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Nishisaka CS, Ventura JP, Bais HP, Mendes R. Role of Bacillus subtilis exopolymeric genes in modulating rhizosphere microbiome assembly. ENVIRONMENTAL MICROBIOME 2024; 19:33. [PMID: 38745256 DOI: 10.1186/s40793-024-00567-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/07/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Bacillus subtilis is well known for promoting plant growth and reducing abiotic and biotic stresses. Mutant gene-defective models can be created to understand important traits associated with rhizosphere fitness. This study aimed to analyze the role of exopolymeric genes in modulating tomato rhizosphere microbiome assembly under a gradient of soil microbiome diversities using the B. subtilis wild-type strain UD1022 and its corresponding mutant strain UD1022eps-TasA, which is defective in exopolysaccharide (EPS) and TasA protein production. RESULTS qPCR revealed that the B. subtilis UD1022eps-TasA- strain has a diminished capacity to colonize tomato roots in soils with diluted microbial diversity. The analysis of bacterial β-diversity revealed significant differences in bacterial and fungal community structures following inoculation with either the wild-type or mutant B. subtilis strains. The Verrucomicrobiota, Patescibacteria, and Nitrospirota phyla were more enriched with the wild-type strain inoculation than with the mutant inoculation. Co-occurrence analysis revealed that when the mutant was inoculated in tomato, the rhizosphere microbial community exhibited a lower level of modularity, fewer nodes, and fewer communities compared to communities inoculated with wild-type B. subtilis. CONCLUSION This study advances our understanding of the EPS and TasA genes, which are not only important for root colonization but also play a significant role in shaping rhizosphere microbiome assembly. Future research should concentrate on specific microbiome genetic traits and their implications for rhizosphere colonization, coupled with rhizosphere microbiome modulation. These efforts will be crucial for optimizing PGPR-based approaches in agriculture.
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Affiliation(s)
- Caroline Sayuri Nishisaka
- Embrapa Environment, Jaguariúna, SP, Brazil
- Graduate Program in Agricultural Microbiology, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - João Paulo Ventura
- Embrapa Environment, Jaguariúna, SP, Brazil
- Graduate Program in Agricultural Microbiology, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Harsh P Bais
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center (BPI), Newark, DE, USA
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Jeyaseelan A, Murugesan K, Thayanithi S, Palanisamy SB. A review of the impact of herbicides and insecticides on the microbial communities. ENVIRONMENTAL RESEARCH 2024; 245:118020. [PMID: 38151149 DOI: 10.1016/j.envres.2023.118020] [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: 09/04/2023] [Revised: 11/23/2023] [Accepted: 12/21/2023] [Indexed: 12/29/2023]
Abstract
Enhancing crop yield to accommodate the ever-increasing world population has become critical, and diminishing arable land has pressured current agricultural practices. Intensive farming methods have been using more pesticides and insecticides (biocides), culminating in soil deposition, negatively impacting the microbiome. Hence, a deeper understanding of the interaction and impact of pesticides and insecticides on microbial communities is required for the scientific community. This review highlights the recent findings concerning the possible impacts of biocides on various soil microorganisms and their diversity. This review's bibliometric analysis emphasised the recent developments' statistics based on the Scopus document search. Pesticides and insecticides are reported to degrade microbes' structure, cellular processes, and distinct biochemical reactions at cellular and biochemical levels. Several biocides disrupt the relationship between plants and their microbial symbionts, hindering beneficial biological activities that are widely discussed. Most microbial target sites of or receptors are biomolecules, and biocides bind with the receptor through a ligand-based mechanism. The biomarker action mechanism in response to biocides relies on activating the receptor site by specific biochemical interactions. The production of electrophilic or nucleophilic species, free radicals, and redox-reactive agents are the significant factors of biocide's metabolic reaction. Most studies considered for the review reported the negative impact of biocides on the soil microbial community; hence, technological development is required regarding eco-friendly pesticide and insecticide, which has less or no impact on the soil microbial community.
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Affiliation(s)
- Aravind Jeyaseelan
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai, 602105, Tamil Nadu, India
| | - Kamaraj Murugesan
- Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology-Ramapuram, Chennai, 600089, Tamil Nadu, India; Life Science Division, Faculty of Health and Life Sciences, INTI International University, Nilai, 71800, Malaysia.
| | - Saranya Thayanithi
- Department of Biotechnology, Rathinam Technical Campus, Coimbatore, 641021, Tamil Nadu, India
| | - Suresh Babu Palanisamy
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai, 602105, Tamil Nadu, India.
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Sokolova EA, Mishukova OV, Hlistun IV, Tromenschleger IN, Tikunov AY, Manakhov AD, Rogaev EI, Savenkov OA, Buyanova MD, Ivanov IV, Smirnova NV, Voronina EN. The Effectiveness of Co-Inoculation by Consortia of Microorganisms Depends on the Type of Plant and the Soil Microbiome. PLANTS (BASEL, SWITZERLAND) 2023; 13:116. [PMID: 38202424 PMCID: PMC10780792 DOI: 10.3390/plants13010116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]
Abstract
The amalgamation of mineral and targeted bacterial preparations represents a new generation of agricultural technology. Inoculation with combined preparations of microorganisms is more effective than inoculation with a single microorganism in stimulating plant growth by providing a more balanced diet for various crops. In this work, the effect of inoculation of 20 consortium variants on the yield indicators of three crops (wheat, buckwheat, corn) and the soil microbiome in the open field was investigated. The soil microbiome was defined by 16S rRNA sequences through NGS. The species richness of the soil microbial community (alpha diversity) was similar for all studied samples. A beta-diversity analysis revealed that the microbial diversity of three soil samples (C.bw, F.bw and Soil.bw) differed significantly from all others. At the phylum level, the number of Acidobacteriota and Firmicutes in these samples was increased. For the combination "Consortium C (Rothia endophytic GMG9 and Azotobacter chroococcum GMG39)-buckwheat", a systemic positive improvement in all growth and yield indicators was observed. The soil of the site where buckwheat grew, inoculated by Consortium C, contained significantly more available phosphorus than all other soil samples. Such results can be explained both by the direct action of a consortium of phosphate-immobilizing and nitrogen-fixing bacteria and acidification of the medium due to an increase in phylum Acidobacteriota bacteria in the soil.
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Affiliation(s)
- Ekaterina Alexeevna Sokolova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.V.M.); (I.V.H.); (I.N.T.); (A.Y.T.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Olga Viktorovna Mishukova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.V.M.); (I.V.H.); (I.N.T.); (A.Y.T.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Inna Viktorovna Hlistun
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.V.M.); (I.V.H.); (I.N.T.); (A.Y.T.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Irina Nikolaevna Tromenschleger
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.V.M.); (I.V.H.); (I.N.T.); (A.Y.T.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Artem Yurievich Tikunov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.V.M.); (I.V.H.); (I.N.T.); (A.Y.T.)
| | - Andrey Dmitrievich Manakhov
- Department of Genetics, Centre for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sirius, Russia; (A.D.M.); (E.I.R.)
| | - Evgeny Ivanovich Rogaev
- Department of Genetics, Centre for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sirius, Russia; (A.D.M.); (E.I.R.)
| | - Oleg Alexandrovich Savenkov
- Institute of Soil Science and Agrochemistry, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.A.S.); (M.D.B.)
| | - Maria Dmitrievna Buyanova
- Institute of Soil Science and Agrochemistry, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.A.S.); (M.D.B.)
| | - Ilya Vladimirovich Ivanov
- Institute of Soil Science and Agrochemistry, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.A.S.); (M.D.B.)
| | - Natalya Valentinovna Smirnova
- Institute of Soil Science and Agrochemistry, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.A.S.); (M.D.B.)
| | - Elena Nikolaevna Voronina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.V.M.); (I.V.H.); (I.N.T.); (A.Y.T.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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