Biology subjects

Chille, E. E.

Publications and source records attributed to Chille, E. E..

4 recordsLinked to original sources

bioRxiv2026

Multi-omics data of a weedy coral species from Ulithi Atoll (Micronesia) to investigate the impact of human disturbance on coral health and resilience

BackgroundCoral reefs are among the most biodiverse ecosystems on Earth yet face an increasing risk of collapse under climate change and intensifying anthropogenic pressures. Although there is strong evidence that stressors such as overfishing, sedimentation, and wastewater runoff can drive shifts in coral community structure, few studies have investigated the molecular mechanisms underlying these shifts. Integrating data across multiple layers of biological organization, from the genome to the proteome and metabolome, offers a powerful approach to understanding how coral physiology and resilience are impacted by human activities. FindingsHere, we present high-coverage whole genome sequencing (Montipora only) together with untargeted metabolomic and proteomic datasets from three coral genera (Acropora, Pocillopora, and Montipora) that inhabit Ulithi Atoll, Yap State, FSM. Ulithi Atoll is an ideal system for investigating how anthropogenic pressures influence coral molecular ecology and adaptation, with extensive historical ecological data available through the long-term research program of the One People One Reef collaborative to connect multi-omics data with macroecological trends. Following data cleaning and quality control, all datasets exhibited minimal technical variation among samples, providing a comprehensive baseline for future research on coral resilience across a mosaic of natural and anthropogenic stressors. ConclusionsThese data provide a resource for examining how anthropogenic pressures influence coral physiology and resilience across environmental gradients. They also allow the identification of biomarkers of chronic stress that may inform the development of point-of-care diagnostic tools for coral health and contribute to evidence-based reef conservation and management strategies.

genomics↗

bioRxiv2025

Metaproteome analysis of the coral holobiont demonstrates algal symbiont dampening under thermal stress

The accelerating loss of coral reefs worldwide due to anthropogenic climate change has led to a myriad of studies aimed at understanding the basis of coral resilience to support reef conservation. Here, we integrate physiological measurements with proteomic and metabolomic profiles to examine species-specific responses to increased temperature in three sympatric reef-building corals from the Great Barrier Reef: Acropora hyacinthus, Porites lobata, and Stylophora pistillata. We find species-specific stress response strategies with A. hyacinthus, a thermally sensitive species, exhibiting rapid decline in endosymbiont physiology, coupled with a one-third reduction in protein abundance. In contrast, P. lobata displayed a delayed physiological response to stress and a muted proteome response, suggesting greater resilience. S. pistillata initially showed minor shifts in the proteome followed by colony "bail-out". Overall, we observed markedly different responses in most biochemical pathways in the three coral species. Nonetheless, some known biomarkers of stress, including heat-shock proteins, showed conserved responses to thermal stress with differences in temporal abundance reflecting bleaching resistance. Our results underscore the species-specific nature of coral responses to thermal stress and highlight proteomic signatures associated with symbiosis breakdown, offering mechanistic insights into coral bleaching susceptibility and resilience.

microbiology↗

bioRxiv2021

Energetics but not development is impacted in coral embryos exposed to ocean acidification

In light of the chronic stress and mass mortality reef-building corals face under climate change, it is critical to understand the processes essential to reef persistence and replenishment, including coral reproduction and development. Here we quantify gene expression and size sensitivity to ocean acidification across a set of developmental stages in the rice coral, Montipora capitata. Embryos and swimming larvae were exposed to pH treatments 7.8 (Ambient), 7.6 (Low) and 7.3 (Xlow) from fertilization to 9 days post-fertilization. Embryo and larval volume, and stage-specific gene expression were compared between treatments to determine the effects of acidified seawater on early development. While there was no measurable size differentiation between fertilized eggs and prawn chips exposed to pH 7.8, 7.6, and 7.3, early gastrula and planula raised in reduced pH treatments were significantly smaller than those raised in ambient seawater, suggesting an energetic cost to developing under low pH. However, no differentially expressed genes emerged until 9 days post-fertilization. Notably, gene expression patterns of larvae developing at pH 7.8 and pH 7.3 were more similar than those developing at pH 7.6. Larvae from pH 7.6 showed upregulation of genes involved in cell division, regulation of transcription, lipid metabolism, and oxidative stress in comparison to the other two treatments. While low pH appears to increase energetic demands and trigger oxidative stress, the developmental process is robust to this at a molecular level, with swimming larval stage reached in all pH treatments. Summary statementThis developmental time series tracks the physiological and transcriptomic outcomes of early coral development under ambient pH (pH 7.8), and two low pH conditions (pH 7.6 and 7.3).

physiology↗

bioRxiv2021

Developmental series of gene expression clarifies maternal mRNA provisioning and maternal-to-zygotic transition in the reef-building coral Montipora capitata

BackgroundMaternal mRNA provisioning of oocytes regulates early embryogenesis. Maternal transcripts are degraded as zygotic genome activation (ZGA) intensifies, a phenomenon known as the maternal-to-zygotic transition (MZT). Here, we examine gene expression over nine developmental stages in the Pacific rice coral, Montipora capitata, from eggs and embryos at 1, 4, 9, 14, 22, and 36 hours-post-fertilization (hpf), as well as swimming larvae (9d), and adult colonies. ResultsWeighted Gene Coexpression Network Analysis revealed four expression peaks, identifying the maternal complement, two waves of the MZT, and adult expression. Gene ontology enrichment revealed maternal mRNAs are dominated by cell division, methylation, biosynthesis, metabolism, and protein/RNA processing and transport functions. The first MZT wave occurs from [~]4-14 hpf and is enriched in terms related to biosynthesis, methylation, cell division, and transcription. In contrast, functional enrichment in the second MZT wave, or ZGA, from 22 hpf-9dpf, includes ion/peptide transport and cell signaling. Finally, adult expression is enriched for functions related to signaling, metabolism, and ion/peptide transport. Our proposed MZT timing is further supported by expression of enzymes involved in zygotic transcriptional repression (Kaiso) and activation (Sox2), which peak at 14 hpf and 22 hpf, respectively. Further, DNA methylation writing (DNMT3a) and removing enzymes (TET1) peak and remain stable past [~]4 hpf, indicating that methylome programming occurs before 4 hpf. ConclusionsOur high-resolution insight into the coral maternal mRNA and MZT provides essential information regarding setting the stage for, and the sensitivity of, developmental success and parental carryover effects under increasing environmental stress.

developmental biology↗