Microbial Diversity | del Campo Lab - Microbial Ecology and Evolution

Marine animal microbiomes

Sun, 30 Jun 2024 00:00:00 +0000

We study the microbial communities associated with marine model organisms, combining metabarcoding, genomics, and transcriptomics to understand how microbiomes contribute to host physiology and the broader ocean carbon cycle.

Biomineralisation in the Gulf Toadfish microbiome

Marine teleost fish precipitate CaCO₃ in their intestines as part of their osmoregulatory strategy, a process that may account for up to 15% of total calcium carbonate deposition in the ocean. Despite its significance, the molecular mechanisms driving this reaction remain unknown — no candidate genes have been identified in the fish genome or transcriptome of the Gulf Toadfish (Opsanus beta), the primary model for studying this process.

We are testing the hypothesis that gut microbiota — rather than the fish itself — are responsible for intestinal carbonate precipitation. Bacteria are well-established agents of calcium carbonate deposition in marine environments, and their role in analogous processes (such as kidney stone formation) has been documented in mammals. Using a combination of 16S/18S metabarcoding, metagenomics, and transcriptomics, we are characterising the microbial communities of the toadfish gut and identifying candidate bacteria driving CaCO₃ deposition. Understanding this process is critical for accurate modelling of ocean carbon dynamics and for exploring marine microbiome-based carbon sequestration strategies.

Key publications

Oehlert AM, Garza J, Nixon S, et al., including Javier del Campo & Grosell M (2024). Implications of dietary carbon incorporation in fish carbonates for the global carbon cycle. Science of the Total Environment, 916, 169895.

Preprint: Symbiotic bacteria support calcium carbonate precipitation in the Gulf Toadfish gut. bioRxiv (2025).

The microbiome of the California sea hare

Photo by Elizabeth Whitson

The California sea hare, Aplysia californica, is a well-studied model organism in neurobiology and neuroscience. Despite deep knowledge of its physiology, anatomy, and ethology, little is known about its microbiome. In collaboration with the National Resource for Aplysia at the Rosenstiel School of Marine and Atmospheric Science, we are exploring for the first time the prokaryotic and microeukaryotic communities associated with this organism using a genomic, metabarcoding approach. These data will allow us to investigate how the microbiome influences behaviour, ageing, and other characteristics of this important model animal.

The Montseny Brook Newt microbiome

Tue, 28 Sep 2021 00:00:00 +0000

Chytridiomycosis has already caused the disappearance of more than 200 amphibian species around the planet. These diseases — caused by chytrid fungi and exacerbated by climate change, globalisation, and the exotic pet trade — are predicted to drive many more amphibian populations to extinction in the coming years.

Calotriton arnoldi, the Montseny Brook Newt, is the only European salamander classified as Critically Endangered by the IUCN and the most threatened amphibian in Europe. Described in 2005, it is known only from a handful of mountain streams in the Montseny Natural Park (Catalonia), with an occupation area of just 10 km². A recent outbreak of the chytrid fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal) in the Montnegre i el Corredor Natural Park, just 15 km south of Montseny, poses a direct and imminent threat to this species.

Our goal is to identify bacterial candidates from C. arnoldi’s skin microbiome that could serve as probiotics under a bioaugmentation strategy to fight Bsal infection. We compare the microbiomes of C. arnoldi with those of Triturus marmoratus and Salamandra salamandra individuals associated with disease resistance. Based on these comparisons, we will isolate bacteria from skin swab samples and screen them for antifungal activity against Bsal cultures, building a collection of candidate probiotics to protect this critically endangered newt.

PR2 — A reference 18S rRNA sequence database

Wed, 27 Apr 2016 00:00:00 +0000

The PR2 database was initiated in 2010 in the frame of the BioMarks project, building on work developed over the previous decade in the Plankton Group at the Station Biologique de Roscoff. Its aim is to provide a reference database of carefully annotated 18S rRNA sequences using eight unique taxonomic fields (from kingdom to species). It currently contains over 184,000 sequences, with metadata fields including geo-localisation, culture or environmental origin, host type, and more.

Annotation of PR2 is performed by experts from each taxonomic group. An important partner in this effort is EukRef, which has merged its bioinformatics pipelines and workshop-based curation efforts with PR2. EukRef has built tools used during multiple workshops dedicated to specific taxonomic groups, including ciliates, choanoflagellates, and others.

Key publications

Laure Guillou et al. (2013). The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Research.

Javier del Campo et al. (2018). EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. PLOS Biology.

Issues and contributions

Report issues or contribute on GitHub.