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Open AccessArticle

Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning

1
Department of Plant Sciences, University of California, Davis, CA 95616, USA
2
Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
3
100 K Pathogen Genome Project, University of California, Davis, CA 95616, USA
*
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(12), 2043; https://doi.org/10.3390/microorganisms8122043
Received: 10 November 2020 / Revised: 8 December 2020 / Accepted: 17 December 2020 / Published: 20 December 2020
(This article belongs to the Section Plant Microbe Interactions)
Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived from the atmosphere via an undefined nitrogen fixation mechanism. The diazotrophic microbiota associated with the plant’s mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized by our group where we found 23 lactococci capable of biological nitrogen fixation (BNF) without containing any of the proposed essential genes for this trait (nifHDKENB). To determine the genes in Lactococcus associated with this phenotype, we selected 70 lactococci from the dairy industry that are not known to be diazotrophic to conduct a comparative population genomic analysis. This showed that the diazotrophic lactococcal genomes were distinctly different from the dairy isolates. Examining the pangenome followed by genome-wide association study and machine learning identified genes with the functions needed for BNF in the maize isolates that were absent from the dairy isolates. Many of the putative genes received an ‘unknown’ annotation, which led to the domain analysis of the 135 homologs. This revealed genes with molecular functions needed for BNF, including mucilage carbohydrate catabolism, glycan-mediated host adhesion, iron/siderophore utilization, and oxidation/reduction control. This is the first report of this pathway in this organism to underpin BNF. Consequently, we proposed a model needed for BNF in lactococci that plausibly accounts for BNF in the absence of the nif operon in this organism. View Full-Text
Keywords: Lactococcus lactis; biological nitrogen fixation; maize; pangenome; GWAS; random forests; lactococci; lactic acid bacteria; plant/microbe association Lactococcus lactis; biological nitrogen fixation; maize; pangenome; GWAS; random forests; lactococci; lactic acid bacteria; plant/microbe association
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MDPI and ACS Style

Higdon, S.M.; Huang, B.C.; Bennett, A.B.; Weimer, B.C. Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning. Microorganisms 2020, 8, 2043. https://doi.org/10.3390/microorganisms8122043

AMA Style

Higdon SM, Huang BC, Bennett AB, Weimer BC. Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning. Microorganisms. 2020; 8(12):2043. https://doi.org/10.3390/microorganisms8122043

Chicago/Turabian Style

Higdon, Shawn M.; Huang, Bihua C.; Bennett, Alan B.; Weimer, Bart C. 2020. "Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning" Microorganisms 8, no. 12: 2043. https://doi.org/10.3390/microorganisms8122043

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