Microbial community multi-omic analysis of marsh sediment following enrichment with crustacean shell compost

Nutrient availability influences microbial processes in natural environments, notably biogeochemical cycling and microbial community structure. Short-term, functional responses of microbial communities to nutrient pulses in coastal communities are not fully understood, especially in temperate environments undergoing climate driven changes. A 48-hour microcosm experiment was carried out in which paired metagenomic and metatranscriptomic sequencing was employed to elucidate how decomposition of chitin rich substrates, namely crab and lobster shell compost, alter salt marsh microbiome structure and function. Within 48 hours of amendment a notable shift in community function was observed, including increased chitin degradation, altered stress-response, and enhanced sporulation. These responses coincided with marked decreases in genes regulating key biogeochemical processes, including carbon fixation, sulfur oxidation and reduction, and other metabolic pathways. After addition of shell compost, changes in microbial community structure and increased incidence of virulence-associated genes were also observed, accompanied by measurable transcriptional activation, notably aerolysin A (aerA), which encodes the pore-forming exotoxin aerolysin. These results support shifts in both community composition and function in temperate salt marsh sediment microbiomes following chitin-rich nutrient addition. It is concluded that temperate coastal systems are sensitive to organic nutrient enrichment, with the potential for ecological and public-health relevant consequences. These effects may be particularly significant given chitin is among the most abundant and readily available bionutrients in aquatic ecosystems.