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

Luz K. Medina-Cordoba, View ORCID ProfileAroon T. Chande, Lavanya Rishishwar, Leonard W. Mayer, Lina C. Valderrama-Aguirre, Augusto Valderrama-Aguirre, John Christian Gaby, Joel E. Kostka, View ORCID ProfileI. King Jordan
doi: https://doi.org/10.1101/780809
Luz K. Medina-Cordoba
aSchool of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
bPanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
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Aroon T. Chande
aSchool of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
bPanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
cApplied Bioinformatics Laboratory, Atlanta, Georgia, USA
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  • ORCID record for Aroon T. Chande
Lavanya Rishishwar
aSchool of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
bPanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
cApplied Bioinformatics Laboratory, Atlanta, Georgia, USA
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Leonard W. Mayer
bPanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
cApplied Bioinformatics Laboratory, Atlanta, Georgia, USA
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Lina C. Valderrama-Aguirre
bPanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
dLaboratory of Microorganismal Production (Bioinoculums), Department of Field Research in Sugarcane, INCAUCA S.A.S., Cali, Valle del Cauca, Colombia
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Augusto Valderrama-Aguirre
bPanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
eBiomedical Research Institute (COL0082529), Cali, Valle del Cauca, Colombia
fUniversidad Santiago de Cali, Cali, Colombia
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John Christian Gaby
aSchool of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
gFaculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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Joel E. Kostka
aSchool of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
bPanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
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  • For correspondence: king.jordan@biology.gatech.edu joel.kostka@biology.gatech.edu
I. King Jordan
aSchool of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
bPanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
cApplied Bioinformatics Laboratory, Atlanta, Georgia, USA
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  • ORCID record for I. King Jordan
  • For correspondence: king.jordan@biology.gatech.edu joel.kostka@biology.gatech.edu
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ABSTRACT

Previous studies have shown that the sugarcane microbiome harbors diverse plant growth promoting (PGP) microorganisms, including nitrogen-fixing bacteria, and the objective of this study was to design a genome-enabled approach to prioritize sugarcane associated nitrogen-fixing bacteria according to their potential as biofertilizers. Using a systematic high throughput approach, 22 pure cultures of nitrogen-fixing bacteria were isolated and tested for diazotrophic potential by PCR amplification of nitrogenase (nifH) genes, common molecular markers for nitrogen fixation capacity. Genome sequencing confirmed the presence of intact nitrogenase nifH genes and operons in the genomes of 18 of the isolates. Isolate genomes also encoded operons for phosphate solubilization, siderophore production operons, and other PGP phenotypes. Klebsiella pneumoniae strains comprised 14 of the 22 nitrogen-fixing isolates, and four others were members of closely related genera to Klebsiella. A computational phenotyping approach was developed to rapidly screen for strains that have high potential for nitrogen fixation and other PGP phenotypes while showing low risk for virulence and antibiotic resistance. The majority of sugarcane isolates were below a genotypic and phenotypic threshold, showing uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six prioritized strains were experimentally evaluated for PGP phenotypes: nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid and indole acetic acid. Results from the biochemical assays were consistent with the computational phenotype predictions for these isolates. Our results indicate that computational phenotyping is a promising tool for the assessment of benefits and risks associated with bacteria commonly detected in agricultural ecosystems.

IMPORTANCE A genome-enabled approach was developed for the prioritization of native bacterial isolates with the potential to serve as biofertilizers for sugarcane fields in Colombia’s Cauca Valley. The approach is based on computational phenotyping, which entails predictions related to traits of interest based on bioinformatic analysis of whole genome sequences. Bioinformatic predictions of the presence of plant growth promoting traits were validated with experimental assays and more extensive genome comparisons, thereby demonstrating the utility of computational phenotyping for assessing the benefits and risks posed by bacterial isolates that can be used as biofertilizers. The quantitative approach to computational phenotyping developed here for the discovery of biofertilizers has the potential for use with a broad range of applications in environmental and industrial microbiology, food safety, water quality, and antibiotic resistance studies.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 24, 2019.
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Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields
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
bioRxiv 780809; doi: https://doi.org/10.1101/780809
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Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields
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
bioRxiv 780809; doi: https://doi.org/10.1101/780809

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