DNA extraction from coral reef sediment bacteria for the polymerase chain reaction

A rapid and effective method for the direct extraction of high molecular weight amplifiable DNA from two coral reef sediments was developed. DNA was amplified by the polymerase chain reaction (PCR) using 16S rDNA specific primers. The amplicons were digested with HaeIII, HinP1I and MspI and separated using polyacrylamide gel electrophoresis and silver staining. The resulting amplified ribosomal DNA restriction analysis (ARDRA) patterns were used as a fingerprint to discern differences between the coral reef sediment samples. Results indicated that ARDRA is an effective method for determining differences within the bacterial community amongst different environmental samples.     

The effect of warming and benthic community acclimation on coral reef carbonate sediment metabolism and dissolution

Coral Reefs - Global warming (and the consequent increase in sea surface temperature) is expected to modify rates of gross primary production (GPP), respiration (R), and net calcium carbonate...     

Regenerative functions and microbial ecology of coral reefs: Labelled bacteria in a coral reef microcosm

Representative coral reef organisms and substrata assembled in a laboratory microcosm removed radioactively labelled bacteria from water circulated over them. A similar experiment with a reef clam and its algal-encrusted base gave similar results. Biochemical fractionation of selected organisms in these experiments suggested digestion and possible assimilation of bacterial proteins. In view of previous results concerning the microbial ecology of coral reefs, it is suggested that reef infaunal metazoa are adapted to utilize internal sedimentary processes and regenerative functioning through suspension- (and deposit-)feeding mechanisms. A model ecosystem is presented to suggest the possible feedback of these mechanisms as they operate within a reef.     

High herbivory despite high sediment loads on a fringing coral reef

Coral Reefs - Algal turfs are expected to increasingly dominate the benthos of coral reefs in the Anthropocene, becoming important sources of reef productivity. The sediments trapped within algal...     

Effects of sediment deposition on the seaweed Sargassum on a fringing coral reef

 Coral reef degradation may involve shifts from coral to algal dominance and may be caused in part by increased sediment loads. Inshore fringing reef flats in the central Great Barrier Reef region are often subjected to periods of high sedimentation and are often dominated by macroalgae such as Sargassum. Experiments reported here examine the impacts of sediments on the recruitment, growth, survival, degeneration and vegetative regeneration of Sargassum microphyllum on a fringing coral reef flat in the central Great Barrier Reef. Comparison of three levels of sediment deposition (experimental addition, control (ambient condition) and experimental removal) showed that increased amounts of sediment significantly decreased rates of recruitment, growth, survival and vegetative regeneration, but not degeneration of S. microphyllum. In addition, the regenerative ability of S. microphyllum thalli with short, persistent erect branches (untreated) was compared with that of thalli experimentally cut back to the holdfast. This experimental damage significantly reduced regeneration. Accepted: 6 October 1997     

Coral reef encruster communities and carbonate production in cryptic and exposed coral reef habitats along a gradient of terrestrial disturbance

Encrusting calcareous organisms such as bryozoans, crustose coralline algae (CCA), foraminiferans, and serpulid worms are integral components of tropical framework-building reefs. They can contribute calcium carbonate to the reef framework, stabilise the substrate, and promote larval recruitment of other framework-building species (e.g. coral recruits). The percentage cover of encrusting organisms and their rates of carbonate production (g m⁻² year⁻¹) were assessed at four sites within a coastal embayment, along a gradient of riverine influence (high-low). As the orientation and type of substrate is thought to influence recruitment of encrusting organisms, organisms recruiting to both natural (the underside of platy corals) and experimental substrates were assessed. The effect of substrate exposure under different levels of riverine influence was assessed by orientating experimental substrates to mimic cryptic and exposed reef habitats (downwards-facing vs upwards-facing tiles) at each site. Cryptic experimental tiles supported similar encruster assemblages to those recruiting to the underneath (cryptic side) of platy corals, suggesting that tiles can be used as an experimental substrate to assess encruster recruitment in reef systems. Encruster cover, in particular CCA, and carbonate production was significantly higher at low-impact (clear water), high wave energy sites when compared to highly riverine impacted (turbid water), low wave energy sites. Cryptically orientated substrates supported a greater diversity of encrusting organisms, in particular serpulid worms and bryozoans. The inverse relationships observed between riverine inputs and encrusters (total encruster cover and carbonate production) have implications for both the current and future rates and styles of reefal framework production.     

Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians

Ascidians are ecologically important components of marine ecosystems yet the ascidian microbiota remains largely unexplored beyond a few model species. We used 16S rRNA gene tag pyrosequencing to provide a comprehensive characterization of microbial symbionts in the tunic of 42 Great Barrier Reef ascidian samples representing 25 species. Results revealed high bacterial biodiversity (3 217 unique operational taxonomic units (OTU_0.03) from 19 described and 14 candidate phyla) and the widespread occurrence of ammonia-oxidizing Thaumarchaeota in coral reef ascidians (24 of 25 host species). The ascidian microbiota was clearly differentiated from seawater microbial communities and included symbiont lineages shared with other invertebrate hosts as well as unique, ascidian-specific phylotypes. Several rare seawater microbes were markedly enriched (200–700 fold) in the ascidian tunic, suggesting that the rare biosphere of seawater may act as a conduit for horizontal symbiont transfer. However, most OTUs (71%) were rare and specific to single hosts and a significant correlation between host relatedness and symbiont community similarity was detected, indicating a high degree of host-specificity and potential role of vertical transmission in structuring these communities. We hypothesize that the complex ascidian microbiota revealed herein is maintained by the dynamic microenvironments within the ascidian tunic, offering optimal conditions for different metabolic pathways such as ample chemical substrate (ammonia-rich host waste) and physical habitat (high oxygen, low irradiance) for nitrification. Thus, ascidian hosts provide unique and fertile niches for diverse microorganisms and may represent an important and previously unrecognized habitat for nitrite/nitrate regeneration in coral reef ecosystems.     

Diversity and abundance of ammonia-oxidizing archaea and bacteria in polluted mangrove sediment

Ammonia oxidation by microorganisms is a critical process in the nitrogen cycle. Recent research results show that ammonia-oxidizing archaea (AOA) are both abundant and diverse in a range of ecosystems. In this study, we examined the abundance and diversity of AOA and ammonia-oxidizing beta-proteobacteria (AOB) in estuarine sediments in Hong Kong for two seasons using the ammonia monooxygenase A subunit gene (amoA) as molecular biomarker. Relationships between diversity and abundance of AOA and AOB and physicochemical parameters were also explored. AOB were more diverse but less abundant than AOA. A few phylogenetically distinct amoA gene clusters were evident for both AOA and AOB from the mangrove sediment. Pearson moment correlation analysis and canonical correspondence analysis (CCA) were used to explore physicochemical parameters potentially important to AOA and AOB. Metal concentrations were proposed to contribute potentially to the distributions of AOA while total phosphorus (TP) was correlated to the distributions of AOB. Quantitative PCR estimates indicated that AOA were more abundant than AOB in all samples, but the ratio of AOA/AOB (from 1.8 to 6.3) was smaller than most other studies by one to two orders. The abundance of AOA or AOB was correlated with pH and temperature while the AOA/AOB ratio was with the concentrations of ammonium. Several physicochemical factors, rather than any single one, affect the distribution patterns suggesting that a combination of factors is involved in shaping the dynamics of AOA and AOB in the mangrove ecosystem.     

Algae sediment dynamics are mediated by herbivorous fishes on a nearshore coral reef

Coral Reefs - Epilithic algae are a ubiquitous component of coral reefs. Components of the epilithic algal matrix (EAM) can have a significant influence on coral settlement and benthic feeding by...     

An introduction to the biogeochemical cycling of calcium and substitutive strontium in living coral reef mesocosms

The coral reef mesocosms designed by the Smithsonian Institution's Dr. Walter Adey, his Marine System Laboratory personnel, and staff members of the Pittsburgh Aqua-Zoo simulate most of the physical, chemical, and biological parameters found in natural Caribbean coral reefs. After developing the mesocosm in Pittsburgh, an evaluation and comparison between natural reef seawater sources and closed mesocosm seawater conditions indicated that an additional parameter should be investigated. It was hypothesized that, given time, the aragonite- and calcite (CaCO₃ crystal forms)-producing organisms in the closed mesocosms could deplete the seawater of available Ca²⁺ and substitutive Sr²⁺. Atomic absorption spectrophotometry was utilized to determine concentrations in the seawater over time. Results showed a substantial reduction in dissolved Ca and Sr in the mesocosm after approximately two years. Dissolved aragonitic Halimeda algae parts were put into the system for replacive purposes. In terms of the biogeochemical cycling of Ca²⁺ and Sr²⁺, the coral reef mesocosm organisms behaved similarly to natural reefs, which have a constant supply of dissolved Ca²⁺ and Sr²⁺. Further research utilizing radiolabeled sources of Ca²⁺, Sr²⁺, and Mg²⁺, in conjunction with in vivo scanning electron microscopy (SEM) and growth increment studies, are recommended for determining the exact biogeochemical pathways for these elements in coral reefs, and to quantify growth parameters. © 1993 Wiley-Liss, Inc.     

Long‐term population dynamics of a coral reef gastropod and responses to disturbance

The age‐specific density of the red‐lipped stromb Strombus luhuanus (Mollusca: Gastropoda) was monitored over 13 years (1981–1993) at four locations on the intertidal reef flat at Heron Island, Great Barrier Reef. Densities were highly variable, but there were persistent, location‐specific differences in population density, age structure and adult body size, the latter indicating that the populations were not extensively linked by adult movement. There was relatively high recruitment at most locations in 1984, 1989 and 1993, each occurring approximately 2 years after El Niño/Southern Oscillation events, although recruit density during these years varied in both space and time. The studied strombs experienced three disturbance events: (i) experimental harvesting at two locations (1984–1985); (ii) siltation from a harbour dredging operation (1987–1988); and (iii) a severe cyclone (1992). Resilience to harvesting at a local scale (0.5–2 ha) was high: density had recovered within a year, due to immigration of adults and older juveniles. Strombus luhuanus responded much more strongly to broad‐scale changes to its environment than to localized harvesting. After dredging, there was a progressive density decline coupled with low recruitment at two locations, and a later decline at a third location, followed by a recruitment‐driven rebound after the cyclone. Generalized environmental effects of siltation and the cyclone were also reflected in substantial changes in algal cover. Long‐term variations in environmental conditions probably cause high temporal variation over large spatial scales through effects on the survival of larvae or recruits. Localized short‐term field monitoring of such species would give a misleading picture of key factors affecting population dynamics.     

Large‐scale coral reef rehabilitation after blast fishing in Indonesia

The severely degraded condition of many coral reefs worldwide calls for active interventions to rehabilitate their physical and biological structure and function, in addition to effective management of fisheries and no‐take reserves. Rehabilitation efforts to stabilize reef substratum sufficiently to support coral growth have been limited in size. We documented a large coral reef rehabilitation in Indonesia aiming to restore ecosystem functions by increasing live coral cover on a reef severely damaged by blast fishing and coral mining. The project deployed small, modular, open structures to stabilize rubble and to support transplanted coral fragments. Between 2013 to 2015, approximately 11,000 structures covering 7,000 m² were deployed over 2 ha of a reef at a cost of US$174,000. Live coral cover on the structures increased from less than 10% initially to greater than 60% depending on depth, deployment date and location, and disturbances. The mean live coral cover in the rehabilitation area in October 2017 was higher than reported for reefs in many other areas in the Coral Triangle, including marine protected areas, but lower than in the no‐take reference reef. At least 42 coral species were observed growing on the structures. Surprisingly, during the massive coral bleaching in other regions during the 2014–2016 El Niño–Southern Oscillation event, bleaching in the rehabilitation area was less than 5% cover despite warm water (≥30°C). This project demonstrates that coral rehabilitation is achievable over large scales where coral reefs have been severely damaged and are under continuous anthropogenic disturbances in warming waters.     

Suspended sediment impairs habitat choice and chemosensory discrimination in two coral reef fishes

Increasing sediment onto coral reefs has been identified as a major source of habitat degradation, and yet little is known about how it affects reef fishes. In this study, we tested the hypothesis that sediment-enriched water impairs the ability of larval damselfish to find suitable settlement sites. At three different experimental concentrations of suspended sediment (45, 90, and 180 mg l⁻¹), pre-settlement individuals of two species (Pomacentrus amboinensis and P. moluccensis) were not able to select their preferred habitat. In a clear water environment (no suspended sediment), both species exhibit a strong preference for live coral over partially dead and dead coral, choosing live coral 70 and 80% of the time, respectively. However, when exposed to suspended sediment, no habitat choice was observed, with individuals of both species settling on live coral, partially dead, and dead coral, at the same frequency. To determine a potential mechanism underlying these results, we tested chemosensory discrimination in sediment-enriched water. We demonstrated that sediment disrupts the ability of this species to respond to chemical cues from different substrata. That is, individuals of P. moluccensis prefer live coral to dead coral in clear water, but in sediment-enriched water, chemical cues from live and dead coral were not distinguished. These results suggest that increasing suspended sediment in coral reef environments may reduce settlement success or survival of coral reef fishes. A sediment-induced disruption of habitat choice may compound the effects of habitat loss on coral reefs.     

Ability to home in small site‐attached coral reef fishes

The ability of two common, site‐attached coral‐reef fishes to return to their home corals after displacement was investigated in a series of field experiments at One Tree Island, southern Great Barrier Reef. The humbug Dascyllus aruanus was displaced up to 250 m, with 42% of individuals returning home, irrespective of body size, displacement, direction (up or across currents) and route complexity, while for the lemon damselfish Pomacentrus moluccensis 35% of individuals returned overall, with 33% from the greatest displacement, 100 m along a reef edge. Given that the home range of both species is <1 m², over their 10+ year life span, the mechanisms and motivations for such homing ability are unclear but it may allow resilience if fishes are displaced by storm events, allowing rapid return to home corals.     

Mixed asexual and sexual reproduction in the Indo‐Pacific reef coral Pocillopora damicornis

Pocillopora damicornis is one of the best studied reef‐building corals, yet it's somewhat unique reproductive strategy remains poorly understood. Genetic studies indicate that P. damicornis larvae are produced almost exclusively parthenogenetically, and yet population genetic surveys suggest frequent sexual reproduction. Using microsatellite data from over 580 larvae from 13 colonies, we demonstrate that P. damicornis displays a mixed reproductive strategy where sexual and asexual larvae are produced simultaneously within the same colony. The majority of larvae were parthenogenetic (94%), but most colonies (10 of the 13) produced a subset of their larvae sexually. Logistic regression indicates that the proportion of sexual larvae varied significantly with colony size, cycle day, and calendar day. In particular, the decrease in sexual larvae with colony size suggests that the mixed reproductive strategy changes across the life of the coral. This unique shift in reproductive strategy leads to increasingly asexual replications of successful genotypes, which (in contrast to exclusive parthenogens) have already contributed to the recombinant gene pool.     

First description of the neuro‐anatomy of a larval coral reef fish Amphiprion ocellaris

The present study described the neuro‐anatomy of a larval coral reef fish Amphiprion ocellaris and hypothesized that morphological changes during the transition from the oceanic environment to a reef environment (i.e. recruitment) have the potential to be driven by changes to environmental conditions and associated changes to cognitive requirements. Quantitative comparisons were made of the relative development of three specific brain areas (telencephalon, mesencephalon and cerebellum) between 6 days post‐hatch (dph) larvae (oceanic phase) and 11 dph (at reef recruitment). The results showed that 6 dph larvae had at least two larger structures (telencephalon and mesencephalon) than 11 dph larvae, while the size of cerebellum remained identical. These results suggest that the structure and organization of the brain may reflect the cognitive demands at every stage of development. This study initiates analysis of the relationship between behavioural ecology and neuroscience in coral reef fishes.     

Differential modification of seawater carbonate chemistry by major coral reef benthic communities

Ocean acidification (OA) resulting from uptake of anthropogenic CO₂ may negatively affect coral reefs by causing decreased rates of biogenic calcification and increased rates of CaCO₃ dissolution and bioerosion. However, in addition to the gradual decrease in seawater pH and Ω _a resulting from anthropogenic activities, seawater carbonate chemistry in these coastal ecosystems is also strongly influenced by the benthic metabolism which can either exacerbate or alleviate OA through net community calcification (NCC = calcification – CaCO₃ dissolution) and net community organic carbon production (NCP = primary production ? respiration). Therefore, to project OA on coral reefs, it is necessary to understand how different benthic communities modify the reef seawater carbonate chemistry. In this study, we used flow-through mesocosms to investigate the modification of seawater carbonate chemistry by benthic metabolism of five distinct reef communities [carbonate sand, crustose coralline algae (CCA), corals, fleshy algae, and a mixed community] under ambient and acidified conditions during summer and winter. The results showed that different communities had distinct influences on carbonate chemistry related to the relative importance of NCC and NCP. Sand, CCA, and corals exerted relatively small influences on seawater pH and Ω _a over diel cycles due to closely balanced NCC and NCP rates, whereas fleshy algae and mixed communities strongly elevated daytime pH and Ω _a due to high NCP rates. Interestingly, the influence on seawater pH at night was relatively small and quite similar across communities. NCC and NCP rates were not significantly affected by short-term acidification, but larger diel variability in pH was observed due to decreased seawater buffering capacity. Except for corals, increased net dissolution was observed at night for all communities under OA, partially buffering against nighttime acidification. Thus, algal-dominated areas of coral reefs and increased net CaCO₃ dissolution may partially counteract reductions in seawater pH associated with anthropogenic OA at the local scale.     

Model of a coral reef ecosystem

The results of modelling of a coral reef ecosystem at French Frigate Shoals and independent field measures of benthic primary productivity indicate relatively good agreement between food required by consumer trophic levels and organic carbon produced by primary producers. Based upon the high internal predation necessary for the model to match primary production estimates, we reason that the ecosystem is primarily regulated from the top down by forces of predation and that primary production appears to be controlled by nutrients, rate limits, and the distribution of space and habitat. In spite of relatively high primary productivity, potential yield at the top of the food chain is low because of high internal predation and high trophic complexity (6 trophic levels). Fishery yield might be maximized by harvesting low on the food chain particularly if top carnivores can be cropped to release predator pressure on selected prey. Agreement between field measures of metabolism and model (ECOPATH) results provides reasonable confidence that the model can be used as one tool for resource management.     

Enhanced fast-start performance and anti-predator behaviour in a coral reef fish in response to suspended sediment exposure

Coral Reefs - Declining water quality, in particular elevated suspended sediments, poses a significant threat to coastal coral reefs. We exposed juvenile anemonefish (Amphiprion melanopus) to two...     

Marine plants in a coral reef ecosystem

Based on a review of the literature and our own data, marine plants are shown to play an important role in the formation and sustaining of coral reefs, which are one of coastal tropical ecosystems of the World Ocean. The important ecosystem roles of marine plants include primary production and recycling of organic matter, the construction of the hard base of a coral reef, the fixation of dissolved molecular nitrogen in sea-water, the formation of an initial link in the food chain, the provision of a habitat for marine animals, and the protection of the reef against destructive wave action.