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

Shawn M Higdon1, Bihua C Huang2,3, Alan B Bennett1

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Researchers discovered novel genes in Lactococcus bacteria enabling biological nitrogen fixation (BNF) in Sierra Mixe maize, independent of the typical nif genes. This finding reveals a new pathway for BNF in these microbes.

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Area of Science:

  • Microbiology
  • Genomics
  • Plant Science

Background:

  • Sierra Mixe maize utilizes atmospheric nitrogen via an unknown mechanism.
  • Associated diazotrophic microbiota, including 23 lactococci, were previously identified.
  • These lactococci fix nitrogen without the canonical *nifHDKENB* genes.

Purpose of the Study:

  • To identify the genes responsible for biological nitrogen fixation (BNF) in *Lactococcus* associated with Sierra Mixe maize.
  • To compare the genomes of diazotrophic *Lactococcus* with non-diazotrophic dairy isolates.
  • To elucidate the novel pathway for BNF in *Lactococcus*.

Main Methods:

  • Comparative population genomic analysis of 70 dairy *Lactococcus* isolates and maize-associated strains.
  • Pangenome analysis, genome-wide association study (GWAS), and machine learning.
  • Domain analysis of putative genes and homologs.

Main Results:

  • Diazotrophic *Lactococcus* genomes are distinct from dairy isolates.
  • GWAS and machine learning identified unique genes for BNF in maize isolates.
  • Domain analysis revealed genes involved in carbohydrate catabolism, host adhesion, and iron utilization.

Conclusions:

  • A novel pathway for BNF in *Lactococcus* has been identified, independent of the *nif* operon.
  • This pathway involves mucilage carbohydrate breakdown, adhesion, and redox control.
  • The findings provide the first model for *nif*-independent BNF in *Lactococcus*.