Ontogenetic variation in the gut microbiota of <i>Kyphosus sydneyanus</i> : a comparative analysis

Gut microbiota can be shaped by host-related (e.g., species, diet) and environmental (e.g., habitat, geography) factors. Gut microbiota of the herbivorous fish family Kyphosidae vary between individuals and gut sections and can be influenced by diet and geography. Temperate <i>Kyphosus sydneyanus</i> are abundant on rocky reefs of northeastern New Zealand, where adults mainly consume Phaeophyceae, whereas juveniles typically feed on Rhodophyta and Chlorophyceae. We compared the gut microbiota of <i>K. sydneyanus</i> adults and juveniles to investigate the relative effects of ontogeny versus diet on bacterial community composition. We used 16S rRNA gene amplicon sequencing and ddPCR quantification to determine the following: (i) ontogenetic variation in gut microbiota of <i>K. sydneyanus</i>, (ii) shared microbial taxa, and (iii) processes influencing bacterial community assembly, given the lack of vertical transmission. To further explore dietary effects, we also compared these data to the gut microbiota of adult <i>K. sectatrix</i>, which are rare tropical vagrants to northeastern New Zealand. Juvenile <i>K. sydneyanus</i> exhibited greater dietary similarity to <i>K. sectatrix</i> adults than conspecific adults. Overall, <i>K. sydneyanus</i> gut microbiota diversity increased with fish size, and <i>K. sydneyanus</i> adults had a more diverse gut microbiota than <i>K. sectatrix</i> adults. Estimated absolute abundances and community structure varied considerably across individuals. <i>K. sydneyanus</i> juveniles had relative abundances more similar to those from adult <i>K. sectatrix</i> than adult conspecifics. However, a comparison of amplicon sequence variants (ASVs) showed that juveniles of <i>K. sydneyanus</i> shared more ASVs with conspecific adults. This suggests that historical contingency and selection are important drivers of community assembly.IMPORTANCEMost marine animals undergo external fertilization (e.g., fish) and lack mechanisms for vertical transmission of gut microbiota. Consequently, host-related and environmental factors can play important roles in community assembly. The gut microbiota of the herbivorous marine fish family Kyphosidae varies between individual fish, host species, diet, and geographic location. Juvenile <i>Kyphosus sydneyanus</i> shared more dietary similarity with adult <i>K. sectatrix</i> than adult conspecifics. Comparing gut communities of juvenile and adult <i>K. sydneyanus</i> and adult <i>K. sectatrix</i> collected from the same locations differentiates some of the causal factors involved in bacterial community assembly. Results suggest that the host diet has a strong influence on bacterial diversity and composition. In addition, historical contingency and environmental selection play a significant role in shaping gut microbiota through host ontogeny.