Coral Reef Benthos Research Articles

Microbiome of Sri Lankan Coral Reefs: An Indian Ocean Island Subjected to a Gradient of Natural and Anthropogenic Impacts

Coral reefs around Sri Lanka have coexisted with human communities for thousands of years and are a continual source of food, economic productivity, and tourism. Although these reef systems sustain nearby populations, little is known about the presence or functional role of microbial communities on reefs dominated by hard corals or fleshy algae. Coral reef benthos cover was recorded, and reef-associated water samples were collected, sequenced and analyzed from seven coral reefs around Sri Lanka. Microbial metagenomes were analyzed to reveal both the taxonomic and metabolic makeup of the microbial communities present at each site. A metagenomic analysis of microbial phyla showed that Alphaproteobacteria and Gammaproteobacteria were most abundant, constituting up to 79.4% of microbial communities. At the order level, Rhodobacterales dominated the microbial communities across all sites, with the exception of the Paraviwella coral reef, where the order Alteromonadales dominated. A Principal Component Analysis (PCA) was performed using metagenomic sequence data to find the possible trends of interactions and drivers of taxonomic and metabolic community structure. This study is the first microbial metagenome dataset of coral reef associated water from the Indian Ocean continental island, Sri Lanka. These data further confirm the need for a comprehensive study of reefs in Sri Lanka aimed at elucidating the processes involved in microbial energy utilization.

Coral Reef Benthos Classification Using Data from a Short-Range Multispectral Sensor

A five-band short-range multispectral sensor (MicaSense RedEdge-M) was adapted to an underwater housing and used to obtain data from coral reef benthos. Artificial illumination was required to obtain data from most of the spectral range of the sensor; the optimal distance for obtaining these data was 0.5 m, from the sensor to the bottom. Multispectral orthomosaics were developed using structure-from-motion software; these have the advantage of producing ultra-high spatial resolution (down to 0.4 × 0.4 mm/pixel) images over larger areas. Pixel-based supervised classification of a multispectral (R, G, B, RE bands) orthomosaic accurately discriminated among different benthic components; classification schemes defined 9 to 14 different benthic components such as brown algae, green algae, sponges, crustose coralline algae, and different coral species with high accuracy (up to 84% overall accuracy, and 0.83 for Kappa and Tau coefficients). The least useful band acquired by the camera for this underwater application was the near-infrared (820–860 nm) associated with its rapid absorption in the water column. Further testing is required to explore possible applications of these multispectral orthomosaics, including the assessment of the health of coral colonies, as well as the automation of their processing.

Interaction effects of crude oil and nutrient exposure on settlement of coral reef benthos

Anthropogenic stressors increasingly cause ecosystem-level changes to sensitive marine habitats such as coral reefs. Intensification of coastal development and shipping traffic can increase nutrient and oil pollution on coral reefs, yet these two stressors have not been studied in conjunction. Here, we simulate a disturbance scenario exposing carbonate settlement tiles to nutrient and oil pollution in a full-factorial design with four treatments: control, nutrients, oil, and combination to examine community structure and net primary productivity (NPP) of pioneer communities throughout 28 weeks. Compared to the control treatment oil pollution decreased overall settlement and NPP, while nutrients increased turf algae and NPP. However, the combination of these two stressors resulted in similar community composition and NPP as the control. These results indicate that pioneer communities may experience shifts due to nutrient enrichment, and/or oil pollution. However, the timing and duration of an event will influence recovery trajectories requiring further study.

Effects of the cleaner fish Labroides dimidiatus on grazing fishes and coral reef benthos

Territorial and roving grazing fishes farm, and feed on, algae, sediment, or detritus, thus exerting different influences on benthic community structure, and are common clients of cleaner fish. Whether cleaners affect grazing-fish diversity and abundance, and indirectly the benthos, was tested using reefs maintained free of the bluestreak cleaner wrasseLabroides dimidiatusfor 8.5 yr (removals) compared with controls. We quantified fish abundance per grazing functional group, foraging rates of roving grazers, cleaning rates of roving grazers byL. dimidiatus, reef benthos composition, and fouling material on settlement tiles. Abundances of ‘intensive’ and ‘extensive’ territorial farmers, non-farmers, parrotfishes andAcanthurusspp. were lower on removal than control reefs, but this was not the case for ‘indeterminate’ farmers andCtenochaetus striatus. Foraging rates ofAcanthurusspp. andC. striatuswere unaffected by cleaner presence or cleaning duration. This suggests some robustness of the grazers’ foraging behaviour to loss of cleaners.Acanthurusspp. foraged predominantly on sediment and detritus, whereasC. striatusand parrotfishes grazed over algal turfs. Nevertheless, benthic community structure and amount of organic and inorganic material that accumulated over 3.5 mo on tiles were not affected by cleaner presence. Thus, despite greater abundances of many roving grazers, and consequently higher grazing rates being linked to the presence of cleaners, the benthos was not detectably affected by cleaners. This reveals that the positive effect of cleaners on fish abundance is not associated with a subsequent change in the benthos as predicted. Rather, it suggests a resilience of benthic community structure to cleaner-fish loss, possibly related to multiple antagonistic effects of different grazer functional groups. However, losing cleaners remains a problem for reefs, as the lack of cleaning has adverse consequences for fish physiology and populations.

Baseline Assessment of Marine Litter and Microplastic Ingestion by Cold-Water Coral Reef Benthos at the East Mingulay Marine Protected Area (Sea of the Hebrides, Western Scotland)

The extent of marine litter and microplastic occurrence across ocean biomes and species remains poorly characterised, particularly in remote deep-water ecosystems. The present study in the East Mingulay Special Area of Conservation (a Marine Protected Area in the Sea of the Hebrides, western Scotland) used historic surveys and benthic samples to obtain baseline levels of anthropogenic debris and microparticle ingestion. Most debris identified in the MPA was fisheries related. A total of 11% of benthic macrofauna from Mingulay Reef Area 1 and Banana Reef had ingested microplastics, with no statistically significant effect of feeding guild, station, or reef, on ingestion rates. However, ingestion rate was highest at a station located in a topographic hollow along a gentle sloping area with strong variable ocean currents where fine-scale interactions between bathymetry and hydrography may have helped trap and focus microparticles. Raman spectroscopy of microparticles revealed several types of polymers being ingested, tentatively identified as polypropylene (PP), polyurethane (PU), polystyrene (PS), and polyethylene terephthalate (PET). Besides establishing a baseline assessment of marine litter and microparticles in a deep-water setting, the approach demonstrates the utility of using historic data and specimens collected for other purposes to expand the geographic and ecosystem coverage for larger more regional-scale and even basin-wide assessments such as those needed to inform Good Environmental Status in European waters as called for by the Marine Strategy Framework Directive.

Hyperspectral Shallow-Water Remote Sensing with an Enhanced Benthic Classifier

Hyperspectral remote sensing inversion models utilize spectral information over optically shallow waters to retrieve optical properties of the water column, bottom depth and reflectance, with the latter used in benthic classification. Accuracy of these retrievals is dependent on the spectral endmember(s) used to model the bottom reflectance during the inversion. Without prior knowledge of these endmember(s) current approaches must iterate through a list of endmember—a computationally demanding task. To address this, a novel lookup table classification approach termed HOPE-LUT was developed for selecting the likely benthic endmembers of any hyperspectral image pixel. HOPE-LUT classifies a pixel as sand, mixture or non-sand, then the latter two are resolved into the three most likely classes. Optimization subsequently selects the class (out of the three) that generated the best fit to the remote sensing reflectance. For a coral reef case, modeling results indicate very high benthic classification accuracy (>90%) for depths less than 4 m of common coral reef benthos. These accuracies decrease substantially with increasing depth due to the loss of bottom information, especially the spectral signatures. We applied this technique to hyperspectral airborne imagery of Heron Reef, Great Barrier Reef and generated benthic habitat maps with higher classification accuracy compared to standard inversion models.

Scaling up Ecological Measurements of Coral Reefs Using Semi-Automated Field Image Collection and Analysis

Ecological measurements in marine settings are often constrained in space and time, with spatial heterogeneity obscuring broader generalisations. While advances in remote sensing, integrative modelling and meta-analysis enable generalisations from field observations, there is an underlying need for high-resolution, standardised and geo-referenced field data. Here, we evaluate a new approach aimed at optimising data collection and analysis to assess broad-scale patterns of coral reef community composition using automatically annotated underwater imagery, captured along 2 km transects. We validate this approach by investigating its ability to detect spatial (e.g., across regions) and temporal (e.g., over years) change, and by comparing automated annotation errors to those of multiple human annotators. Our results indicate that change of coral reef benthos can be captured at high resolution both spatially and temporally, with an average error below 5%, among key benthic groups. Cover estimation errors using automated annotation varied between 2% and 12%, slightly larger than human errors (which varied between 1% and 7%), but small enough to detect significant changes among dominant groups. Overall, this approach allows a rapid collection of in-situ observations at larger spatial scales (km) than previously possible, and provides a pathway to link, calibrate, and validate broader analyses across even larger spatial scales (10–10,000 km2).

Mapping Coral Reef Benthos, Substrates, and Bathymetry, Using Compact Airborne Spectrographic Imager (CASI) Data

This study used a reef-up approach to map coral reef benthos, substrates and bathymetry, with high spatial resolution hyperspectral image data. It investigated a physics-based inversion method for mapping coral reef benthos and substrates using readily available software: Hydrolight and ENVI. Compact Airborne Spectrographic Imager (CASI) data were acquired over Heron Reef in July 2002. The spectral reflectance of coral reef benthos and substrate types were measured in-situ, and using the HydroLight 4.2 radiative transfer model a spectral reflectance library of subsurface reflectance was simulated using water column depths from 0.5–10.0 m at 0.5 m intervals. Using the Spectral Angle Mapper algorithm, sediment, benthic micro-algae, algal turf, crustose coralline algae, macro-algae, and live coral were mapped with an overall accuracy of 65% to a depth of around 8.0 m; in waters deeper than 8.0 m the match between the classified image and field validation data was poor. Qualitative validation of the maps showed accurate mapping of areas dominated by sediment, benthic micro-algae, algal turf, live coral, and macro-algae. A bathymetric map was produced for water column depths 0.5–10.0 m, at 0.5 m intervals, and showed high correspondence with in-situ sonar data (R2 value of 0.93).

Warning Signals of Regime Shifts as Intrinsic Properties of Endogenous Dynamics

Ecosystem dynamics can exhibit large, nonlinear changes after small changes in an environmental parameter that passes a critical threshold. These regime shifts are often associated with loss of biodiversity and ecosystem services. Because critical thresholds for regime shifts are hard to determine with precision, some recent studies have focused on deriving signals from dynamics leading up to the thresholds. Models in these studies depend on using noise terms independent of system parameters and variables to add stochasticity. However, demographic stochasticity, an important source of random variability, arises directly from system dynamics. In this study, a framework is developed for modeling demographic stochasticity in a mechanistic way, incorporating system variables and parameters. This framework is applied to a deterministic, dynamic model of a coral reef benthos. The resulting stochastic model indicates that increasing variance-but not skewness-is consistently found in system dynamics approaching a critical threshold of grazing pressure. Even if the threshold is breached, attraction of transient dynamics by a saddle point provides an opportunity for regime shift reversal by management intervention. These results suggest that early warning signals of regime shifts can arise intrinsically in endogenous dynamics and can be detected without reliance on random environmental forcings.

Spectral reflectance of coral reef benthos and substrate assemblages on Heron Reef, Australia

Studies investigating the spectral reflectance of coral reef benthos and substrates have focused on the measurement of pure endmembers, where the entire field of view (FOV) of a spectrometer is focused on a single benthos or substrate type. At the spatial scales of the current satellite sensors, the heterogeneity of coral reefs even at a sub-metre scale means that many individual image pixels will be made up of a mixture of benthos and substrate types. If pure endmember spectra are used as training data for image classification, there is a spatial discrepancy, because many pixels will have a mixed endmember spectral reflectance signature. This study investigated the spectral reflectance of coral reef benthos and substrates at a spatial scale directly linked to the pixel size of high spatial resolution imaging systems, by incorporating multiple benthos and substrate types into the spectrometer FOV in situ. A total of 334 spectral reflectance signatures were measured of 19 assemblages of the coral reef benthos and substrate types. The spectra were analysed for separability using first derivative values, and a discrimination decision tree was designed to identify the assemblages. Using the decision tree, it was possible to identify 15 assemblages with a mean overall classification accuracy of 62.6%.

Microbial diversity associated with four functional groups of benthic reef algae and the reef‐building coral Montastraea annularis

The coral reef benthos is primarily colonized by corals and algae, which are often in direct competition with one another for space. Numerous studies have shown that coral-associated Bacteria are different from the surrounding seawater and are at least partially species specific (i.e. the same bacterial species on the same coral species). Here we extend these microbial studies to four of the major ecological functional groups of algae found on coral reefs: upright and encrusting calcifying algae, fleshy algae, and turf algae, and compare the results to the communities found on the reef-building coral Montastraea annularis. It was found using 16S rDNA tag pyrosequencing that the different algal genera harbour characteristic bacterial communities, and these communities were generally more diverse than those found on corals. While the majority of coral-associated Bacteria were related to known heterotrophs, primarily consuming carbon-rich coral mucus, algal-associated communities harboured a high percentage of autotrophs. The majority of algal-associated autotrophic Bacteria were Cyanobacteria and may be important for nitrogen cycling on the algae. There was also a rich diversity of photosynthetic eukaryotes associated with the algae, including protists, diatoms, and other groups of microalgae. Together, these observations support the hypothesis that coral reefs are a vast landscape of distinctive microbial communities and extend the holobiont concept to benthic algae.

Coral mucus as an efficient trap for picoplanktonic cyanobacteria: implications for pelagic–benthic coupling in the reef ecosystem

Although the planktonic community of coral reefs is dominated by picoplankton (e.g. the cyanobacterium Synechococcus), it was long believed to play only a marginal role in pelagic- benthic coupling, as its minute size (0.2 to 2.0 µm) and negligible sinking rate render it largely unavailable for the filter-feeding reef benthos. However, scleractinian corals have been shown to continuously release mucus that functions as an efficient trap and important carrier for particulate matter within the reef ecosystem. This study investigates the trapping potential of coral mucus for picoplankton in the laboratory and in the field. Freshly released mucus of Fungia corals already con- tained background levels of pelagic and/or associated synechococcoid cyanobacteria (1.0 ± 0.2 × 10 4 cells ml -1 ). Mesocosm experiments in flow-through tanks revealed up to 46-fold picoplankton enrichment in aged mucus aggregates, while laboratory experiments with rotated chambers con- firmed the pelagic source of these mucus enrichments. Addition of coral mucus resulted in a signifi- cant increase in clearance rates (32 to 52% h -1 ) of the initial Synechococcus spp. population com- pared to clearance found in non-mucus chambers (6 to 18% h -1 ). Drifting mucus aggregates originating from Acropora corals collected in situ exhibited high Synechococcus enrichment (up to 4.6 × 10 6 cells ml -1 ) compared to the surrounding seawater (2.1 ± 0.8 × 10 4 cells ml -1 ), indicating effi- cient picoplankton enrichment by 2 orders of magnitude. The ensuing rapid sedimentation (0.5 to 1 cm s -1 ) of enriched aggregates highlights the importance of coral mucus as a so far overlooked vector enhancing the flux of pelagic picoplankton to the coral reef benthos.

PHOTOSYNTHETIC SYMBIONTS AND ENERGY SUPPLY DETERMINE OCTOCORAL BIODIVERSITY IN CORAL REEFS.

Many coral reef organisms live in symbiotic relationships with photosynthetic microalgae. This symbiosis extends the energy resources available to reef organisms, thereby potentially influencing biodiversity. In octocorals, about one-half of the taxa contain photosynthetic symbionts while the rest do not, and thus octocorals are an ideal model to assess the relationships between biodiversity, spatial and environmental factors, and photosynthetic symbionts. Data collected from 1106 sites on the Great Barrier Reef, Australia, between 12° and 24° S showed that taxa with photosynthetic symbionts (phototrophs) had higher abundances, wider ranges, and a wider spread of locations than taxa without symbionts (heterotrophs). In phototrophic assemblages, spatial turnover comprised both exchange and loss of taxa, and their richness was high across a broad range of environmental conditions. In contrast, heterotrophs were uncommon, had short ranges, and were located where energy supply was highest and disturbance lowest. Turnover between heterotrophic assemblages comprised taxonomic loss rather than exchange of taxa. The biodiversity patterns and differences between phototrophic and heterotrophic octocorals are similar to those recorded in more spatially limited studies of phototrophic sponges and hard corals, and heterotrophic sponges. This study therefore suggests that the association, or not, with photosynthetic symbionts, and spatial and environmental factors related to energy supply and disturbance are principal drivers of biodiversity, community composition, and ranges of coral reef benthos.

Response of the coral reef benthos and herbivory to fishery closure management and the 1998 ENSO disturbance

The hypothesis that herbivory is higher in areas without fishing and will increase the rate at which hard coral communities return to pre-disturbance conditions was tested in and out of the marine protected areas (MPA) of Kenya after the 1998 El Niño Southern Oscillation (ENSO). Herbivory was estimated by assay and biomass methods, and both methods indicated higher herbivory in fishery closures. Despite higher herbivory, the effect of the ENSO disturbance was larger within these closures, with reefs undergoing a temporary transition from dominance by hard and soft coral to a temporary dominance of turf and erect algae that ended in the dominance of calcifying algae, massive Porites, Pocillopora and a few faviids six years after the disturbance. The fished reefs changed the least but had a greater cover of turf and erect algae and sponge shortly after the disturbance. Higher herbivory in the fishery closures reduced the abundance and persistence of herbivore-susceptible erect algae and created space and appropriate substratum for recruiting corals. Nonetheless, other post-settlement processes may have had strong influences such that annual rates of coral recovery were low ( approximately 2%) and not different between the management regimes. Recovery, as defined as and measured by the return to pre-disturbance coral cover and the dominant taxa, was slower in fishery closures than unmanaged reefs.

Modification of benthic communities by territorial damselfish: a multi-species comparison

The effects of territorial damselfish on coral reef benthos have been well-studied for a few relatively large-bodied species with visually distinct territories. Despite a growing body of research demonstrating their abundance, and their effects on algae, corals and other grazers, there has been little research on the effects of the territorial damselfish community as a whole. This study investigated the space occupation, territory composition, and diet of ten damselfish species at three locations: Magnetic and Orpheus Islands (Great Barrier Reef), and Kimbe Bay (Papua New Guinea). Territories were measured, and the composition of benthic communities inside and outside territories was assessed both in situ and from algal collections. The stomach contents of territorial damselfishes were also quantified. Although the larger, previously well-studied species had the most visible effect on the benthic community in their territories, all the smaller species also significantly affected the algal composition, normally with an increase of palatable algae. However, the composition of algal assemblages inside the territories of different species varied considerably. Damselfish territories were highly individual, not just among species, but also among locations. Diets were diverse and indicated a greater degree of omnivory and detritivory than previously thought. At all locations, territories occupied a substantial proportion of the substratum: >25% on Magnetic Island, >50% at Orpheus Island, and ∼50% in Kimbe Bay. Within individual zones, this figure was as high as 70%. The contribution of territorial damselfishes to a range of benthic patterns and processes is considerable, and future benthic studies may need to distinguish more closely between territory and non-territory areas.

A "Reef-Up" approach to classifying coral habitats from IKONOS imagery

Monitoring coral reef benthos with satellites has typically followed a sensor-down approach, with the classification algorithm driven by statistics derived from the imagery. I adopt a method, drawing on statistics derived from hyperspectral optical field measurements of substrate reflectance to train image classification. In order to calibrate the satellite data with direct physical measurements of reflectivity, it is necessary to process both the imagery and in situ data to common units of albedo. Building upon a proof-of-concept study conducted by the author in the Red Sea, the link is made by correcting the remote sensing data for the effect of varying bathymetry using in situ measurement of water column optical properties and a digital elevation model constructed from a vessel-based acoustic survey, thereby yielding units of substrate reflectance. Extensive ground verification of the predictive benthic habitat map resulting from image classification showed that eight substrate classes were resolved with an overall accuracy of 69% down to a depth of 6 m, including live and dead coral framework. As compared to conventional from-image classification techniques, the reef-up method offers the potential for higher thematic accuracy while maintaining a greater degree of flexibility for repeat survey using platforms of higher spectral and spatial resolution, expected to come online in the near future. The fact that image acquisition and optical ground-truthing did not occur concurrently, is of particular relevance in confirming that in situ measurements can be made independent of image acquisition and retrospectively linked to appropriate substrate classes. Considering the wealth of hyperspectral data already acquired for shallow reef facies, the work highlights the potential of the reef-up approach for quantifying substrate distribution in coral environments using both air- and spaceborne platforms.

Spectral unmixing of coral reef benthos under ideal conditions

Hyperspectral remote sensing has shown promise for detailed discrimination of coral reef substratum types, but, by necessity, it samples at pixel scales larger than reef substratum patch sizes. Spectral unmixing techniques have been successful in resolving subpixel areal cover in terrestrial environments. However, the application of spectral unmixing on coral reefs is fundamentally challenging, due not only to the water column, but also to the potentially large number of spectrally similar and ecologically significant end-member (substratum) classes involved. A controlled ex-situ experiment was conducted using field-spectrometer data to assess the accuracy of spectral unmixing techniques to estimate the areal cover of small-scale ( 0.64, i.e. r >0.8). The most successful analyses were based on derivatives of down-sampled data, implying that spectral unmixing benefits more from spectral smoothing and judicious choice of band locations than from high spectral resolution per se. Although these results show that changes in coral and algal cover can be determined by unmixing their spectra, the method is not yet an operational remote sensing tool. Primary empirical research is needed before taking the next step, which is to incorporate a water column, of variable depth, above the sea bed.

Particle removal by coral reef communities: picoplankton is a major source of nitrogen

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 257:13-23 (2003) - doi:10.3354/meps257013 Particle removal by coral reef communities: picoplankton is a major source of nitrogen M. Ribes1,3,*, R. Coma2, M. J. Atkinson1, R. A. Kinzie III1 1Hawaii Institute of Marine Biology, University of Hawaii, PO Box 1346, Coconut Island, Kaneohe 96744, Hawaii, USA 2Centre d¹Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, PO Box 118, 17300 Blanes, Girona, Spain 3Present address: Institut de Ciències del Mar (CMIMA-CSIC), Pg. Marítim 37-49, 08003 Barcelona, Spain *Email: mribes@icm.csic.es ABSTRACT: Removal and uptake of planktonic particulate organic matter by coral reef benthos is widely recognized as an important pathway for carbon and nutrients. We placed 3 natural assemblages of coral reef benthos, including 3 species of corals with associated sponges, ascidians, actinians, and bryozoans, in a long flume (24 x 0.4 x 0.3 m). Water was re-circulated at various speeds (5, 13, 22, and 32 cm s-1) over 6 h, and the disappearance of particles (pico-, nano-, microplankton and detrital particles) were measured using flow cytometry and microscopy. Control communities consisted of dead coral skeletons. Rates of removal of all particles were proportional to their concentrations. The first-order rate constant for the decrease in particle concentration ranged from 36 to 97 x 10-6 m s-1 (mean ± SD = 63 ± 16 x 10-6 m s-1), with 71% of this variation explained by particle type. Water velocity had no significant effect on these rate constants. Living particles contributed 96% of the total nitrogen removal, with picoplankton (cells 0.2 to 2 µm) accounting for 92%. Overall, nitrogen removal from particles (8.8 to 10.3 mmol N m-2 d-1) appears to be similar in magnitude to that of dissolved inorganic nitrogen; thus, picoplankton is a major source of nitrogen for these coral reef assemblages. KEY WORDS: Benthos · Coral reef communities · Nutrients · Particle removal Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 257. Online publication date: August 07, 2003 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2003 Inter-Research.

Linkage of small-scale spatial variations in DOC, inorganic nutrients and bacterioplankton growth with different coral reef water types

This study focuses on links of dissolved organic carbon (DOC), inorganic nutrients (DIN and DIP) and bacterioplankton growth with specific coral reef water types. At 5 reef stations along the SW coast of Curacao (Netherlands Antilles), 6 different water types (4 reef water types (live coral surface contact water, reef crevice water, reef bottom water, reef overlying water) and 2 reference water types collected offshore from each station at 2 and 8 m depth) were analysed for DOC, DIN and DIP, bacterial production and abundance. Consistent patterns were found: reef waters were enhanced in DIN, DIP and specific bacterial growth rate (µn) compared to offshore waters. DOC, DIP, and µn were higher close to the reef bottom than in the reef overlying water. Coral surface contact water was significantly enhanced in DOC compared to reef crevice and reef bottom water, suggest- ing that the major source of DOC in reef waters are the live corals. DIN concentration was highest in reef crevice water, suggesting that crevices are the major net N-regenerating spaces on reefs, more important than the reef bottom between corals. Small-scale DIP distribution suggested net P regen- eration in reef crevice and coral surface contact water. The highest specific growth rates of bacterio- plankton were found in the coral surface contact water, with slightly lower rates in reef crevice water. Experiments showed that the labile DOC fraction (LDOC) in reef crevice water was substantially smaller than in coral surface contact and reef overlying water, which suggests that crevices are apparently sinks of LDOC. In reef crevice and reef bottom water the low substrate LDOC:DIN ratios suggest that LDOC might be the growth-limiting factor of bacterioplankton in these water types. In coral surface contact and reef overlying water the substrate LDOC:DIN ratios of more than 40 (and LDOC:DIP ratios of over 800) and the significant relations between µn and DIN (DIP) suggest nutrient limitation of bacterioplankton growth in these water types. This study clearly illustrates the close link in reef waters between coral reef benthos and bacterioplankton trophodynamics.

Measurement and prediction of mass transfer to experimental coral reef communities

The uptake of nutrients (N and P) into coral reef communities is proposed to be limited by diffusion through concentration‐depleted boundary layers between the water and organisms, or what is termed “mass transfer limitation.” The mass transfer rate is a physical limit to the rate of nutrient uptake. Maximum uptake rates by highly rough biological surfaces have not yet been evaluated. Engineering correlations indicate that increased surface roughness should increase mass transfer, although it has been difficult to quantify roughness of living corals. In this paper, the effects of highly rough coral surfaces on mass transfer were investigated by using dissolution of gypsum (plaster‐of‐paris) from flat smooth surfaces and coral skeletons. The gypsum dissolution rates were measured as an increase in concentration of calcium ions in freshwater recirculating over experimental surfaces. Stanton numbers (Stm, a dimensionless number giving the ratio of uptake rate per unit area to the rate of advection of the substance past the uptake surface) of experimental smooth surfaces ranged from 2.6 to 3.5 × 10−5 and were the same as values in the engineering literature for smooth surfaces. Stm for coral‐shaped surfaces ranged from 70 × 10−5 at 0.03 m s−1 to 17 × 10−5 at velocities up to 0.50 m s−1 and were in general 9 ± 1 times that of smooth surfaces. The measured Stm for each coral‐shaped surface was the same as the predicted Stm (±10%) calculated from measured friction and roughness using a correlation of heat transfer. Stm for ammonia uptake on living coral reef communities show the same relationship between mass transfer, friction, and roughness as the coral‐shaped gypsum surfaces. The transport rates of nutrients to reef surfaces are controlled by large‐scale roughness, typically associated with coral heads, and not small‐scale roughness elements on the organisms, nor biological alterations of diffusive boundary layers. Nutrient uptake and possibly other metabolic exchange rates arc governed by concentration, water velocity, and friction dissipated over the reef, denoting that coral reef community metabolism is physically forced.