Metatranscriptomics-based investigation of bacterial community dynamics across a dissolved organic matter gradient in southern Lake Michigan

Bacterial communities in freshwater ecosystems play a critical role in biogeochemical and food web dynamics. However, our understanding of environmental controls on bacterial community function, particularly in large lakes, is limited. We characterized Lake Michigan water chemistry, bacterial community function, and substrate preferences to better understand bacteria-water chemistry relationships. Using metatranscriptomics, we investigated bacterioplankton gene expression in surface waters across a nearshore-to-offshore transect during 2017–2018. Additionally, we measured nutrients, dissolved organic carbon (DOC), chromophoric dissolved organic matter (DOM), as well as changes in major fluorescent DOM components across this transect. The results highlighted similarities in inorganic N and P measurements and a minor reduction in DOC levels from nearshore to offshore. However, significant changes in the composition of DOM were observed across the transect, including a higher presence of terrestrially derived and high-molecular-weight DOM in the nearshore. These differences in DOM quality were associated with the differential expression of several gene families between nearshore and offshore bacterioplankton. Notably, genes involved in the acquisition of various DOM, N, and P substrates, including peptidases, proteases, and transporter genes for amino acids, nucleobases, sugars, urea, and inorganic phosphate, were over-represented in the offshore bacterioplankton. A focused analysis of all the transporter gene expression for C, N, and P substrates revealed similar trends—higher expression of DOM transporter genes in the offshore versus nearshore. When viewed in the context of changing DOM quality across the transect, these results imply that offshore bacterial communities are more substrate-limited (particularly C) than in nearshore and are investing more energy in acquiring DOM substrates. IMPORTANCE Various environmental, geological, and climatic factors influence bacterial community dynamics in freshwater ecosystems in complex and interactive ways. It thus becomes challenging in microbial ecology studies to disentangle the specific effects of these factors on microbial community function. Spatial environmental gradients in large lake ecosystems can provide a unique opportunity to test important questions about bacterial function and water chemistry relationships in a relatively consistent geological and climatic framework. Lake Michigan, one of the five largest lakes in the world, is one such example. The lake has witnessed significant ecological changes in the last few decades, and the impact of these changes on the physico-chemical environment and bacterioplankton function is not fully understood. In a relatively novel approach for freshwater systems, this study assesses Lake Michigan bacterial metabolism using robust transcriptomics techniques in the context of rich environmental data, including characterization of the lake chromophoric DOM and fluorescent DOM pool.