Microbial biogeochemistry is an exciting field that spans multiple environments and time scales, using data collected from the field and from laboratory experiments. In the Kharbush lab, we use organic molecules or biomarkers produced by microbes to bridge the gap between how microbes live and interact with each other in their environment (microbial ecology) with large scale cycling of carbon and nutrients (biogeochemistry). Because of its importance to water quality and its connection to climate change, much of the research in our lab focuses on understanding how different microbes acquire and use nitrogen.
We use a combination of analytical chemistry, isotope geochemistry, and molecular biology techniques, as well as developing new methods to widen the “analytical window” of what we can measure. See our facilities and instrumentation here.
Our research aims to connect intracellular metabolic processes with organismal ecology. This not only improves biomarker applications, but also contributes to overall understanding of microbial ecology and will allow better prediction and modeling of carbon and nitrogen cycling in the environment.
Research directions
Harmful cyanobacterial blooms and nitrogen
Cyanobacterial harmful algal blooms (CHABs) and the toxins they produce are a growing worldwide threat to freshwater ecosystems. These blooms are usually caused by excessive inputs of nutrients (nitrogen and phosphorous) in runoff from land. We are exploring how nutrient type such as inorganic vs. organic forms of nitrogen, as well as abiotic stressors like pH changes, are important for determining which algal species become dominant, and may therefore be important in promoting the growth of harmful species over others.
Relavant publications: Patterns in sources and forms of nitrogen in a large eutrophic lake during a cyanobacterial harmful algal bloom (2023)
Winter nitrogen cycling in Lake Erie
Global climate change is leading to shorter cold periods with less ice cover. A critical knowledge gap is how changing winters will alter biogeochemical cycling in seasonally ice-covered aquatic environments, including the Great Lakes. Nitrification is a critical process observed to occur at higher rates during winter, because the light-limited conditions under ice are hypothesized to favor growth of nitrifiers over photoautotrophs, potentially driving under-ice nitrate accumulation that shapes the spring phytoplankton bloom. We are measuring winter nitrification rates to determine how winter nitrification may impact phytoplankton community structure and how rates change with ice phenology.
C and N cycling at Middle Island Sinkhole, Lake Huron
MIS is a modern anoxic system dominated by cyanobacterial mats, some of which are capable of both oxygenic and anoxygenic photosynthesis, as well as chemoautotrophic sulfur oxidizing bacteria. The photo to the left shows the mat in July of 2022 (photo credit NOAA).
Nitrogen isotope signatures of phytoplankton and bacterial biomarkers
Biomarkers are molecules that are produced by a specific organism or metabolic process. Similar to genomic markers, detection of biomarker molecules in the environment can indicate the presence of the producing organism or metabolism. Chemical biomarkers, however, differ in two important ways from genomic markers: they are often preserved far beyond the lifespan of the producing organisms, and they record isotopic information. Isotope values of biomarkers can be used to trace carbon and nitrogen cycling by specific organisms.
Phytoplankton-bacteria metabolic interactions
Phytoplankton communities contain complex assemblages of both microalgae and bacteria, which interact to exchange nutrients and other cellular metabolites. Especially in freshwater systems, these metabolic interactions and their potential impact on the proliferation of harmful cyanobacteria are not well understood.
Relevant publications: Microbiome processing of organic nitrogen input supports growth and cyanotoxin production of Microcystis aeruginosa cultures (2024)
Uptake of Phytoplankton-Derived Carbon and Cobalamins by Novel Acidobacteria Genera in Microcystis Blooms Inferred from Metagenomic and Metatranscriptomic Evidence (2022)