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Lookup NU author(s): Abbie Affleck, Dr Theresa RuegerORCiD
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
© 2026 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd. Microbial symbionts influence ecological and evolutionary processes in their multicellular hosts; yet they remain poorly characterised in marine systems. Sponges host exceptionally diverse microbiomes, potentially providing rich microbial reservoirs for their residents. The tusked goby (Risor ruber), an obligate sponge-dweller, and its sponge hosts provide an ideal model to investigate the causes and consequences of shared microbial taxa in host–resident systems. Using 16S rRNA sequencing, we characterised the microbiomes of R. ruber skin and gut, their sponge hosts, a non-obligate, sponge-associated goby (Elacatinus prochilos) and seawater. We quantified microbial overlap among hosts, examined ontogenetic patterns of shared microbiomes across goby body size and assessed the putative ecological benefits of shared microbial taxa for R. ruber. We reveal more than 500 microbial ASVs shared between R. ruber and their sponge hosts. The unique microbial overlap between R. ruber and their sponge hosts far exceeded overlap with E. prochilos and seawater. Shared taxa are putatively linked to nutrient acquisition, vitamin biosynthesis and pathogen defence, suggesting potential benefits for R. ruber from inhabiting microbially rich sponges. The proportion of the shared microbiome between R. ruber gut and sponges declines with goby body size, which suggests that the goby may undergo ontogenetic changes in diet or gut development. Thus, sponges provide more than shelter: they may function as microbial reservoirs and nutritional sources for residents. These findings underscore the need to protect microbially rich habitats and further study host–resident microbial interactions in marine systems and beyond.
Author(s): Bunholi IV, Affleck A, Johnson K, Ortega R, Freeman CJ, Rueger T, Casey JM
Publication type: Article
Publication status: Published
Journal: Molecular Ecology
Year: 2026
Volume: 35
Issue: 16
Online publication date: 20/08/2026
Acceptance date: 12/08/2026
Date deposited: 01/09/2026
ISSN (print): 0962-1083
ISSN (electronic): 1365-294X
Publisher: John Wiley and Sons Inc.
URL: https://doi.org/10.1111/mec.70523
DOI: 10.1111/mec.70523
Data Access Statement: All related metadata and code are available on GitHub https://github.com/Bunholi/Risor_Sponge_Microbiome. Raw sequence reads are deposited to NCBI SRA BioSample Project PRJNA1333385 under accession numbers from SAMN51794804 to SAMN51794936. This research was conducted in the Caribbean in compliance with relevant national regulations and consistent with the principles of the Convention on Biological Diversity and the Nagoya Protocol. Collaborations with regional researchers ensured that local ecological knowledge and context informed study design, fieldwork and data interpretation. Student co-authors from a local academic institution contributed to specimen collection and identification and were included to promote capacity building and strengthen regional expertise in marine science. Research findings will be made publicly available through open-access databases, contributing to both local and global understanding of host-resident interactions in marine systems.
PubMed id: 42622370
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