Coral and Marine Ecosystems Studies

This paper introduces RootPainter, an interactive machine learning tool for marine image analysis, demonstrating its accuracy and efficiency in measuring sponges in underwater images.

This study uses a process-based model to show that environmental fluctuations and conspecific density-dependence, not species interactions, drive coral reef fish community dynamics.

This paper develops a coral disease risk forecasting system using ecological and environmental data to predict disease risk in coral reefs, showing improved accuracy compared to previous systems.

This study investigates whether changes in gene body methylation (GBM) correlate with gene expression plasticity in corals during heat acclimatization, finding no significant association.

This study examines transcriptomic responses to sediment stress in branching and massive corals across different locations, finding species-specific and morphological differences in gene expression.

This study measures calcification and productivity in mesophotic reefs to assess their response to carbonate chemistry variability.

This study identifies a vertically transmitted, tissue-associated bacterial symbiont in the coral Pocillopora acuta, providing insights into its genomic features and potential benefits to the host.

The paper identifies a Philaster sp. parasite responsible for mass mortality of sea urchins across the Caribbean and Mediterranean, showing its rapid global spread and potential for long-range transmission.

This study analyzes the diversity and functional potential of chlamydiae associated with cnidarians using metabarcoding and metagenome-assembled genomes, revealing an obligate intracellular lifestyle and lack of unique genes.

This paper predicts the spatio-temporal distribution of deep-sea coral and sponge microbiomes using environmental, host, and microbiome data across 214 years.

This study examines how coral hosts, symbiotic algae, and bacteria respond to daily temperature fluctuations and continuous warming, finding that diurnal fluctuations may reduce heat stress and bacterial response changes.

The paper shows that DNA from non-viable bacteria can bias diversity estimates in corals, using PMA treatment to distinguish viable from non-viable DNA.

The paper synthesizes data to show herbivore biomass affects benthic condition and that management actions can increase parrotfish biomass, supporting herbivore management for reef resilience.

The paper analyzes genetic variation and reproductive strategies in two sympatric Hawaiian coral species, finding one is strictly sexual and the other predominantly asexual with triploid clades.

This study examines how thermal stress affects gene expression across different life stages of corals, finding stage-specific responses that may influence adaptation to climate change.

The paper shows that glucose from symbiotic algae supports nitrogen assimilation in Aiptasia, enabling survival in nutrient-poor environments.

The paper identifies SNVs in coral sperm and somatic tissue, suggesting lifelong stem cell renewal and lineage selection in corals.

This study shows that thermal preconditioning in corals enhances antioxidant defenses via BI-1 regulation of GR, reducing oxidative DNA damage during heat stress.

This study uses RNA-seq to analyze the physiological responses of Porites lobata to fragmentation and outplanting, revealing rapid wound regeneration and growth phases with specific metabolic and stress responses.

This paper presents the first draft reference genome of the mustard hill coral, Porites astreoides, using long-read sequencing and provides functional annotations to support comparative genomic studies and coral conservation efforts.

This study uses DNA barcoding to identify coral species in aquarium collections, finding that 44% could be identified to species level and 80% provisionally, highlighting biases in reference databases.

The paper investigates Symbiodiniaceae cell density in two black coral species from Madagascar using microscopy and molecular methods, finding low densities and suggesting antipatharians may not rely on high symbiont abundance.

The paper uses metabolomics to identify metabolic markers of stony coral tissue loss disease in Montastraea cavernosa, revealing differences between healthy, diseased, and recovered corals.

This paper introduces Reef Cover, a coral reef classification system for global habitat mapping using remote sensing data, demonstrating its application in the Pacific Islands.

The paper examines physiological and transcriptomic differences in a single coral colony, finding distinct functional roles in different polyp locations due to environmental gradients.

The paper identifies gene expression patterns associated with disease resistance and long-term growth in corals from a marine sanctuary, showing no trade-off between resistance and calcification.

This study presents the Ostreobium nuclear genome and metatranscriptomic analysis to understand its adaptations to the coral skeleton environment and its role in coral holobiont dynamics.

The paper identifies genetic adaptations in coral holobionts from the Great Barrier Reef's inshore regions linked to Holocene climate change.

The paper analyzes transcriptomic responses of Acropora palmata and its symbionts to disease exposure, finding consistent innate immune gene expression despite yearly disease variability.

This paper develops a field-friendly framework for characterizing coral holobionts using nanopore sequencing and bioinformatics pipelines, revealing reef-scale bacterial networks and host-specific associations.