Metatranscriptomics reveals a shift in microbial community composition and function during summer months in a coastal marine environment

Abstract

Temperate coastal marine waters are often thermally stratified from spring through fall, but can be dynamic and disrupted by tidal currents and wind-driven upwelling. These mixing events introduce deeper, cooler water with a higher partial pressure of CO₂ (pCO₂), and its associated microbial communities to the surface. Anecdotally, there have been concerns that these changes in water quality as well as in microbial composition and activity may be involved in mass mortality events of Pacific oysters (Crassostrea gigas) on the East Coast of Vancouver Island, British Columbia. Therefore, improved understanding of the composition and microbial activity of marine waters associated with seasons and abiotic variables may be useful in managing these mortality events. To characterize both compositional and functional changes associated with abiotic factors, here we generate a reference metatranscriptome from the Strait of Georgia over the representative seasons and analyze metatranscriptomic profiles of the microorganisms present within intake water containing different pCO₂ levels at a shellfish hatchery in British Columbia from June through October. Abiotic factors studied include pH, temperature, alkalinity, aragonite, calcite and pCO₂. Community composition changes were observed to occur at broad taxonomic levels, and most notably to vary with temperature and pCO₂. Functional gene expression profiles indicated a strong difference between early (June-July) and late summer (August-October) associated with viral activity. The taxonomic data suggests this could be due to the termination of cyanobacteria and phytoplankton blooms by viral lysis in the late season. Functional analysis indicated fewer differentially expressed transcripts associated with abiotic variables (e.g., pCO₂) than with the temporal effect. Microbial composition and activity in these waters varies with both short-term effects observed alongside abiotic variation as well as long-term effects observed across seasonal changes, as captured in the samples analyzed here. The analysis of both taxonomy and functional gene expression simultaneously in the same samples (i.e., metatranscriptomics) provided a more comprehensive view for monitoring water bodies than either would in isolation.