Biology subjects

van Oppen, M. J.

Publications and source records attributed to van Oppen, M. J..

7 recordsLinked to original sources

bioRxiv2026

Diverse H2O2-scavenging phenotypes of coral-associated bacteria reveal candidates for bleaching mitigation

There is growing interest in manipulating coral-associated bacteria to enhance coral thermal bleaching tolerance. Reactive oxygen species (ROS), particularly hydrogen peroxide (H2O2), are major drivers of coral bleaching, therefore, coral-associated bacteria capable of scavenging H2O2 may help reduce bleaching. Bacterial candidates are commonly selected through genome inference and occasionally phenotypic assays, but how well these approaches predict H2O2-scavenging capacity is unknown. We screened 29 bacterial strains isolated from the scleractinian corals Acropora loripes and Galaxea fascicularis for genome-inferred H2O2-scavenging pathways and in vitro activity using an ABTS radical-scavenging assay, H2O2 tolerance (the highest H2O2 concentration that allows bacterial growth), H2O2 removal from the medium, and qualitative catalase activity. Although all strains encoded at least two complete H2O2-scavenging pathways, genomic prediction did not consistently align with in vitro scavenging activity. Growth under H2O2 exposure was strongly coupled with H2O2 scavenging, but these traits showed no correlation with ABTS inhibition or catalase activity inferred from bubble formation. The top-ranked phenotypes, based on H2O2 tolerance and scavenging, were observed in Roseovarius, Roseibium, Ruegeria, and Muricauda strains, which tolerated 5-50 mM H2O2. These genera are common associates of microalgae, including coral endosymbionts, which are key sources of excess ROS during thermal stress. Among these, Roseovarius and Muricauda also showed high ABTS inhibition (>97%), indicating broader antioxidant capacity that may be advantageous within the complex oxidative environment of thermally stressed corals. Strains combining strong H2O2 scavenging with broad antioxidant activity may therefore represent the most promising candidates for subsequent validation within the coral holobiont.

microbiology↗

bioRxiv2026

Rapid thermal adaptation in coral photosymbionts draws on standing variation and recombination

Bleaching tolerance in corals depends in part on the thermal tolerance of their microalgal symbionts. Laboratory evolution has increased the thermal tolerance of the symbiont Cladocopium proliferum in ~120 generations, but the genetic basis of that response was unknown. We compared single nucleotide polymorphisms in transcriptomes of three heat-evolved C. proliferum strains and one wild-type (unselected) strain from the same progenitor. We found 15,640 polymorphic loci, but no variant was both private to a strain and consistent across its replicates, which indicates that new mutations contributed little to the response in expressed sequences. Instead, allele frequencies at 350 loci differed significantly between strains, and linkage patterns indicated recombination had occurred within scaffolds both before and after the strains were separated. Selection and recombination of variation already present in the progenitor therefore underpinned the rapid thermal adaptation. Experimental evolution for reef restoration should start from genetically diverse cultures rather than single cell isolates.

evolutionary biology↗

bioRxiv2025

Genomic prediction of symbiotic interactions between two Endozoicomonas clades and their coral host, Acropora loripes

BackgroundThe bacterial genus Endozoicomonas is a predominant member of the coral microbiome, widely recognised for its ubiquity and ability to form high-density aggregates within coral tissues. Hence, investigating its metabolic interplay with coral hosts offers critical insights into its ecological roles and contributions to coral health and resilience. ResultsUsing long- and short-read whole-genome sequencing of 11 Endozoicomonas strains from Acropora loripes, genome sizes were found to range between 5.8 and 7.1 Mbp. Phylogenomic analysis identified two distinct clades within the family Endozoicomonadaceae. Metabolic reconstruction uncovered clade-specific pathways, including the degradation of holobiont-derived carbon and lipids (e.g., galactose, starch, triacylglycerol, D-glucuronate), latter of suggest involvement of Endozoicomonas in host sex-type steroid hormone metabolism. A clade-specific type 6 Secretion System (T6SS) and predicted effector molecules were identified, potentially facilitating coral-bacterium symbiosis. Additionally, genomic analyses revealed diverse phosphorus acquisition strategies, implicating Endozoicomonas in holobiont phosphorus cycling and stress responses. ConclusionsThis study reveals clade-specific genomic signatures of Endozoicomonas supporting its mutualistic lifestyle within corals. Findings suggests possible roles in nutrient cycling, reproductive health, and stress resilience, offering novel insights into coral holobiont functioning and potential strategies for reef restoration.

genomics↗

bioRxiv2024

Differential aggregation patterns of Endozoicomonas within tissues of the coral Acropora loripes

Bacteria in the genus Endozoicomonas are well-known coral symbionts commonly found as clusters within tissues of several coral species. Mapping the spatial distribution of these microbial communities is critical to gaining a holistic understanding of the potential role they may play within the coral host. This study focuses on characterising bacterial aggregates associated with the common reef-building coral, Acropora loripes, from the central Great Barrier Reef, Australia. A conventional cultivation-based method was employed to establish a pure culture collection of 11 undescribed Endozoicomonas strains isolated from A. loripes. Subsequent 16S rRNA gene sequence analysis revealed their classification into two distinct phylogenetic clades. To resolve their spatial distribution in hospite, clade-specific fluorescence in situ hybridisation probes were designed. Aggregates were consistently observed in the gastrodermal tissue layers surrounding the upper and lower gastrovascular cavity and were predominantly formed by cells from the same phylogenetic clade, with a minor proportion of aggregates formed by Endozoicomonas from both targeted clades. Furthermore, a clear distinction in aggregation pattern was observed; one clade exhibited clusters with regular and contained growth patterns, whereas the other formed clusters lacking clear boundaries and having irregular shapes. Scanning electron microscopy revealed the presence of a membrane of unknown origin associated with bacterial aggregates in two instances, suggesting potential structural or functional differences in these aggregates. These contrasting morphological features underscore the need for comprehensive investigations into the underlying mechanisms governing bacterial aggregate formation in corals.

ecology↗

bioRxiv2022

Flow cytometry-based biomarker assay for in vitro identification of heat tolerance conferring coral symbionts

Corals tolerance to high temperature stress largely depends on their symbiotic microalgae (Symbiodiniaceae). However, the contributing microalgal traits are largely unclear. Here we compare the in vitro cellular profiles of seven Cladocopium C1acro microalgal strains (derived from the same ancestral strain) during a four-week exposure to 27{degrees}C or 31{degrees}C. One was an unselected wild-type strain (WT), three were selected at 31{degrees}C for nine years and shown to confer thermal tolerance on the coral host (SS+) and three others were similarly selected but did not confer tolerance (SS-). Flow cytometry was used to measure the intracellular stress indicators reactive oxygen species (ROS), reduced glutathione (rGSH) and mitochondrial-membrane potential ({Delta}{Psi}m), as well as cell size/shape and photosynthetic pigments. Cell densities and photosynthetic efficiency ({Phi}PSII, Fv/Fm) were also measured. WT showed the highest levels of intracellular ROS and {Delta}{Psi}m, lowest rGSH and largest cell sizes at both temperatures. SS+ strains had the lowest ROS and highest rGSH values and a unique pattern of correlations among parameters at 31{degrees}C. Our results support previous reports implicating the role of microalgal ROS, {Delta}{Psi}m and rGSH in holobiont thermal tolerance and suggest flow cytometry is a useful pre-screening tool for identifying microalgal strains with enhanced thermal tolerance.

microbiology↗

bioRxiv2020

Cryptic diversity masks ecologically distinct coral species on tropical reefs

Coral reefs are the epitome of species diversity, yet the number of described scleractinian coral species, the framework-builders of coral reefs, remains moderate by comparison. DNA sequencing studies are rapidly challenging this notion by exposing a wealth of undescribed diversity, but the evolutionary and ecological significance of this diversity remains largely unclear. Here, we present an annotated genome for one of the most ubiquitous corals in the Indo-Pacific (Pachyseris speciosa), and uncover through a comprehensive genomic and phenotypic assessment that it comprises morphologically indistinguishable, but ecologically divergent cryptic lineages. Demographic modelling based on whole-genome resequencing disproved that morphological crypsis was due to recent divergence, and instead indicated ancient morphological stasis. Although the lineages occur sympatrically across shallow and mesophotic habitats, extensive genotyping using a rapid diagnostic assay revealed differentiation of their ecological distributions. Leveraging "common garden" conditions facilitated by the overlapping distributions, we assessed physiological and quantitative skeletal traits and demonstrated concurrent phenotypic differentiation. Lastly, spawning observations of genotyped colonies highlighted the potential role of temporal reproductive isolation in the limited admixture, with consistent genomic signatures in genes related to morphogenesis and reproduction. Overall, our findings demonstrate how ecologically and phenotypically divergent coral species can evolve despite morphological stasis, and provide new leads into the potential mechanisms facilitating such divergence in sympatry. More broadly, they indicate that our current taxonomic framework for reef-building corals may be scratching the surface of the ecologically relevant diversity on coral reefs, consequently limiting our ability to protect or restore this diversity effectively.

evolutionary biology↗

bioRxiv2020

Development of a free radical scavenging probiotic to mitigate coral bleaching

Corals are colonized by symbiotic microorganisms that exert a profound influence on the animals health. One noted symbiont is a single-celled alga (from the family Symbiodiniaceae), which provides the coral with most of its fixed carbon. During thermal stress, hyperactivity of photosynthesis results in a toxic accumulation of reactive oxygen species (ROS). If not scavenged by the antioxidant network, ROS may trigger a signaling cascade ending with the coral host and algal symbiont disassociating; this process is known as bleaching. Our goal was to construct a probiotic comprised of host-associated bacteria able to neutralize free radicals such as ROS. Using the coral model, the anemone Exaiptasia diaphana, and pure bacterial cultures isolated from the model animal, we identified six strains with high free radical scavenging ability belonging to the families Alteromonadaceae, Rhodobacteraceae, Flavobacteriaceae, and Micrococcaceae. In parallel, we established a "negative" probiotic consisting of genetically related strains with poor free radical scavenging capacities. From their whole genome sequences, we explored genes of interest that may contribute to their potential beneficial roles, which may help facilitate the therapeutic application of a bacterial probiotic. In particular, the occurrence of key pathways that are known to influence ROS in each of the strains has been inferred from the genomes sequences and are reported here. IMPORTANCECoral bleaching is tightly linked to the production of reactive oxygen species (ROS), which accumulates to a toxic level in algae-harboring host cells leading to coral-algal dissociation. Interventions targeting ROS accumulation, such as the application of exogenous antioxidants, have shown promise for maintaining the coral-algal partnership. With the feasibility of administering antioxidants directly to corals being low, we aim to develop a probiotic to neutralize toxic ROS during a thermal stress event. This probiotic can be tested with corals or a coral model to assess its efficacy in improving coral resistance to environmental stress.

bioengineering↗