What are the processes contributing to the maintenance of microbial diversity?
Ecological Responses. It is now well established that various biotic and abiotic factors influence microbial biogeographic patterns at the community level. However, the mechanisms maintaining these patterns are largely unknown. First, I am interested in linking the fine-scale genetic variation among closely-related taxa to variation in ecologically-relevant traits (Chase et al. 2017). Variation in these traits should translate to differential distributions across environments, where the environment selects for specific clades (and traits) under variable conditions. By delineating ecotypes, or fine-scale genetic clusters sharing ecologically-relevant phenotypic traits, we can map environmental distributions to link this variation to spatial distributions (Chase et al. 2018). Inevitably, I am interested in elucidating the importance of key environmental parameters contributing to niche differentiation.
We are also interested in processes that are independent of environmental selection, including stochastic or neutral processes, that also contribute to community dynamics. By controlling dispersal with field manipulation experiments, we can quantify the effects of stochasticity on the beta-diversity in bacterial communities (Albright et al. 2019). Our observations indicated that stochastic effects on beta-diversity were not attenuated at the functional level, as measured by genetic functional potential and extracellular enzyme activity.
By expanding a trait-based approach to other bioactive taxa, we can effectively target biochemically novel lineages for focused natural product discovery efforts. Similar to work in soils, marine sediment actinomycetes, particularly Streptomyces, have become the most prolific source of antibiotics identified to date. Despite the deep history and intensive work done in Streptomyces, we have identified a novel marine lineage, MAR4, that are enriched in genes that encode the biosynthesis of hybrid isoprenoids (i.e., prenyltransferases; PTases) and vanadium-dependent chloroperoxidase (VHPO) enzymes (Sweeney et al. 2024). Most of the MAR4 natural products are known for their antibacterial properties, such as the napyradiomycin family of meroterpenoids that exhibit potent and rapid bactericidal activity. However, the biosynthesis of many of the known molecules, particularly in relation to the BGCs that encode them, remains ambiguous. We are currently working to link the observed genomic signatures in MAR4 strains to their chemical diversity, with a focus on halogenated compounds.
Jennifer Martiny - UC Irvine [link]
Paul Jensen - Scripps Institution of Oceanography [link]
Steve Allison - UC Irvine [link]
Eoin Brodie - Lawrence Berkeley National Laboratory [link]
Ulas Karaoz - Lawrence Berkeley National Laboratory [link]
Adam Martiny - UC Irvine [link]
Bradley Moore - Scripps Institution of Oceanography [link]
Martin Polz - University of Vienna, formerly MIT [link]
Alejandra Rodriguez-Verdugo - UC Irvine [link]
Kathleen Smits - Southern Methodist University [link]
Katrine Whiteson - UC Irvine [link]