Transitions: Metagenomics of aquatic biofilms: evaluating linkages between autotrophic and heterotrophic microbial diversity and function

This Transitions to Excellence in Molecular and Cellular Biosciences research grant will support implementation of cutting-edge molecular techniques into the research and teaching program of a mid-career scientist allowing her to adopt empowering technologies that are not accessible in her current research environment. Rapid advances in molecular techniques have facilitated widespread taxonomic characterization of microbial communities.

Current research is quickly moving beyond just characterizing diversity (who is there?), towards a focus on linking individual species with their functional properties (what do they do?). However, the study of some microbial communities remain relatively unexplored with respect to diversity or function. This is particularly true for benthic biofilms (i.e., assemblage of algae, bacteria, and fungi) in freshwater ecosystems.

The overarching goal of this research is to use molecular techniques to bridge the gap between microbial community composition and functioning within natural environments. Findings from this research will make significant contributions to an understanding of, and ability to, link microbial diversity with ecosystem function. By providing data from natural microbial communities to publically available repositories, this project will facilitate improved taxonomic resolution and genomic library construction.

These data may also be useful beyond their ecological application given that identification of novel microbial associations in natural environments could facilitate the design of synthetic microbial communities as a tool for industrial cultivation and biotechnology. In addition to charting new conceptual ground in molecular ecology, this project will provide research experiences for graduate and undergraduate students from under-represented groups.

Many ecosystem processes (e.g., carbon cycling) are mediated by microorganisms and understanding how microbial functions scale up to the ecosystem level is an important goal in ecology. Boreal peatlands provide a model ecosystem to examine relationships between microbial structure and function owing to their role in global carbon storage. In this project, researchers will use molecular techniques to examine both the eukaryotic and prokaryotic diversity of the biofilm microbiome and identify functional traits along a hydrologic gradient and relate changes in microbiome structure and function to peatland carbon dioxide (CO2) emissions.

Biofilm composition and metabolism are strongly influenced by differences in hydrologically mediated environmental conditions with consequences for net CO2 emissions. Conditions that promote a higher proportion of autotrophic (algae) biofilm results in greater CO2 uptake from the atmosphere, whereas a biofilm dominated by heterotrophic microorganisms (bacteria and fungi) promotes greater CO2 emissions.

The composition of autotrophic and heterotrophic components of the biofilm are intricately linked and perturbations to one portion of the biofilm community can cascade through the rest. Therefore, it is anticipated that changes in gene expression that control metabolic functions within the autotrophic component of the biofilm will be reflected in the make-up and functioning of the heterotrophic component of the biofilm and vice versa.

This project is expected to reveal the influence of environmental conditions on gene expression within the autotrophic and heterotrophic components of the biofilm. Further, this research is likely to facilitate the discovery of correlated patterns of abundance between certain eukaryotic and prokaryotic microbes, and link trait-mediated metabolic functions at the community level.

Using metagenomic approaches to evaluate how abiotic and biotic interactions shape microbial communities and microbial-mediated biogeochemical processes addresses a critical knowledge gap in the field of aquatic microbiology and will provide a better understanding of how aquatic microbes participate in biogeochemical cycling within peatlands. Methodological procedures will be integrated into college curriculum, providing opportunities for a diversity of students to gain exposure to ecological molecular techniques and applications that will prepare them for the increasing use of applied microbiology in industry, environmental monitoring, and management careers.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.