Establishing microbial baselines to identify indicators of coral reef health

Microorganisms make a significant contribution to reef ecosystem health and resilience via their critical role in mediating nutrient transformations, their interactions with macro-organisms and their provision of chemical cues that underpin the recruitment of diverse reef taxa. However, environmental changes often cause compositional and functional shifts in microbial communities that can have flow-on consequences for microbial-mediated processes. These microbial alterations may impact the health of specific host organisms and can have repercussions for the functioning of entire coral ecosystems. Assessing changes in reef microbial communities should therefore provide an early indicator of ecosystem impacts and would underpin the development of diagnostic tools that could help forecast shifts in coral reef health under different environmental states. Monitoring, management and active restoration efforts have recently intensified and diversified in response to global declines in coral reef health. Here we propose that regular monitoring of coral reef microorganisms could provide a rapid and sensitive platform for identifying declining ecosystem health that can complement existing management frameworks. By summarising the most common threats to coral reefs, with a particular focus on the Great Barrier Reef, and elaborating on the role of microbes in coral reef health and ecosystem stability, we highlight the diagnostic applicability of microbes in reef management programs. Fundamental to this objective is the establishment of microbial baselines for Australia's coral reefs.AIMS@JCU PhD Scholarship; GBRMPA Science Management Research Award; Advance Queensland PhD Scholarship; Portuguese Science and Technology Foundation (FCT) [SFRH/BPD/110285/2015

Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes

Microbially mediated processes contribute to coral reef resilience yet, despite extensive characterisation of microbial community variation following environmental perturbation, the effect on microbiome function is poorly understood. We undertook metagenomic sequencing of sponge, macroalgae and seawater microbiomes from a macroalgae-dominated inshore coral reef to define their functional potential and evaluate seasonal shifts in microbially mediated processes. In total, 125 high-quality metagenome-assembled genomes were reconstructed, spanning 15 bacterial and 3 archaeal phyla. Multivariate analysis of the genomes relative abundance revealed changes in the functional potential of reef microbiomes in relation to seasonal environmental fluctuations (e.g. macroalgae biomass, temperature). For example, a shift from Alphaproteobacteria to Bacteroidota-dominated seawater microbiomes occurred during summer, resulting in an increased genomic potential to degrade macroalgal-derived polysaccharides. An 85% reduction of Chloroflexota was observed in the sponge microbiome during summer, with potential consequences for nutrition, waste product removal, and detoxification in the sponge holobiont. A shift in the Firmicutes:Bacteroidota ratio was detected on macroalgae over summer with potential implications for polysaccharide degradation in macroalgal microbiomes. These results highlight that seasonal shifts in the dominant microbial taxa alter the functional repertoire of host-associated and seawater microbiomes, and highlight how environmental perturbation can affect microbially mediated processes in coral reef ecosystems.Australian Government Department of Industry, Innovation and Science; Advance Queensland PhD Scholarship Great Barrier Reef Marine Park Authority Management Award National Environmental Science Program (NESP)info:eu-repo/semantics/publishedVersio

Quantifying capture and ingestion of live feeds across three coral species

Nutrient acquisition through heterotrophy is critical for the health of reef-building corals. The optimization of exogenous nutrition protocols to support a diversity of aquaculture corals requires improved techniques to assess feeding rates. Here, we compared the feeding rates of three coral species (Acropora millepora, Pocillopora acuta and Galaxea fascicularis) fed Artemia salina through capture rate (indirect) and dissection (direct) approaches, with direct detection and enumeration within dissected polyps facilitated by fluorescent microbeads ingested by the Artemia. When A. millepora was provided Artemia at 3 individuals ml−1 for one hour, the calculated capture rates (0.7 ind. polyp−1 h−1) overestimated prey ingested compared to prey detected directly within polyps (0.2 ind. polyp−1 h−1), and ingestion varied significantly between genotypes. In contrast, for P. acuta, capture rate calculations (1 ind. polyp−1 h−1) underestimated prey detected within polyps (3.5 ind. polyp−1 h−1) and ingestion did not vary between genotypes. For G. fascicularis, the feeding rates were similar as calculated by both capture rates (59 ind. polyp−1 h−1) and by polyp dissections (75 ind. polyp−1 h−1). Results from this study provide valuable insights into coral feeding rates of different coral species that can improve prey enrichment and feeding strategies for nutritional supplementation of corals in captivity

A stratified transect approach captures reef complexity with canopy-forming organisms

On the Great Barrier Reef (GBR), persistent changes to reef communities have begun to be documented, and on inshore reefs these shifts may favour the proliferation of macroalgae. Critical to understanding changes to reef community structure in response to anthropogenic impacts is developing effective methods to accurately document the abundance of different reef organisms. Effective monitoring must be time and cost efficient, replicable, and able to sufficiently and accurately detect disturbances to allow development of strategies to mitigate their impacts. Traditional techniques to document coral reef communities (i.e. photo-quadrats, benthic intercept transects) rely on planar views, which tend to either over- or under-represent canopy-forming organisms. As canopy-forming organisms are likely to be affected by anthropogenic influences (corals negatively, algae positively), it is essential for monitoring programs to implement methods sufficient to document changes to the vertical dimension of coral reefs. Here we build on previous work to document the canopy effect in coral-dominated ecosystems and propose a new survey approach suitable for implementation in algal-dominated systems. A vertically stratified transect, modified from a traditional point intercept transect, captures benthic and canopy-forming members of reef communities and provides information on three-dimensional complexity. To test the capability of the new method to detect changes in vertical reef structure, seaweed was removed from experimental quadrats and monitoring techniques were applied before and after four months of regrowth. A stratified method more accurately captured the three-dimensional change resulting from algal canopy growth, while resolving the over- and under-representation of algal biomass in two traditional techniques. We propose that a stratified transect method improves abundance estimates of canopy-forming organisms whilst maintaining data compatibility with traditional methods

High diversity of microplankton surrounds deep-water coral reef in the Norwegian Sea

Coral reefs that exist in the depths of the oceans are surrounded by Eukarya, Archaea and bacterial communities that may play an important role in the nutrition and health of the reef. The first interdomain community structure of planktonic organisms in seawater from a deep-water coral reef is described. Community profiling and analysis of ribosomal RNA gene sequences from a coral reef system at 350 m depth in the Norwegian Sea revealed a rich diversity of Eukarya and Bacteria and a moderate diversity of Archaea. Most sequences affiliated with marine microplankton from deep-sea to cold-surface regions, with many sequences being similar to those described in studies of mesopelagic and oxygen minimum zones. Dominant phylotypes belonged to the Alveolata (group I, II, dinoflagellates), Stramenopiles (silicoflagellates), Alphaproteobacteria (Pelagibacter ubique), Gammaproteobacteria (ARCTIC96BD-19), Bacteroidetes (Flavobacteria) and mesophilic Crenarchaeota (Nitrosopumilus maritimus). Several rare and novel members of the community fell into distinct phylogenetic groups. The inferred function of dominant community members suggested autotrophs that utilise light, ammonium or sulphide, and lifestyles based on host associations. The high diversity reflected a microplankton community structure, which is significantly different from that of microplankton collected at the same depth at a pelagic station away from reefs

Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis

Genotype-specific contributions to the environmental tolerance and disease susceptibility of corals are widely accepted. Yet our understanding of how host genotype influences the composition and stability of the coral microbiome subjected to environmental fluctuations is limited. To gain insight into the community dynamics and environmental stability of microbiomes associated with distinct coral genotypes, we assessed the microbial community associated with Acropora tenuis under single and cumulative pressure experiments. Experimental treatments comprised either a single pulse of reduced salinity (minimum of 28 psu) or exposure to the cumulative pressures of reduced salinity (minimum of 28 psu), elevated seawater temperature (+2°C), elevated pCO2(900 ppm), and the presence of macroalgae. Analysis of 16S rRNA gene amplicon sequence data revealed that A. tenuis microbiomes were highly host-genotype specific and maintained high compositional stability irrespective of experimental treatment. On average, 48% of the A. tenuis microbiome was dominated by Endozoicomonas. Amplicon sequence variants (ASVs) belonging to this genus were significantly different between host individuals. Although no signs of stress were evident in the coral holobiont and the vast majority of ASVs remained stable across treatments, a microbial indicator approach identified 26 ASVs belonging to Vibrionaceae, Rhodobacteraceae, Hahellaceae, Planctomycetes, Phylobacteriaceae, Flavobacteriaceae, and Cryomorphaceae that were significantly enriched in corals exposed to single and cumulative stressors. While several recent studies have highlighted the efficacy of microbial indicators as sensitive markers for environmental disturbance, the high host-genotype specificity of coral microbiomes may limit their utility and we therefore recommend meticulous control of host-genotype effects in coral microbiome research

Biological controls to manage Acropora-eating flatworms in coral aquaculture

Coral aquaculture is expanding to supply the marine ornamental trade and active coral reef restoration. A common pest of Acropora corals is the Acropora-eating flatworm Prosthiostomum acroporae, which can cause colonial mortality at high infestation densities on Acropora spp. We investigated the potential of 2 biological control organisms in marine aquaria for the control of P. acroporae infestations. A. millepora fragments infested with adult polyclad flatworms (5 flatworms fragment(-1)) or single egg clusters laid on Acropora skeleton were cohabited with either sixline wrasse Pseudocheilinus hexataenia or the peppermint shrimp Lysmata vittata and compared to a control (i.e. no predator) to assess their ability to consume P. acroporae at different life stages over 24 h. P. hexataenia consumed 100% of adult flatworms from A. millepora fragments (n = 9; 5 flatworms fragment(-1)), while L. vittata consumed 82.0 +/- 26.36% of adult flatworms (mean +/- SD; n= 20). Pseudocheilinus hexataenia did not consume any Prosthiostomum acroporae egg capsules, while L. vittata consumed 63.67 +/- 43.48% (n = 20) of egg capsules on the Acropora skeletons. Mean handling losses in controls were 5.83% (shrimp system) and 3.50% (fish system) of flatworms and 2.39% (fish system) and 3.50% (shrimp system) of egg capsules. Encounters between L. vittata and P. hexataenia result in predation of P. acroporae on an Acropora coral host and represent viable biological controls for reducing infestations of P. acroporae in aquaculture systems

Implications of ocean acidification for marine microorganisms from the free-living to the host-associated

Anthropogenic CO2 emissions are causing oceans to become more acidic, with consequences for all marine life including microorganisms. Studies reveal that from the microbes that occupy the open ocean to those intimately associated with their invertebrate hosts changing ocean chemistry will alter the critical functions of these important organisms. Our current understanding indicates that bacterial communities associated with their host will shift as pH drops by another 0.2–0.4 units over the next 100 years. It is unclear what impacts this will have for host health, however, increased vulnerability to disease seems likely for those associated with reef corals. Natural CO2 seeps have provided a unique setting for the study of microbial communities under OA in situ, where shifts in the bacterial communities associated with corals at the seep are correlated with a decline in abundance of the associated coral species. Changes to global biogeochemical cycles also appear likely as photosynthesis and nitrogen fixation by pelagic microbes becomes enhanced under low pH conditions. However, recent long-term studies have shown that pelagic microbes are also capable of evolutionary adaptation, with some physiological responses to a decline in pH restored after hundreds of generations at high pCO2 levels. The impacts of ocean acidification (OA) also will not work in isolation, thus synergistic interactions with other potential stressors, such as rising seawater temperatures, will likely exacerbate the microbial response to OA. This review discusses our existing understanding of the impacts of OA on both pelagic and host-associated marine microbial communities, whilst highlighting the importance of controlled laboratory studies and in situ experiments, to fill the current gaps in our knowledge

Settlement of larvae from four families of corals in response to a crustose coralline alga and its biochemical morphogens

Healthy benthic substrates that induce coral larvae to settle are necessary for coral recovery. Yet, the biochemical cues required to induce coral settlement have not been identified for many taxa. Here we tested the ability of the crustose coralline alga (CCA) Porolithon onkodes to induce attachment and metamorphosis, collectively termed settlement, of larvae from 15 ecologically important coral species from the families Acroporidae, Merulinidae, Poritidae, and Diploastreidae. Live CCA fragments, ethanol extracts, and hot aqueous extracts of P. onkodes induced settlement (>10%) for 11, 7, and 6 coral species, respectively. Live CCA fragments were the most effective inducer, achieving over 50% settlement for nine species. The strongest settlement responses were observed in Acropora spp.; the only non-acroporid species that settled over 50% were Diploastrea heliopora, Goniastrea retiformis, and Dipsastraea pallida. Larval settlement was reduced in treatments with chemical extracts compared with live CCA, although high settlement (>50%) was reported for six acroporid species in response to ethanol extracts of CCA. All experimental treatments failed (< 10%) to induce settlement in Montipora aequituberculata, Mycedium elephantotus, and Porites cylindrica. Individual species responded heterogeneously to all treatments, suggesting that none of the cues represent a universal settlement inducer. These results challenge the commonly-held notion that CCA ubiquitously induces coral settlement, and emphasize the critical need to assess additional cues to identify natural settlement inducers for a broad range of coral taxa