Foster, N. L. | Search bioRxiv

bioRxiv2026

A metagenomic exploration of the bacterial community composition of two deep-sea Pheronema carpenteri sponge aggregations from the North Atlantic; insights into ecosystem services

AimsSponge microbiomes have been extensively studied, in part due to their potential as sources of novel antimicrobials and other biologics, with most research focusing on Demosponges. Here, we investigate the Hexactinellid sponge Pheronema carpenteri, previously identified as a promising source of antibiotic-producing bacteria. MethodsUsing next-generation sequencing of bacterial 16S rRNA genes and a single sponge metagenome, we examined the composition of bacterial communities of P. carpenteri sponges recovered from the Porcupine Seabight, along with local water and sediment samples. ResultsOur results show that P. carpenteri harbours a microbiome abundant in Proteobacteria (47.1-59.4%) and Actinobacteria (11.5-27.5%), with consistent intra-aggregation similarities and structured intra-sponge communities. A metagenomic analysis revealed the presence of several nitrogen cycling genes (nirK, nosZ, nirS homologues of proteobacterial origin), supporting a suggestion that these sponges may play a role in nitrogen cycling, while biosynthetic gene clusters (BGCs) were limited (4 complete clusters). Notably, bacterial community structures within P. carpenteri aggregations resemble those observed in both low and high microbial abundance (LMA/HMA) sponges. ConclusionsHexactinellids are traditionally considered LMA sponges, so identifying species that deviate from this dichotomy provides new insights into sponge microbiome ecology. Integrating Hexactinellids into both culture-dependent and culture-independent studies will advance our broader understanding of sponge-associated microbial diversity and could inform biodiscovery programmes in marine environments. Impact StatementOur findings support the suggestion that a combination of culture-based and molecular analyses is required to generate a comprehensive picture of the biosynthetic potential of P. carpenteri sponges. We also reveal insights into the ecosystem services that sponge microbiomes may contribute towards. These observations could facilitate a deeper understanding of the biotechnological and environmental value of key marine resources.

microbiology↗

bioRxiv2019

A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses

Video and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has led to the development of personal, group, or institution level reference image catalogues of operational taxonomic units (OTUs) or morphospecies. Lack of standardisation among these reference catalogues has led to problems with observer bias and the inability to combine datasets across studies. In addition, lack of a common reference standard is stifling efforts in the application of artificial intelligence to taxon identification. Using the North Atlantic deep sea as a case study, we propose a database structure to facilitate standardisation of morphospecies image catalogues between research groups and support future use in multiple front-end applications. We also propose a framework for coordination of international efforts to develop reference guides for the identification of marine species from images. The proposed structure follows the Darwin Core standard to allow integration with existing databases. We suggest a management framework where high-level taxonomic groups are curated by a regional team, consisting of both end users and taxonomic experts. We identify a mechanism by which overall quality of data within a common reference guide could be raised over the next decade. Finally, we discuss the role of a common reference standard in advancing marine ecology and supporting sustainable use of this ecosystem.

ecology↗