Application of Next-Generation Sequencing for the Determination of the Bacterial Community in the Gut Contents of Brackish Copepod Species (Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus)

SIMPLE SUMMARY: Copepods are important components of marine coastal food chains, supporting fishery resources by providing prey items mainly for fish. Copepods interact with small microorganisms via feeding on phytoplankton. DNA methods can determine the gut contents of copepods and provide important information regarding how copepods interact with phytoplankton and bacteria. In the present study, we designed a method for extracting the gut content DNA from small-sized copepods that are important in coastal and brackish areas. Based on DNA analyses, Rhodobacteraceae, which is common in marine waters and sediments, was most abundant in the gut contents of the three copepod species (Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus). However, the detailed composition of bacteria was different among species and locations. The results suggested that environmental variables and species-specific feeding behaviour can affect the gut bacterial community. The bacteria play an important role in digestion and in the overall degradation and release of metabolites to the outside water. Further analyses with advanced methods regarding DNA isolation from small microorganisms and identification skills using a DNA library for better understanding of biological interactions and matter cycling in marine food webs are required. ABSTRACT: The gut bacterial communities of copepods can affect metabolic processes, and consequently, their activity can be related to the release of organic substances to the environment. Hence, they are important for organic matter cycling in marine coast food webs. However, information regarding the variation in gut bacterial communities based on copepod species and environmental variations is limited. We analysed the differences in gut bacterial communities from dominant copepod species, i.e., Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus, in a brackish reservoir. The core bacteria among the copepod species and locations consisted of the following main operational taxonomic units (OTUs): Novosphingobium capsulatum and the family Rhodobacteraceae belonging to Alphaproteobacteria, which is abundant in seawater and freshwater aquatic ecosystems as a zooplankton-associated bacterial community. The bacterial community composition of each copepod (except the core species) showed high variability. The bacterial community diversity differed depending on the copepod species and the sites’ environmental conditions, especially salinity, e.g., compositional variations in the bacterial community of P. inopinus were high at sites with low salinity. Therefore, the gut bacterial community of each copepod species responds differently to the environment.