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In response to climate change, biodiversity patterns in the oceans are predicted to shift rapidly, thus increasing the need for efficient monitoring methods. Environmental DNA (eDNA) metabarcoding recently emerged as a potent and cost-effective candidate to answer this challenge. We targeted three molecular markers to determine multicellular metazoan communities from two timepoints across a long-standing transect in the Southern Hemisphere, the Munida Observational Time Series. We detected four community types across the successive water masses—neritic, sub-tropical, frontal, and sub-Antarctic—crossed by the transect, together with important community differences between the two sampling points. From indicator species analysis, we found diversity patterns were mostly driven by planktonic organisms. Mesopelagic communities differed from surface-water communities in the sub-Antarctic water mass, with at-depth communities dominated by single-cellular organisms. We evaluate the ability of eDNA to detect species-compositional changes across surface and depth gradients and lay the foundations for using this technique in multi-trophic environmental monitoring efforts across long time series. We observed community differences across time and space. More intensive sampling will be critical to fully capture diversity across marine gradients, but this multi-trophic method represents an invaluable opportunity to understand shifts in marine biota.

It has been widely shown that oyster reefs enhance local biodiversity and fisheries production. To determine the importance of intertidal remnant estuarine oyster reefs compared to unstructured sandy habitats over small spatial scales (

Marine water temperatures are increasing globally, with eastern Australian estuaries warming faster than predicted. There is growing evidence that this rapid warming of coastal waters is increasing the abundance and virulence of pathogenic members of the Vibrionaceae, posing a significant health risk to both humans and aquatic organisms. Fish disease, notably outbreaks of emerging pathogens in response to environmental perturbations such as heatwaves, have been recognised in aquaculture settings. Considerably less is known about how rising sea surface temperatures will impact the microbiology of wild fish populations, particularly those within estuarine systems that are more vulnerable to warming. We used a combination of Vibrio-specific quantitative PCR and amplicon sequencing of the 16S rRNA and hsp60 genes to examine seawater and fish (Pelates sexlineatus) gut microbial communities across a quasi-natural experimental system, where thermal pollution from coal-fired power stations creates a temperature gradient of up to 6 °C, compatible with future predicted temperature increases. At the warmest site, fish hindgut microbial communities were in a state of dysbiosis characterised by shifts in beta diversity and a proliferation (71.5% relative abundance) of the potential fish pathogen Photobacterium damselae subsp. damselae. Comparable patterns were not identified in the surrounding seawater, indicating opportunistic proliferation within estuarine fish guts under thermal stress. A subsequent evaluation of predicted future warming-related risk due to pathogenic Vibrionaceae in temperate estuarine fish demonstrated that warming is likely to drive opportunistic pathogen increases in the upper latitudinal range of this estuarine fish, potentially impacting adaptations to future warming. These findings represent a breakthrough in our understanding of the dynamics of emerging pathogens in populations of wild aquatic organisms within environments likely to experience rapid warming under future climate change.

Estuaries are critical habitats subject to a range of stressors requiring effective management. Microbes are gaining recognition as effective environmental indicators, however, the response of host associated communities to stressors remains poorly understood. We examined microbial communities from seawater, sediments and the estuarine fish Pelates sexlineatus, in Australia's largest urbanised estuary, and hypothesised that anthropogenic contamination would be reflected in the microbiology of these sample types. The human faecal markers Lachno3 and HF183 were not detected, indicating negligible influence of sewage, but a gradient in copy numbers of the class 1 integron (intI-1), which is often used as a marker for anthropogenic contamination, was observed in sediments and positively correlated with metal concentrations. While seawater communities were not strongly driven by metal contamination, shifts in the diversity and composition of the fish gut microbiome were observed, with statistical links to levels of metal contamination (F2, 21 = 1.536, p

Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.

As marine heatwaves increasingly threaten coral reefs worldwide, some extreme reef environments naturally expose corals to high-temperature fluctuations and can therefore provide important insights into the mechanisms underlying coral heat tolerance. Coral reefs in the Kimberley region in northwest Australia experience the world’s largest tropical tides and are therefore exposed to highly fluctuating temperatures in the intertidal. In contrast, the subtidal remains mostly submerged, resulting in moderate daily temperature fluctuations. A marine heatwave in 2016 triggered wide-spread bleaching in the Kimberley. Intertidal corals bleached less and recovered faster than adjacent subtidal corals; however, the mechanisms underlying this differential bleaching and recovery response remain poorly understood. Here we assessed both host- and symbiont-based indicators of bleaching resilience in the coral Acropora aspera. We tagged visibly healthy and bleached colonies from both environments in April 2016 and measured symbiont community composition, cell density, chlorophyll a, total biomass and host tissue energy reserves (lipids, protein and carbohydrates) during bleaching in April and in November 2016. Bleaching severity was higher in the subtidal than in intertidal, and while Cladocopium dominated all corals, symbiont community compositions differed significantly between environments and between bleached and healthy subtidal corals. Interestingly, bleaching resilience seemed decoupled from energy reserves, even though high levels of energy reserves and/or sufficient consumption during bleaching are widely thought to increase resistance to and recovery from bleaching. Although all bleached/recovered corals showed a general pattern of catabolizing protein reserves, distinct environment-specific trends were observed: subtidal corals that suffered extensive mortality also catabolized energy-poor carbohydrate reserves. In contrast, intertidal corals recovered rapidly after bleaching and maintained energy reserves. Total biomass remained unchanged between bleached and healthy corals in both environments. Overall, the findings of this study demonstrate that the consumption of energy reserves during bleaching is not always a reliable indicator of bleaching resilience.

Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate-related threats and as such there is a pressing need for cost-effective whole-ecosystem surveying to baseline biodiversity, study assemblage changes and ultimately develop sustainable management plans. We investigated the utility of eDNA metabarcoding as a high-resolution, multitrophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI)-a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seawater samples collected from 42 sites within a 140 km2 area. Our assays successfully detected a wide range of bony fish and elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across the island ecosystem and demonstrating the localisation of eDNA signals, despite extensive tidal and oceanic movements. In addition, we document putative new occurrence records for 46 taxa and compare the efficiency of our eDNA approach to visual survey techniques at CKI. Our study demonstrates the utility of a multimarker metabarcoding approach in capturing multitrophic biodiversity across an entire coral reef atoll and sets an important baseline for ongoing monitoring and management.

Cumulative anthropogenic pressures have triggered a global decline in the health of marine ecosystems, and coral reefs, in particular, are in crisis. With climate and population-related pressures predicted to intensify in the coming decades, it is increasingly crucial to develop cost-effective and accurate monitoring tools to document changes to these important ecosystems. Environmental DNA (eDNA) coupled with metabarcoding is a powerful tool for surveying a wide variety of biota. Here, we develop a baseline eDNA toolkit targeting scleractinian corals and validate its performance in conjunction with data derived on traditional diver-based visual surveys at the Cocos (Keeling) Islands. Three assays targeting the ITS2 and 16S barcoding regions were designed, which broadly detected diversity within Scleractinia and Porifera. Our eDNA assays recovered 78 ITS2 operational taxonomic units (OTUs) from 25 scleractinian genera which is comparable to the level of diversity recorded on visual surveys (68 species from 26 genera). There were some notable differences in the species detected using eDNA versus visual records that may relate to either misidentifications, intragenic variation, differential assay performance or cryptic species. Our data demonstrate that a multi-assay eDNA analytical approach, applied on surface water collections, represents a powerful and complementary way to survey diversity that can also reveal fine scale spatial differentiation in community composition. With further refinement and improved reference databases, we envisage eDNA to become a powerful complement to visual surveys and to play a key role in monitoring the health and diversity of complex coral reefs ecosystems.

Background The utility of environmental DNA (eDNA) metabarcoding surveys to accurately detect species depends on the degree of DNA dispersal. Multiple marine studies have observed only minimal eDNA transport by horizontal water movement across small spatial scales, leading to the conclusion that spatially specific eDNA signals accurately resemble in‐field species assemblages along a horizontal axis. Marine communities, however, are also structured vertically according to depth. In marine environments displaying permanent water stratification, vertical zonation patterns may be more apparent and present on smaller spatial scales (i.e., meters) than horizontal community structuring. The scale at which eDNA signals differ along a vertical transect and the accuracy of eDNA metabarcoding in revealing naturally stratified communities have yet to be assessed. Methods and results In this study, we determined the ability of eDNA metabarcoding surveys to distinguish vertically localized community assemblages. To test this, we sampled three vertical transects along a steep rock wall at three depths (0 m, 4 m, 15 m), covering two distinct communities that were separated by near‐permanent water column stratification in the form of a strong halocline at ~3 m. Using three metabarcoding assays, our eDNA metabarcoding survey detected 54 taxa, across 46 families and 7 phyla, including 19 fish, 15 crustacean, and 8 echinoderm species. Ordination and cluster analyses show distinct eDNA signals across the halocline for all three replicate transects, suggesting that vertical dispersal of eDNA between communities was limited. Furthermore, eDNA signals of individual taxa were only retrieved within their observed vertical distribution, providing biological validation for the obtained results. Our results demonstrate, for the first time, the need to take into consideration oceanographic (e.g. water column stratification) and biological processes (e.g. vertical community structuring) when designing sampling strategies for marine eDNA metabarcoding surveys.

An impact assessment of oceanic effluent releases from Belmont wastewater treatment works (WWTW) in Newcastle, Australia, was undertaken. Benthic infaunal assemblages in sandy sediments of ~25 m water depth were examined, at sites adjacent to the release point, and at increasing distances up to 2 km in both a NE and SW direction over five consecutive years (2016-2020). Localised impacts were evident for infaunal assemblages, with sites within 20 m of the outfall ("Impact" site types) exhibiting lower taxa richness and Shannon diversity, higher abundances of polychaetes and/or nematodes, higher polychaete ratios, and shifts in assemblage composition in comparison to sites at greater distances during some years. Taxa with increased localised abundances at the outfall were identified as indicators for monitoring impacts, including deposit-feeding polychaetes (Families Polygordiidae, Paraonidae and Dorvilleidae) and Phylum Nematoda. Future infaunal monitoring could include molecular tools and paired sediment analyses.

Advances in high-throughput sequencing (HTS) are revolutionizing monitoring in marine environments by enabling rapid, accurate and holistic detection of species within complex biological samples. Research institutions worldwide increasingly employ HTS methods for biodiversity assessments. However, variance in laboratory procedures, analytical workflows and bioinformatic pipelines impede the transferability and comparability of results across research groups. An international experiment was conducted to assess the consistency of metabarcoding results derived from identical samples and primer sets using varying laboratory procedures. Homogenized biofouling samples collected from four coastal locations (Australia, Canada, New Zealand and the USA) were distributed to 12 independent laboratories. Participants were asked to follow one of two HTS library preparation workflows. While DNA extraction, primers and bioinformatic analyses were purposefully standardized to allow comparison, many other technical variables were allowed to vary among laboratories (e.g., amplification protocols, type of instrument used, etc.). Despite substantial variation observed in raw results, the primary signal in the data was consistent, with the samples grouping strongly by geographic origin for all datasets. Simple post-hoc data clean-up by removing low quality samples gave the best improvement in sample classification for nuclear 18S rRNA gene data, with an overall 92.81% correct group attribution. For mitochondrial COI gene data, the best classification result (95.58%) was achieved after correction for contamination errors. The identified critical methodological factors that introduced the greatest variability (preservation buffer, sample defrosting, template concentration, DNA polymerase, PCR enhancer) should be of great assistance in standardizing future comparative biodiversity studies using metabarcoding.

Diet studies provide base understanding of trophic structure and are a valuable initial step for many fields of marine ecology, including conservation and fisheries biology. Considerable complexity in marine trophic structure can exist due to the presence of highly mobile species with long life spans. Mobula rays are highly mobile, large, planktivorous elasmobranchs that are frequently caught either directly or as bycatch in fisheries, which, combined with their conservative life history strategy, makes their populations susceptible to decline in intensely fished regions. Effective management of these iconic and vulnerable species requires an understanding of the diets that sustain them, which can be difficult to determine using conventional sampling methods. We use three DNA metabarcode assays to identify 44 distinct taxa from the stomachs (n = 101) of four sympatric Mobula ray species (Mobula birostris, Mobula tarapacana, Mobula japanica, and Mobula thurstoni) caught over 3 years (2013–2015) in a direct fishery off Bohol in the Philippines. The diversity and incidence of bony fishes observed in ray diets were unprecedented. Nevertheless, rays showed dietary overlap, with krill (Euphausia) dominating their diet. Our results provide a more detailed assessment of sympatric ray diets than was previously described and reveal the complexity that can exist in food webs at critical foraging habitats.

Coral reefs are severely threatened by climate change and recurrent mass bleaching events, highlighting the need for a better understanding of the factors driving recovery and resilience both at the community and species level. While temperature variability has been shown to promote coral heat tolerance, it remains poorly understood how this influences coral recovery capacity. Similarly, few studies have investigated how the presence of cryptic species influences bleaching and recovery responses. Using an integrated ecological, physiological and genomic approach, we examined the recovery of both coral communities and their dominant species from the 2016 mass bleaching event in the macrotidal Kimberley region, NW Australia. We show that recovery of coral communities inhabiting adjacent but environmentally contrasting reef habitats differed dramatically following unprecedented bleaching in 2016. Both intertidal (thermally extreme) and subtidal (thermally moderate) habitats experienced extensive bleaching (72-81%), but subtidal coral communities had a greater percentage of severely bleached corals than the intertidal community (76% versus 53%). Similarly, subtidal Acropora aspera corals suffered much greater losses of chlorophyll a than intertidal conspecifics (96% versus 46%). The intertidal coral community fully recovered to its pre-bleaching configuration within six months, whereas the adjacent subtidal suffered extensive mortality (68% loss of live coral cover). Despite the presence of three cryptic genetic lineages in the dominant coral species, the physiological response of A. aspera was independent of host cryptic genetic diversity. Furthermore, both intertidal and subtidal A. aspera harbored symbionts in the genus Cladocopium (previously clade C). Our findings highlight the important role of tidally-controlled temperature variability in promoting coral recovery capacity, and we propose that shallow reef environments characterized by strong environmental gradients may generally promote coral resilience to extreme climatic events. Thermally variable reef environments may therefore provide important spatial refugia for coral reefs under rapid climate change.

Maintaining the accretion potential and three dimensional structure of coral reefs is a priority but reef-building scleractinian corals are highly threatened and retreating. Hence future reefs are predicted to be dominated by non-constructional taxa. Since the Late Triassic however, other non-scleractinian anthozoans such as Heliopora have contributed to tropical and subtropical reef-building. Heliopora is an ancient and highly conserved reef building octocoral genus within the monospecific Family Helioporidae, represented by a single extant species – H. coerulea, Pallas, 1766. Here we show integrated morphological, genomic and reproductive evidence to substantiate the existence of a second species within the genus Heliopora. Importantly, some individuals of the new species herein described as Heliopora hiberniana sp. nov. feature a white skeleton indicating that the most diagnostic and conserved Heliopora character (the blue skeleton) can be displaced. The new species is currently known only from offshore areas in north Western Australia, which is a part of the world where coral bleaching events have severely impacted the scleractinian community over the last two decades. Field observations indicate individuals of both H. coerulea and H. hiberniana sp. nov. were intact after the 2016 Scott Reef thermal stress event, and we discuss the possibility that bleaching resistant non-scleractinian reef builders such as Heliopora could provide new ecological opportunities for the reconfiguration of future reefs by filling empty niches and functional roles left open by the regression of scleractinian corals.

Significance The mode and tempo of extinctions and extirpations after the first contact phase of human settlements is a widely debated topic. As the last major landmass to be settled by humans, New Zealand offers a unique lens through which to study interactions of people and biota. By analyzing ancient DNA from more than 5,000 nondiagnostic and fragmented bones from 38 subfossil assemblages, we describe species and patterns that have been missed by morphological approaches. We report the identification of five species of whale from an archaeological context in New Zealand and describe the prehistoric kākāpō population structure. Taken together, this study demonstrates insights into subsistence practices and extinction processes and demonstrates the value of genetic analyses of fossil assemblages., New Zealand’s geographic isolation, lack of native terrestrial mammals, and Gondwanan origins make it an ideal location to study evolutionary processes. However, since the archipelago was first settled by humans 750 y ago, its unique biodiversity has been under pressure, and today an estimated 49% of the terrestrial avifauna is extinct. Current efforts to conserve the remaining fauna rely on a better understanding of the composition of past ecosystems, as well as the causes and timing of past extinctions. The exact temporal and spatial dynamics of New Zealand’s extinct fauna, however, can be difficult to interpret, as only a small proportion of animals are preserved as morphologically identifiable fossils. Here, we conduct a large-scale genetic survey of subfossil bone assemblages to elucidate the impact of humans on the environment in New Zealand. By genetically identifying more than 5,000 nondiagnostic bone fragments from archaeological and paleontological sites, we reconstruct a rich faunal record of 110 species of birds, fish, reptiles, amphibians, and marine mammals. We report evidence of five whale species rarely reported from New Zealand archaeological middens and characterize extinct lineages of leiopelmatid frog (Leiopelma sp.) and kākāpō (Strigops habroptilus) haplotypes lost from the gene pool. Taken together, this molecular audit of New Zealand’s subfossil record not only contributes to our understanding of past biodiversity and precontact Māori subsistence practices but also provides a more nuanced snapshot of anthropogenic impacts on native fauna after first human arrival.

Aim To describe, model and assess the relative importance of environmental and climatic factors likely influencing the regional distribution of coral cover and assemblages with contrasting life histories and susceptibilities to bleaching. Location We compiled the first comprehensive empirical dataset for coral communities in the south-eastern Indian Ocean (SEIO), incorporating information from 392 sites along the western coast of Australia and offshore atolls/islands across ~19° of latitude. Methods We assessed hard coral cover and community composition to genus using point-intercept transects or point-count analysis of digital images taken along transects. We explored spatial variation in environmental conditions and in composition of corals with contrasting life histories. After de-trending the temporal patterns, we assessed the relative importance of environmental metrics to coral cover, life histories and bleaching susceptibility using a full subsets model-selection approach with generalized additive mixed models, accounting for both temporal and among site variation. Results The distribution of temperature, light, the frequency of temperature anomalies and tropical cyclones appear to be drivers of coral community structure. Functional diversity of low- to mid-latitude coral communities may convey some resilience to thermal stress, while higher latitude communities dominated by Competitive and Bleaching-Susceptible taxa may lack this functional resilience. These patterns likely reflect varying historical exposure to cyclones and temperature anomalies. Main conclusions As evident in recent years, changing background conditions and regimes of disturbance in coming decades will shift the distribution, functional diversity and resilience of coral reefs throughout the SEIO. The rate and magnitude of environmental change will ultimately determine the future of the tropical reefs and whether the higher latitude reefs provide some refuge from climate change. Our study highlights the need to quantify the distributional properties of key environmental metrics to better understand and predict reef condition through coming decades.

Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using ‘tree of life’ (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing ‘universal’ PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra- and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs.

Relatively small volumes of water may contain sufficient environmental DNA (eDNA) to detect target aquatic organisms via genetic sequencing. We therefore assessed the utility of eDNA to document the diversity of coral reef fishes in the central Red Sea. DNA from seawater samples was extracted, amplified using fish-specific 16S mitochondrial DNA primers, and sequenced using a metabarcoding workflow. DNA sequences were assigned to taxa using available genetic repositories or custom genetic databases generated from reference fishes. Our approach revealed a diversity of conspicuous, cryptobenthic, and commercially relevant reef fish at the genus level, with select genera in the family Labridae over-represented. Our approach, however, failed to capture a significant fraction of the fish fauna known to inhabit the Red Sea, which we attribute to limited spatial sampling, amplification stochasticity, and an apparent lack of sequencing depth. Given an increase in fish species descriptions, completeness of taxonomic checklists, and improvement in species-level assignment with custom genetic databases as shown here, we suggest that the Red Sea region may be ideal for further testing of the eDNA approach.

The analysis of apex predator diet has the ability to deliver valuable insights into ecosystem health, and the potential impacts a predator might have on commercially relevant species. The Australian sea lion (Neophoca cinerea) is an endemic apex predator and one of the world's most endangered pinnipeds. Given that prey availability is vital to the survival of top predators, this study set out to understand what dietary information DNA metabarcoding could yield from 36 sea lion scats collected across 1,500 km of its distribution in southwest Western Australia. A combination of PCR assays were designed to target a variety of potential sea lion prey, including mammals, fish, crustaceans, cephalopods, and birds. Over 1.2 million metabarcodes identified six classes from three phyla, together representing over 80 taxa. The results confirm that the Australian sea lion is a wide-ranging opportunistic predator that consumes an array of mainly demersal fauna. Further, the important commercial species Sepioteuthis australis (southern calamari squid) and Panulirus cygnus (western rock lobster) were detected, but were present in

Dinoflagellates of the family Symbiodiniaceae form mutualistic symbioses with marine invertebrates such as reef-building corals, but also inhabit reef environments as free-living cells. Most coral species acquire Symbiodiniaceae horizontally from the surrounding environment during the larval and/or recruitment phase, however the phylogenetic diversity and ecology of free-living Symbiodiniaceae on coral reefs is largely unknown. We coupled environmental DNA sequencing and genus-specific qPCR to resolve the community structure and cell abundances of free-living Symbiodiniaceae in the water column, sediment, and macroalgae and compared these to coral symbionts. Sampling was conducted at two time points, one of which coincided with the annual coral spawning event when recombination between hosts and free-living Symbiodiniaceae is assumed to be critical. Amplicons of the internal transcribed spacer (ITS2) region were assigned to 12 of the 15 Symbiodiniaceae genera or genera-equivalent lineages. Community compositions were separated by habitat, with water samples containing a high proportion of sequences corresponding to coral symbionts of the genus Cladocopium, potentially as a result of cell expulsion from in hospite populations. Sediment-associated Symbiodiniaceae communities were distinct, potentially due to the presence of exclusively free-living species. Intriguingly, macroalgal surfaces displayed the highest cell abundances of Symbiodiniaceae, suggesting a key role for macroalgae in ensuring the ecological success of corals through maintenance of a continuum between environmental and symbiotic populations of Symbiodiniaceae.

Proteins and carbohydrates have profound impacts on the ecology of gut microbiota, but disentangling the single and interactive effects of different dietary constituents is challenging. Here, we used a multidimensional approach, the Geometric Framework, to study the interactions between nutrition and bacterial abundances with respect to protein and carbohydrate intakes in field cricket, Teleogryllus oceanicus. Our study revealed that species richness decreased as crickets consumed more macronutrients, and species evenness peaked at high intake of protein-rich diets. Sex and protein:carbohydrate (P:C) ratios in diets were the primary factors influencing the gut bacterial community, but most of the microbial operational taxonomic units (OTUs) that were significantly different between males and females were present in low abundance. In contrast, protein intake had a greater influence than carbohydrate consumption on the relative abundances of the core bacterial taxa, as an increase in dietary protein availability could remove the growth constraint imposed by limited nitrogen. Taken together, the use of the Geometric Framework provides a deeper insight into how nutritional intakes influence the relative abundances of gut microbes, and could be a useful tool to integrate the study of gut microbiome and fitness traits in a host.

This study investigated differences in Symbiodinium diversity in the scleractinian coral species Agaricia lamarcki between shallow (20–25 m) and mesophotic (50–70 m) depths in the Northern Caribbean. Corals were sampled in each of four shallow sites (20–25 m; n = 18) and three mesophotic sites (50–70 m; n = 18) from Mona Island (Puerto Rico) and the US Virgin Islands during a mesophotic exploratory cruise and from the La Parguera shelf edge, off Southwestern Puerto Rico. Symbiodinium diversity was assessed using internal transcribed spacer 2 sequences clustered into operational taxonomic units (OTUs). Clustering resulted in eight clade C OTUs and one clade D OTU. Of these, there were three common Symbiodinium OTUs consisting of C3 and D1a.N14 in shallow reefs and C11.N4 in mesophotic reefs. Statistical tests (permutational multivariate analysis of variance and analysis of similarity) showed significant differences between clade C Symbiodinium OTUs in A. lamarcki colonies located at shallow and mesophotic depths, indicating symbiont zonation. Symbiodinium diversity in A. lamarcki from the Northern Caribbean is comparable to previous reports in the Southern Caribbean for this species. This is the first report of the thermal tolerant species Symbiodinium trenchii (D1a) in A. lamarcki.

Pocillopora damicornis is one of the most extensively studied coral species globally, but high levels of phenotypic plasticity within the genus make species identification based on morphology alone unreliable. As a result, there is a compelling need to develop cheap and time-effective molecular techniques capable of accurately distinguishing P. damicornis from other congeneric species. Here, we develop a fluorescence-based quantitative real-time PCR (qPCR) assay to genotype a single nucleotide polymorphism that accurately distinguishes P. damicornis from other morphologically similar Pocillopora species. We trial the assay across colonies representing multiple Pocillopora species and then apply the assay to screen samples of Pocillopora spp. collected at regional scales along the coastline of Western Australia. This assay offers a cheap and time-effective alternative to Sanger sequencing and has broad applications including studies on gene flow, dispersal, recruitment and physiological thresholds of P. damicornis.

High-throughput sequencing is revolutionizing our ability to comprehensively characterize free-living and symbiotic Symbiodiniaceae, a diverse dinoflagellate group that plays a critical role in coral reef ecosystems. Most studies however, focus on a single marker for metabarcoding Symbiodiniaceae, potentially missing important ecological traits that a combination of markers may capture. In this proof-of-concept study, we used a small set of symbiotic giant clam (Tridacna maxima) samples obtained from nine French Polynesian locations and developed a multiplex metabarcoding method that pools and simultaneously sequences multiple Symbiodiniaceae genes for in-depth biodiversity assessments. Our results showed that the technique effectively recovered very similar proportions of sequence reads and dominant Symbiodiniaceae clades among the three multiplexed genes investigated per sample, and captured varying levels of phylogenetic resolution enabling a more comprehensive assessment of the diversity present. Multiplex metabarcoding offers significant analytical cost savings while providing exceptional phylogenetic information and sequence coverage.

Background Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion Overall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance.

Effective biomonitoring is critical for driving management outcomes that ensure long-term sustainability of the marine environment. In recent years, environmental DNA (eDNA), coupled with metabarcoding methodologies, has emerged as a promising tool for generating biotic surveys of marine ecosystems, including those under anthropogenic pressure. However, more empirical data are needed on how to best implement eDNA field sampling approaches to maximize their utility for each specific application. The effect of the substrate chosen for eDNA sampling on the diversity of marine taxa detected by DNA metabarcoding has not yet been systematically analysed, despite aquatic systems being those most commonly targeted for eDNA studies. We investigated the effect of four commonly used eDNA substrates to explore taxonomic diversity: (a) surface water, (b) marine sediment, (c) settlement plates and (d) planktonic tows. With a focus on coastal ports, 332 eDNA samples from Australia (Indian and Southern oceans) and Kazakhstan (Caspian Sea) were collected and analysed by multi-assay DNA metabarcoding. Across study locations, between 30% and 52% of eukaryotic families detected were unique to a particular substrate and