Research

While we are always taking on new projects, below are some of the key themes in our research. 

Theme 1: Biogeochemical cycling and trophic state development in warm water ecosystems  

Our understanding of tropical aquatic ecology and the key mechanisms behind regime shifts (such as eutrophication) lags behind that of temperate systems. Our research works to correct this imbalance while advancing our broader understanding of aquatic ecosystem biogeochemistry. One unique feature of many tropical lakes is the high temperatures (> 20 °C) of the anoxic water column in lakes which maintain stable seasonal stratification. These warm and anoxic conditions support anaerobic metabolisms that are otherwise thermally constrained at higher latitudes. 

Fadum, JM, B Steele, MRV Ross, and EK Hall. 2025.“Coordinated in situ lake sampling concurrent with satellite acquisition days provides a mechanism for addressing data scarcity: A case study from Lake Yojoa, Honduras”. Acta Limnologica Brasiliensia 37, e2,  http://doi.org/10.1590/S2179-975X6924 

Fadum, JM, MA Borton, RA Daly, KC Wrighton, and EK Hall. 2024. “Nitrogen metabolisms of warm, anoxic waters revealed using genome resolved metatranscriptomics”. mSystems 9(2), e01059-23, https://doi.org/10.1128/msystems.01059-23    

Fadum, JM and EK Hall. 2023. “Nitrogen is unlikely to consistently limit primary productivity in most tropical lakes”. Ecosphere 14(3), e4451, https://doi.org/10.1002/ecs2.4451

Fadum, JM, MN Waters, and EK Hall. 2023. “Trophic state resilience to hurricane disturbance of Lake Yojoa, Honduras. Scientific Reports 13(1), e5681, https://doi.org/10.1038/s41598-023-32712-3

Theme 2: Cryptic biogeochemical impacts of aquaculture 

Organic matter (OM) loading is a ubiquitous effect of finfish aquaculture. One important ecological implication of OM loading (whether from aquaculture or terrestrial sources) is that it alters the biogeochemical transformations that dictate the degree to which bioavailable N is retained in an ecosystem as inorganic N, or else converted to N2O (a potent greenhouse gas) or N2. The biogeochemical impacts of aquaculture (beyond bulk nutrient additions) are poorly understood and even more poorly reflected in current sustainability standards. This has led to negative environmental consequences and ecosystem degradation, even from sustainably accredited operations. 

Fadum, JM, MRV Ross, EA Tenorio, CA Barby, and EK Hall. 2025. “Nutrient loading from a sustainably certified aquaculture operation dwarfs annual nutrient inputs from a large multi-use watershed, Lake Yojoa, Honduras”. Earth’s Future 13(3), e2024EF004807, https://doi.org/10.1029/2024EF004807 

Fadum, JM, EK Hall, E Litchman, and EJ Zakem. 2024. “Aquaculture as a global perturbation experiment”. Limnology & Oceanography Letters 9(4), 317-323, https://doi.org/10.1002/lol2.10384 

Fadum, JM and EK Hall. 2022. “The interaction of physical structure and nutrient loading drives ecosystem change in a large tropical lake over 40 years”. Science of The Total Environment, 830, e154454, https://doi.org/10.1016/j.scitotenv.2022.154454 

Theme 3: Redox-based approaches to understanding ecological change in aquatic environments 

Eutrophication, the deleterious growth of algae fueled by excessive nutrient additions, is one of the most pervasive anthropogenically driven changes in both inland and coastal ecosystems. Our research advances our understanding of the drivers of eutrophication (as well as its impact on the aquatic microbiome) by moving beyond nutrient flux quantification and developing a robust understanding of the microbially mediated biogeochemical pathways which underpin these ecosystem-scale changes. In addition to empirical observations, we use and develop theoretical and numerical models to better understand the mechanisms driving trophic state change in aquatic ecosystems.

Fadum, JM, X Sun, and EJ Zakem. 2025. “Redox-constrained microbial ecology dictates nitrogen loss versus retention”. ISME Communications. ycaf219, https://doi.org/10.1093/ismeco/ycaf219 

Fadum, JM, EJ Zakem, and JM Beman. 2026. "Predictable genomic architecture of anaerobic nitrogen loss and retention in natural marine ecosystems". in preparation.