Investigating the function of the ubiquitous Acidobacteria in terrestrial environments

Members of the phylum Acidobacteria are found in soils worldwide. They comprise a monophyletic phylum of astonishing diversity, similar to the proteobacteria, with 26 currently recognized subdivisions. Their common occurrence and high abundance based on ribosomal gene sequences suggests that they are likely a major component of the microbial community in soil and play ecologically significant roles in the soil environment. However, their roles remain largely unknown due to the limited number of cultivated representatives and a paucity of information on their genetic potential (genomic and metagenomic information). The overarching goal of this project is to elucidate the ecophysiology and therefore the success and ubiquity of members of the phylum Acidobacteria in terrestrial ecosystems by combining genomic, growth-based, molecular and single-cell functional analyses. Our goal is to better link the genetic potential of acidobacteria with their in situ functions in the soil. We have a unique opportunity to analyze the genomes of multiple strains in subdivisions 1 and 3 to understand the genetic potential across representatives of these dominant subdivisions due to a successfully awarded Joint Genome Institute Community Sequencing Project. We will annotate strains to identify the acidobacteria "pan-genome" in parallel to confirmatory growth experiments in the laboratory. Of particular note is the ability of select acidobacteria strains for improved growth under reduced oxygen concentrations as well as growth in `floc` structures. Our preliminary genome analysis of the available acidobacteria genomes indicate that strains Ellin6076, KBS 83, KBS 96, A. capsulatum, and T. roseus strain KBS 63 harbor the catalytic subunit of cbb3 a high-affinity terminal cytochrome oxidase (ccoN) which allow them to detect oxygen at a low Km. The presence of this terminal oxidase could allow acidobacteria to thrive in environments with low O2 concentrations, such as flocs or soil aggregates. We will explore the single-cell activity of acidobacteria that grow in flocs and the presence and activity of acidobacteria across soil aggregates of different size-classes using a combination of expression assays, single-cell isotope analysis and O2 microsensor measurements. We will use the gained information to optimize isolation strategies for acidobacteria from the soil. The expected scientific outcome include: (1) identify genes that help explain their ubiquity in soils (i.e. C and N cycling genes, high-affinity terminal oxidases); (2) develop acidobacterial primers for functional gene analysis and expression studies in environmental samples, linking genome potential with environmental function; (3) explore microaerophily in the acidobacteria with growth-based testing and environmental in situ studies combined with NanoSIMS analysis; and (4) develop additional cultivation/enrichment strategies to isolate additional strains in this phylum.

Members of the phylum Acidobacteria are found in soils worldwide. They comprise a monophyletic phylum of astonishing diversity with 26 currently recognized subdivisions. Their common occurrence and high abundance suggest that they are likely a major component of the microbial community in soil and play ecologically significant roles in the soil environment. However, their roles remain largely unknown due to the limited number of cultivated representatives and a paucity of information on their genetic potential. Soils represent habitats with unpredictable conditions, confronting soil microorganisms with suboptimal conditions for growth. Remarkably, certain microbial groups such as the Acidobacteria are abundant and ubiquitous across many soils, yet the reasons for their persistence remain elusive. Using a combination of genomic, growth-based, enzyme kinetics and molecular analyses, we identified key features in acidobacterial strains, which help to explain their ubiquity and success in the soil. A large-scale comparative genome analysis including 24 acidobacterial strains revealed a diverse repertoire for both, carbon and nitrogen utilization. Furthermore, multiple soil acidobacteria harbored the potential to scavenge atmospheric concentrations of hydrogen due to a high-affinity hydrogenase, a proposed mechanism for energy generation under nutrient-limiting conditions. This capability was supported in growth experiments, in which hydrogen was consumed in stationary phase at and below atmospheric levels in tandem with hydrogenase gene expression. Limited access to oxygen is another potential stress factor for soil microorganisms, as oxygen is often depleted e.g. in larger soil aggregates. Low- and high-affinity respiratory oxygen reductases were detected in soil acidobacterial genomes, suggesting the capacity for growing across different oxygen gradients. However, against our initial theory, low-affinity reductases were able to respire oxygen at extremely low concentrations. The possibility to respire with the same enzymes at very different oxygen concentrations represents another example of their adaptation to the fluctuating soil habitat. In this project, we have performed the largest acidobacterial comparative genomics analysis, followed by growth-based experiments to test suggested physiologies. In doing so, we explored their relationship with oxygen and provided evidence that another prevalent and abundant group of soil bacteria contribute to atmospheric hydrogen uptake. This work revealed traits that provide soil acidobacteria with physiological versatility, presumably allowing flexibility and thus can explain their success in soil.