Benthic copepod guts as a selective microbial microhabitat in marine sediments

The gut microbiome of the benthic copepod Platychelipus littoralis, a key species in the intertidal mudflats of western Europe, was characterized throughout a 1 yr period. It was hypothesized that benthic copepods living in sediment would have core microbial taxa in their gut microbiome, in accordance with the gut microbiomes of pelagic copepods living in the water column, but that this community might change rapidly. Copepods were isolated from sediment, and after a starvation period, the guts were microdissected. The copepod gut was found to be a selective microbial microhabitat, significantly different in microbiome composition from the sediment, with lower species richness and evenness. Although microbial cell counts were low in copepod guts, the gut microbiome was stable between 24 and 48 h of egestion. Diatoms were the main food source of the copepods, as confirmed by fatty acid biomarkers. Core bacterial species in the gut belonged to Rhodobacteraceae, Flavobacteriaceae and Saprospiraceae, known as degraders of complex organic compounds. Bacteria were not a significant food source themselves, but core bacterial taxa were potentially involved in food-assisted degradation. This study elucidated bacteria-copepod interactions, relevant for the food web ecology of benthic systems and potentially the optimization of copepod culturing.