Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields

Abstract Previous studies have shown the sugarcane microbiome harbors diverse plant growth promoting microorganisms, including nitrogen-fixing bacteria (diazotrophs), which can serve as biofertilizers. The genomes of 22 diazotrophs from Colombian sugarcane fields were sequenced to investigate potent...

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Autores principales:	Luz K. Medina-Cordoba, Aroon T. Chande, Lavanya Rishishwar, Leonard W. Mayer, Lina C. Valderrama-Aguirre, Augusto Valderrama-Aguirre, John Christian Gaby, Joel E. Kostka, I. King Jordan
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/252dea7e7a7740c1ad8c2ca0106b9f0d
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spelling	oai:doaj.org-article:252dea7e7a7740c1ad8c2ca0106b9f0d2021-12-02T14:53:43ZGenomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields10.1038/s41598-021-88380-82045-2322https://doaj.org/article/252dea7e7a7740c1ad8c2ca0106b9f0d2021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-88380-8https://doaj.org/toc/2045-2322Abstract Previous studies have shown the sugarcane microbiome harbors diverse plant growth promoting microorganisms, including nitrogen-fixing bacteria (diazotrophs), which can serve as biofertilizers. The genomes of 22 diazotrophs from Colombian sugarcane fields were sequenced to investigate potential biofertilizers. A genome-enabled computational phenotyping approach was developed to prioritize sugarcane associated diazotrophs according to their potential as biofertilizers. This method selects isolates that have potential for nitrogen fixation and other plant growth promoting (PGP) phenotypes while showing low risk for virulence and antibiotic resistance. Intact nitrogenase (nif) genes and operons were found in 18 of the isolates. Isolates also encode phosphate solubilization and siderophore production operons, and other PGP genes. The majority of sugarcane isolates showed uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six strains with the highest overall genotype scores were experimentally evaluated for nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid, and indole acetic acid. Results from the biochemical assays were consistent and validated computational phenotype predictions. A genotypic and phenotypic threshold was observed that separated strains by their potential for PGP versus predicted pathogenicity. Our results indicate that computational phenotyping is a promising tool for the assessment of bacteria detected in agricultural ecosystems.Luz K. Medina-CordobaAroon T. ChandeLavanya RishishwarLeonard W. MayerLina C. Valderrama-AguirreAugusto Valderrama-AguirreJohn Christian GabyJoel E. KostkaI. King JordanNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Luz K. Medina-Cordoba Aroon T. Chande Lavanya Rishishwar Leonard W. Mayer Lina C. Valderrama-Aguirre Augusto Valderrama-Aguirre John Christian Gaby Joel E. Kostka I. King Jordan Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields
description	Abstract Previous studies have shown the sugarcane microbiome harbors diverse plant growth promoting microorganisms, including nitrogen-fixing bacteria (diazotrophs), which can serve as biofertilizers. The genomes of 22 diazotrophs from Colombian sugarcane fields were sequenced to investigate potential biofertilizers. A genome-enabled computational phenotyping approach was developed to prioritize sugarcane associated diazotrophs according to their potential as biofertilizers. This method selects isolates that have potential for nitrogen fixation and other plant growth promoting (PGP) phenotypes while showing low risk for virulence and antibiotic resistance. Intact nitrogenase (nif) genes and operons were found in 18 of the isolates. Isolates also encode phosphate solubilization and siderophore production operons, and other PGP genes. The majority of sugarcane isolates showed uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six strains with the highest overall genotype scores were experimentally evaluated for nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid, and indole acetic acid. Results from the biochemical assays were consistent and validated computational phenotype predictions. A genotypic and phenotypic threshold was observed that separated strains by their potential for PGP versus predicted pathogenicity. Our results indicate that computational phenotyping is a promising tool for the assessment of bacteria detected in agricultural ecosystems.
format	article
author	Luz K. Medina-Cordoba Aroon T. Chande Lavanya Rishishwar Leonard W. Mayer Lina C. Valderrama-Aguirre Augusto Valderrama-Aguirre John Christian Gaby Joel E. Kostka I. King Jordan
author_facet	Luz K. Medina-Cordoba Aroon T. Chande Lavanya Rishishwar Leonard W. Mayer Lina C. Valderrama-Aguirre Augusto Valderrama-Aguirre John Christian Gaby Joel E. Kostka I. King Jordan
author_sort	Luz K. Medina-Cordoba
title	Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields
title_short	Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields
title_full	Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields
title_fullStr	Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields
title_full_unstemmed	Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields
title_sort	genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from colombian sugarcane fields
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/252dea7e7a7740c1ad8c2ca0106b9f0d
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Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields

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