Unraveling the Genomic and Environmental Diversity of the UbiquitousSolirubrobacter

Abstract

2.AbstractSolirubrobacter, a genus within the Actinobacteriota phylum, is commonly found in soils and rhizospheres yet remains unexplored despite its widespread presence and diversity, as revealed through metagenomic studies. Previously recognized as a prevalent soil bacterium, our study delved into phylogenomics, pangenomics, environmental diversity, and bacterial interactions ofSolirubrobacter. Analyzing the limited genomic sequences available for this genus, we uncovered a pangenome consisting of 19,645 protein families, with 2,644 constituting a strict core genome. While reported isolates do not exhibit motility, we intriguingly discovered the presence of flagellin genes, albeit with an incomplete flagellum assembly pathway. Our examination of 16S ribosomal genes unveiled a considerable diversity (3,166 operational taxonomic units OTUs) ofSolirubrobacterin Mexican soils, and co-occurrence network analysis indicated its extensive connectivity with other bacterial taxa. Through phylogenomic analysis, we delved into the relatedness of sequenced strains and notably dismissed ASM999324v1 as a member of this genus. Our investigation extended to the metagenomic diversity ofSolirubrobacteracross various environments, affirming its pervasive presence in rhizospheres and certain soils. This broader pangenomic view revealed genes linked to transcription, signal transduction, defense mechanisms, and carbohydrate metabolism, highlightingSolirubrobacter’sadaptability. We observed thatSolirubrobacter’sprevalence in rhizospheres is geographically indiscriminate, prompting intriguing questions about its potential interactions with plants and the biotic and abiotic determinants of its soil occurrence. Given its richness and diversity,Solirubrobactermight be a versatile yet overlooked keystone species in its environments, meriting further recognition and study.3.Impact statementThis study explored the enigmatic world ofSolirubrobacter, a widespread microbe commonly found in soils and plants across various regions. Despite its prevalence, little is known about its genetic diversity and functionality and how it thrives in diverse environments. Our research unveils the genetic secrets ofSolirubrobacter, shedding light on its adaptability and ecological interactors and roles. We showed thatSolirubrobacterenvironmental prevalence makes it a good candidate for studying the genetic basis of being a successful microbe associated with soil and plants.4.Data summaryData, scripts and statistical analysis available in GitHub:https://github.com/genomica-fciencias-unam/SolirubrobacterSequences, phylogenetic analysis, raw data structures:https://doi.org/10.6084/m9.figshare.2444652116S rRNA gene raw data:https://www.ncbi.nlm.nih.gov/sra/PRJNA603586https://www.ncbi.nlm.nih.gov/sra/PRJNA603590Shotgun metagenomes:https://www.ncbi.nlm.nih.gov/bioproject/603603All supporting data, code, and protocols are within the article, supplementary files, and described repositories.