Insights into the genome of Methylobacterium sp. NMS14P, a novel bacterium for growth promotion of maize, chili, and sugarcane

A novel methylotrophic bacterium designated as NMS14P was isolated from the root of an organic coffee plant ( Coffea arabica ) in Thailand. The 16S rRNA sequence analysis revealed that this new isolate belongs to the genus Methylobacterium , and its novelty was clarified by genomic and comparative g...

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Published inPloS one Vol. 18; no. 2; p. e0281505
Main Authors Jirakkakul, Jiraporn, Khoiri, Ahmad Nuruddin, Duangfoo, Thanawat, Dulsawat, Sudarat, Sutheeworapong, Sawannee, Petsong, Kantiya, Wattanachaisaereekul, Songsak, Paenkaew, Prasobsook, Tachaleat, Anuwat, Cheevadhanarak, Supapon, Prommeenate, Peerada
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 07.02.2023
Public Library of Science (PLoS)
Subjects
ABC transporter
Acetic acid
Agriculture
Agrochemicals
Analysis
Bacteria
Biofertilizers
Biofilms
Biology and Life Sciences
Biomedical materials
Biosynthesis
Chemotaxis
Chromosomes
Coffee
Colonization
Consortia
Corn
Crop yields
Cytokinins
Edible Grain - genetics
Engineering and Technology
Experiments
Fertilizers
Genes
Genomes
Genomic analysis
Host plants
Hot peppers
In vivo methods and tests
Indoleacetic acid
Jalapeno
Management
Metabolism
Metabolites
Methylobacterium
Methylobacterium - genetics
Mosses
Oxidation
Phosphatase
Phylogeny
Physical Sciences
Plant growth
Plasmids
Quorum sensing
RNA, Ribosomal, 16S - genetics
rRNA 16S
Saccharum - genetics
Secondary metabolites
Seeds
Sequence analysis
Soil fertility
Solubilization
Sugarcane
Sulfur
Sustainable agriculture
Trehalose
Urea
Zea mays - genetics
Thailand
United States > US
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Abstract A novel methylotrophic bacterium designated as NMS14P was isolated from the root of an organic coffee plant ( Coffea arabica ) in Thailand. The 16S rRNA sequence analysis revealed that this new isolate belongs to the genus Methylobacterium , and its novelty was clarified by genomic and comparative genomic analyses, in which NMS14P exhibited low levels of relatedness with other Methylobacterium- type strains. NMS14P genome consists of a 6,268,579 bp chromosome, accompanied by a 542,519 bp megaplasmid and a 66,590 bp plasmid, namely pNMS14P1 and pNMS14P2, respectively. Several genes conferring plant growth promotion are aggregated on both chromosome and plasmids, including phosphate solubilization, indole-3-acetic acid (IAA) biosynthesis, cytokinins (CKs) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, sulfur-oxidizing activity, trehalose synthesis, and urea metabolism. Furthermore, pangenome analysis showed that NMS14P possessed the highest number of strain-specific genes accounting for 1408 genes, particularly those that are essential for colonization and survival in a wide array of host environments, such as ABC transporter, chemotaxis, quorum sensing, biofilm formation, and biosynthesis of secondary metabolites. In vivo tests have supported that NMS14P significantly promoted the growth and development of maize, chili, and sugarcane. Collectively, NMS14P is proposed as a novel plant growth-promoting Methylobacterium that could potentially be applied to a broad range of host plants as Methylobacterium -based biofertilizers to reduce and ultimately substitute the use of synthetic agrochemicals for sustainable agriculture.
AbstractList A novel methylotrophic bacterium designated as NMS14P was isolated from the root of an organic coffee plant ( Coffea arabica ) in Thailand. The 16S rRNA sequence analysis revealed that this new isolate belongs to the genus Methylobacterium , and its novelty was clarified by genomic and comparative genomic analyses, in which NMS14P exhibited low levels of relatedness with other Methylobacterium- type strains. NMS14P genome consists of a 6,268,579 bp chromosome, accompanied by a 542,519 bp megaplasmid and a 66,590 bp plasmid, namely pNMS14P1 and pNMS14P2, respectively. Several genes conferring plant growth promotion are aggregated on both chromosome and plasmids, including phosphate solubilization, indole-3-acetic acid (IAA) biosynthesis, cytokinins (CKs) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, sulfur-oxidizing activity, trehalose synthesis, and urea metabolism. Furthermore, pangenome analysis showed that NMS14P possessed the highest number of strain-specific genes accounting for 1408 genes, particularly those that are essential for colonization and survival in a wide array of host environments, such as ABC transporter, chemotaxis, quorum sensing, biofilm formation, and biosynthesis of secondary metabolites. In vivo tests have supported that NMS14P significantly promoted the growth and development of maize, chili, and sugarcane. Collectively, NMS14P is proposed as a novel plant growth-promoting Methylobacterium that could potentially be applied to a broad range of host plants as Methylobacterium -based biofertilizers to reduce and ultimately substitute the use of synthetic agrochemicals for sustainable agriculture.
A novel methylotrophic bacterium designated as NMS14P was isolated from the root of an organic coffee plant (Coffea arabica) in Thailand. The 16S rRNA sequence analysis revealed that this new isolate belongs to the genus Methylobacterium, and its novelty was clarified by genomic and comparative genomic analyses, in which NMS14P exhibited low levels of relatedness with other Methylobacterium-type strains. NMS14P genome consists of a 6,268,579 bp chromosome, accompanied by a 542,519 bp megaplasmid and a 66,590 bp plasmid, namely pNMS14P1 and pNMS14P2, respectively. Several genes conferring plant growth promotion are aggregated on both chromosome and plasmids, including phosphate solubilization, indole-3-acetic acid (IAA) biosynthesis, cytokinins (CKs) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, sulfur-oxidizing activity, trehalose synthesis, and urea metabolism. Furthermore, pangenome analysis showed that NMS14P possessed the highest number of strain-specific genes accounting for 1408 genes, particularly those that are essential for colonization and survival in a wide array of host environments, such as ABC transporter, chemotaxis, quorum sensing, biofilm formation, and biosynthesis of secondary metabolites. In vivo tests have supported that NMS14P significantly promoted the growth and development of maize, chili, and sugarcane. Collectively, NMS14P is proposed as a novel plant growth-promoting Methylobacterium that could potentially be applied to a broad range of host plants as Methylobacterium-based biofertilizers to reduce and ultimately substitute the use of synthetic agrochemicals for sustainable agriculture.
A novel methylotrophic bacterium designated as NMS14P was isolated from the root of an organic coffee plant (Coffea arabica) in Thailand. The 16S rRNA sequence analysis revealed that this new isolate belongs to the genus Methylobacterium, and its novelty was clarified by genomic and comparative genomic analyses, in which NMS14P exhibited low levels of relatedness with other Methylobacterium-type strains. NMS14P genome consists of a 6,268,579 bp chromosome, accompanied by a 542,519 bp megaplasmid and a 66,590 bp plasmid, namely pNMS14P1 and pNMS14P2, respectively. Several genes conferring plant growth promotion are aggregated on both chromosome and plasmids, including phosphate solubilization, indole-3-acetic acid (IAA) biosynthesis, cytokinins (CKs) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, sulfur-oxidizing activity, trehalose synthesis, and urea metabolism. Furthermore, pangenome analysis showed that NMS14P possessed the highest number of strain-specific genes accounting for 1408 genes, particularly those that are essential for colonization and survival in a wide array of host environments, such as ABC transporter, chemotaxis, quorum sensing, biofilm formation, and biosynthesis of secondary metabolites. In vivo tests have supported that NMS14P significantly promoted the growth and development of maize, chili, and sugarcane. Collectively, NMS14P is proposed as a novel plant growth-promoting Methylobacterium that could potentially be applied to a broad range of host plants as Methylobacterium-based biofertilizers to reduce and ultimately substitute the use of synthetic agrochemicals for sustainable agriculture.A novel methylotrophic bacterium designated as NMS14P was isolated from the root of an organic coffee plant (Coffea arabica) in Thailand. The 16S rRNA sequence analysis revealed that this new isolate belongs to the genus Methylobacterium, and its novelty was clarified by genomic and comparative genomic analyses, in which NMS14P exhibited low levels of relatedness with other Methylobacterium-type strains. NMS14P genome consists of a 6,268,579 bp chromosome, accompanied by a 542,519 bp megaplasmid and a 66,590 bp plasmid, namely pNMS14P1 and pNMS14P2, respectively. Several genes conferring plant growth promotion are aggregated on both chromosome and plasmids, including phosphate solubilization, indole-3-acetic acid (IAA) biosynthesis, cytokinins (CKs) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, sulfur-oxidizing activity, trehalose synthesis, and urea metabolism. Furthermore, pangenome analysis showed that NMS14P possessed the highest number of strain-specific genes accounting for 1408 genes, particularly those that are essential for colonization and survival in a wide array of host environments, such as ABC transporter, chemotaxis, quorum sensing, biofilm formation, and biosynthesis of secondary metabolites. In vivo tests have supported that NMS14P significantly promoted the growth and development of maize, chili, and sugarcane. Collectively, NMS14P is proposed as a novel plant growth-promoting Methylobacterium that could potentially be applied to a broad range of host plants as Methylobacterium-based biofertilizers to reduce and ultimately substitute the use of synthetic agrochemicals for sustainable agriculture.
Audience Academic
Author Sutheeworapong, Sawannee
Wattanachaisaereekul, Songsak
Duangfoo, Thanawat
Prommeenate, Peerada
Paenkaew, Prasobsook
Jirakkakul, Jiraporn
Dulsawat, Sudarat
Tachaleat, Anuwat
Cheevadhanarak, Supapon
Khoiri, Ahmad Nuruddin
Petsong, Kantiya
AuthorAffiliation 5 Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
4 School of Food Industry, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand
1 Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
3 Department of Food Technology, Faculty of Technology, Khon Kaen University, Khon Kaen, Thailand
Universidade de Coimbra, PORTUGAL
2 Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
AuthorAffiliation_xml – name: 3 Department of Food Technology, Faculty of Technology, Khon Kaen University, Khon Kaen, Thailand
– name: 4 School of Food Industry, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand
– name: Universidade de Coimbra, PORTUGAL
– name: 5 Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
– name: 2 Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
– name: 1 Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/36749783$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
Copyright Copyright: © 2023 Jirakkakul 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.
COPYRIGHT 2023 Public Library of Science
2023 Jirakkakul 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. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
2023 Jirakkakul et al 2023 Jirakkakul et al
2023 Jirakkakul 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. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
Copyright_xml – notice: Copyright: © 2023 Jirakkakul 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.
– notice: COPYRIGHT 2023 Public Library of Science
– notice: 2023 Jirakkakul 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. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
– notice: 2023 Jirakkakul et al 2023 Jirakkakul et al
– notice: 2023 Jirakkakul 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. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
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License Copyright: © 2023 Jirakkakul 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.
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SSID ssj0053866
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Snippet A novel methylotrophic bacterium designated as NMS14P was isolated from the root of an organic coffee plant ( Coffea arabica ) in Thailand. The 16S rRNA...
A novel methylotrophic bacterium designated as NMS14P was isolated from the root of an organic coffee plant (Coffea arabica) in Thailand. The 16S rRNA sequence...
A novel methylotrophic bacterium designated as NMS14P was isolated from the root of an organic coffee plant ( Coffea arabica ) in Thailand. The 16S rRNA...
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pubmed
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SubjectTerms ABC transporter
Acetic acid
Agriculture
Agrochemicals
Analysis
Bacteria
Biofertilizers
Biofilms
Biology and Life Sciences
Biomedical materials
Biosynthesis
Chemotaxis
Chromosomes
Coffee
Colonization
Consortia
Corn
Crop yields
Cytokinins
Edible Grain - genetics
Engineering and Technology
Experiments
Fertilizers
Genes
Genomes
Genomic analysis
Host plants
Hot peppers
In vivo methods and tests
Indoleacetic acid
Jalapeno
Management
Metabolism
Metabolites
Methylobacterium
Methylobacterium - genetics
Mosses
Oxidation
Phosphatase
Phylogeny
Physical Sciences
Plant growth
Plasmids
Quorum sensing
RNA, Ribosomal, 16S - genetics
rRNA 16S
Saccharum - genetics
Secondary metabolites
Seeds
Sequence analysis
Soil fertility
Solubilization
Sugarcane
Sulfur
Sustainable agriculture
Trehalose
Urea
Zea mays - genetics
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Title Insights into the genome of Methylobacterium sp. NMS14P, a novel bacterium for growth promotion of maize, chili, and sugarcane
URI https://www.ncbi.nlm.nih.gov/pubmed/36749783
https://www.proquest.com/docview/2774144907
https://www.proquest.com/docview/2774267909
https://pubmed.ncbi.nlm.nih.gov/PMC9904496
https://doaj.org/article/150367ff150f4c60804f1f58ce8d6a95
http://dx.doi.org/10.1371/journal.pone.0281505
Volume 18
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