Linking differences in microbial network structure with changes in coral larval settlement

Coral cover and recruitment have decreased on reefs worldwide due to climate change-related disturbances. Achieving reliable coral larval settlement under aquaculture conditions is critical for reef restoration programmes; however, this can be challenging due to the lack of reliable and universal larval settlement cues. To investigate the role of microorganisms in coral larval settlement, we undertook a settlement choice experiment with larvae of the coral Acropora tenuis and microbial biofilms grown for different periods on the reef and in aquaria. Biofilm community composition across conditioning types and time was profiled using 16S and 18S rRNA gene sequencing. Co-occurrence networks revealed that strong larval settlement correlated with diverse biofilm communities, with specific nodes in the network facilitating connections between modules comprised of low- vs high-settlement communities. Taxa associated with high-settlement communities were identified as Myxoccales sp., Granulosicoccus sp., Alcanivoraceae sp., unassigned JTB23 sp. (Gammaproteobacteria), and Pseudovibrio denitrificans. Meanwhile, taxa closely related to Reichenbachiella agariperforans, Pleurocapsa sp., Alcanivorax sp., Sneathiella limmimaris, as well as several diatom and brown algae were associated with low settlement. Our results characterise high-settlement biofilm communities and identify transitionary taxa that may develop settlement-inducing biofilms to improve coral larval settlement in aquaculture.

Future ocean conditions induce necrosis, microbial dysbiosis and nutrient cycling imbalance in the reef sponge Stylissa flabelliformis

Oceans are rapidly warming and acidifying in the context of climate change, threatening sensitive marine biota including coral reef sponges. Ocean warming (OW) and ocean acidification (OA) can impact host health and associated microbiome, but few studies have investigated these effects, which are generally studied in isolation, on a specific component of the holobiont. Here we present a comprehensive view of the consequences of simultaneous OW and OA for the tropical sponge Stylissa flabelliformis. We found no interactive effect on the host health or microbiome. Furthermore, OA (pH 7.6 versus pH 8.0) had no impact, while OW (31.5 °C versus 28.5 °C) caused tissue necrosis, as well as dysbiosis and shifts in microbial functions in healthy tissue of necrotic sponges. Major taxonomic shifts included a complete loss of archaea, reduced proportions of Gammaproteobacteria and elevated relative abundances of Alphaproteobacteria. OW weakened sponge-microbe interactions, with a reduced capacity for nutrient exchange and phagocytosis evasion, indicating lower representations of stable symbionts. The potential for microbially-driven nitrogen and sulphur cycling was reduced, as was amino acid metabolism. Crucially, the dysbiosis annihilated the potential for ammonia detoxification, possibly leading to accumulation of toxic ammonia, nutrient imbalance, and host tissue necrosis. Putative defence against reactive oxygen species was greater at 31.5 °C, perhaps as microorganisms capable of resisting temperature-driven oxidative stress were favoured. We conclude that healthy symbiosis in S. flabelliformis is unlikely to be disrupted by future OA but will be deeply impacted by temperatures predicted for 2100 under a "business-as-usual" carbon emission scenario.

Benthic micro- and macro-community succession and coral recruitment under overfishing and nutrient enrichment

Herbivory and nutrient availability are fundamental drivers of benthic community succession in shallow marine systems, including coral reefs. Despite the importance of early community succession for coral recruitment and recovery, studies characterizing the impact of top-down and bottom-up drivers on micro- and macrobenthic communities at scales relevant to coral recruitment are lacking. Here, a combination of tank and field experiments were used to assess the effects of herbivore exclusion and nutrient enrichment on micro- to macrobenthic community succession and subsequent coral recruitment success. Herbivore exclusion had the strongest effect on micro- and macrobenthic community succession, including a community shift toward copiotrophic and potentially opportunistic/pathogenic microorganisms, an increased cover of turf and macroalgae, and decreased cover of crustose coralline algae. Yet, when corals settled prior to the development of a macrobenthic community, rates of post-settlement survival increased when herbivores were excluded, benefiting from the predation refugia provided by cages during their vulnerable early post-settlement stage. Interestingly, survival on open tiles was negatively correlated with the relative abundance of the bacterial order Rhodobacterales, an opportunistic microbial group previously associated with stressed and diseased corals. Development of micro- and macrobenthic communities in the absence of herbivory, however, led to reduced coral settlement. In turn, there were no differences in post-settlement survival between open and caged treatments for corals settled on tiles with established benthic communities. As a result, open tiles experienced marginally higher recruitment rates, driven primarily by the higher initial number of settlers on open tiles compared to caged tiles. Overall, we reveal that the primary interaction driving coral recruitment is the positive effect of herbivory in creating crustose coralline algae (CCA)-dominated habitats, free of fleshy algae and associated opportunistic microbes, to enhance coral settlement. The negative direct and indirect impact of fish predation on newly settled corals was outweighed by the positive effect of herbivory on the initial rate of coral settlement. In turn, the addition of nutrients further altered benthic community succession in the absence of herbivory, reducing coral post-settlement survival. However, the overall impact of nutrients on coral recruitment dynamics was minor relative to herbivory.

A genomic view of the microbiome of coral reef demosponges

Sponges underpin the productivity of coral reefs, yet few of their microbial symbionts have been functionally characterised. Here we present an analysis of ~1200 metagenome-assembled genomes (MAGs) spanning seven sponge species and 25 microbial phyla. Compared to MAGs derived from reef seawater, sponge-associated MAGs were enriched in glycosyl hydrolases targeting components of sponge tissue, coral mucus and macroalgae, revealing a critical role for sponge symbionts in cycling reef organic matter. Further, visualisation of the distribution of these genes amongst symbiont taxa uncovered functional guilds for reef organic matter degradation. Genes for the utilisation of sialic acids and glycosaminoglycans present in sponge tissue were found in specific microbial lineages that also encoded genes for attachment to sponge-derived fibronectins and cadherins, suggesting these lineages can utilise specific structural elements of sponge tissue. Further, genes encoding CRISPR and restriction-modification systems used in defence against mobile genetic elements were enriched in sponge symbionts, along with eukaryote-like gene motifs thought to be involved in maintaining host association. Finally, we provide evidence that many of these sponge-enriched genes are laterally transferred between microbial taxa, suggesting they confer a selective advantage within the sponge niche and therefore play a critical role in host ecology and evolution.

Simulated future conditions of ocean warming and acidification disrupt the microbiome of the calcifying foraminifera Marginopora vertebralis across life stages

Foraminifera host diverse microbial communities that can shift in response to changing environmental conditions. To characterize climate change impacts on the foraminifera microbiome across life stages, we exposed adult Marginopora vertebralis (Large Benthic Foraminifera) to pCO₂ and temperature scenarios representing present-day, 2050 and 2100 levels and raised juveniles under present-day and 2050 conditions. While treatment condition had no significant effect on the seawater microbial communities, exposure to future scenarios significantly altered both adult and juvenile microbiomes. In adults, divergence between present-day and 2050 or 2100 conditions was primarily driven by a reduced relative abundance of Oxyphotobacteria under elevated temperature and pCO₂ . In juveniles, the microbial shift predominantly resulted from changes in the proportion of Proteobacteria. Indicator species analysis identified numerous treatment-specific indicator taxa, most of which were indicative of present-day conditions. Oxyphotobacteria, previously reported as putative symbionts of foraminifera, were indicative of present-day and 2050 conditions in adults, but of present-day conditions only in juveniles. Overall, we show that the sensitivity of the M. vertebralis microbiome to climate change scenarios extends to both life stages and primarily correlates with declines in Oxyphotobacteria and shifts in Proteobacteria under elevated temperature and pCO₂ .

Thermal stress modifies the marine sponge virome

Marine sponges can form stable partnerships with a wide diversity of microbes and viruses, and this high intraspecies symbiont specificity makes them ideal models for exploring how host-associated viromes respond to changing environmental conditions. Here we exposed the abundant Great Barrier Reef sponge Rhopaloiedes odorabile to elevated seawater temperature for 48 h and utilised a metaviromic approach to assess the response of the associated viral community. An increase in endogenous retro-transcribing viruses within the Caulimorviridae and Retroviridae families was detected within the first 12 h of exposure to 32 °C, and a 30-fold increase in retro-transcribing viruses was evident after 48 h at 32 °C. Thermally stressed sponges also exhibited a complete loss of ssDNA viruses which were prevalent in field samples and sponges from the control temperature treatment. Despite these viromic changes, functional analysis failed to detect any loss or gain of auxiliary metabolic genes, indicating that viral communities are not providing a direct competitive advantage to their host under thermal stress. In contrast, endogenous sponge retro-transcribing viruses appear to be replicating under thermal stress, and consistent with retroviral infections in other organisms, may be contributing to the previously described rapid decline in host health evident at elevated temperature.

HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts

Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments.

Host-associated coral reef microbes respond to the cumulative pressures of ocean warming and ocean acidification

Key calcifying reef taxa are currently threatened by thermal stress associated with elevated sea surface temperatures (SST) and reduced calcification linked to ocean acidification (OA). Here we undertook an 8 week experimental exposure to near-future climate change conditions and explored the microbiome response of the corals Acropora millepora and Seriatopora hystrix, the crustose coralline algae Hydrolithon onkodes, the foraminifera Marginopora vertebralis and Heterostegina depressa and the sea urchin Echinometra sp. Microbial communities of all taxa were tolerant of elevated pCO₂/reduced pH, exhibiting stable microbial communities between pH 8.1 (pCO₂ 479–499 μatm) and pH 7.9 (pCO₂ 738–835 μatm). In contrast, microbial communities of the CCA and foraminifera were sensitive to elevated seawater temperature, with a significant microbial shift involving loss of specific taxa and appearance of novel microbial groups occurring between 28 and 31 °C. An interactive effect between stressors was also identified, with distinct communities developing under different pCO₂ conditions only evident at 31 °C. Microbiome analysis of key calcifying coral reef species under near-future climate conditions highlights the importance of assessing impacts from both increased SST and OA, as combinations of these global stressors can amplify microbial shifts which may have concomitant impacts for coral reef structure and function.

Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens

Sponges are well known for hosting dense and diverse microbial communities, but how these associations vary with biogeography and environment is less clear. Here we compared the microbiome of an ecologically important sponge species, Carteriospongia foliascens, over a large geographic area and identified environmental factors likely responsible for driving microbial community differences between inshore and offshore locations using co-occurrence networks (NWs). The microbiome of C. foliascens exhibited exceptionally high microbial richness, with more than 9,000 OTUs identified at 97% sequence similarity. A large biogeographic signal was evident at the OTU level despite similar phyla level diversity being observed across all geographic locations. The C. foliascens bacterial community was primarily comprised of Gammaproteobacteria (34.2% ± 3.4%) and Cyanobacteria (32.2% ± 3.5%), with lower abundances of Alphaproteobacteria, Bacteroidetes, unidentified Proteobacteria, Actinobacteria, Acidobacteria and Deltaproteobacteria. Co-occurrence NWs revealed a consistent increase in the proportion of Cyanobacteria over Bacteroidetes between turbid inshore and oligotrophic offshore locations, suggesting that the specialist microbiome of C. foliascens is driven by environmental factors.

Natural volcanic CO2 seeps reveal future trajectories for host-microbial associations in corals and sponges

Atmospheric carbon dioxide (CO₂) levels are rapidly rising causing an increase in the partial pressure of CO₂ (pCO₂) in the ocean and a reduction in pH known as ocean acidification (OA). Natural volcanic seeps in Papua New Guinea expel 99% pure CO₂ and thereby offer a unique opportunity to explore the effects of OA in situ. The corals Acropora millepora and Porites cylindrica were less abundant and hosted significantly different microbial communities at the CO₂ seep than at nearby control sites <500 m away. A primary driver of microbial differences in A. millepora was a 50% reduction of symbiotic Endozoicomonas. This loss of symbiotic taxa from corals at the CO₂ seep highlights a potential hurdle for corals to overcome if they are to adapt to and survive OA. In contrast, the two sponges Coelocarteria singaporensis and Cinachyra sp. were ∼40-fold more abundant at the seep and hosted a significantly higher relative abundance of Synechococcus than sponges at control sites. The increase in photosynthetic microbes at the seep potentially provides these species with a nutritional benefit and enhanced scope for growth under future climate scenarios (thus, flexibility in symbiosis may lead to a larger niche breadth). The microbial community in the apparently pCO₂-sensitive sponge species S. massa was not significantly different between sites. These data show that responses to elevated pCO₂ are species-specific and that the stability and flexibility of microbial partnerships may have an important role in shaping and contributing to the fitness and success of some hosts.

Temperature: a prolonged confounding factor on cholinesterase activity in the tropical reef fish Acanthochromis polyacanthus

Cholinesterase activity usually decreases in fish exposed to anticholinesterase compounds such as organophosphate and carbamate pesticides. Here we show that tropical reef fish Acanthochromis polyacanthus (or spiny damsel) also exhibits a decrease in ChE activity when exposed to elevated temperature from 28°C to 32°C or 34°C after 4 days. We further demonstrate that the decline persists even after 7 days of recovery at control temperature. This is the first report of a drop in ChE activity in fish as temperature increases. Our results strongly suggest the need for long-term monitoring of water temperature in the field prior to sampling A. polyacanthus for toxicology studies, as temperature is a prolonged and confounding factor for ChE activity in this species.

Sulfur-oxidizing bacterial populations within cyanobacterial dominated coral disease lesions

This study investigated the diversity and quantitative shifts of sulfur-oxidizing bacteria (SOB) during the onset of black band disease (BBD) in corals using quantitative PCR (qPCR) and cloning approaches targeting the soxB gene, involved in sulfur oxidation. Four Montipora sp. coral colonies identified with lesions previously termed cyanobacterial patches (CP) (comprising microbial communities different from those of BBD lesions), was monitored in situ as CP developed into BBD. The overall abundance of SOB in both CP and BBD lesions were very low and near the detection limit of the qPCR assay, although consistently indicated that SOB populations decreased as the lesions transitioned from CP to BBD. Phylogenetic assessment of retrieved soxB genes showed that SOB in both CP and BBD lesions were dominated by one sequence type, representing > 70% of all soxB gene sequences and affiliated with members of the Rhodobacteraceae within the α-Proteobacteria. This study represents the first assessment targeting SOB within BBD lesions and clearly shows that SOB are not highly diverse or abundant in this complex microbial mat. The lack of oxidation of reduced sulfur compounds by SOB likely aids the accumulation of high levels of sulfide at the base of the BBD mat, a compound contributing to the pathogenicity of BBD lesions.

Near-future ocean acidification causes differences in microbial associations within diverse coral reef taxa

Microorganisms form symbiotic partnerships with a diverse range of marine organisms and can be critical to the health and survival of their hosts. Despite the importance of these relationships, the sensitivity of symbiotic microbes to ocean acidification (OA) is largely unknown and this needs to be redressed to adequately predict marine ecosystem resilience in a changing climate. We adopted a profiling approach to explore the sensitivity of microbes associated with coral reef biofilms and representatives of three ecologically important calcifying invertebrate phyla [corals, foraminifera and crustose coralline algae (CCA)] to OA. The experimental design for this study comprised four pHs consistent with current IPCC predictions for the next few centuries (pHNIST 8.1, 7.9, 7.7, 7.5); these pH/pCO₂ conditions were produced in flow-through aquaria using CO₂ bubbling. All reduced pH/increased pCO₂ treatments caused clear differences in the microbial communities associated with coral, foraminifera, CCA and reef biofilms over 6 weeks, while no visible signs of host stress were detected over this period. The microbial communities of coral, foraminifera, CCA and biofilms were significantly different between pH 8.1 (pCO₂ = 464 μatm) and pH 7.9 (pCO₂ = 822 μatm), a concentration likely to be exceeded by the end of the present century. This trend continued at lower pHs/higher pCO₂. 16S rRNA gene sequencing revealed variable and species-specific changes in the microbial communities with no microbial taxa consistently present or absent from specific pH treatments. The high sensitivity of coral, foraminifera, CCA and biofilm microbes to OA conditions projected to occur by 2100 is a concern for reef ecosystems and highlights the need for urgent research to assess the implications of microbial shifts for host health and coral reef processes.

Same, same but different: symbiotic bacterial associations in GBR sponges

Symbioses in marine sponges involve diverse consortia of microorganisms that contribute to the health and ecology of their hosts. The microbial communities of 13 taxonomically diverse Great Barrier Reef (GBR) sponge species were assessed by DGGE and 16S rRNA gene sequencing to determine intra and inter species variation in bacterial symbiont composition. Microbial profiling revealed communities that were largely conserved within different individuals of each species with intra species similarity ranging from 65–100%. 16S rRNA gene sequencing revealed that the communities were dominated by Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Nitrospira, and Cyanobacteria. Sponge-associated microbes were also highly host-specific with no operational taxonomic units (OTUs) common to all species and the most ubiquitous OTU found in only 5 of the 13 sponge species. In total, 91% of the OTUs were restricted to a single sponge species. However, GBR sponge microbes were more closely related to other sponge-derived bacteria than they were to environmental communities with sequences falling within 50 of the 173 previously defined sponge-(or sponge-coral) specific sequence clusters (SC). These SC spanned the Acidobacteria, Actinobacteria, Proteobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Gemmatimonadetes, Nitrospira, and the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum. The number of sequences assigned to these sponge-specific clusters across all species ranged from 0 to 92%. No relationship between host phylogeny and symbiont communities were observed across the different sponge orders, although the highest level of similarity was detected in two closely related Xestospongia species. This study identifies the core microbial inhabitants in a range of GBR sponges thereby providing the basis for future studies on sponge symbiotic function and research aiming to predict how sponge holobionts will respond to environmental perturbation.

Effects of chlorpyrifos on cholinesterase activity and stress markers in the tropical reef fish Acanthochromis polyacanthus

Tropical coastal ecosystems, including the Great Barrier Reef (GBR) of Australia are increasingly threatened by pollution; yet few studies have investigated the sensitivity of GBR species to these pollutants. Here we exposed juveniles of the tropical reef fish Acanthochromis polyacanthus (spiny damselfish) to three concentrations of the insecticide chlorpyrifos (CPF) and measured (i) muscle cholinesterase (ChE) activity; (ii) hepatic glutathione-S-transferase (GST) activity; and (iii) coenzyme Q (CoQ) redox balance, after 6h and 96h of exposure. After 96h, muscle ChE activity was significantly inhibited by 26%, 49% and 53% when fish were exposed to 1, 10 or 100μg/L CPF, respectively. Muscle ChE characterization revealed three types of ChEs, including two atypical forms. Hepatic CoQ antioxidant form significantly increased at 10μg/L after 6h of exposure, potentially demonstrating an early response to CPF-induced oxidative stress in liver. Hepatic GST was not affected by CPF exposure.

Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms

Marine sponges often contain diverse and abundant communities of microorganisms including bacteria, archaea and eukaryotic microbes. Numerous 16S rRNA-based studies have identified putative 'sponge-specific' microbes that are apparently absent from seawater and other (non-sponge) marine habitats. With more than 7500 sponge-derived rRNA sequences (from clone, isolate and denaturing gradient gel electrophoresis data) now publicly available, we sought to determine whether the current notion of sponge-specific sequence clusters remains valid. Comprehensive phylogenetic analyses were performed on the 7546 sponge-derived 16S and 18S rRNA sequences that were publicly available in early 2010. Overall, 27% of all sequences fell into monophyletic, sponge-specific sequence clusters. Such clusters were particularly well represented among the Chloroflexi, Cyanobacteria, 'Poribacteria', Betaproteobacteria and Acidobacteria, and in total were identified in at least 14 bacterial phyla, as well as the Archaea and fungi. The largest sponge-specific cluster, representing the cyanobacterium 'Synechococcus spongiarum', contained 245 sequences from 40 sponge species. These results strongly support the existence of sponge-specific microbes and provide a suitable framework for future studies of rare and abundant sponge symbionts, both of which can now be studied using next-generation sequencing technologies.

The larval sponge holobiont exhibits high thermal tolerance

Marine sponges are critical components of benthic environments; however, their sessile habit, requirement to filter large volumes of water and complex symbiotic partnerships make them particularly vulnerable to the effects of global climate change. We assessed the effect of elevated seawater temperature on bacterial communities in larvae of the Great Barrier Reef sponge, Rhopaloeides odorabile. In contrast to the strict thermal threshold of 32°C previously identified in adult R. odorabile, larvae exhibit a markedly higher thermal tolerance, with no adverse health effects detected at temperatures below 36°C. Similarly, larval microbial communities were conserved at temperatures up to 34°C with a highly significant shift occurring after 24 h at 36°C. This shift involved the loss of previously described symbionts (in particular the Nitrospira, Chloroflexi and a Roseobacter lineage) and the appearance of new Gammaproteobacteria not detected at lower temperatures. Here, we demonstrated that sponge larvae maintain highly stable symbioses at seawater temperatures exceeding those that are predicted under current climate change scenarios. In addition, by revealing that the shift in microbial composition occurs in conjunction with necrosis and mortality of larvae at 36°C we have provided additional evidence of the strong link between host health and the stability of symbiont communities.