Freshwater bacteria are diverse and play an important role in the function of stream ecosystems. Yet interactions among different elements of freshwater microbial communities (e.g., pelagic, benthic, host-associated) are yet to be fully elucidated. Here we investigate the diversity, composition, and function of bacterial communities of stream water, stream epilithic biofilm, and the gut microbiome of a biofilm grazing fish, ayu (Plecoglossus altivelis). We aimed to determine if epilithic biofilm bacterial communities change due to the density and/or feeding behaviour of ayu and to determine the degree to which local biofilm bacterial communities shape the ayu gut microbiome.
Our study locations were two tributaries of Chikuma River, near Ueda, Nagano (Yodagawa and Sangawa). We sampled epilithic biofilm from stones with and without ayu feeding marks from several sites along a gradient of ayu density. Ayu were caught by local fishermen and the fecal matter sampled by squeezing the sides of the fish. We also sampled the water column bacterial community by filtering 1L of water (from the high density and ayu absent locations only). Bacterial metabarcoding of the 16S rRNA V4 region using primers 515F and 806R was performed by an external provider (GikenBio).
We detected a total of 3216 bacterial taxa. Water samples had the highest mean taxa richness (mean+-SD; 456.00 +- 78.1), followed by the ayu gut (294.10 +-  84.1) and biofilm (245.80 +- 76.3). The overall composition of these three communities was significantly different (p = 0.001). There were also significant differences in bacterial diversity (p = 0.0005) and composition (p = 0.001) of our two study streams. In Yodagawa, biofilm bacterial diversity tended to increase downstream (which were also the sites with higher ayu density), but only on stones without feeding marks (adjR2 = 0.119, p = 0.160). In both streams, biofilm bacterial diversity was significantly lower on stones that had ayu feeding marks (p = 0.0145). The ayu gut microbiome community differed significantly between fish from the two streams (p = 0.010) and was more diverse in fish from Sangawa (mean+-SD, 346.20+-72.7 compared to 224.80+-23.0, p = 0.008). Fish gut microbiome communities more closely resembled the environmental bacterial community of their river of residence (Sangawa – water and Yodagawa – biofilm, p = 0.006). Overall our results suggest that the feeding behaviour of ayu reduces the diversity of bacterial biofilm communities on stones and in turn contributes to the diversity of the ayu gut microbiome.