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      A Review on the Biotechnological Applications of the Operational Group Bacillus amyloliquefaciens

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          Abstract

          Bacteria under the operational group Bacillus amyloliquefaciens (OG Ba) are all Gram-positive, endospore-forming, and rod-shaped. Taxonomically, the OG Ba belongs to the Bacillus subtilis species complex, family Bacillaceae, class Bacilli, and phylum Firmicutes. To date, the OG Ba comprises four bacterial species: Bacillus amyloliquefaciens, Bacillus siamensis, Bacillus velezensis and Bacillus nakamurai. They are widely distributed in various niches including soil, plants, food, and water. A resurgence in genome mining has caused an increased focus on the biotechnological applications of bacterial species belonging to the OG Ba. The members of OG Ba are known as plant growth-promoting bacteria (PGPB) due to their abilities to fix nitrogen, solubilize phosphate, and produce siderophore and phytohormones, as well as antimicrobial compounds. Moreover, they are also reported to produce various enzymes including α-amylase, protease, lipase, cellulase, xylanase, pectinase, aminotransferase, barnase, peroxidase, and laccase. Antimicrobial compounds that able to inhibit the growth of pathogens including non-ribosomal peptides and polyketides are also produced by these bacteria. Within the OG Ba, various B. velezensis strains are promising for use as probiotics for animals and fishes. Genome mining has revealed the potential applications of members of OG Ba for removing organophosphorus (OPs) pesticides. Thus, this review focused on the applicability of members of OG Ba as plant growth promoters, biocontrol agents, probiotics, bioremediation agents, as well as producers of commercial enzymes and antibiotics. Here, the bioformulations and commercial products available based on these bacteria are also highlighted. This review will better facilitate understandings of members of OG Ba and their biotechnological applications.

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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            Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

            The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity between the genomes of two strains, this technique is tedious and error-prone and cannot be used to incrementally build up a comparative database. Recent technological progress in the area of genome sequencing calls for bioinformatics methods to replace the wet-lab DDH by in-silico genome-to-genome comparison. Here we investigate state-of-the-art methods for inferring whole-genome distances in their ability to mimic DDH. Algorithms to efficiently determine high-scoring segment pairs or maximally unique matches perform well as a basis of inferring intergenomic distances. The examined distance functions, which are able to cope with heavily reduced genomes and repetitive sequence regions, outperform previously described ones regarding the correlation with and error ratios in emulating DDH. Simulation of incompletely sequenced genomes indicates that some distance formulas are very robust against missing fractions of genomic information. Digitally derived genome-to-genome distances show a better correlation with 16S rRNA gene sequence distances than DDH values. The future perspectives of genome-informed taxonomy are discussed, and the investigated methods are made available as a web service for genome-based species delineation.
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              Biocontrol mechanism by root-associated Bacillus amyloliquefaciens FZB42 – a review

              Bacillus amyloliquefaciens subsp. plantarum FZB42 is a Gram-positive model bacterium for unraveling plant–microbe interactions in Bacilli. In addition, FZB42 is used commercially as biofertilizer and biocontrol agent in agriculture. Genome analysis of FZB42 revealed that nearly 10% of the FZB42 genome is devoted to synthesizing antimicrobial metabolites and their corresponding immunity genes. However, recent investigations in planta demonstrated that – except surfactin – the amount of such compounds found in vicinity of plant roots is relatively low, making doubtful a direct function in suppressing competing microflora including plant pathogens. These metabolites have been also suspected to induce changes within the rhizosphere microbial community, which might affect environment and plant health. However, sequence analysis of rhizosphere samples revealed only marginal changes in the root microbiome, suggesting that secondary metabolites are not the key factor in protecting plants from pathogenic microorganisms. On the other hand, adding FZB42 to plants compensate, at least in part, changes in the community structure caused by the pathogen, indicating an interesting mechanism of plant protection by beneficial Bacilli. Sub-lethal concentrations of cyclic lipopeptides and volatiles produced by plant-associated Bacilli trigger pathways of induced systemic resistance (ISR), which protect plants against attacks of pathogenic microbes, viruses, and nematodes. Stimulation of ISR by bacterial metabolites is likely the main mechanism responsible for biocontrol action of FZB42.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                Microorganisms
                Microorganisms
                microorganisms
                Microorganisms
                MDPI
                2076-2607
                17 March 2021
                March 2021
                : 9
                : 3
                : 614
                Affiliations
                [1 ]Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; syazwanngalimat@ 123456gmail.com (M.S.N.); radinshafierul@ 123456yahoo.com (R.S.R.Y.); malikaladilbaharudin@ 123456gmail.com (M.M.A.-a.B.)
                [2 ]Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; nsmy211195@ 123456gmail.com (S.M.Y.); murnimarlina@ 123456upm.edu.my (M.K.)
                [3 ]Laboratory of Sustainable Aquaculture, International Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia, Port Dickson 71050, Negeri Sembilan, Malaysia
                [4 ]Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; aqlima@ 123456upm.edu.my
                [5 ]Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
                Author notes
                [* ]Correspondence: suriana@ 123456upm.edu.my ; Tel.: +603-97698298
                Author information
                https://orcid.org/0000-0001-8751-7026
                https://orcid.org/0000-0002-6639-6656
                https://orcid.org/0000-0002-7625-3704
                https://orcid.org/0000-0003-4027-5730
                Article
                microorganisms-09-00614
                10.3390/microorganisms9030614
                8002464
                33802666
                9715836c-ddcf-45c9-a8c3-62e0980fdb4e
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 22 January 2021
                : 26 February 2021
                Categories
                Review

                plant growth-promoting bacteria,biocontrol agent,enzymes,antimicrobial compounds,probiotics,bioremediation,bacillus amyloliquefaciens,bacillus velezensis,bacillus siamensis,bacillus nakamurai

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