Life Sciences Seminar: Elucidating the eco-evolutionary dynamics of microbial systems

Elucidating the eco-evolutionary dynamics of microbial systems: experimental and computational approaches

Dr. Angela Oliverio
Computational Biologist
Data Sciences Team
Invitae, Boulder, CO

This research leverages ‘omics approaches and predictive modeling. Dr. Olivierio will discuss the building of a predictive atlas of soil bacteria and protists from over 200 soils collected around the world. Using metagenomic sequencing, soil microbes were profiled to model their distribution patterns and potential functional global contributions using machine learning approaches. This work begins to establish approaches using functional ‘omics and modeling in both natural and experimental microbial systems to elucidate eco-evolutionary dynamics.

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Abstract:
The importance of soil microbes to soil health and fertility, nutrient cycling, and agricultural productivity is well recognized. However, predicting the ecologies, functional roles, and spatial distributions of microbial communities remains difficult. It remains challenging to develop a mechanistic understanding due to the sheer complexity of microbial systems. For example, there are often thousands of microbial species in a system and also many cross-trophic and indirect interactions amongst microbes. Additionally, there can also be strong feedback loops between microbes and their environments which are difficult to disentangle. To tackle this complexity towards a predictive understanding of microbial systems, we have developed two complementary approaches in natural and experimental systems leveraging ‘omics approaches and predictive modeling towards biological insight. First, using natural field systems, we began to identify the distributions of the most abundant soil bacteria (Delgado-Baquerizo, Oliverio et al., 2018, Science) and protists (Oliverio et al., 2020, Science Advances) from > 200 soils globally – and build a global atlas of soil taxa. Using a combination of high-throughput amplicon sequencing coupled with shotgun metagenomic sequencing, we taxonomically and functionally profiled soil communities. We then identified the niches of particular taxa via random forest modeling with soil and site level metadata (e.g. soil pH, nutrients, climatic variables, etc.). Once we identified the niches of individual lineages, we were able to classify soil microbial taxa into ecological categories and determine significant co-occurrence patterns using a network analyses approach, and quantify the potential contributions of different functional groups to belowground. Second, using experimental sourdough starters as model microbial systems, we have begun to identify some mechanisms that drive community assembly processes. Sourdough starter microbiomes are great candidates to study community ecology and evolution in the lab because communities are highly reproducible and readily culturable. In collaboration with colleagues at Tufts and NC State, we have started to develop sourdough starters as a model system. We found that biotic interactions and not environmental factors best predicted the structure of sourdough systems collected globally from citizen scientists (Landis & Oliverio et al., 2021, eLife). Likewise, we discovered that an under-appreciated group of sourdough bacteria, the acetic acid bacteria, drive emergent properties of starter systems including rates of dough-rise and aroma profiles. Taken together, this work begins to establish approaches using functional ‘omics and modeling in both natural and experimental microbial systems to identify what mechanisms drive eco-evolutionary dynamics in microbial systems.

Speaker Bio:
Dr. Angela Oliverio is a computational biologist currently working at Invitae on the data science team within Oncology. In her current position she leads a team in developing data infrastructure and leveraging large genomic datasets in order to predict cancer recurrence. Dr. Oliverio obtained her BA in Biology from Smith College, and her PhD from the University of Colorado in Ecology and Evolution, working with Dr. Noah Fierer. She received the NSF graduate research fellowship to fund her graduate studies, where she researched the macroecological patterns and functional contributions of microbial systems across spatial scales. To address these questions, she leveraged functional ‘omics approaches including metagenomics and metabolomics along with large-scale experiments. Her research lies at the intersections of computational biology, metagenomics, soil microbiology, and global change.

Intended Audience:
Undergraduates, graduates, and experts. Those with interest in the topic.