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Diversity of the Microbacteriaceae, with focus on the plant pathogenic genera Clavibacter and Leifsonia, based on environmental 16S data

Thais Galhardo Egreja Ribeiro Silva: Department of Plant Pathology, University of Nebraska

<div>The family Microbacteriaceae, which contains numerous plant pathogens, are gram-positive bacteria with predominantly high GC content. The most notable genera in this family are pathogens of economically important monocots. For example, <em>Clavibacter</em> is the causal agent of Goss’s bacterial wilt and leaf blight in corn and <em>Leifsonia</em> is the causal agent of ratoon stunting disease (RSD) in sugarcane. Taxonomic and phylogenetic diversity of this bacterial family has lagged behind those of other pathogens despite the prevalence of the Microbacteriaceae in many environments (e.g. plant tissue, thermal hot springs, and ocean water). In order to characterize this important family, we mined approximately 1.4 billion 16S sequences that had been deposited into NCBI’s SRA raw data repository. These were then clustered into 53,696,442 sample-specific OTUs (operational taxonomic units) using the QIIME pipeline. Of those initial OTUs, 180,806 OTUs showed 95% synteny to OTUs designated as members of the Microbacteriaceae from cultural studies and deposited in the SILVAngs database. A consensus tree was generated from 1,568 MCMC Bayesian phylogenies and consisted of four major sub-familiar lineages which do not conform to previously described subfamilies. We hypothesize that pathogenicity is dependent on genomic diversity and/or the presence of integrated mobile elements.</div>