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Genome analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management
The Bacillus amyloliquefaciens subsp. plantarum strain UCMB5113 is a Gram-positive rhizobacterium that can colonize plant roots and stimulate plant growth and defense based on unknown mechanisms. This reinforcement of plants may provide protection to various forms of biotic and abiotic stress. To de...
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| Published in: | PloS one 2014-08, Vol.9 (8), p.e104651 |
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| creator | Niazi, Adnan Manzoor, Shahid Asari, Shashidar Bejai, Sarosh Meijer, Johan Bongcam-Rudloff, Erik |
| description | The Bacillus amyloliquefaciens subsp. plantarum strain UCMB5113 is a Gram-positive rhizobacterium that can colonize plant roots and stimulate plant growth and defense based on unknown mechanisms. This reinforcement of plants may provide protection to various forms of biotic and abiotic stress. To determine the genetic traits involved in the mechanism of plant-bacteria association, the genome sequence of UCMB5113 was obtained by assembling paired-end Illumina reads. The assembled chromosome of 3,889,532 bp was predicted to encode 3,656 proteins. Genes that potentially contribute to plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis and siderophore production were identified. Moreover, annotation identified putative genes responsible for non-ribosomal synthesis of secondary metabolites and genes supporting environment fitness of UCMB5113 including drug and metal resistance. A large number of genes encoding a diverse set of secretory proteins, enzymes of primary and secondary metabolism and carbohydrate active enzymes were found which reflect a high capacity to degrade various rhizosphere macromolecules. Additionally, many predicted membrane transporters provides the bacterium with efficient uptake capabilities of several nutrients. Although, UCMB5113 has the possibility to produce antibiotics and biosurfactants, the protective effect of plants to pathogens seems to be indirect and due to priming of plant induced systemic resistance. The availability of the genome enables identification of genes and their function underpinning beneficial interactions of UCMB5113 with plants. |
| doi_str_mv | 10.1371/journal.pone.0104651 |
| format | article |
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This reinforcement of plants may provide protection to various forms of biotic and abiotic stress. To determine the genetic traits involved in the mechanism of plant-bacteria association, the genome sequence of UCMB5113 was obtained by assembling paired-end Illumina reads. The assembled chromosome of 3,889,532 bp was predicted to encode 3,656 proteins. Genes that potentially contribute to plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis and siderophore production were identified. Moreover, annotation identified putative genes responsible for non-ribosomal synthesis of secondary metabolites and genes supporting environment fitness of UCMB5113 including drug and metal resistance. A large number of genes encoding a diverse set of secretory proteins, enzymes of primary and secondary metabolism and carbohydrate active enzymes were found which reflect a high capacity to degrade various rhizosphere macromolecules. Additionally, many predicted membrane transporters provides the bacterium with efficient uptake capabilities of several nutrients. Although, UCMB5113 has the possibility to produce antibiotics and biosurfactants, the protective effect of plants to pathogens seems to be indirect and due to priming of plant induced systemic resistance. The availability of the genome enables identification of genes and their function underpinning beneficial interactions of UCMB5113 with plants.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0104651</identifier><identifier>PMID: 25119988</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Acetic acid ; Acetoin ; Analysis ; Annotations ; Antibiotics ; Arabidopsis ; Arabidopsis - growth & development ; Arabidopsis - microbiology ; Bacillus ; Bacillus - genetics ; Bacillus amyloliquefaciens ; Bacillus subtilis ; Bacteria ; Bacterial genetics ; Bacterial Proteins - genetics ; Base Sequence ; Biofilms ; Biofilms - growth & development ; Bioinformatics ; Bioinformatics and Systems Biology ; Bioinformatik och systembiologi ; Biology and Life Sciences ; Biosurfactants ; Biosynthesis ; Brassica napus - growth & development ; Brassica napus - microbiology ; Breeding of animals ; Carbohydrate metabolism ; Carbohydrates ; Cluster Analysis ; Computational Biology ; Enzymes ; Fitness ; Genes ; Genetics ; Genetics and Breeding ; Genetik och förädling ; Genome, Bacterial - genetics ; Genomes ; Genomics ; Growth ; Indoleacetic acid ; Macromolecules ; Metabolism ; Metabolites ; Microbiology ; Microorganisms ; Mikrobiologi ; Molecular Sequence Annotation ; Molecular Sequence Data ; Motility ; Nucleotide sequence ; Nutrients ; Organic acids ; Pathogens ; Phylogenetics ; Phylogeny ; Plant biology ; Plant Biotechnology ; Plant growth ; Plant metabolites ; Plant protection ; Plant roots ; Plant Roots - microbiology ; Priming ; Proteins ; Reproductive fitness ; Rhizosphere ; Secondary metabolites ; Sequence Analysis, DNA ; Species Specificity ; Stress management ; Växtbioteknologi</subject><ispartof>PloS one, 2014-08, Vol.9 (8), p.e104651</ispartof><rights>COPYRIGHT 2014 Public Library of Science</rights><rights>2014 Niazi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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growth & development</subject><subject>Brassica napus - microbiology</subject><subject>Breeding of animals</subject><subject>Carbohydrate metabolism</subject><subject>Carbohydrates</subject><subject>Cluster Analysis</subject><subject>Computational Biology</subject><subject>Enzymes</subject><subject>Fitness</subject><subject>Genes</subject><subject>Genetics</subject><subject>Genetics and Breeding</subject><subject>Genetik och förädling</subject><subject>Genome, Bacterial - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Growth</subject><subject>Indoleacetic acid</subject><subject>Macromolecules</subject><subject>Metabolism</subject><subject>Metabolites</subject><subject>Microbiology</subject><subject>Microorganisms</subject><subject>Mikrobiologi</subject><subject>Molecular Sequence Annotation</subject><subject>Molecular Sequence Data</subject><subject>Motility</subject><subject>Nucleotide sequence</subject><subject>Nutrients</subject><subject>Organic acids</subject><subject>Pathogens</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant biology</subject><subject>Plant Biotechnology</subject><subject>Plant growth</subject><subject>Plant metabolites</subject><subject>Plant protection</subject><subject>Plant roots</subject><subject>Plant Roots - microbiology</subject><subject>Priming</subject><subject>Proteins</subject><subject>Reproductive fitness</subject><subject>Rhizosphere</subject><subject>Secondary metabolites</subject><subject>Sequence Analysis, DNA</subject><subject>Species Specificity</subject><subject>Stress management</subject><subject>Växtbioteknologi</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNqNk29r1EAQxoMotla_geiCIPjizt3b_PWF0B5aC5WCtb5dJpvJ3ZZNNu5uWutH8FM79a7lAgoSyCSzv-fZzGQnSZ4LPheyEG8v3eh7sPPB9Tjngqd5Jh4k-6KSi1m-4PLhzvNe8iSES84zWeb542RvkQlRVWW5n_w6xt51yICsboIJzLXsCLSxdgwMuhvrrPk-Yksp7AM7H-swzNlgoY_gx45dLD8fkZl8x4D5tfnpatARvaGluIbITDd4d4VhI2Er767jmnZrWIgeQ2Ad7bzCDvv4NHnUgg34bBsPkouPH74uP81Oz45PloenM11IHmdQFlXR5lXFi0LqYlE1WFeQNxp11eiSY1EIirLkUHCBrS6hAcBGAtJ7jvIgebnxHawLatvGoESWSWosIUScbIjGwaUavOnA3ygHRv1JOL9S4KPRFlWdV0KnaZsWdC94A7qqy6ZuAVsuqromr9nGK1zjMNYTt2DHGvxtUAFVznkqiX-__bqx7pCq6qMHO5FNV3qzVit3pVJBJYuSDF5tDbyjPxfiP0rcUiugKkzfOjLTnQlaHaaizDI6IhVR879QdDXYGU0HrzWUnwjeTATERPwRVzCGoE7Ov_w_e_Ztyr7eYdcINq6Ds2M0rg9TMN2A2rsQPLb3nRNc3c7NXTfU7dyo7dyQ7MVu1-9Fd4MifwPFsRcj</recordid><startdate>20140813</startdate><enddate>20140813</enddate><creator>Niazi, Adnan</creator><creator>Manzoor, Shahid</creator><creator>Asari, Shashidar</creator><creator>Bejai, Sarosh</creator><creator>Meijer, Johan</creator><creator>Bongcam-Rudloff, Erik</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>5PM</scope><scope>ADTPV</scope><scope>AOWAS</scope><scope>DOA</scope></search><sort><creationdate>20140813</creationdate><title>Genome analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management</title><author>Niazi, Adnan ; Manzoor, Shahid ; Asari, Shashidar ; Bejai, Sarosh ; Meijer, Johan ; Bongcam-Rudloff, Erik</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c730t-a8797f6990773c729deb9a6dcec9dc80e771dc8380a701efc8adaaed3ae7016e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Acetic acid</topic><topic>Acetoin</topic><topic>Analysis</topic><topic>Annotations</topic><topic>Antibiotics</topic><topic>Arabidopsis</topic><topic>Arabidopsis - growth & development</topic><topic>Arabidopsis - microbiology</topic><topic>Bacillus</topic><topic>Bacillus - genetics</topic><topic>Bacillus amyloliquefaciens</topic><topic>Bacillus subtilis</topic><topic>Bacteria</topic><topic>Bacterial genetics</topic><topic>Bacterial Proteins - genetics</topic><topic>Base Sequence</topic><topic>Biofilms</topic><topic>Biofilms - growth & development</topic><topic>Bioinformatics</topic><topic>Bioinformatics and Systems Biology</topic><topic>Bioinformatik och systembiologi</topic><topic>Biology and Life Sciences</topic><topic>Biosurfactants</topic><topic>Biosynthesis</topic><topic>Brassica napus - growth & development</topic><topic>Brassica napus - microbiology</topic><topic>Breeding of animals</topic><topic>Carbohydrate metabolism</topic><topic>Carbohydrates</topic><topic>Cluster Analysis</topic><topic>Computational Biology</topic><topic>Enzymes</topic><topic>Fitness</topic><topic>Genes</topic><topic>Genetics</topic><topic>Genetics and Breeding</topic><topic>Genetik och förädling</topic><topic>Genome, Bacterial - 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This reinforcement of plants may provide protection to various forms of biotic and abiotic stress. To determine the genetic traits involved in the mechanism of plant-bacteria association, the genome sequence of UCMB5113 was obtained by assembling paired-end Illumina reads. The assembled chromosome of 3,889,532 bp was predicted to encode 3,656 proteins. Genes that potentially contribute to plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis and siderophore production were identified. Moreover, annotation identified putative genes responsible for non-ribosomal synthesis of secondary metabolites and genes supporting environment fitness of UCMB5113 including drug and metal resistance. A large number of genes encoding a diverse set of secretory proteins, enzymes of primary and secondary metabolism and carbohydrate active enzymes were found which reflect a high capacity to degrade various rhizosphere macromolecules. Additionally, many predicted membrane transporters provides the bacterium with efficient uptake capabilities of several nutrients. Although, UCMB5113 has the possibility to produce antibiotics and biosurfactants, the protective effect of plants to pathogens seems to be indirect and due to priming of plant induced systemic resistance. The availability of the genome enables identification of genes and their function underpinning beneficial interactions of UCMB5113 with plants.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25119988</pmid><doi>10.1371/journal.pone.0104651</doi><oa>free_for_read</oa></addata></record> |
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| ispartof | PloS one, 2014-08, Vol.9 (8), p.e104651 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1553137016 |
| source | Publicly Available Content (ProQuest); PubMed Central |
| subjects | Acetic acid Acetoin Analysis Annotations Antibiotics Arabidopsis Arabidopsis - growth & development Arabidopsis - microbiology Bacillus Bacillus - genetics Bacillus amyloliquefaciens Bacillus subtilis Bacteria Bacterial genetics Bacterial Proteins - genetics Base Sequence Biofilms Biofilms - growth & development Bioinformatics Bioinformatics and Systems Biology Bioinformatik och systembiologi Biology and Life Sciences Biosurfactants Biosynthesis Brassica napus - growth & development Brassica napus - microbiology Breeding of animals Carbohydrate metabolism Carbohydrates Cluster Analysis Computational Biology Enzymes Fitness Genes Genetics Genetics and Breeding Genetik och förädling Genome, Bacterial - genetics Genomes Genomics Growth Indoleacetic acid Macromolecules Metabolism Metabolites Microbiology Microorganisms Mikrobiologi Molecular Sequence Annotation Molecular Sequence Data Motility Nucleotide sequence Nutrients Organic acids Pathogens Phylogenetics Phylogeny Plant biology Plant Biotechnology Plant growth Plant metabolites Plant protection Plant roots Plant Roots - microbiology Priming Proteins Reproductive fitness Rhizosphere Secondary metabolites Sequence Analysis, DNA Species Specificity Stress management Växtbioteknologi |
| title | Genome analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-24T10%3A02%3A48IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genome%20analysis%20of%20Bacillus%20amyloliquefaciens%20Subsp.%20plantarum%20UCMB5113:%20a%20rhizobacterium%20that%20improves%20plant%20growth%20and%20stress%20management&rft.jtitle=PloS%20one&rft.au=Niazi,%20Adnan&rft.aucorp=Sveriges%20lantbruksuniversitet&rft.date=2014-08-13&rft.volume=9&rft.issue=8&rft.spage=e104651&rft.pages=e104651-&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0104651&rft_dat=%3Cgale_plos_%3EA418552519%3C/gale_plos_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c730t-a8797f6990773c729deb9a6dcec9dc80e771dc8380a701efc8adaaed3ae7016e3%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=1553137016&rft_id=info:pmid/25119988&rft_galeid=A418552519&rfr_iscdi=true |