From single cells to microbial populations: Disentangling microbial interactions and functions through integrated omics techniques

Abstract

Microbial communities play a central role in global geochemical cycles, environmental engineering systems, and human health. However, how microbial communities perform their in-situ activities and what are the biotic (e.g., species interactions) and abiotic controls remain challenging to elucidate and manipulate. The availability of high-throughput sequencing techniques to assess environmental DNA and mRNA levels (functional omics), in combination with new computational tools for analysis of the resulting sequences, provide new opportunities to dissect complex microbial interactions within natural and engineered systems. In this work, we developed a series of new computational tools and pipelines to integrate (microbial) single-cell genomics, metagenomics and metatranscriptomic data from complex ecosystems and recover information on microbial diversity and functional potential (Tsementzi et al, Env. Microb. Reports, 2014). We subsequently applied these techniques to unravel the roles of two highly specialized microbes within complex microbial communities: (a) Dehaloccoides mcartyi is the only organism known to date that can perform complete reductive dechlorination of chlorinated contaminants. This critical function for bioremediation applications depends on the poorly understood roles of co-occurring, diverse helper microbial species and complex species interactions. Using integrated omic techniques on natural and engineered mixed communities, we explored the role of community members as well as the strain genomic heterogeneity of D. mcartyi in dechlorination activity. (b) The ubiquitous SAR11 bacteria comprise the most abundant organisms in the ocean surface. While SAR11 have been known to only respire oxygen and oxidize small organic molecules, recent findings revealed that these organisms persist in high abundance within extended anoxic water masses formed in oceanic Oxygen Minimum Zones (OMZ). Integrated omic analysis elucidated a previously unrecognized anaerobic metabolism for these cells related to nitrate respiration (Tsementzi et al, Nature, 2016). These findings link SAR11 to pathways of ocean nitrogen loss, and thus, have important implications for our understanding of OMZs and global nutrient cycling