Biology subjects

Laffy, P. W.

Publications and source records attributed to Laffy, P. W..

5 recordsLinked to original sources

bioRxiv2026

No-take marine reserves promote oligotrophic reef bacterioplankton communities across the Great Barrier Reef

Australias Great Barrier Reef is a biodiversity hotspot critical to ocean health, yet it faces increasing threats from climate change and localised impacts requiring effective conservation and management action. Rezoning of the Great Barrier Reef Marine Park in 2004 expanded No-Take Marine Reserves (NTMRs) to restrict extractive activities like fishing and collecting, creating one of the largest networks of marine reserves globally. Benefits like increased biomass of fisheries-targeted species and improved coral community health metrics have been reported, though the effects of zoning on water chemistry and seawater microbiology remain unexplored. Using data from the Great Barrier Reef Microbial Genomics Database, we investigated the structure of seawater microbiomes on 48 offshore reefs within NTMRs and fished reefs. A supervised classification method (MINT sPLS-DA) identified 350 indicator species that predict zoning with [~]71% accuracy (range 58-85%). Microbial communities broadly reflected reef states, with NTMR zones enriched in streamlined microbial oligotrophs (Pelagibacter and SAR86) correlating with higher cover of hard coral, crustose coralline algae, and herbivore fish abundance under lower nutrient conditions. By contrast, fished reefs harbored opportunists (Flavobacteriales, especially UA16, and Pseudomonadales) associating with elevated nutrients and turf algae cover. Co-occurrence networks revealed stronger competitive interactions in fished reefs, where nutrient-responsive taxa may outcompete other microbes, underscoring the need to investigate how these shifts influence reef nutrient cycling and function. Our findings reveal ecosystem-wide effects of marine zoning beyond fish protection, with distinct seawater microbiomes between fished reefs and NTMRs, which will help build decision tools for more targeted reef health monitoring assessments.

microbiology↗

bioRxiv2026

Conserved transcriptomic heat stress response signatures in coral recruits selectively bred from thermally distinct broodstock in a low-differentiation system

Thermal history provenancing can guide the choice of parental broodstock for selective breeding of corals from distinct reefs and has been proposed as an intervention for enhancing climate resilience. However, the genetic and molecular mechanisms underlying resultant offspring responses to heat stress, particularly during early life stages, remain poorly understood. Here, we generated Acropora tersa larvae and recruits by crossing parental colonies from the historically warmer Martin Reef and cooler Davies Reef and assessed the effects of within- and between-reef crosses on genetic diversity and transcriptional responses to heat stress. Genome-wide single nucleotide polymorphism analyses showed that broodstock from Martin and Davies Reefs were weakly differentiated (FST = 0.008) and exhibited comparable heterozygosity, as did all larval offspring groups. Transcriptomic analyses of recruits exposed to heat stress (32 {degrees}C for 36 days) revealed that both within- and between-reef offspring groups activated conserved stress-response pathways, with seven genotype-independent heat-responsive genes detected across all offspring groups. Differential expression and enrichment analyses showed induction of defence, protein homeostasis, intracellular transport, and metabolic processes alongside repression of growth- and signalling-related functions, consistent with the Type A General Coral Stress Response. Taken together, these findings suggest that the benefits of thermal history provenancing-informed selective breeding may be limited in low-differentiation systems and that targeted pre-screening of broodstock may help capture functional genetic variation relevant to restoration applications.

genomics↗

bioRxiv2026

Enhanced survival and lower growth in assisted gene flow corals during a marine heatwave driven by local adaptation

Recent increases in the frequency of mass coral bleaching and mortality events have caused shifts in species composition and rapid global reef decline. Genetic-based techniques, like assisted gene flow (AGF), offer the potential to enhance corals climate readiness by introducing genetic variation associated with heat tolerance into vulnerable populations. This method remains untested in the wild during a marine heatwave. To this end, we selectively bred AGF corals by crossing parent Acropora tersa corals collected across five Great Barrier Reef (GBR) locations spanning a thermal and bleaching gradient. Breeding produced intra- and inter-regional offspring that were then deployed to a central GBR reef. This deployment reef was subsequently hit by a marine heatwave (>31.4{degrees}C for 17 days and >6 Degree Heating Weeks). Heat tolerance-associated traits (survival, growth, and bleaching) were compared between AGF offspring and a native control cross over the 95 days in the wild. Overall, AGF offspring had 4x greater odds of survival compared to controls, and 2x greater odds compared to northern juveniles. Growth rates were 14% higher in control juveniles compared to the mean growth rate across all AGF crosses. Interestingly, heat-stress assays (32{degrees}C) of the parental adult corals showed similar patterns to their offspring, with higher survival and lower bleaching of corals from warmer northern reefs. Taken together, these findings providing critical support that the selective breeding of AGF corals can provide enhanced survival under marine heatwave conditions in the wild. It also suggests further evaluation is needed for trait-specific responses to effectively match donor and recipient reefs in restoration planning.

ecology↗

bioRxiv2025

The planktonic microbiome of the Great Barrier Reef

Large genome databases have markedly improved our understanding of marine microorganisms. Although these resources have focused on prokaryotes, genomes from many dominant marine lineages, such as Pelagibacter and Prochlorococcus, are conspicuously underrepresented. Here, we present the Great Barrier Reef Microbial Genomes Database (GBR-MGD) comprising 5,283 prokaryotic genomes obtained from GBR seawater samples using Nanopore sequencing, including a collection of high quality genomes of underrepresented groups. We show that standard short read assemblies miss these populations due to a combination of strain heterogeneity and low GC% sequencing bias. The GBR-MGD also comprises 20 chromosome-level picoeukaryote and 808,585 viral genomes, including a newly described clade of marine Crassvirales. We demonstrate the use of the GBR-MGD to identify indicator taxa that can reliably predict the effects of reef management practices, such as the establishment of marine protected zones.

genomics↗

bioRxiv2024

Environmental, host, and symbiont drivers of heat tolerance in a species complex of reef-building corals

Reef-building coral populations are under unprecedented threat from climate warming. Yet, variation in coral heat tolerance exists whereby some colonies can cope with higher sea temperatures than others and thus may hold unique value for conservation and restoration. Here, we quantify variation in heat tolerance of an ecologically important tabular coral species complex across the Great Barrier Reef (GBR) while also measuring genomic variation in the coral host and symbiont partners. Coral bleaching and photochemical traits were measured in 569 colonies within the Acropora hyacinthus species complex from 17 reefs following exposure to standardized acute heat stress assays. We detected substantial variation in heat tolerance, where individual colony thermal thresholds differed by up to 7.3{degrees}C and 5.7{degrees}C among and within reefs, respectively. Sea surface temperature climatology was the strongest predictor of heat tolerance, where colonies from warmer northern and inshore reefs typically exhibited the highest thermal thresholds, while colonies from cooler southern reefs were able to tolerate greater temperature increases relative to their local summer temperatures. Heat tolerance was also positively associated with exposure to thermal stress in the weeks preceding measurements. Assignment of colonies to host genomic clusters revealed four putative species within the A. hyacinthus complex that did not vary in their responses to experimental heat stress. Symbiodiniaceae communities within colonies were comprised primarily of Cladocopium ITS2 variants that differed spatially but had minimal effect on heat tolerance. Between 36 - 80% of heat tolerance variation was explained by environmental, host, and symbiont genomic predictors, leaving 20 - 64% to be explained by additional underlying drivers such as functional genomic variation not measured here. These results may be used to inform conservation and restoration actions, including targeting heat tolerant individuals for selective breeding, and will provide a foundation for evaluating the genomic basis of heat tolerance.

ecology↗