Inter-cluster competition and resource partitioning may govern the ecology of Frankia

Microbes live in a complex communal ecosystem. The structural complexity of microbial community reflects diversity, functionality as well as habitat type. Delineation of ecologically important microbial populations along with exploration of their roles in environmental adaptation or host-microbe interaction has a crucial role in modern microbiology. In this scenario, reverse ecology (the use of genomics to study ecology) plays a pivotal role. Some studies have reported the presence of other non-Frankia genus from the same root nodule from where the Frankia was isolated. Since co-existance of two different genus in one small niche should maintain a strict direct interaction, it will be interesting to utilize the concept of reverse ecology in this scenario.Here, we exploited an ‘R’ package, the RevEcoR, to resolve the issue of co-existing microbes which are proven to be a crucial tool for identifying the nature of their relationship (competition or complementation) persisting among them. Our target organism here is Frankia, a nitrogen-fixing actinobacterium popular for its genetic and host specificity nature. According to their plant host, Frankia has already been subdivided into four clusters CI, CII, CIII and CIV. Our results revealed a strong competing nature of CI Frankia. The competition index between CI and CIII was greater than other studied Frankia clusters. The other interesting result was the co-occurrence of C-II and C-IV groups. It was revealed that these two groups follow the theory of resource partitioning in their lifestyle. Metabolic analysis along with their differential transporter machinery validated our hypothesis of resource partitioning among C-II and C-IV group.