Environmental Genomics
Zodletone Spring is a sulfide and sulfur-rich spring in southwestern Oklahoma. We have been actively researching the diversity of Zoldetone Spring for almost two decades. Due to its unique geochemistry and environmental gradients, spatial sampling in Zodletone Spring can substitute for inaccessible temporal time scales. Our current research is focusing on using the spring as a portal to characterize organisms that thrived on Earth prior to the great oxygenation event. Here is a publication from our lab on this topic.
Specifically, we are using meta-omics approaches to identify and characterize novel bacterial lineages prevalent in Zodletone Spring. In samples representing “ancient” pre-oxygenated geological eons, we have uncovered an unprecedented level of diversity and a unique microbial community dominated by taxa that are extremely rare in various current biomes on Earth. Further, we have discovered that many of these novel genera are involved in a unique sulfur cycle in the spring using precursors that are rare nowadays, but prevalent in the spring, as well as on ancient, pre-oxygenated earth (e.g. sulfite, thiosulfate, tetrathionate, and sulfur). We continue to characterize this unique community in Zodletone Spring using state-of-the-art genomic, transcriptomic, proteomic, and culturomic approaches.
Currently, our focus is on:
- Methodological improvements of genome recovery from metagenomes.
- Assessing the viriome landscape in Zodletone Spring.
- Assessing novel secondary metabolites production capacity in unique members of the microbial community in Zodletone Spring.
- Utilization of novel culture-based (culturomics) approaches to isolate and characterize novel microbial taxa in the spring.
A phylocentric strategy for characterizing yet-uncultured microbial taxa
Culture-independent diversity surveys have clearly shown that a large swath of microbial lineages on Earth remains uncultured. During the last decade, our laboratory has been active in using various environmental genomics and bioinformatic approaches in elucidating the metabolic role of various lineages. We use a phylocentric strategy where genomes belonging to the same lineage are characterized to provide a pangenomic view of the lineage’s collective characteristics and capacities. Such a strategy also allows for examining the relative role played by niche versus phylogeny in shaping microbial genomes and metabolic abilities. Our emphasis is on lineages thriving in anaerobic settings. Prior efforts have examined members of the phyla OP11 (Patesibacteria), WS3 (Latescibacteria), OP8 (Aminicenantes), OP1 (Bipolaricaulota), LCP89, UBP10 (Binatota), Myxococcota, Desulfobacterota, Krumholzibacterota, Mcinerneybacteria, and the archaeal phylum Diapherotrites. Current projects are focusing on characterizing the genomic content of novel lineages within the candidate phyla radiation (CPR) group and the phylum Acidobacteriota.