Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning
| Autor: | Shawn M. Higdon, Bart C. Weimer, Alan B. Bennett, Bihua C. Huang |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Microbiology (medical)
random forests pangenome Operon Lactococcus Population plant/microbe association plant Biology Machine learning computer.software_genre maize Microbiology Genome Article 03 medical and health sciences Virology Genetics GWAS education Lactococcus lactis lcsh:QH301-705.5 Gene 030304 developmental biology microbe association lactococci 0303 health sciences education.field_of_study 030306 microbiology business.industry Human Genome biological nitrogen fixation biology.organism_classification lactic acid bacteria lcsh:Biology (General) Nitrogen fixation Diazotroph Artificial intelligence business computer |
| Zdroj: | Microorganisms Microorganisms, vol 8, iss 12 Volume 8 Issue 12 Microorganisms, Vol 8, Iss 2043, p 2043 (2020) |
| ISSN: | 2076-2607 |
| Popis: | 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&rsquo 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 &lsquo unknown&rsquo 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|