Gut Microbiota and Feeding Patterns of the Antarctic Fairy Shrimp (Branchinecta gaini Daday, 1910): A Metabarcoding Perspective

Understanding how feeding ecology and environmental conditions shape gut microbiota is essential for interpreting host–microbe interactions in extreme environments. Here, we investigated the diet and gut-associated bacterial communities of the Antarctic fairy shrimp Branchinecta gaini across multiple postglacial freshwater ponds on King George Island. We combined microscopic gut content analysis with 18 S and 16 S rRNA gene metabarcoding and distinguished between gut content and gut tract–associated bacterial fractions in pooled, pond-level samples to assess the relative roles of diet, host filtering, and environmental context in structuring gut-associated communities. Our results reveal pronounced dietary flexibility of B. gaini , with strong site-specific differences in consumed eukaryotic taxa reflecting local resource availability. This trophic variability was mirrored by highly variable gut-associated bacterial communities, characterized by low taxonomic overlap among ponds and the absence of a stable core microbiota at the pooled sample level. Although bacterial assemblages differed between gut contents and gut tract, consistent at the composite-sample scale, this pattern suggests limited evidence for strong host filtering. Gut-associated communities retained pond-specific signatures, indicating a dominant role of environmental sourcing. Environmental drivers influenced different aspects of gut microbiome organization: hydrological connectivity and associated conductivity gradients were linked to shifts in bacterial community composition, whereas water temperature showed a non-linear association with bacterial alpha diversity but not with overall community structure. Water pH showed no detectable effect on either metric. Together, these findings indicate that gut-associated bacterial communities of B. gaini , as captured by pooled samples, largely reflect environmentally acquired assemblages shaped by opportunistic feeding and local environmental filtering. This ecological flexibility may represent a key strategy enabling persistence of B. gaini across highly heterogeneous Antarctic freshwater ecosystems.