MEPS prepress abstract   -  DOI: https://doi.org/10.3354/meps14800

ABSTRACT: The gut microbiome of the benthic copepod Platychelipus littoralis, a key species in 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 this community might change rapidly. Copepods were isolated from sediment, and after a starvation period, 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. The main food source of the copepods were diatoms, as was confirmed by fatty acid biomarkers. Core bacterial species of 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.