stressors to favour the survival of microbial community that can biodegrade and detoxify them in the distillery sludge. This study confirmed that the treatment of the distillery waste was not sufficiently effective and provided new metagenomic information on its impact on the surrounding microbial community. It also offered new insights into potential bioremediation candidates.
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Affiliation(s)
- Sonam Tripathi
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar Central University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Diane Purchase
- Department of Natural Sciences, Faculty of Science and Technology, Middlesex University, The Burroughs, London, NW4 4BT, UK
| | - Sarah Al-Rashed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O 2455, Riyadh, 11451, Saudi Arabia
| | - Ram Chandra
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar Central University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India.
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Behera BK, Dehury B, Rout AK, Patra B, Mantri N, Chakraborty HJ, Sarkar DJ, Kaushik NK, Bansal V, Singh I, Das BK, Rao AR, Rai A. Metagenomics study in aquatic resource management: Recent trends, applied methodologies and future needs. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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22
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Mehta P, Yadav M, Ahmed V, Goyal K, Pandey R, Chauhan NS. Culture-Independent Exploration of the Hypersaline Ecosystem Indicates the Environment-Specific Microbiome Evolution. Front Microbiol 2021; 12:686549. [PMID: 34777269 PMCID: PMC8581802 DOI: 10.3389/fmicb.2021.686549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 09/30/2021] [Indexed: 01/08/2023] Open
Abstract
Sambhar Salt Lake, situated in the state of Rajasthan, India is a unique temperate hypersaline ecosystem. Exploration of the salt lake microbiome will enable us to understand microbiome functioning in nutrient-deprived extreme conditions, as well as enrich our understanding of the environment-specific microbiome evolution. The current study has been designed to explore the Sambhar Salt Lake microbiome with a culture-independent multi-omics approach to define its metagenomic features and prevalent metabolic functionaries. The rRNA feature and protein feature-based phylogenetic reconstruction synchronously (R = 0.908) indicated the dominance of the archaea (Euryarchaeota) and bacteria (Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria). Metabolic reconstruction identified selective enrichment of the protein features associated with energy harvesting and stress tolerance (osmotic, oxidative, metal/metalloid, heat/cold, antibiotic, and desiccation). Metabolites identified with metabolome analysis confirmed physiological adaptation of the lake microbiome within a hypersaline and nutrient-deprived environment. Comparative metagenomics of the 212 metagenomes representing freshwater, alkaline, and saline ecosystem microbiome indicated the selective enrichment of the microbial groups and genetic features. The current study elucidates microbiome functioning within the nutrient-deprived harsh ecosystems. In summary, the current study harnessing the strength of multi-omics and comparative metagenomics indicates the environment-specific microbiome evolution.
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Affiliation(s)
- Priyanka Mehta
- Genomics and Molecular Medicine, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Monika Yadav
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Vasim Ahmed
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Khushboo Goyal
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Rajesh Pandey
- Genomics and Molecular Medicine, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
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Kumar N, Mittal A, Yadav M, Sharma S, Kumar T, Chakraborty R, Sengupta S, Chauhan NS. Photocatalytic TiO 2/CdS/ZnS nanocomposite induces Bacillus subtilis cell death by disrupting its metabolism and membrane integrity. Indian J Microbiol 2021; 61:487-496. [PMID: 34744204 DOI: 10.1007/s12088-021-00973-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 08/08/2021] [Indexed: 12/24/2022] Open
Abstract
Titanium dioxide (TiO2) is widely characterized for its application in clinical diagnostics, therapeutics, cosmetics, nutrition, and environment management. Despite enormous potential, its dependence on ultraviolet (UV) light for photocatalytic activity limits its commercialization. Accordingly in the present study, a photo catalytically superior ternary complex of TiO2 with Cadmium sulfide/Zinc sulfide (CdS/ZnS) has been synthesized, as well as, characterized for photo-induced antimicrobial activity. The band gap of crystalline TiO2/CdS/ZnS nanocomposite has been reduced (2.26 eV) and nanocomposite has shown the optimal photo-activation at 590 nm. TiO2 nanocomposite has significant bactericidal activity in visible light (P < 0.01). Exposure of the TiO2 nanocomposite affected the cellular metabolism by altering the 1681 metabolic features (P < 0.001) culminating in poor cellular survivability. Additionally, photo-induced reactive oxygen species generation through nanocomposite disrupts the microbial cellular structure. The present study synthesized photocatalytic nanocomposite as well as unveiled the holistic cellular effect of theTiO2/CdS/ZnS nanocomposite. Additionally, the present study also indicated the potential application of TiO2/CdS/ZnS nanocomposite for sustainable environment management, therapeutics, and various industries. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-021-00973-z.
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Affiliation(s)
- Naveen Kumar
- Department of Chemistry, Maharshi Dayanand University, Rohtak, Haryana India
| | - Anuj Mittal
- Department of Chemistry, Maharshi Dayanand University, Rohtak, Haryana India
| | - Monika Yadav
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana India
| | - Shankar Sharma
- Department of Chemistry, Maharshi Dayanand University, Rohtak, Haryana India
| | - Tarun Kumar
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana India
| | - Rahul Chakraborty
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shantanu Sengupta
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana India
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Luo Z, Zhong Q, Han X, Hu R, Liu X, Xu W, Wu Y, Huang W, Zhou Z, Zhuang W, Yan Q, He Z, Wang C. Depth-dependent variability of biological nitrogen fixation and diazotrophic communities in mangrove sediments. MICROBIOME 2021; 9:212. [PMID: 34702367 PMCID: PMC8549172 DOI: 10.1186/s40168-021-01164-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/17/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND Nitrogen-fixing prokaryotes (diazotrophs) contribute substantially to nitrogen input in mangrove sediments, and their structure and nitrogen fixation rate (NFR) are significantly controlled by environmental conditions. Despite the well-known studies on diazotrophs in surficial sediments, the diversity, structure, and ecological functions of diazotrophic communities along environmental gradients of mangrove sediment across different depths are largely unknown. Here, we investigated how biological nitrogen fixation varied with the depth of mangrove sediments from the perspectives of both NFR and diazotrophic communities. RESULTS Through acetylene reduction assay, nifH gene amplicon and metagenomic sequencing, we found that the NFR increased but the diversity of diazotrophic communities decreased with the depth of mangrove sediments. The structure of diazotrophic communities at different depths was largely driven by salinity and exhibited a clear divergence at the partitioning depth of 50 cm. Among diazotrophic genera correlated with NFR, Agrobacterium and Azotobacter were specifically enriched at 50-100 cm sediments, while Anaeromyxobacter, Rubrivivax, Methylocystis, Dickeya, and Methylomonas were more abundant at 0-50 cm. Consistent with the higher NFR, metagenomic analysis demonstrated the elevated abundance of nitrogen fixation genes (nifH/D/K) in deep sediments, where nitrification genes (amoA/B/C) and denitrification genes (nirK and norB) became less abundant. Three metagenome-assembled genomes (MAGs) of diazotrophs from deep mangrove sediments indicated their facultatively anaerobic and mixotrophic lifestyles as they contained genes for low-oxygen-dependent metabolism, hydrogenotrophic respiration, carbon fixation, and pyruvate fermentation. CONCLUSIONS This study demonstrates the depth-dependent variability of biological nitrogen fixation in terms of NFR and diazotrophic communities, which to a certain extent relieves the degree of nitrogen limitation in deep mangrove sediments. Video Abstract.
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Affiliation(s)
- Zhiwen Luo
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Qiuping Zhong
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Xingguo Han
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092, Zurich, Switzerland
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Xingyu Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Wenjun Xu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510530, PR China
| | - Yongjie Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510530, PR China
| | - Weiming Huang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Wei Zhuang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.
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Li H, La S, Zhang X, Gao L, Tian Y. Salt-induced recruitment of specific root-associated bacterial consortium capable of enhancing plant adaptability to salt stress. THE ISME JOURNAL 2021; 15:2865-2882. [PMID: 33875820 PMCID: PMC8443564 DOI: 10.1038/s41396-021-00974-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 03/12/2021] [Accepted: 04/06/2021] [Indexed: 02/01/2023]
Abstract
Salinity is a major abiotic stress threatening crop production. Root-derived bacteria (RDB) are hypothesized to play a role in enhancing plant adaptability to various stresses. However, it is still unclear whether and how plants build up specific RDB when challenged by salinity. In this study, we measured the composition and variation in the rhizosphere and endophyte bacteria of salt-sensitive (SSs) and salt-resistant (SRs) plants under soil conditions with/without salinity. The salt-induced RDB (both rhizobiomes and endophytes) were isolated to examine their effects on the physiological responses of SSs and SRs to salinity challenge. Moreover, we examined whether functional redundancy exists among salt-induced RDB in enhancing plant adaptability to salt stress. We observed that although SSs and SRs recruited distinct RDB and relevant functions when challenged by salinity, salt-induced recruitment of specific RDB led to a consistent growth promotion in plants regardless of their salinity tolerance capacities. Plants employed a species-specific strategy to recruit beneficial soil bacteria in the rhizosphere rather than in the endosphere. Furthermore, we demonstrated that the consortium, but not individual members of the salt-induced RDB, provided enduring resistance against salt stress. This study confirms the critical role of salt-induced RDB in enhancing plant adaptability to salt stress.
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Affiliation(s)
- Hong Li
- grid.22935.3f0000 0004 0530 8290Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, P. R. China
| | - Shikai La
- grid.22935.3f0000 0004 0530 8290Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, P. R. China
| | - Xu Zhang
- grid.22935.3f0000 0004 0530 8290Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, P. R. China
| | - Lihong Gao
- grid.22935.3f0000 0004 0530 8290Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, P. R. China
| | - Yongqiang Tian
- grid.22935.3f0000 0004 0530 8290Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, P. R. China
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Lu Q, Ge G, Sa D, Wang Z, Hou M, Jia YS. Effects of salt stress levels on nutritional quality and microorganisms of alfalfa-influenced soil. PeerJ 2021; 9:e11729. [PMID: 34316396 PMCID: PMC8286062 DOI: 10.7717/peerj.11729] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 06/15/2021] [Indexed: 12/27/2022] Open
Abstract
Background Globally, there is a large amount of salinized land. These soils have varying degrees of salt stress, causing ionic toxicity and osmotic stress on plants. However, it is not clear how different degrees of salt stress affect plant nutrients and microbial communities. Thus, a comprehensive understanding of plant major nutrients and microbial communities response to salt stress is desirable. Results We analyzed the main nutrients of the salt-tolerant ZhongMu No. 3 alfalfa variety planted in a salt stress environment. In mild and moderate group, the protein content and fatty acid content of alfalfa were the highest, indicating the best nutritional value. The severe group of salt stress affected the growth and development of alfalfa, as manifested by a decrease in the nutritional quality of alfalfa. Pseudomonas and Sphingobacterium that from alfalfa stem and leaf endophytes also increased with an increase in salt stress. In contrast, Sphingomonas, Methylobacterium, and Rhizobium decrease with increasing salt stress. Methylobacterium and Rhizobium have extremely significant differences in response to salt stress, and Exiquobacterium also shows significant differences. Conclusions Soil salinity would be an important factor beyond which alfalfa nutrient quality and microbial community structure change. This study identified key levels of salt stress that may affect the nutrient quality and microbial community structure. These findings enhance our understanding of the effects of salt stress on the nutritional quality of alfalfa and provide a reference for the sustainable use of salinized soil in the future.
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Affiliation(s)
- Qiang Lu
- College of Grassland and Resources and Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, China
| | - GenTu Ge
- College of Grassland and Resources and Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, China
| | - DuoWen Sa
- College of Grassland and Resources and Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, China
| | - ZhiJun Wang
- College of Grassland and Resources and Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, China
| | - MeiLing Hou
- College of Agriculture, Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia Autonomous Region, China
| | - Yu Shan Jia
- College of Grassland and Resources and Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region, China
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Guan Y, Jiang N, Wu Y, Yang Z, Bello A, Yang W. Disentangling the role of salinity-sodicity in shaping soil microbiome along a natural saline-sodic gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142738. [PMID: 33097264 DOI: 10.1016/j.scitotenv.2020.142738] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 05/16/2023]
Abstract
Increasing salinity and sodicity have been recognized as threats to soil fertility and crop yield worldwide. In recent years, salt-affected soils have received great attentions due to the shortage of arable land. This study therefore aims to characterize soil bacterial community, assembly process and co-occurrence network along natural saline-sodic gradients across Songnen Plain, Northeast China. As revealed by Miseq sequencing, 8482 bacterial OTUs were annotated at 97% identity across 120 soil samples. Our results indicated that soil salinity-sodicity not only significantly decreased bacterial richness and but also impacted bacterial community composition. The dominant bacterial phyla included Proteobacteria (28.89%), Actinobacteria (19.96%) and Gemmatimonadetes (16.71%). By applying threshold indicator species analysis (TITAN), OTUs from Gemmatimonadetes were found to be the taxa with the most prevalent and strongest preference for high salinity-sodicity. Null model analysis revealed that the majority (76.4%) of βNTI values were below -2 or above 2, indicating deterministic process was dominant across all samples. Notably, deterministic process contributed to a greater extent in higher saline-sodic soils. The bacterial co-occurrence network was more complex in slightly saline-sodic soils than in moderately and extremely saline-sodic soils, reflected by more nodes, more hubs and stronger connections, which was mainly driven by soil pH. These results provide strong evidence that salinity-sodicity was a key determinant in shaping soil bacterial community, assembly process and co-occurrence network pattern.
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Affiliation(s)
- Yupeng Guan
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Nana Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Yanxiang Wu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Zhongzan Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Wei Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China.
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Tailoring Next Generation Plant Growth Promoting Microorganisms as Versatile Tools beyond Soil Desalinization: A Road Map towards Field Application. SUSTAINABILITY 2021. [DOI: 10.3390/su13084422] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Plant growth promoting bacteria (PGPB) have been the target of intensive research studies toward their efficient use in the field as biofertilizers, biocontrol, and bioremediation agents among numerous other applications. Recent trends in the field of PGPB research led to the development of versatile multifaceted PGPB that can be used in different field conditions such as biocontrol of plant pathogens in metal contaminated soils. Unfortunately, all these research efforts lead to the development of PGPB that failed to perform in salty environments. Therefore, it is urgently needed to address this drawback of these PGPB toward their efficient performance in salinity context. In this paper we provide a review of state-of-the-art research in the field of PGPB and propose a road map for the development of next generation versatile and multifaceted PGPB that can perform in salinity. Beyond soil desalinization, our study paves the way towards the development of PGPB able to provide services in diverse salty environments such as heavy metal contaminated, or pathogen threatened. Smart development of salinity adapted next generation biofertilizers will inevitably allow for mitigation and alleviation of biotic and abiotic threats to plant productivity in salty environments.
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Sharma P, Tripathi S, Chandra R. Metagenomic analysis for profiling of microbial communities and tolerance in metal-polluted pulp and paper industry wastewater. BIORESOURCE TECHNOLOGY 2021; 324:124681. [PMID: 33454444 DOI: 10.1016/j.biortech.2021.124681] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/02/2021] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
This work aimed to study the profiling and efficiency of microbial communities and their abundance in the pulp and paper industry wastewater, which contained toxic metals, high biological oxygen demands, chemical oxygen demand, and ions contents. Sequence alignment of the 16S rRNA V3-V4 variable region zone with the Illumina MiSeq framework revealed 25356 operating taxonomical units (OTUs) derived from the wastewater sample. The major phyla identified in wastewater were Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi, Actinobacteria, Spirochetes, Patesibacteria, Acidobacteria, and others including unknown microbes. The study showed the function of microbial communities essential for the oxidation and detoxifying of complex contaminants and design of effective remediation techniques for the re-use of polluted wastewater. Findings demonstrated that the ability of different classes of microbes to adapt and survive in metal-polluted wastewater irrespective of their relative distribution, as well as further attention can be provided to its use in the bioremediation process.
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Affiliation(s)
- Pooja Sharma
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow 226 025, Uttar Pradesh, India
| | - Sonam Tripathi
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow 226 025, Uttar Pradesh, India
| | - Ram Chandra
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow 226 025, Uttar Pradesh, India.
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30
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Yao R, Yang J, Wang X, Xie W, Zheng F, Li H, Tang C, Zhu H. Response of soil characteristics and bacterial communities to nitrogen fertilization gradients in a coastal salt‐affected agroecosystem. LAND DEGRADATION & DEVELOPMENT 2021; 32:338-353. [PMID: 0 DOI: 10.1002/ldr.3705] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/26/2020] [Indexed: 05/22/2023]
Affiliation(s)
- Rongjiang Yao
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science, Chinese Academy of Sciences (CAS) Nanjing 210008 PR China
| | - Jinsong Yang
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science, Chinese Academy of Sciences (CAS) Nanjing 210008 PR China
| | - Xiangping Wang
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science, Chinese Academy of Sciences (CAS) Nanjing 210008 PR China
| | - Wenping Xie
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science, Chinese Academy of Sciences (CAS) Nanjing 210008 PR China
| | - Fule Zheng
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science, Chinese Academy of Sciences (CAS) Nanjing 210008 PR China
- University of Chinese Academy of Sciences Beijing 100049 PR China
| | - Hongqiang Li
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science, Chinese Academy of Sciences (CAS) Nanjing 210008 PR China
- University of Chinese Academy of Sciences Beijing 100049 PR China
| | - Cong Tang
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science, Chinese Academy of Sciences (CAS) Nanjing 210008 PR China
- University of Chinese Academy of Sciences Beijing 100049 PR China
| | - Hai Zhu
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science, Chinese Academy of Sciences (CAS) Nanjing 210008 PR China
- University of Chinese Academy of Sciences Beijing 100049 PR China
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Isolation of gene conferring salt tolerance from halophilic bacteria of Lunsu, Himachal Pradesh, India. J Genet Eng Biotechnol 2020; 18:57. [PMID: 33025336 PMCID: PMC7538504 DOI: 10.1186/s43141-020-00070-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/08/2020] [Indexed: 12/20/2022]
Abstract
Background Halophiles offer an attractive source of genes conferring salt tolerance. Halobacillus trueperi SS1 strain of Lunsu, Himachal Pradesh, India, a strict halophile, was exploited to isolate and clone the genes for salt tolerance. The genomic library of BamH1 digest of H. trueperi SS1 was constructed in pUC19, and recombinants were screened for salt tolerance on an LB medium containing ampicillin (100 μg/ml) and NaCl (0 to 1.5 M). Results One recombinant clone named as salt-tolerant clone (STC) conferred salt tolerance to host Escherichia coli/DH5α, which showed growth in the LB medium supplemented with ampicillin and 1.2 M NaCl. Restriction digestion and PCR analysis revealed the presence of an insert of approximately 2000 bp in the STC. DNA sequencing of the 2-kb insert on both strands yielded a sequence of 2301 nucleotides. Protein BLAST analysis of 2301-bp sequence of H. trueperi SS1 present in STC showed 97% identity to multidrug transport ATP binding/permease protein of Halobacillus karajensis. The insert contained in STC was subcloned into pGEX4T2 vector, and the recombinant clone STC/pGEX4T2 conferred salt tolerance to the bacterial host E. coli. Conclusions The present study led to the isolation of salt tolerance gene encoding a putative multidrug transport ATP binding/permease protein from H. trueperi SS1. The salt tolerance gene can be subcloned for transferring salt tolerance traits into agricultural crop plants for cultivation in saline and coastal lands.
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Kumar S, Paul D, Bhushan B, Wakchaure GC, Meena KK, Shouche Y. Traversing the "Omic" landscape of microbial halotolerance for key molecular processes and new insights. Crit Rev Microbiol 2020; 46:631-653. [PMID: 32991226 DOI: 10.1080/1040841x.2020.1819770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Post-2005, the biology of the salt afflicted habitats is predominantly studied employing high throughput "Omic" approaches comprising metagenomics, transcriptomics, metatranscriptomics, metabolomics, and proteomics. Such "Omic-based" studies have deciphered the unfamiliar details about microbial salt-stress biology. The MAGs (Metagenome-assembled genomes) of uncultured halophilic microbial lineages such as Nanohaloarchaea and haloalkaliphilic members within CPR (Candidate Phyla Radiation) have been reconstructed from diverse hypersaline habitats. The study of MAGs of such uncultured halophilic microbial lineages has unveiled the genomic basis of salt stress tolerance in "yet to culture" microbial lineages. Furthermore, functional metagenomic approaches have been used to decipher the novel genes from uncultured microbes and their possible role in microbial salt-stress tolerance. The present review focuses on the new insights into microbial salt-stress biology gained through different "Omic" approaches. This review also summarizes the key molecular processes that underlie microbial salt-stress response, and their role in microbial salt-stress tolerance has been confirmed at more than one "Omic" levels.
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Affiliation(s)
- Satish Kumar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India.,ICAR-National Institute of Abiotic Stress Management, Baramati, Pune, India
| | - Dhiraj Paul
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Bharat Bhushan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - G C Wakchaure
- ICAR-National Institute of Abiotic Stress Management, Baramati, Pune, India
| | - Kamlesh K Meena
- ICAR-National Institute of Abiotic Stress Management, Baramati, Pune, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
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Effects of Different Fertilizer Treatments on Rhizosphere Soil Microbiome Composition and Functions. LAND 2020. [DOI: 10.3390/land9090329] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fertilization influences the soil microbiome. However, little is known about the effects of long-term fertilization on soil microbial metabolic pathways. In this study, we investigated the soil microbiome composition and function and microbial participation in the N cycle according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) functional annotation of different genes in a metagenomic analysis after long-term fertilization. Fertilizer application significantly changed the soil C/N ratio. Chemical fertilizer (NPK) treatment decreased soil pH, and chemical fertilizer combined with straw (NPK+S0.5) treatment increased ammonium nitrogen (NH4+-N) but decreased nitrate nitrogen (NO3−-N). NPK, NPK+S0.5 and S0.5 applications did not change the soil microbiome composition or dominant phylum but changed the relative abundances of microbiome components. Moreover, fertilizer significantly influenced metabolic processes, cellular processes and single-organism processes. Compared with a no-fertilizer treatment (CK), the NPK treatment resulted in more differentially expressed gene (DEG) pathways than the NPK+S0.5 and S0.5 treatments, and these pathways significantly correlated with soil nitrate nitrogen (NO3−-N), available phosphorus (AP) and the moisture content of soil (MC). KEGG analysis found that fertilizer application mainly affected the ribosome, photosynthesis and oxidative phosphorylation pathways. S0.5 and NPK+S0.5 increased microbial nitrogen fixation, and NPK and NPK+S0.5 decreased amoA and amoB and accelerated denitrification. Thus, organic fertilizer increased N fixation and nitrification, and inorganic N fertilizer accelerated denitrification. We found that the function of the soil microbiome under different fertilizer applications could be important for the rational application of fertilizer and for environmental and sustainable development.
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Petrova SN, Andronov EE, Belimov AA, Beregovaya YV, Denshchikov VA, Minakov DL. Prokaryotic Community Structure in the Rapeseed (Brassica napus L.) Rhizosphere Depending on Addition of 1-Aminocyclopropane-1-Carboxylate-Utilizing Bacteria. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720010117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Comparative genomics analysis of Nitriliruptoria reveals the genomic differences and salt adaptation strategies. Extremophiles 2019; 24:249-264. [PMID: 31820112 DOI: 10.1007/s00792-019-01150-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/25/2019] [Indexed: 12/22/2022]
Abstract
The group Nitriliruptoria, recently classified as a separate class of phylum Actinobacteria, has five members at present, which belong to halophilic or halotolerant Actinobacteria. Here, we sequenced the genomes of Egicoccus halophilus EGI 80432T and Egibacter rhizosphaerae EGI 80759T, and performed a comparative genomics approach to analyze the genomic differences and salt adaptation mechanisms in Nitriliruptoria. Phylogenetic analysis suggested that Euzebya tangerina F10T has a closer phylogenetic relationship to Euzebya rosea DSW09T, while genomic analysis revealed highest genomic similarity with Nitriliruptor alkaliphilus ANL-iso2T and E. halophilus EGI 80432T. Genomic differences of Nitriliruptoria were mainly observed in genome size, gene contents, and the amounts of gene in per functional categories. Furthermore, our analysis also revealed that Nitriliruptoria possess similar synthesis systems of solutes, such as trehalose, glutamine, glutamate, and proline. On the other hand, each member of Nitriliruptoria species possesses specific mechanisms, K+ influx and efflux, betaine and ectoine synthesis, and compatible solutes transport to survive in various high-salt environments.
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Jaiswal S, Gautam RK, Singh RK, Krishnamurthy SL, Ali S, Sakthivel K, Iquebal MA, Rai A, Kumar D. Harmonizing technological advances in phenomics and genomics for enhanced salt tolerance in rice from a practical perspective. RICE (NEW YORK, N.Y.) 2019; 12:89. [PMID: 31802312 PMCID: PMC6892996 DOI: 10.1186/s12284-019-0347-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/06/2019] [Indexed: 05/12/2023]
Abstract
Half of the global human population is dependent on rice as a staple food crop and more than 25% increase in rice productivity is required to feed the global population by 2030. With increase in irrigation, global warming and rising sea level, rising salinity has become one of the major challenges to enhance the rice productivity. Since the loss on this account is to the tune of US$12 billion per annum, it necessitates the global attention. In the era of technological advancement, substantial progress has been made on phenomics and genomics data generation but reaping benefit of this in rice salinity variety development in terms of cost, time and precision requires their harmonization. There is hardly any comprehensive holistic review for such combined approach. Present review describes classical salinity phenotyping approaches having morphological, physiological and biochemical components. It also gives a detailed account of invasive and non-invasive approaches of phenomic data generation and utilization. Classical work of rice salinity QLTs mapping in the form of chromosomal atlas has been updated. This review describes how QTLs can be further dissected into QTN by GWAS and transcriptomic approaches. Opportunities and progress made by transgenic, genome editing, metagenomics approaches in combating rice salinity problems are discussed. Major aim of this review is to provide a comprehensive over-view of hitherto progress made in rice salinity tolerance research which is required to understand bridging of phenotype based breeding with molecular breeding. This review is expected to assist rice breeders in their endeavours by fetching greater harmonization of technological advances in phenomics and genomics for better pragmatic approach having practical perspective.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India
| | - R K Gautam
- Division of Field Crop Improvement & Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, 744105, India.
| | - R K Singh
- Division of Plant Breeding Genetics and Biotechnology, International Rice Research Institute, DAPO Box 7777, Los Banos, Metro Manila, Philippines
| | - S L Krishnamurthy
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India
| | - S Ali
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India
| | - K Sakthivel
- Division of Field Crop Improvement & Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, 744105, India
| | - M A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, PUSA, New Delhi, 110012, India.
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Anand G, Bisaria VS, Sharma S. Impact of abiotic stressors on native rhizospheric bacterial community of Cajanus cajan. J Basic Microbiol 2019; 60:4-13. [PMID: 31682282 DOI: 10.1002/jobm.201900378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 09/09/2019] [Accepted: 10/04/2019] [Indexed: 01/03/2023]
Abstract
Salinity and drought are the major abiotic stresses that limit agricultural productivity. Application of plant growth promoting rhizobacteria (PGPR) is an attractive technology but with the bottlenecks of reduced efficacy and survivability in the environment. For increased efficiency of PGPR strains, the impact of stresses on the native bacterial community needs to be studied. Experimentally induced stresses would be ideal to assess the immediate perturbances in the structure of soil bacterial community. Hence, the study focused on the effect of experimentally-induced salinity, and drought stress on rhizospheric bacterial community of Cajanus cajan. A plant growth experiment was set up to induce salinity and drought stresses. Shifts in the bacterial community were assessed by a culture-independent technique of denaturing gradient gel electrophoresis using 16S ribosomal RNA gene and transcript as markers, leading to a comparison of the resident with the active bacterial community. The impact on plant was evaluated by measurement of plant biometrics. Further, salinity and drought-stressed conditions led to distinct shifts in native and active rhizospheric bacterial community, corresponding to the higher decline at induction of stresses, and stabilization at later time points. The study encompasses the perturbations in the active and resident rhizospheric bacterial community caused by the induction of two different abiotic stresses along the plant's growth.
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Affiliation(s)
- Gautam Anand
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Virendra S Bisaria
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
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Salinity Is a Key Determinant for Soil Microbial Communities in a Desert Ecosystem. mSystems 2019; 4:mSystems00225-18. [PMID: 30801023 PMCID: PMC6372838 DOI: 10.1128/msystems.00225-18] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/29/2019] [Indexed: 11/20/2022] Open
Abstract
Belowground microorganisms are indispensable components for nutrient cycling in desert ecosystems, and understanding how they respond to increased salinity is essential for managing and ameliorating salinization. Our sequence-based data revealed that microbial diversity decreased with increasing salinity, and certain salt-tolerant phylotypes and phenotypes showed a positive relationship with salinity. Using a null modeling approach to estimate microbial community assembly processes along a salinity gradient, we found that salinity imposed a strong selection pressure on the microbial community, which resulted in a dominance of deterministic processes. Studying microbial diversity and community assembly processes along salinity gradients is essential in understanding the fundamental ecological processes in desert ecosystems affected by salinization. Soil salinization is a growing environmental problem caused by both natural and human activities. Excessive salinity in soil suppresses growth, decreases species diversity, and alters the community composition of plants; however, the effect of salinity on soil microbial communities is poorly understood. Here, we characterize the soil microbial community along a natural salinity gradient in Gurbantunggut Desert, Northwestern China. Microbial diversity linearly decreased with increases in salinity, and community dissimilarity significantly increased with salinity differences. Soil salinity showed a strong effect on microbial community dissimilarity, even after controlling for the effects of spatial distance and other environmental variables. Microbial phylotypes (n = 270) belonging to Halobacteria, Nitriliruptoria, [Rhodothermi], Gammaproteobacteria, and Alphaproteobacteria showed a high-salinity niche preference. Out of nine potential phenotypes predicted by BugBase, oxygen-related phenotypes showed a significant relationship with salinity content. To explore the community assembly processes, we used null models of within-community (nearest-taxon index [NTI]) and between-community (βNTI) phylogenetic composition. NTI showed a significantly negative relationship with salinity, suggesting that the microbial community was less phylogenetically clustered in more-saline soils. βNTI, the between-community analogue of NTI, showed that deterministic processes have overtaken stochastic processes across all sites, suggesting the importance of environmental filtering in microbial community assembly. Taken together, these results suggest the importance of salinity in soil microbial community composition and assembly processes in a desert ecosystem. IMPORTANCE Belowground microorganisms are indispensable components for nutrient cycling in desert ecosystems, and understanding how they respond to increased salinity is essential for managing and ameliorating salinization. Our sequence-based data revealed that microbial diversity decreased with increasing salinity, and certain salt-tolerant phylotypes and phenotypes showed a positive relationship with salinity. Using a null modeling approach to estimate microbial community assembly processes along a salinity gradient, we found that salinity imposed a strong selection pressure on the microbial community, which resulted in a dominance of deterministic processes. Studying microbial diversity and community assembly processes along salinity gradients is essential in understanding the fundamental ecological processes in desert ecosystems affected by salinization.
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Stratford M, Steels H, Novodvorska M, Archer DB, Avery SV. Extreme Osmotolerance and Halotolerance in Food-Relevant Yeasts and the Role of Glycerol-Dependent Cell Individuality. Front Microbiol 2019; 9:3238. [PMID: 30687253 PMCID: PMC6333755 DOI: 10.3389/fmicb.2018.03238] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/13/2018] [Indexed: 12/19/2022] Open
Abstract
Osmotolerance or halotolerance are used to describe resistance to sugars and salt, or only salt, respectively. Here, a comprehensive screen of more than 600 different yeast isolates revealed that osmosensitive species were equally affected by NaCl and glucose. However, the relative toxicity of salt became increasingly prominent in more osmoresistant species. We confirmed that growth inhibition by glucose in a laboratory strain of Saccharomyces cerevisiae occurred at a lower water activity (Aw) than by salt (NaCl), and pre-growth in high levels of glucose or salt gave enhanced cross-resistance to either. Salt toxicity was largely due to osmotic stress but with an additive enhancement due to effects of the relevant cation. Almost all of the yeast isolates from the screen were also noted to exhibit hetero-resistance to both salt and sugar, whereby high concentrations restricted growth to a small minority of cells within the clonal populations. Rare resistant colonies required growth for up to 28 days to become visible. This cell individuality was more marked with salt than sugar, a possible further reflection of the ion toxicity effect. In both cases, heteroresistance in S. cerevisiae was strikingly dependent on the GPD1 gene product, important for glycerol synthesis. In contrast, a tps1Δ deletant impaired for trehalose showed altered MIC but no change in heteroresistance. Effects on heteroresistance were evident in chronic (but not acute) salt or glucose stress, particularly relevant to growth on low Aw foods. The study reports diverse osmotolerance and halotolerance phenotypes and heteroresistance across an extensive panel of yeast isolates, and indicates that Gpd1-dependent glycerol synthesis is a key determinant enabling growth of rare yeast subpopulations at low Aw, brought about by glucose and in particular salt.
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Affiliation(s)
- Malcolm Stratford
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Hazel Steels
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - David B Archer
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Simon V Avery
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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Exopolysaccharides and Biofilms in Mitigating Salinity Stress: The Biotechnological Potential of Halophilic and Soil-Inhabiting PGPR Microorganisms. SOIL BIOLOGY 2019. [DOI: 10.1007/978-3-030-18975-4_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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