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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 method

Corals and the reef ecosystems that they support are in global decline due to increasing anthropogenic pressures such as climate change1. However, effective reef conservation strategies are hampered by a limited mechanistic understanding of coral biology and the functional roles of the diverse microbial communities that underpin coral health2,3. Here, we present an integrated genomic characterization of the coral species Porites lutea and its microbial partners. High-quality genomes were recovered from P. lutea, as well as a metagenome-assembled Cladocopium C15 (the dinoflagellate symbiont) and 52 bacterial and archaeal populations. Comparative genomic analysis revealed that many of the bacterial and archaeal genomes encode motifs that may be involved in maintaining association with the coral host and in supplying fixed carbon, B-vitamins and amino acids to their eukaryotic partners. Furthermore, mechanisms for ammonia, urea, nitrate, dimethylsulfoniopropionate and taurine transformation were identified that interlink members of the holobiont and may be important for nutrient acquisition and retention in oligotrophic waters. Our findings demonstrate the critical and diverse roles that microorganisms play within the coral holobiont and underscore the need to consider all of the components of the holobiont if we are to effectively inform reef conservation strategies.

Although the early coral reef-bleaching warning system (NOAA/USA) is established, there is no feasible treatment that can minimize temperature bleaching and/or disease impacts on corals in the field. Here, we present the first attempts to extrapolate the widespread and well-established use of bacterial consortia to protect or improve health in other organisms (e.g., humans and plants) to corals. Manipulation of the coral-associated microbiome was facilitated through addition of a consortium of native (isolated from Pocillopora damicornis and surrounding seawater) putatively beneficial microorganisms for corals (pBMCs), including five Pseudoalteromonas sp., a Halomonas taeanensis and a Cobetia marina-related species strains. The results from a controlled aquarium experiment in two temperature regimes (26 °C and 30 °C) and four treatments (pBMC; pBMC with pathogen challenge – Vibrio coralliilyticus, VC; pathogen challenge, VC; and control) revealed the ability of the pBMC consortium to partially mitigate coral bleaching. Significantly reduced coral-bleaching metrics were observed in pBMC-inoculated corals, in contrast to controls without pBMC addition, especially challenged corals, which displayed strong bleaching signs as indicated by significantly lower photopigment contents and Fv/Fm ratios. The structure of the coral microbiome community also differed between treatments and specific bioindicators were correlated with corals inoculated with pBMC (e.g., Cobetia sp.) or VC (e.g., Ruegeria sp.). Our results indicate that the microbiome in corals can be manipulated to lessen the effect of bleaching, thus helping to alleviate pathogen and temperature stresses, with the addition of BMCs representing a promising novel approach for minimizing coral mortality in the face of increasing environmental impacts.

Human-induced environmental changes have been linked directly with loss of biodiversity. Coral reefs, which have been severely impacted by anthropogenic activities over the last few decades, exemplify this global problem and provide an opportunity to develop research addressing key knowledge gaps through “omics”-based approaches. While many stressors, e.g., global warming, ocean acidification, overfishing, and coastal development have been identified, there is an urgent need to understand how corals function at a basic level in order to conceive strategies for mitigating future reef loss. In this regard, availability of fully sequenced genomes has been immensely valuable in providing answers to questions of organismal biology. Given that corals are metaorganisms comprised of the coral animal host, its intracellular photosynthetic algae, and associated microbiota (i.e., bacteria, archaea, fungi, viruses), these efforts must focus on entire coral holobionts. The Reef Future Genomics 2020 (ReFuGe 2020) Consortium has formed to sequence hologenomes of 10 coral species representing different physiological or functional groups to provide foundation data for coral reef adaptation research that is freely available to the research community.

Diverse and abundant bacterial populations play important functional roles in the multi-partite association of the coral holobiont. The specificity of coral-associated assemblages remains unclear, and little is known about the inheritance of specific bacteria from the parent colony to their offspring. This study investigated if broadcast spawning and brooding corals release specific and potentially beneficial bacteria with their offspring to secure maintenance across generations. Two coral species, Acropora tenuis and Pocillopora damicornis, were maintained in 0.2 μm filtered seawater during the release of their gametes and planulae, respectively. Water samples, excluding gametes and planulae, were subsequently collected, and bacterial diversity was assessed through a pyrosequencing approach amplifying a 470-bp region of the 16S rRNA gene including the variable regions 1–3. Compared to the high bacterial diversity harboured by corals, only a few taxa of bacteria were released by adult corals. Both A. tenuis and P. damicornis released similar bacteria, and the genera Alteromonas and Roseobacter were abundant in large proportions in the seawater of both species after reproduction. This study suggests that adult corals may release bacteria with their offspring to benefit the fitness in early coral life stages.

Globally, reef-building corals are the most prolific producers of dimethylsulphoniopropionate (DMSP)1, 2, a central molecule in the marine sulphur cycle and precursor of the climate-active gas dimethylsulphide3, 4. At present, DMSP production by corals is attributed entirely to their algal endosymbiont, Symbiodinium2. Combining chemical, genomic and molecular approaches, we show that coral juveniles produce DMSP in the absence of algal symbionts. DMSP levels increased up to 54% over time in newly settled coral juveniles lacking algal endosymbionts, and further increases, up to 76%, were recorded when juveniles were subjected to thermal stress. We uncovered coral orthologues of two algal genes recently identified in DMSP biosynthesis, strongly indicating that corals possess the enzymatic machinery necessary for DMSP production. Our results overturn the paradigm that photosynthetic organisms are the sole biological source of DMSP, and highlight the double jeopardy represented by worldwide declining coral cover, as the potential to alleviate thermal stress through coral-produced DMSP declines correspondingly.

The waters surrounding coral reef ecosystems are generally poor in nutrients, yet their levels of primary production are comparable with those reported from tropical rain forests. One explanation of this paradox is the efficient cycling of nutrients between the coral host, its endosymbiotic alga Symbiodinium and a wide array of microorganisms. Despite their importance for the animals' fitness, the cycling of nutrients in early coral life stages and the initial establishment of partnerships with the microbes involved in these processes has received little scrutiny to date. Nitrogen is an essential but limited nutrient in coral reef ecosystems. In order to assess the early nutrient exchange between bacteria and corals, coral larvae of the species Pocillopora damicornis were incubated with two coral-associated bacteria (Alteromonas sp., or Vibrio alginolyticus), prelabeled with the stable nitrogen isotope N-15. The incorporation and translocation of nitrogen from Vibrio- and Alteromonas bacteria into P. damicornis coral larvae and specifically into the coral-symbiotic Symbiodinium were detected by nanoscale secondary ion mass spectrometry (NanoSIMS). A significant increase in the amount of enriched N-15 (two to threefold compared to natural abundance) was observed in P. damicornis larvae within 8h of incubation for both bacterial treatments (one-way ANOVA, F-5,F-53=18.03, P=0.004 for Alteromonas sp. and F-5,F-53=18.03, P=0.0001 for V. alginolyticus). These findings reveal that coral larvae acquire nutrients previously taken up from the environment by bacteria. The additional nitrogen may increase the survival rate and fitness of the developing coral and therefore contribute to the successful maintenance of coral reefs.

Bacteria associated with three coral species, Acropora tenuis, Pocillopora damicornis and Tubastrea faulkneri, were assessed before and after coral mass spawning on Ningaloo Reef in Western Australia. Two colonies of each species were sampled before and after the mass spawning event and two additional samples were collected for P. damicornis after planulation. A variable 470 bp region of the 16 S rRNA gene was selected for pyrosequencing to provide an understanding of potential variations in coral-associated bacterial diversity and community structure. Bacterial diversity increased for all coral species after spawning as assessed by Chao1 diversity indicators. Minimal changes in community structure were observed at the class level and data at the taxonomical level of genus incorporated into a PCA analysis indicated that despite bacterial diversity increasing after spawning, coral-associated community structure did not shift greatly with samples grouped according to species. However, interesting changes could be detected from the dataset; for example, α-Proteobacteria increased in relative abundance after coral spawning and particularly the Roseobacter clade was found to be prominent in all coral species, indicating that this group may be important in coral reproduction.

Coral-associated microbial communities from three coral species (Pocillopora damicornis, Acropora tenuis and Favites abdita) were examined every 3 months (January, March, June, October) over a period of 1 year on Ningaloo Reef, Western Australia. Tissue from corals was collected throughout the year and additional sampling of coral mucus and seawater samples was performed in January. Tissue samples were also obtained in October from P. damicornis coral colonies on Rottnest Island off Perth, 1200 km south of Ningaloo Reef, to provide comparisons between coral-microbial associates in different locations. The community structures of the coral-associated microorganisms were analysed using phylogenetic analysis of 16S rRNA gene clone libraries, which demonstrated highly diverse microbial profiles among all the coral species sampled. Principal component analysis revealed that samples grouped according to time and not species, indicating that coral-microbial associations may be a result of environmental drivers such as oceanographic characteristics, benthic community structure and temperature. Tissue samples from P. damicornis at Rottnest Island revealed similarities in bacteria to the samples at Ningaloo Reef. This study highlights that coral-associated microbial communities are highly diverse; however, the complex interactions that determine the stability of these associations are not necessarily dependent on coral host specificity. © 2010 Federation of European Microbiological Societies.

Hydrocarbon seeps provide inputs of petroleum hydrocarbons to widespread areas of the Timor Sea. Alkanes constitute the largest proportion of chemical components found in crude oils, and therefore genes involved in the biodegradation of these compounds may act as bioindicators for this ecosystem's response to seepage. To assess alkane biodegradation potential, the diversity and distribution of alkane hydroxylase (alkB) genes in sediments of the Timor Sea were studied. Deduced AlkB protein sequences derived from clone libraries identified sequences only distantly related to previously identified AlkB sequences, suggesting that the Timor Sea maybe a rich reservoir for novel alkane hydroxylase enzymes. Most sequences clustered with AlkB sequences previously identified from marine Gammaproteobacteria though protein sequence identities averaged only 73% (with a range of 60% to 94% sequence identities). AlkB sequence diversity was lower in deep water (>400 m) samples off the continental slope than in shallow water (<100 m) samples on the continental shelf but not significantly different in response to levels of alkanes. Real-time PCR assays targeting Timor Sea alkB genes were designed and used to quantify alkB gene targets. No correlation was found between gene copy numbers and levels of hydrocarbons measured in sediments using sensitive gas chromatography-mass spectrometry techniques, probably due to the very low levels of hydrocarbons found in most sediment samples. Interestingly, however, copy numbers of alkB genes increased substantially in sediments exposed directly to active seepage even though only low or undetectable concentrations of hydrocarbons were measured in these sediments in complementary geochemical analyses due to efficient biodegradation.

Aims: Vibrio harveyi is an important pathogen, causing potential devastation to marine aquaculture. This organism, however, is extremely difficult to identify because it is phenotypically diverse. Biochemical identification can involve many tests and take weeks to perform. The aim of this work is to develop a PCR that can reduce the number of biochemical tests, and the time taken, to get a definitive identification of this organism. Methods and Results: The PCR was developed using 16S rDNA sequences from a number of V. harveyi strains, and other vibrios. The described test gave positive results for all strains of V. harveyi tested. However, some strains of V. alginolyticus also gave positive results and a small number of biochemical tests were required to differentiate between these two species. This indicated that preisolation of the bacteria was needed and therefore the test was not applicable to the testing of mixed populations directly. Conclusion, Significance and Impact of the Study: The duration of identification of this species was significantly reduced from a number of weeks to a few days. Hence, diagnosis of affected animals will be faster and earlier treatment can be administered which may increase the survival rate from vibriosis.