Deterministic and stochastic processes influencing gut microbiome assembly in Pygoscelis papua penguins

This study uses a multi-kingdom metabarcoding framework to investigate algal DNA signatures in Gentoo penguin (Pygoscelis papua) guano as a proxy for combined dietary and environmental exposure. Pre-processed 18S phyloseq objects were analysed in R (v4.3.2) using packages including phyloseq, edgeR, vegan, and ggplot2. A dietary proxy (percent crustacean; Eumalacostraca) was derived from metazoan reads and incorporated into sample metadata.Algal communities were isolated by removing metazoan taxa and filtering low-abundance features. Community structure was assessed using Bray-Curtis distances and PERMANOVA (adonis2; 9,999 permutations; colony-stratified), with repeated rarefaction (≥250 and ≥500 reads) to evaluate sensitivity to sequencing depth. Ordination (PCoA) was used for visualisation. Taxon-level associations with dietary signal were tested using linear models with Benjamini-Hochberg correction.Results indicate weak but significant community-level associations with diet, alongside stronger taxon-specific responses, consistent with hybrid assembly driven by stochastic environmental effects and selective dietary filtering. Weak Mantel correlations between algal and bacterial communities suggest partially dependent structuring processes.