First metabarcoding characterization of seabird guano microbiomes along the Peruvian coast: environmental filtering shapes taxonomically simplified but functionally stable communities

Abstract

Seabird guano from the islands off the Peruvian coast constitutes an organic fertilizer resource of recognized strategic importance; however, the microbial communities associated with this substrate had remained entirely uncharacterized. The present study provides the first comprehensive, cultureindependent characterization of bacterial and fungal communities in guano collected from 13 guanoproducing zones along the Peruvian coastline, encompassing deposits from the Guanay cormorant (Leucocarbo bougainvillii) and the Peruvian booby (Sula variegata), the two dominant and representative guano-producing bird species. Using 16S rRNA and ITS amplicon metabarcoding, combined with physicochemical analysis and functional prediction through FAPROTAX, and FUNGuild, we found that bacterial communities were consistently dominated by Bacillota (> 90%), particularly the order Bacillales, with halotolerant and endospore-forming genera, among which Saccharomonospora was notably abundant; this genus exhibited the strongest positive correlation with potassium content (+ 0.80, p 95%), with Aspergillus as the only genus showing a significant positive differential-abundance signal in Guanay cormorant guano relative to Peruvian booby guano. Within this exploratory framework, although the overall composition of bacterial and fungal communities did not differ significantly between the two bird species, differential abundance analysis identified specific bacterial taxa, including Pseudomonas, Atopostipes, and Lentibacillus, as significantly enriched in Guanay cormorant guano, revealing microbial differences that, while subtle, are ecologically relevant across host species. The predicted functional profile suggested a broadly stable metabolic repertoire oriented towards organic matter mineralization and nitrogen transformation across samples. These findings provide a first microbiological baseline for the evidence-based management of Peruvian island guano as a sustainable biofertilization resource.