Award: OCE-1948058

Microbial communities in lake sediments can provide insight into modern and recent water column processes as well as watershed land-use and water quality. This project sought to better understand how organic matter from different types of biomass including cyanobacteria (e.g. Microcystis in Lake Erie vs picocyanobacteria in Lake Superior) influences carbon export and impacts the ability of heterotrophic bacteria in the water column and sediment to break down that organic matter and remove (anthropogenic) nitrogen from the system.

We examined microbial communities in sediments in lakes across land-use and nutrient status gradients, including Lake Superior and Lake Erie. Lakes in our study varied in how impacted they are by harmful cyanobacterial blooms. Cyanobacterial production, especially during blooms, has a potentially strong impact on carbon and nitrogen cycling, particularly if cyanobacterial biomass is exported to the sediments. We sought to examine how nutrient status would impact sediment microbial community composition and biogeochemical cycling to better understand the fate of biomass from the the water column (including cyanobacteria and their subsequent biomass that can end up in the sediments) and surrounding landscapes (terrestrial organic matter). 

We investigated sediment microbial communities in lakes in the Minnesota's Sentinel Lakes in a Changing Environment (SLICE) program that spanned four of the seven Environmental Protection Agency/Commission for Environmental Cooperation’s (level III) ecological regions: western corn belt, north central hardwood forest, northern lakes and forests, and the Canadian shield. These regions can be distinguished by underlying geology, soils, vegetation, and land use. Microbial communities clustered by ecological region and land use rather than any individual lake properties such as total phosphorous or fixed nitrogen concentration. 

Recent research has highlighted the role carbon produced in lakes (from water column primary productivity) can impact sediment biogeochemical cycling and how increasing cyanobacterial blooms might alter biological processes in sediments. Terrestrial organic matter (leaf and tree litter, grasses, living and dead plants, soil, etc.) also impacts lakes by influencing ecosystem metabolism and the structure of food webs. Because lake sediment microbial communities vary by ecological region, organic matter delivery from the surrounding landscape is also likely to vary. To understand how organic matter impacts sediment biogeochemical cycling, we added terrestrial organic matter (leaf litter) to sediment microcosms and examined community composition and methane production (a key microbial process in lake sediments). Sediments were collected from nearshore, open water, and river sites to assess spatial heterogeneity and gradients in delivery of terrestrial organic matter. Contrary to our expectations that methane production rates would be higher in littoral (near-shore) sediments than pelagic ones due to a sediment community structure which is more accustomed to degrading complex organic matter, we found a universal response in methane production in lake sediments. 

The availability of nitrogen in ecosystems can constrain microbial community composition and function and impact the rate of physiological processes in organisms. Nitrogen is an essential element that cycles through various compounds and redox states. The nitrate concentration in Lake Superior has increased over the last century. Given the low concentrations of organic carbon and the depth of oxygen penetration in Lake Superior sediments, we sought to better understand how sediment microorganisms break down organic matter and recycle or remove nitrogen. We used metagenomics and metatranscriptomics to assess the potential and active transformations of nitrogen species by individual organisms in Lake Superior sediments. We observed dynamic and interconnected nitrogen transformations in oxygen-rich, low carbon environments which we can compare to carbon-rich environments such as those in the sediments of the western basin of Lake Erie. In Lake Erie, large cyanobacterial blooms can inhibit the capacity of sediments to perform organic matter respiration and denitrification (which removes from nitrogen from sediments).

Collectively, our data provide valuable context on microbial community composition and function in the sediments from lakes across trophic gradients, how carbon and nitrogen are cycled or recycled, and how these processes are recorded over time. Our data increase current understanding of the environmental factors that impact key sediment microbial processes including carbon and nitrogen cycling. This project trained multiple graduate and undergraduate students and and created outreach content including an at home DNA extraction kit and video along with bioinformatics activities for all ages. The lab also hosted a series of hands-on research activities for Community Outreach, Retention, and Engagement (CORE) Program at UMN. Data have been deposited in public repositories including NCBI. Data and results have been shared through presentations at conferences, a PhD dissertation, and in peer-reviewed publications.

Last Modified: 06/20/2025
Modified by: Trinity Hamilton