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

Abstract

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.

Theobroma cacao L. agricultural soils with natural low and high cadmium (Cd) in Santander (Colombia), contain a persistent shared bacterial composition shaped by multiple soil variables and bacterial isolates highly resistant to Cd concentrations

“…and Staphylococcus sp., thus confirming the greater diversity of Cd-tolerant bacteria present in soils of farms cultivated with cocoa. In addition to their ability to act against Cd, the bacterial genera have important functions at the soil level, for Burkholderia sp., Cupriavidus sp., Enterobacter sp., Klebsiella sp., and Lactococcus sp., the ability to fix N, root nodule formation, and biocontrol ability were reported for some species ( Salles et al., 2006 ; Wolińska et al., 2017 ; Harindintwali et al., 2021 ; Higdon et al., 2020 ); Enterobacter sp., Ralstonia sp., Serratia sp., Bacillus sp., Exiguobacterium sp., and Staphylococcus sp., are considered to have the ability to solubilize phosphates and promote plant growth ( Gupta et al., 2019 ; Hirota et al., 2012 ; Blanco-Vargas et al., 2020 ; Sabaté et al., 2020 ; Pandey and Bhatt, 2016 ; Zhang et al., 2020 ), Escherichia sp. has the ability to produce polysaccharides that interact with soil and plants ( Seo and Matthews, 2014 ), and Dermacoccus sp.…”

Enhancing maize's nitrogen‐fixing potential through ZmSBT3, a gene suppressing mucilage secretion

“…The ancient maize landraces from the Sierra Mixe region of Oaxaca exhibit an impressive capacity for nitrogen fixation, offering a potential way to decrease dependence on nitrogen fertilizers in maize cultivation (Mandimba et al, 1986a, 1986b; Estrada et al, 2002; Van Deynze et al, 2018; Amicucci et al, 2019; Higdon et al, 2020a, 2020b; Sheoran et al, 2021). In contrast to soybean ( Glycine max ) and other legumes, which house diazotrophic bacteria inside underground root nodules, these landraces use a different mechanism: the bacteria live, and fix nitrogen, in mucilage secreted by aerial roots.…”

A thermophilic chemolithoautotrophic bacterial consortium suggests a mutual relationship between bacteria in extreme oligotrophic environments

“…Although nitrogen scavenging cannot be completely ruled out because of the hypothetical presence of unknown metabolic paths (for example, the recent description of a novel mechanism for biological nitrogen fixation by ref. 30 ), we believe that the strict measures employed in the present study would possibly generate insufficient nitrogen (if any) to support bacterial growth and thus would only encourage the growth of true diazotrophs on the N-FIX medium.…”