Data associated with the publication: Major trends and environmental correlates of spatiotemporal shifts in the distribution of genes compared to a biogeochemical model simulation in the Chesapeake Bay

Microorganisms mediate critical biogeochemical transformations that affect the productivity and health of aquatic ecosystems. Metagenomic sequencing can be used to identify how genes change in response to environmental variables. However, relatively few studies directly compare gene changes to biogeochemical model predictions of corresponding processes, especially in dynamic estuarine ecosystems. We aim to understand the major drivers of spatiotemporal shifts in microbial genes and genomes within the water column of the Chesapeake and highlight the largest discrepancies of these observations with our model predictions. We used previously published shotgun metagenomic datasets, collected across multiple months, sites, and water column positions within Chesapeake Bay in 2017, and a metatranscriptomic dataset collected at one site in the Bay in 2010-2011. We found the largest changes in the relative abundance of genes involved in carbon, nitrogen, and sulfur metabolism associated with variables that change with depth and season (e.g. pH, phosphate, water temperature). Several major trends and key relationships between genes and environmental parameters deviate from distributions expected by the model, such as discrepancies between genes mediating nitrification, higher than expected abundance and expression of denitrification genes in aerobic waters, and nitrogen fixation genes in environments with relatively high ammonia but low oxygen concentrations. While more work is needed to determine the biogeochemical consequences of gene abundance deviating from our model predictions, it provides insight into processes that can be targeted for future study to better understand factors that influence gene abundance changes in an important estuarine ecosystem.