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1. Data for Lake Mendota Phosphorus Cycling Model

   https://doi.org/10.6073/pasta/36d0ee7bf67d9dabade404c92be73917  

   Hanson, Paul C; Stillman, Aviah B (January 2019, Environmental Data Initiative)

   There is an opportunity to advance both prediction accuracy and scientific discovery for phosphorus cycling in Lake Mendota (Wisconsin, USA). Twenty years of phosphorus measurements show patterns at seasonal to decadal scales, suggesting a variety of drivers control lake phosphorus dynamics. Our objectives are to produce a phosphorus budget for Lake Mendota and to accurately predict summertime epilimnetic phosphorus using a simple and adaptable modeling approach. We combined ecological knowledge with machine learning in the emerging paradigm, theory-guided data science (TGDS). A mass balance model (PROCESS) accounted for most of the observed pattern in lake phosphorus. However, inclusion of machine learning (RNN) and an ecological principle (PGRNN) to constrain its output improved summertime phosphorus predictions and accounted for long term changes missed by the mass balance model. TGDS indicated additional processes related to water temperature, thermal stratification, and long term changes in external loads are needed to improve our mass balance modeling approach. 

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2. Microbial carbon, sulfur, iron, and nitrogen cycling linked to the potential remediation of a meromictic acidic pit lake

   https://doi.org/10.1038/s41396-022-01320-w  

   Ayala-Muñoz, Diana; Macalady, Jennifer L.; Sánchez-España, Javier; Falagán, Carmen; Couradeau, Estelle; Burgos, William D. (December 2022, The ISME Journal)
3. Modelling the influence of invasive mussels on phosphorus cycling in Lake Michigan

   https://doi.org/10.1016/j.ecolmodel.2019.108920  

   Shen, Chunqi; Liao, Qian; Bootsma, Harvey A. (January 2020, Ecological Modelling)
4. Diversity of sulfur cycling halophiles within the Salton Sea, California’s largest lake

   https://doi.org/10.1186/s12866-025-03839-2  

   Freund, Linton; Hung, Caroline; Topacio, Talyssa M; Diamond, Charles; Fresquez, Alyson; Lyons, Timothy W; Aronson, Emma L (December 2025, BMC Microbiology)

   Abstract BackgroundMicroorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California’s largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022. ResultsWe observed that the water column microbiome significantly varied by season (R² = 0.59,P = 0.003). Temperature (R² = 0.27,P = 0.004), dissolved organic matter (R² = 0.13,P = 0.004), and dissolved oxygen (R² = 0.089,P = 0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria were consistently identified in samples across depths and time points, though their relative abundances fluctuated by season. We found that while sulfur cycling genes were present in all metagenomes, their relative coverages fluctuated by pathway and season throughout the water column. Sulfur oxidation and incomplete sulfur oxidation pathways were conserved in the microbiome across seasons. ConclusionsOur work demonstrates that the microbiome within the Salton Seawater has the capacity to metabolize sulfur species and utilize multiple trophic strategies, such as alternating between chemorganotrophy and chemolithoautrophy, to survive this harsh, fluctuating environment. Together, these results suggest that the Salton Sea microbiome is integral in the geochemical cycling of this ever-changing ecosystem and thus contributes to the seasonal dynamics of the Salton Sea. Further work is required to understand how these environmental bacteria are implicated relationship between the Salton Sea’s sulfur cycle, dust proliferation, and respiratory distress experienced by the local population. 

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5. Letter: Trophic interactions regulate peatland carbon cycling

   https://doi.org/10.1111/ele.13697  

   Wyatt, Kevin H.; McCann, Kevin S.; Rober, Allison R.; Turetsky, Merritt R.; Wang, ed., Shaopeng (February 2021, Ecology Letters)

   Abstract Peatlands are the most efficient natural ecosystems for long‐term storage of atmospheric carbon. Our understanding of peatland carbon cycling is based entirely on bottom‐up controls regulated by low nutrient availability. Recent studies have shown that top‐down controls through predator‐prey dynamics can influence ecosystem function, yet this has not been evaluated in peatlands to date. Here, we used a combination of nutrient enrichment and trophic‐level manipulation to test the hypothesis that interactions between nutrient availability (bottom‐up) and predation (top‐down) influence peatland carbon fluxes. Elevated nutrients stimulated bacterial biomass and organic matter decomposition. In the absence of top‐down regulation, carbon dioxide (CO₂) respiration driven by greater decomposition was offset by elevated algal productivity. Herbivores accelerated CO₂emissions by removing algal biomass, while predators indirectly reduced CO₂emissions by muting herbivory in a trophic cascade. This study demonstrates that trophic interactions can mitigate CO₂emissions associated with elevated nutrient levels in northern peatlands. 

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