Lake or river: environment shapes the ecological adaptation at the level of gene expression in two populations of the freshwater bivalve Diplodon chilensis

Climate change and human impact strongly alter the conditions in fresh water habitats in the Patagonian Andes. We performed in-situ transcriptomics of the freshwater mussel Diplodon chilensis, using Illumina to understand its ecological niche adaptation. This aims at further establishing the use of Diplodon as sentinel organism in environmental change studies. Differential gene expression patterns of 265 identifiable genes across seasonal samples from Paimun lake and Chimehuin river (Northern Patagonia, Argentina) indicated adaptations to different habitats in lake and river to have stronger effects on gene regulation than seasonal change. Seasonal difference in gene regulation were higher in river than in lake bivalves (84 vs. 38 sequences), with strongest effects in the summer reproductive season. Three major categories of differentially expressed genes included growth, metabolic pathway, and immune system/parasite defense genes. Whereas genes upregulated in deep layer lake bivalves support survival under critical conditions of hypoxic episodes, seasonal food availability, and parasite defense, river bivalves invest more strongly into vital ecological processes and display marked seasonal reproduction and growth. The alternative mitochondrial oxidase (AOX) was differentially expressed between sites whereas cytochrome oxidase activity was uniform, pointing at the importance of hypoxia and ecological tolerance in these abundant freshwater mussels. Based on our approach with a minimal number of individuals (three) per site and season, we perceive in situ transcriptomics as the preferred way over hypothesis driven qPCR with preselected genes, to analyze ecological adaptation and stress response in natural mussel populations.