Biology subjects

Croquer, A.

Publications and source records attributed to Croquer, A..

6 recordsLinked to original sources

bioRxiv2026

Genomic characterization reveals high clonal redundancy in two Acropora cervicornis nurseries in the Dominican Republic

Acropora cervicornis is often propagated through fragmentation (i.e., clonal propagation), a common practice implemented by restoration projects. Known as asexual propagation, this strategy may rapidly increase coral cover but reduces genetic variation. We used 2b-RAD sequencing to characterize multilocus genotypic variation among 45 A. cervicornis colonies maintained in two in-situ nurseries (Cap Cana, Acuario) in Punta Cana, Dominican Republic. After reference-based SNP discovery and filtering, 2,515 high-quality SNPs were retained in the dataset. Principal coordinate analysis (PCoA), hierarchical clustering, identity-by-state (IBS) distances, and relatedness estimates identified only three multilocus genets among the 45 colonies (AC1, AC2, and AC3). Of these, AC2 was the most abundant (n = 23; 51.1%), followed by AC3 (n = 14; 31.1%) and lastly AC1 (n = 8; 17.8%). Within-genet IBS distances (0.153-0.227) did not overlap with between-genet distances (0.406-0.497). AC1 and AC2 were detected in both nurseries, whereas AC3 was limited to Acuario. These results reveal substantial clonal redundancy among sampled nursery colonies that determines local reef conservation efforts. These data highlight the value of incorporating genotype identification in nursery-based coral restoration projects.

ecology↗

bioRxiv2026

Proteomic analysis of Stony Coral Tissue Loss Disease demonstrates coral-algal dysbiosis during disease progression

Stony Coral Tissue Loss Disease (SCTLD) has devastated Caribbean reefs, yet the host molecular response to infection is poorly understood. Previous gene expression studies of diseased corals identified shifts in the immune response, apoptosis, and coral-algal dysbiosis. Here, we characterized the proteomic response of Diploria labyrinthiformis to SCTLD by comparing protein abundance in healthy tissue from uninfected colonies and apparently healthy and neighboring diseased tissue from infected colonies. These results were compared with existing metagenomic data from the same samples that previously demonstrated significant shifts in the coral microbiome due to SCTLD. We identified 480 differentially abundant proteins when comparing diseased lesion and healthy tissues, but only 12 between apparently healthy and healthy tissues. Pathway-level analysis provides evidence of immune suppression in apparently healthy tissue, suggesting that host molecular responses precede visible disease progression. Diseased lesion tissues showed wound-healing responses combined with a decreased abundance of proteins involved in symbiosome maintenance and increased oxidative stress responses, consistent with host-algal dysbiosis. This result correlates with the previous metagenomic analysis of these samples which found that infected colonies exhibit distinct algal symbiont communities dominated by Symbiodinium necroappetens, whereas healthy colonies are dominated by Durusdinium trenchii and Breviolum spp. Comparison with existing transcriptomic studies revealed both shared and distinct molecular responses, underscoring the importance of integrating multi-omics approaches to understand coral diseases. Our results suggest that SCTLD in D. labyrinthiformis is associated with early immune suppression, coral-algal dysbiosis, oxidative stress, and subsequent wound-healing responses.

ecology↗

bioRxiv2025

Stony coral tissue loss disease (SCTLD) destabilizes the coral microbiome

Stony coral tissue loss disease (SCTLD) is a rapidly spreading lethal coral disease, the etiology of which remains poorly understood. In this study, using deep metagenomic sequencing, we investigate microbial and viral community dynamics associated with SCTLD progression in the Caribbean stony coral Diploria labyrinthiformis. We assembled 264 metagenome-assembled genomes (MAGs) and correlated their abundance with disease phenotypes, revealing significant shifts in both the prokaryotic microbiome and virome. Our results provide clear evidence of microbial destabilization in diseased corals, suggesting that microbial dysbiosis is an outcome of SCTLD progression. We identified DNA viruses that increase in abundance in infected corals and are present in SCTLD-affected corals at other sites. In addition, we identify the first putative instance of asymptomatic/resistant SCTLD-affected colonies, suggesting potential microbial induced resilience (i.e., beneficial microbiome). Finally, we propose a mechanistic model of SCTLD progression, in which viral dynamics may contribute to a microbiome collapse. These findings provide novel insights into SCTLD pathogenesis and offer consistent molecular signals of disease across diverse geographic sites, presenting new opportunities for disease monitoring and mitigation.

microbiology↗

bioRxiv2020

Status of the pillar coral Dendrogyra cylindrus in Los Roques National Park, Southern Caribbean

Information on the status of the pillar coral Dendrogyra cylindrus across its global distribution range is needed to plan and implement effective conservation interventions at both the national and regional level. Knowledge on the species distribution and abundance on the southernmost edge of its range was limited to qualitative data gathered in the 1980s. In 2014, we started using local ecological knowledge and extensive surveys to assess the status of the pillar coral in Archipelago Los Roques National Park, Venezuela; also evaluating the species representativeness within the MPA according to the level of protection established by the parks zoning. Between 2014 and 2016, we recorded over 1,000 colonies-the highest abundance reported to date for the species- within 14 different habitat types. Disease, bleaching and partial mortality prevalence were below 4%. Size frequency distribution was uni-modal for the MPA and dominated by medium size colonies (40cm -70cm height) suggesting potential for intrinsic population growth. However, the structure of size classes varied among reefs (Pseudo-F=2.70, p=0.03), indicating asynchronous dynamics mostly driven by reef-scale processes. Overall, our results indicate that Los Roques could be a stronghold for the species. But, to maintain the conservation value for coral reefs and the pillar coral, the MPAs zoning designation needs to be urgently revised and the extension of its high-protection zones expanded to increase habitat redundancy as well as the singular habitats composed by thickets of Acropora cervicornis and mounds of Madracis sp. This work confirms the species as extant in one of the four localities within its national range in Venezuela. However, further research on genetic diversity and connectivity among reefs within the MPA is needed to estimate effective population size and assess viability.

ecology↗

bioRxiv2019

Transects, quadrats, or points? What is the best combination to get a precise estimation of a coral community?

The characteristics of coral reef sampling and monitoring are highly variable, with numbers of units and sampling effort varying from one study to another. Numerous works have been carried out to determine an appropriate effect size through statistical power, however, always from a univariate perspective. In this work, we used the pseudo multivariate dissimilarity-based standard error (MultSE) approach to assess the precision of sampling scleractinian coral assemblages in reefs of Venezuela between 2017 and 2018 when using different combinations of number of transects, quadrats and points. For this, the MultSE of 36 sites previously sampled was estimated, using four 30m-transects with 15 photo-quadrats each and 25 random points per quadrat. We obtained that the MultSE was highly variable between sites and is not correlated with the univariate standard error nor with the richness of species. Then, a subset of sites was re-annotated using 100 uniformly distributed points, which allowed the simulation of different numbers of transects per site, quadrats per transect and points per quadrat using resampling techniques. The magnitude of the MultSE stabilized by adding more transects, however, adding more quadrats or points does not improve the estimate. For this case study, the error was reduced by half when using 10 transects, 10 quadrats per transect and 25 points per quadrat. We recommend the use of MultSE in reef monitoring programs, in particular when conducting pilot surveys to optimize the estimation of the community structure.

ecology↗

bioRxiv2018

Analysis of 50 years of coral disease research visualized through the scope of network theory

Coral disease research encompasses five decades of undeniable progress. Since the first descriptions of anomalous signs, we have come to understand multiple processes and environmental drivers that interact with coral pathologies. To gain a better insight into the knowledge we already have, we explored how key topics in coral disease research have been related to each other using network analysis. We reviewed 719 papers and conference proceedings published from 1965 to 2017. From each study, four elements determined our network nodes: 1) studied disease(s); 2) host genus; 3) marine ecoregion(s) associated with the study site; and 4) research objectives. Basic properties of this network confirmed that there is a set of specific topics comprising the majority of research. The top five diseases, genera, and ecoregions studied accounted for over 48% of the research effort in all cases. The community structure analysis identified 15 clusters of topics with different degrees of overlap among them. These clusters represent the typical sets of elements that appear together for a given study. Our results show that while some coral diseases have been studied considering multiple aspects, the overall trend is for most diseases to be understood under a limited range of approaches, e.g. bacterial assemblages have been considerably studied in Yellow and Black band diseases while immune response has been better examined for the aspergillosis-Gorgonia system. Thus, our challenge in the near future is to identify and resolve potential gaps in order to achieve a more comprehensive progress on coral disease research.

ecology↗