Community Genomics, Proteomics and Transcriptomics of Leptospirillum bacteria from a Natural Acidic Microbial Community

Acid mine drainage is a mining-related environmental problem that forms when mineral ores are exposed to air and water, promoting the growth of microorganisms whose metabolism leads to acidification and release of heavy metals. Genomics and proteomics have been used to explore the physiology of the most abundant members of biofilm communities from the Richmond Mine in California, and allowed for assignment of ecological roles they might play within the community. Previous work has shown that colonization starts with the establishment of a Leptospirillum Group II-dominated biofilm. Leptospirillum Group III and other lower abundance community members, including Archaea, appear later as biofilms develop. The objective of this study is to understand the ecological diversity and niche partitioning of Leptospirillum bacteria. Community genomic data collected over a period of 7 years was used to assemble partial genomes of lower abundance organisms. Transcriptomics were used to infer organismal abundances and proteomics data were used to infer expression of predicted proteins. Here we report the partial genome of a new bacterial species that expands the Leptospirillum clade: Leptospirillum Group IV. The new species shares 97% 16S rRNA sequence identity and 70% identity between shared proteins with its closest relative Leptospirillum Group III. The presence of nitrogen fixation and reverse TCA cycle proteins suggest an autotrophic metabolism similar to that of Leptospirillum Group III, while hydrogenase proteins unique to Leptospirillum Group IV suggest an active role in the anaerobic setting. Here we compare the new species with other members of the genus Leptospirillum.