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      Elucidating the effect of biofertilizers on bacterial diversity in maize rhizosphere soil

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          Abstract

          This study was conducted to investigate the effect of biofertilizers on the structure and diversity of the rhizosphere bacterial community of maize. Different biofertilizers were applied to maize. The physical and chemical properties of rhizosphere soil samples were analyzed and the rhizosphere bacteria were analyzed by 16S amplicon sequencing. The results showed that treatment with Bacillus licheniformis and B. amyloliquefaciens as biofertilizers increased the soil organic matter (SOM), total nitrogen, total phosphorus (TP), available phosphorus (AP), and available potassium (AK) contents, indicating that the plant growth-promoting rhizobacteria in the biofertilizers might help the host plant to produce root exudates that, in return, recruit beneficial communities due to available sugars, amino acids, organic acids, vitamins, and polymers. The rhizosphere of maize treated with B. subtilis biofertilizer had the highest diversity and richness. However, the rhizosphere treated with the combined bacterial strains had the lowest diversity and richness, which might be due to the directional increase of the abundance of some bacteria with special functions, but the decrease of the overall bacterial community diversity in the soil. The dominant bacterial phyla were Proteobacteria (32.2%–34.6%), Acidobacteria (15.0%–21.0%), Actinobacteria (13.1%–17.2%), and Gemmatimonadetes (9.0%–10.8%), and the dominant bacterial species were Aciditerrimonas ferrireducens JCM 15389 (4.3%–5.2%), Gemmatimonas aurantiaca (3.2%–4.1%), and Pyrinomonas methylaliphatogenes (2.1%–4.8%). The significantly enriched bacterial functions were associated with amino acid metabolism, sugar metabolism, and energy metabolism pathways. The results of a redundancy analysis showed that SOM, TP, and AK were the main factors affecting the microbial community structure in the maize rhizosphere. In conclusion, the application of biofertilizers increased the diversity and richness of the bacterial community in the maize rhizosphere soil. However, combined strain treatment was failed and not an ideal strategy due to the lowest abundance and diversity.

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          Most cited references55

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          QIIME allows analysis of high-throughput community sequencing data.

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            Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

            S Altschul (1997)
            The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
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              Search and clustering orders of magnitude faster than BLAST.

              Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets. Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch.
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                Author and article information

                Contributors
                Role: Conceptualization
                Role: Formal analysis
                Role: Methodology
                Role: Methodology
                Role: ConceptualizationRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                23 April 2021
                2021
                : 16
                : 4
                : e0249834
                Affiliations
                [1 ] Institute of Applied Chemistry, Shanxi University, Taiyuan, Shanxi Province, China
                [2 ] Institute of Biotechnology, Shanxi University, Taiyuan, Shanxi Province, China
                Government College University, Faisalabad, PAKISTAN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0001-5231-1183
                Article
                PONE-D-20-22399
                10.1371/journal.pone.0249834
                8064744
                33891590
                33ded3ee-4ebd-4bb1-b256-a168c713daac
                © 2021 Wang et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 19 July 2020
                : 25 March 2021
                Page count
                Figures: 5, Tables: 2, Pages: 15
                Funding
                Funded by: The National Key Research and Development Program
                Award ID: 2018YFD0200404-10
                Funded by: The Shanxi Key Research and Development Program
                Award ID: 201803D221005-1
                This work was supported by the National Key Research and Development Program [grant number 2018YFD0200404-10] and the Shanxi Key Research and Development Program [grant number 201803D221005-1].The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Ecology
                Plant Ecology
                Plant-Environment Interactions
                Rhizosphere
                Ecology and Environmental Sciences
                Ecology
                Plant Ecology
                Plant-Environment Interactions
                Rhizosphere
                Biology and Life Sciences
                Plant Science
                Plant Ecology
                Plant-Environment Interactions
                Rhizosphere
                Biology and Life Sciences
                Organisms
                Bacteria
                Bacillus
                Bacillus Subtilis
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Bacterial Pathogens
                Bacillus
                Bacillus Subtilis
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
                Microbial Pathogens
                Bacterial Pathogens
                Bacillus
                Bacillus Subtilis
                Research and Analysis Methods
                Animal Studies
                Experimental Organism Systems
                Prokaryotic Models
                Bacillus Subtilis
                Research and Analysis Methods
                Animal Studies
                Experimental Organism Systems
                Model Organisms
                Maize
                Research and Analysis Methods
                Model Organisms
                Maize
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Grasses
                Maize
                Research and Analysis Methods
                Animal Studies
                Experimental Organism Systems
                Plant and Algal Models
                Maize
                Biology and Life Sciences
                Ecology
                Community Ecology
                Community Structure
                Ecology and Environmental Sciences
                Ecology
                Community Ecology
                Community Structure
                Biology and Life Sciences
                Agriculture
                Agrochemicals
                Fertilizers
                Biology and Life Sciences
                Plant Science
                Lichenology
                Physical Sciences
                Chemistry
                Environmental Chemistry
                Soil Chemistry
                Ecology and Environmental Sciences
                Environmental Chemistry
                Soil Chemistry
                Earth Sciences
                Soil Science
                Soil Chemistry
                Biology and Life Sciences
                Agriculture
                Agricultural Soil Science
                Earth Sciences
                Soil Science
                Agricultural Soil Science
                Custom metadata
                The raw sequencing data are available from the NCBI Sequence Read Archive database (accession number PRJNA596611).

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                Uncategorized

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