What are the processes contributing to the origin and 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. We are 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 trait variation to spatial distributions (Chase et al. 2018). Inevitably, we are interested in elucidating the 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. Despite the deep history and work done in Streptomyces, we identified a novel marine lineage, MAR4, 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 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, such as our recent discovery of the antibiotic indanopyrrole (Sweeney et al. 2024).
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Interested in collaborating on microbial ecology or metagenomics? Contact me to discuss potential partnerships or student opportunities at the graduate and undergraduate levels.
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] April Lukowski - UC San Diego [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] |
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