Biodiversity, population regulation, and the stability of coral-reef fish communities

Assembly rules of coral reef fish communities along the depth gradient

Coral reefs are home to some of the most studied ecological assemblages on the planet. However, differences in large-scale assembly rules have never been studied using empirical quantitative data stratified along the depth gradient of reefs. Consequently, little is known about the small- and regional-scale effects of depth on coral reef assemblages. Using a large dataset of underwater surveys, we observed that the influence of classic biogeographic drivers on the species richness of coral reef fishes changes significantly with depth, shaping distinct assemblages governed by different rules in mesophotic coral ecosystems. We show that a general pattern of decreased taxonomic and functional richness of reef fish assemblages with depth results from convergent filtering of species composition and trophic strategies on deeper reefs across ocean basins and that at smaller scales deep-reef communities are less influenced by regional factors than shallower reefs.

Regulation of open populations of a stream insect through larval density-dependence

In organisms with complex life cycles, the various stages occupy different habitats creating demographically open populations. The dynamics of these populations will depend on the occurrence and timing of stochastic influences relative to demographic density dependence, but understanding of these fundamentals, especially in the face of climate warming, has been hampered by the difficulty of empirical studies.

Using a logically feasible organism, we conducted a replicated density‐perturbation experiment to manipulate late‐instar larvae of nine populations of a stream caddisfly, Zelandopsyche ingens, and measured the resulting abundance over 2 years covering the complete life cycle of one cohort to evaluate influences on dynamics.

Negative density feedback occurred in the larval stage, and was sufficiently strong to counteract variation in abundance due to manipulation of larval density, adult caddis dispersal in the terrestrial environment as well as downstream drift of newly hatched and older larvae in the current. This supports theory indicating regulation of open populations must involve density dependence in local populations sufficient to offset variability associated with dispersal, especially during recruitment, and pinpoints the occurrence to late in the larval life cycle and driven by food resource abundance.

There were large variations in adult, egg mass and early instar abundance that were not related to abundance in the previous stage, or the manipulation, pointing to large stochastic influences. Thus, the results also highlight the complementary nature of stochastic and deterministic influences on open populations. Such density dependence will enhance population persistence in situations where variable dispersal and transitioning between life stages frequently creates mismatches between abundance and the local availability of resources, such as might become more common with climate warming.

Regional heterogeneity in coral species richness and hue reveals novel global predictors of reef fish intra-family diversity

Habitat heterogeneity shapes biological communities, a well-known process in terrestrial ecosystems but substantially unresolved within coral reef ecosystems. We investigated the extent to which coral richness predicts intra-family fish richness, while simultaneously integrating a striking aspect of reef ecosystems-coral hue. To do so, we quantified the coral richness, coral hue diversity, and species richness within 25 fish families in 74 global ecoregions. We then expanded this to an analysis of all reef fishes (4465 species). Considering coral bleaching as a natural experiment, we subsequently examined hue's contribution to fish communities. Coral species and hue diversity significantly predict each family's fish richness, with the highest correlations (> 80%) occurring in damselfish, butterflyfish, emperors and rabbitfish, lower (60-80%) in substrate-bound and mid-water taxa such as blennies, seahorses, and parrotfish, and lowest (40-60%) in sharks, morays, grunts and triggerfish. The observed trends persisted globally. Coral bleaching's homogenization of reef colouration revealed hue's contribution to maintaining fish richness, abundance, and recruit survivorship. We propose that each additional coral species and associated hue provide added ecological opportunities (e.g. camouflage, background contrast for intraspecific display), facilitating the evolution and co-existence of diverse fish assemblages.

Oxygen-dependent changes in binding partners and post-translational modifications regulate the abundance and activity of HIF-1α/2α

Cellular adaptation to low-oxygen environments is mediated in part by the hypoxia-inducible factors (HIFs). Like other transcription factors, the stability and transcriptional activity of HIFs-and consequently, the hypoxic response-are regulated by post-translational modifications (PTMs) and changes in protein-protein interactions. Our current understanding of PTM-mediated regulation of HIFs is primarily based on in vitro protein fragment-based studies typically validated in fragment-expressing cells treated with hypoxia-mimicking compounds. Here, we used immunoprecipitation-based mass spectrometry to characterize the PTMs and binding partners for full-length HIF-1α and HIF-2α under normoxic (21% oxygen) and hypoxic (1% oxygen) conditions. Hypoxia substantially altered the complexity and composition of the HIFα protein interaction networks, particularly for HIF-2α, with the hypoxic networks of both isoforms being enriched for mitochondrial proteins. Moreover, both HIFα isoforms were heavily covalently modified. We identified ~40 PTM sites composed of 13 different types of modification on both HIFα isoforms, including multiple cysteine modifications and an unusual phosphocysteine. More than 80% of the PTMs identified were not previously known and about half exhibited oxygen dependency. We further characterized an evolutionarily conserved phosphorylation of Ser31 in HIF-1α as a regulator of its transcriptional function, and we propose functional roles for Thr406, Thr528, and Ser581 in HIF-2α. These data will help to delineate the different physiological roles of these closely related isoforms in fine-tuning the hypoxic response.

Automated Global Shallow Water Bathymetry Mapping Using Google Earth Engine

Global shallow water bathymetry maps offer critical information to inform activities such as scientific research, environment protection, and marine transportation. Methods that employ satellite-based bathymetric modeling provide an alternative to conventional shipborne measurements, offering high spatial resolution combined with extensive coverage. We developed an automated bathymetry mapping approach based on the Sentinel-2 surface reflectance dataset in Google Earth Engine. We created a new method for generating a clean-water mosaic and a tailored automatic bathymetric estimation algorithm. We then evaluated the performance of the models at six globally diverse sites (Heron Island, Australia; West Coast of Hawaiʻi Island, Hawaiʻi; Saona Island, Dominican Republic; Punta Cana, Dominican Republic; St. Croix, United States Virgin Islands; and The Grenadines) using 113,520 field bathymetry sampling points. Our approach derived accurate bathymetry maps in shallow waters, with Root Mean Square Error (RMSE) values ranging from 1.2 to 1.9 m. This automatic, efficient, and robust method was applied to map shallow water bathymetry at the global scale, especially in areas which have high biodiversity (i.e., coral reefs).

Positive density dependence acting on mortality can help maintain species-rich communities

Conspecific negative density dependence is ubiquitous and has long been recognized as an important factor favoring the coexistence of competing species at local scale. By contrast, a positive density-dependent growth rate is thought to favor species exclusion by inhibiting the growth of less competitive species. Yet, such conspecific positive density dependence often reduces extrinsic mortality (e.g. reduced predation), which favors species exclusion in the first place. Here, using a combination of analytical derivations and numerical simulations, I show that this form of positive density dependence can favor the existence of equilibrium points characterized by species coexistence. Those equilibria are not globally stable, but allow the maintenance of species-rich communities in multispecies simulations. Therefore, conspecific positive density dependence does not necessarily favor species exclusion. On the contrary, some forms of conspecific positive density dependence may even help maintain species richness in natural communities. These results should stimulate further investigations into the precise mechanisms underlying density dependence.

Demographic dynamics of the smallest marine vertebrates fuel coral reef ecosystem functioning

How coral reefs survive as oases of life in low-productivity oceans has puzzled scientists for centuries. The answer may lie in internal nutrient cycling and/or input from the pelagic zone. Integrating meta-analysis, field data, and population modeling, we show that the ocean’s smallest vertebrates, cryptobenthic reef fishes, promote internal reef fish biomass production through extensive larval supply from the pelagic environment. Specifically, cryptobenthics account for two-thirds of reef fish larvae in the near-reef pelagic zone despite limited adult reproductive outputs. This overwhelming abundance of cryptobenthic larvae fuels reef trophodynamics via rapid growth and extreme mortality, producing almost 60% of consumed reef fish biomass. Although cryptobenthics are often overlooked, their distinctive demographic dynamics may make them a cornerstone of ecosystem functioning on modern coral reefs.

The Prevalence and Importance of Competition Among Coral Reef Fishes

Although competition is recognized as a core ecological process, its prevalence and importance in coral reef fish communities have been debated. Here we compile and synthesize the results of 173 experimental tests of competition from 72 publications. We show that evidence for competition is pervasive both within and between species, with 72% of intraspecific tests and 56% of interspecific tests demonstrating a demographically significant consequence of competition (e.g., a decrease in recruitment, survival, growth, or fecundity). We highlight several factors that can interact with the effects of competition and make it more difficult to detect in field experiments. In light of this evidence, we discuss the role of competition in shaping coral reef fish communities and competition's status as one of several processes that contribute to species coexistence. Finally, we consider some of the complex ways that climate change may influence competition, and we provide suggestions for future research.

Understanding the Spatio-Temporal Response of Coral Reef Fish Communities to Natural Disturbances: Insights from Beta-Diversity Decomposition

Understanding how communities respond to natural disturbances is fundamental to assess the mechanisms of ecosystem resistance and resilience. However, ecosystem responses to natural disturbances are rarely monitored both through space and time, while the factors promoting ecosystem stability act at various temporal and spatial scales. Hence, assessing both the spatial and temporal variations in species composition is important to comprehensively explore the effects of natural disturbances. Here, we suggest a framework to better scrutinize the mechanisms underlying community responses to disturbances through both time and space. Our analytical approach is based on beta diversity decomposition into two components, replacement and biomass difference. We illustrate this approach using a 9-year monitoring of coral reef fish communities off Moorea Island (French Polynesia), which encompassed two severe natural disturbances: a crown-of-thorns starfish outbreak and a hurricane. These disturbances triggered a fast logistic decline in coral cover, which suffered a 90% decrease on all reefs. However, we found that the coral reef fish composition remained largely stable through time and space whereas compensatory changes in biomass among species were responsible for most of the temporal fluctuations, as outlined by the overall high contribution of the replacement component to total beta diversity. This suggests that, despite the severity of the two disturbances, fish communities exhibited high resistance and the ability to reorganize their compositions to maintain the same level of total community biomass as before the disturbances. We further investigated the spatial congruence of this pattern and showed that temporal dynamics involved different species across sites; yet, herbivores controlling the proliferation of algae that compete with coral communities were consistently favored. These results suggest that compensatory changes in biomass among species and spatial heterogeneity in species responses can provide further insurance against natural disturbances in coral reef ecosystems by promoting high levels of key species (herbivores). They can also allow the ecosystem to recover more quickly.

Lipid characteristics of five epinephelinae fishes, Epinephelus fasciatus, Epinephelus retouti, Cephalopholis aurantia, Cephalopholis miniatus, and Variola louti, in the Coral Reef

The lipid and fatty acid compositions of the muscle and liver of five Epinephelinae fishes (Epinephelus fasciatus, Epinephelus retouti, Cephalopholis aurantia, Cephalopholis miniatus, and Variola louti) in the coral reef were investigated. The major polyunsaturated fatty acid (PUFA) in the Epinephelinae fish triacylglycerols was 22:6n-3 (docosahexaenoic acid; DHA), which was similar to high levels of DHA in the depot triacylglycerols of highly migratory fishes. In the phospholipids of all specimens, unusually high levels of 20:4n-6 (arachidonic acid; ARA), 22:5n-6 (docosapentaenoic acid; n-6 DPA), and 20:5n-3 (icosapentaenoic acid; EPA) were found with markedly high levels of DHA. Noticeable levels of n-6 long-chain PUFA, such as ARA and n-6 DPA, were found in the muscle and liver polar lipids and suggested a typical profile of the fatty acid composition of coral demersal fishes. The five Epinephelinae fishes were healthful marine foods containing markedly high levels of DHA with noticeable levels of various n-3 and n-6 PUFA.

Density-dependent growth in invasive Lionfish (Pterois volitans)

Direct demographic density dependence is necessary for population regulation and is a central concept in ecology, yet has not been studied in many invasive species, including any invasive marine fish. The red lionfish (Pterois volitans) is an invasive predatory marine fish that is undergoing exponential population growth throughout the tropical western Atlantic. Invasive lionfish threaten coral-reef ecosystems, but there is currently no evidence of any natural population control. Therefore, a manipulative field experiment was conducted to test for density dependence in lionfish. Juvenile lionfish densities were adjusted on small reefs and several demographic rates (growth, recruitment, immigration, and loss) were measured throughout an 8-week period. Invasive lionfish exhibited direct density dependence in individual growth rates, as lionfish grew slower at higher densities throughout the study. Individual growth in length declined linearly with increasing lionfish density, while growth in mass declined exponentially with increasing density. There was no evidence, however, for density dependence in recruitment, immigration, or loss (mortality plus emigration) of invasive lionfish. The observed density-dependent growth rates may have implications for which native species are susceptible to lionfish predation, as the size and type of prey that lionfish consume is directly related to their body size. The absence of density-dependent loss, however, contrasts with many native coral-reef fish species and suggests that for the foreseeable future manual removals may be the only effective local control of this invasion.

Lethal effects of habitat degradation on fishes through changing competitive advantage

Coral bleaching has caused catastrophic changes to coral reef ecosystems around the world with profound ecological, social and economic repercussions. While its occurrence is predicted to increase in the future, we have little understanding of mechanisms that underlie changes in the fish community associated with coral degradation. The present study uses a field-based experiment to examine how the intensity of interference competition between juveniles of two species of damselfish changes as healthy corals degrade through thermal bleaching. The mortality of a damselfish that is a live coral specialist (Pomacentrus moluccensis) increased on bleached and dead coral in the presence of the habitat generalist (Pomacentrus amboinensis). Increased mortality of the specialist was indirectly owing to enhanced aggression by the generalist forcing the specialist higher up and further away from shelter on bleached and dead coral. Evidence from this study stresses the importance of changing interspecific interactions to community dynamics as habitats change.

Long-term field study of sea kraits in New Caledonia: fundamental issues and conservation

This short review focuses on the findings associated with a long-term field study on two species of sea kraits in New Caledonia. Since 2002, more than 30 sites in the lagoon have been sampled, and in most places mark-recapture was implemented. We collected detailed data on more than 14,000 marked individuals (>6000 recaptures) and used different techniques (stable isotopes, bio-logging, analyses of diet). The objective was fundamental: to examine how amphibious snakes cope with both terrestrial and aquatic environments. As access to abundant food is likely the main evolutionary driver for the return transition toward the sea in marine tetrapods, foraging ecology was an important part of the research and novel information was obtained on this subject. Rapidly however, field observations revealed the potential interest of sea kraits for conservation issues. Our results show that these snakes are useful bio-indicators of marine biodiversity; they also provide a useful signal to monitor levels of contamination by heavy metals in the lagoon, and more generally as a means of studying the functioning of reef ecosystems. Importantly, anecdotal observations (e.g., a krait drinking during rain) provided unsuspected physiological insights of general importance to fundamental problems and conservation. One of the lessons of this long-term study is that key results emerged in an unexpected way, but all were dependent on intensive field work.

Functional redundancy patterns reveal non-random assembly rules in a species-rich marine assemblage

The relationship between species and the functional diversity of assemblages is fundamental in ecology because it contains key information on functional redundancy, and functionally redundant ecosystems are thought to be more resilient, resistant and stable. However, this relationship is poorly understood and undocumented for species-rich coastal marine ecosystems. Here, we used underwater visual censuses to examine the patterns of functional redundancy for one of the most diverse vertebrate assemblages, the coral reef fishes of New Caledonia, South Pacific. First, we found that the relationship between functional and species diversity displayed a non-asymptotic power-shaped curve, implying that rare functions and species mainly occur in highly diverse assemblages. Second, we showed that the distribution of species amongst possible functions was significantly different from a random distribution up to a threshold of ∼90 species/transect. Redundancy patterns for each function further revealed that some functions displayed fast rates of increase in redundancy at low species diversity, whereas others were only becoming redundant past a certain threshold. This suggested non-random assembly rules and the existence of some primordial functions that would need to be fulfilled in priority so that coral reef fish assemblages can gain a basic ecological structure. Last, we found little effect of habitat on the shape of the functional-species diversity relationship and on the redundancy of functions, although habitat is known to largely determine assemblage characteristics such as species composition, biomass, and abundance. Our study shows that low functional redundancy is characteristic of this highly diverse fish assemblage, and, therefore, that even species-rich ecosystems such as coral reefs may be vulnerable to the removal of a few keystone species.

Competence-dependent endogenous DNA rearrangement and uptake of extracellular DNA give a natural variant of Streptococcus mutans without biofilm formation

The production of water-insoluble glucan (WIG) enables Streptococcus mutans to survive and persist in the oral niche. WIG is produced from sucrose by glucosyltransferase encoded tandemly by the highly homologous gtfB and gtfC genes. Conversely, a single hybrid gene from the endogenous recombination of gtfB and gtfC is easily generated using RecA, resulting in S. mutans UA159 WIG- (rate of ∼1.0×10(-3)). The pneumococcus recA gene is regulated as a late competence gene. comX gene mutations did not lead to the appearance of WIG- cells. The biofilm collected from the flow cell had more WIG- cells than among the planktonic cells. Among the planktonic cells, WIG- cells appeared after 16 h and increased ∼10-fold after 32 h of cultivation, suggesting an increase in planktonic WIG- cells after longer culture. The strain may be derived from the biofilm environment. In coculture with donor WIG+ and recipient WIG- cells, the recipient cells reverted to WIG+ and acquired an intact gtfBC region from the environment, indicating that the uptake of extracellular DNA resulted in the phenotypic change. Here we demonstrate that endogenous DNA rearrangement and uptake of extracellular DNA generate WIG- cells and that both are induced by the same signal transducer, the com system. Our findings may help in understanding how S. mutans can adapt to the oral environment and may explain the evolution of S. mutans.

Sexual and lifetime selection on body size in a marine fish: the importance of life-history trade-offs

Many field measurements of viability and sexual selection on body size indicate that large size is favoured. However, life-history theory predicts that body size may be optimized and that patterns of selection may often be stabilizing rather than directional. One reason for this discrepancy may be that field estimates of selection tend to focus on limited components of fitness and may not fully measure life-history trade-offs. We use an 8-year, demographic field study to examine both sexual selection and lifetime selection on body size of a coral reef fish (the bicolour damselfish, Stegastes partitus). Selection via reproductive success of adults was very strong (standardized selection differential=1.04). However, this effect was balanced by trade-offs between large adult size and reduced cumulative survival during the juvenile phase. When we measured lifetime fitness (net reproductive rate), selection was strongly stabilizing and only weakly directional, consistent with predictions from life-history theory.

Food partitioning and diet temporal variation in two coexisting sparids, Pagellus erythrinus and Pagellus acarne

Resource partitioning in two congeneric sparids, pandora Pagellus erythrinus and axillary seabream Pagellus acarne, was investigated using stomach content analysis integrated with data on stable isotopes (δ(15) N and δ(13) C). The study was carried out on coastal muddy bottoms in the Gulf of Castellammare (southern Tyrrhenian Sea, western Mediterranean Sea) in seasons (autumn, November 2004; winter, March 2005; spring, early June 2005), at depths between 50 and 100 m. Stomach content analysis suggested low trophic niche overlap between the two species. Pagellus erythrinus mainly preyed on strictly benthic organisms (polychaetes, brachyuran crabs and benthic crustaceans). Although it consumed benthic prey, P. acarne preferred suprabenthic prey such as peracarid crustaceans from the benthic boundary layer a few metres above the bottom. The two species showed different isotopic values, with P. erythrinus exhibiting higher δ(15) N and more enriched δ(13) C than P. acarne, in accordance with its marked benthic behaviour and high predation on carnivore polychaetes. Significant temporal variability in both diet and isotopic values caused trophic differences between the two species. The autumn and winter diet differed from the spring diet and the trophic levels of both species increased from autumn and winter to spring, in accordance with variations in food availability and changes in prey δ(15) N and δ(13) C. These temporal variations may be linked to an increase in energy requirements for reproduction, together with the differing availability of preferred prey throughout the year. Significantly, lower δ(13) C was recorded in fishes collected in winter (March), suggesting the influence of river inputs as a source of particulate organic matter in this zone after the flooding season. In conclusion, these sympatric congeneric fish species displayed clear food partitioning throughout the temporal scale analysed.

Synthesizing mechanisms of density dependence in reef fishes: behavior, habitat configuration, and observational scale

Coral and rocky reef fish populations are widely used as model systems for the experimental exploration of density-dependent vital rates, but patterns of density-dependent mortality in these systems are not yet fully understood. In particular, the paradigm for strong, directly density-dependent (DDD) postsettlement mortality stands in contrast to recent evidence for inversely density-dependent (IDD) mortality. We review the processes responsible for DDD and IDD per capita mortality in reef fishes, noting that the pattern observed depends on predator and prey behavior, the spatial configuration of the reef habitat, and the spatial and temporal scales of observation. Specifically, predators tend to produce DDD prey mortality at their characteristic spatial scale of foraging, but prey mortality is IDD at smaller spatial scales due to attack-abatement effects (e.g., risk dilution). As a result, DDD mortality may be more common than IDD mortality on patch reefs, which tend to constrain predator foraging to the same scale as prey aggregation, eliminating attack-abatement effects. Additionally, adjacent groups of prey on continuous reefs may share a subset of refuges, increasing per capita refuge availability and relaxing DDD mortality relative to prey on patch reefs, where the patch edge could prevent such refuge sharing. These hypotheses lead to a synthetic framework to predict expected mortality patterns for a variety of scenarios. For nonsocial, nonaggregating species and species that aggregate in order to take advantage of spatially clumped refuges, IDD mortality is possible but likely superseded by DDD refuge competition, especially on patch reefs. By contrast, for species that aggregate socially, mortality should be IDD at the scale of individual aggregations but DDD at larger scales. The results of nearly all prior reef fish studies fit within this framework, although additional work is needed to test many of the predicted outcomes. This synthesis reconciles some apparent contradictions in the recent reef fish literature and suggests the importance of accounting for the scale-sensitive details of predator and prey behavior in any study system.

Taxonomic distinctness of demersal fishes of the California current: moving beyond simple measures of diversity for marine ecosystem-based management

Background

Large-scale patterns or trends in species diversity have long interested ecologists. The classic pattern is for diversity (e.g., species richness) to decrease with increasing latitude. Taxonomic distinctness is a diversity measure based on the relatedness of the species within a sample. Here we examined patterns of taxonomic distinctness in relation to latitude (ca. 32–48 °N) and depth (ca. 50–1220 m) for demersal fishes on the continental shelf and slope of the US Pacific coast.

Methodology/Principal Findings

Both average taxonomic distinctness (AvTD) and variation in taxonomic distinctness (VarTD) changed with latitude and depth. AvTD was highest at approximately 500 m and lowest at around 200 m bottom depth. Latitudinal trends in AvTD were somewhat weaker and were depth-specific. AvTD increased with latitude on the shelf (50–150 m) but tended to decrease with latitude at deeper depths. Variation in taxonomic distinctness (VarTD) was highest around 300 m. As with AvTD, latitudinal trends in VarTD were depth-specific. On the shelf (50–150 m), VarTD increased with latitude, while in deeper areas the patterns were more complex. Closer inspection of the data showed that the number and distribution of species within the class Chondrichthyes were the primary drivers of the overall patterns seen in AvTD and VarTD, while the relatedness and distribution of species in the order Scorpaeniformes appeared to cause the relatively low observed values of AvTD at around 200 m.

Conclusions/Significance

These trends contrast to some extent the patterns seen in earlier studies for species richness and evenness in demersal fishes along this coast and add to our understanding of diversity of the demersal fishes of the California Current.

Multi-scale recruitment patterns and effects on local population size of a temperate reef fish

Recruitment of the temperate reef fish Coris julis was studied across the Azores Archipelago (central North Atlantic), over four consecutive recruitment seasons and at three spatial scales: between islands (separated by 100s of km), sites within islands (separated by 10s of km) and transects within sites (separated by 10s of m). At the largest scale (i.e. between islands) spatial recruitment patterns were highly variable, suggesting the influence of stochastic processes. Recruitment was spatially consistent within islands, even though magnitude was unpredictable between years, indicating that processes at meso-scales are probably more deterministic. Recruits settled randomly at the transect scale, probably reflecting habitat homogeneity. It was proposed that large and island-scale patterns reflect larval availability, driven by physical and biological processes occurring in the plankton. No evidence was found for a density-dependent relationship between newly settled and 2 week settled C. julis nor between cumulative recruitment and young-of-the-year. It appears that adult density is limited by larval supply (pre-settlement regulation) at low recruitment sites, and determined by post-settlement, density-dependent processes at high recruitment sites. This work is one of few to investigate multiple spatial and temporal scales of recruitment for a coastal fish species inhabiting isolated, temperate oceanic islands and hence, provides a novel comparison to the many studies of recruitment on coral reefs and other, more connected systems.

Endogenous oxidative stress produces diversity and adaptability in biofilm communities

Many bacterial species are capable of biofilm growth, in which cells live and replicate within multicellular community groups. Recent work shows that biofilm growth by a wide variety of bacterial species can generate genetic diversity in microbial populations. This finding is significant because the presence of diverse subpopulations can extend the range of conditions in which communities can thrive. Here, we used biofilms formed by the pathogen Pseudomonas aeruginosa to investigate how this population diversity is produced. We found that some cells within biofilms incur double-stranded DNA breaks caused by endogenous oxidative stress. Genetic variants then result when breaks are repaired by a mutagenic mechanism involving recombinatorial DNA repair genes. We hypothesized that the mutations produced could promote the adaptation of biofilm communities to changing conditions in addition to generating diversity. To test this idea, we exposed biofilms to an antibiotic and found that the oxidative stress-break repair mechanism increased the emergence of antibiotic-resistant bacteria. The diversity and adaptability produced by this mechanism could help biofilm communities survive in harsh environments.

Density-dependent effects on hatching success of the olive ridley turtle, Lepidochelys olivacea

Historically, the olive ridley arribada at Playa Nancite, Costa Rica, was one of the largest olive ridley arribadas in the eastern Pacific with 70,000 nesting females in a year. Recently the Nancite arribada drastically declined. We hypothesized that the population decline at Playa Nancite could have been due to low hatching success as a result of the high density of nests on the beach, such that recruitment to the population was insufficient to balance losses. To test this hypothesis, we examined density-dependent effects on hatching success and their underlying mechanisms by experimentally manipulating nest densities in experimental plots on the nesting beach. We set up four nest-density treatments in five experimental blocks. We measured effects of density on hatching success, CO(2) and O(2) concentrations and temperature both within nests and in sand adjacent to nests frequently during incubation. Experimental nest densities affected hatching success with the highest density having the lowest hatching success. Higher nest density led to lower O(2) levels and higher CO(2) levels in the nest with greater changes in the latter part of the incubation. Highest temperatures occurred in high-density areas. Temperatures were lower in sand surrounding the nest than in the nest. Effects of density on temperature, CO(2) and O(2) were confirmed at a naturally high-density nesting beach, Playa La Flor, Nicaragua. Long-term failure in production of hatchlings due to historic high densities may have contributed to the decline of arribadas on Playa Nancite. Thus, density-dependent population control would have operated at the embryonic life stage in this population of olive ridley turtles.

Selective mortality of a coral reef damselfish: role of predator-competitor synergisms

Phenotypic variability within cohorts of juvenile organisms can serve as the basis for selective mortality. Previous studies have demonstrated the important role that predators play in this process but not the impact of competitors on selective predation. We use a combination of lab and field studies to evaluate the effect of the presence of adult competitor damselfish (Dascyllus aruanus and Pomacentrus moluccensis; family Pomacentridae) on the selective mortality of newly-arrived (settled) lemon damselfish (P. moluccensis) by resident predator fishes (Pseudochromis fuscus Pseudochromidae and Cheilodipterus quinquelineatus Apogonidae). Lab trials consisted of mesocosm experiments in which the behaviour, mortality, and physiological condition (measured as lipid content) of surviving P. moluccensis settlers from each of three treatments: (1) predators absent, (2) predators present, and (3) predators and competitors present, were compared. The field study involved stocking newly settled P. moluccensis on natural bommies (patch reefs) which had either been subject to a partial removal of resident fish (predators and competitors) or left alone. Results indicated there was very strong condition-based selective mortality in both the lab and field trials. In both cases there was a strong positive relationship between mortality and the lipid content of surviving fish; implying low-condition fish were selectively removed. The mesocosm trials indicated that the strength of mortality as well as condition selectivity was higher when competitors were present than when they were absent. Behavioural observations in the mesocosm study suggest that attention by juvenile P. moluccensis to the movements and occasional chases of the competitors (especially D. aruanus) reduced their vigilance to the predators. These results suggest the important and interactive roles which condition of newly settled reef fish and interspecific competition can play in the outcomes of post-settlement predation.

HABITAT COMPLEXITY MODIFIES POST-SETTLEMENT MORTALITY AND RECRUITMENT DYNAMICS OF A MARINE FISH

For species that have an open population structure, local population size may be strongly influenced by a combination of propagule supply and post-settlement survival. While it is widely recognized that supply of larvae (or recruits) is variable and that variable recruitment may affect the relative contribution of pre- and post-settlement factors, less effort has been made to quantify how variation in the strength of post-settlement mortality (particularly density-dependent mortality) will affect the importance of processes that determine population size. In this study, I examined the effects of habitat complexity on mortality of blue rockfish (Sebastes mystinus) within nearshore reefs off central California. I first tested whether variation in habitat complexity (measured as three-dimensional complexity of rocky substrate) affected the magnitude of both density-independent and density-dependent mortality. I then used limitation analysis to quantify how variation in habitat complexity alters the relative influence of recruitment, density-independent mortality, and density-dependent mortality in determining local population size. Increased habitat complexity was associated with a reduction in both density-independent and density-dependent mortality. At low levels of habitat complexity, limitation analysis revealed that mortality was strong and recruitment had relatively little influence on population size. However, as habitat complexity increased, recruitment became more important. At the highest levels of habitat complexity, limitation by recruitment was substantial, although density-dependent mortality was ultimately the largest constraint on population size. In high-complexity habitats, population dynamics may strongly reflect variation in recruitment even though fluctuations may be dampened by density-dependent mortality. By affecting both density-independent and density-dependent mortality, variation in habitat complexity may result in qualitative changes in the dynamics of populations. These findings suggest that the relative importance of pre- vs. post-settlement factors may be determined by quantifiable habitat features, rather than ambient recruitment level alone. Because the magnitude of recruitment fluctuations can affect species coexistence and the persistence of populations, habitat-driven changes in population dynamics may have important consequences for both community structure and population viability.

Positive indirect effects of reef fishes on kelp performance: the importance of mesograzers

It has been suggested that microcarnivorous reef fishes may play an important role in giant kelp forest communities by preventing infestations of mesograzers that could severely impact or potentially destroy recovering kelp forests after extreme disturbance events. However, these trophic linkages, specifically the direct and indirect effects of fishes on the biomass of mesograzers, grazing intensity, and the performance of giant kelp, have not been sufficiently quantified and evaluated as to their importance and in the absence of such disturbance events. We examined experimentally the effects of mesograzers on the growth and performance of giant kelp in the presence and absence of their fish predators near Santa Catalina Island, California (U.S.A.). Mesograzer biomass and grazing intensity were significantly higher when fishes were excluded from giant kelp, which in turn, lowered kelp performance. This pattern was consistent both on experimental plots of kelp as habitat isolates, and on a continuous reef. Moreover, the abundance of mesograzers was inversely related to the abundance of kelp perch among several kelp-forested reefs, suggesting that these effects can occur at larger spatial scales. Because of differences in the diet and behavior of two microcarnivorous fishes, the kelp perch and señorita, we conducted an experiment manipulating each species and its density independently to determine their separate effects on mesograzers and kelp performance. Concurrently we examined the growth and mortality of juvenile kelp. Grazing intensity decreased, estimates of kelp performance increased, and the growth of juvenile kelp increased with increasing densities of fish but with no detectable effects between fishes. Our results demonstrate that these microcarnivorous fishes have positive indirect effects on kelp performance by reducing mesograzer biomass and grazing intensity, and the early life stages of other fishes also may be important. More specifically, these fishes have a positive effect on the density of fronds of giant kelp that can result in greater recruitment success and the abundance of kelp-associated invertebrates and fishes. Indeed, this study suggests that mesograzers have the potential to be one of the most important herbivores in kelp forest ecosystems.

Hierarchical organization via a facilitation cascade in intertidal cordgrass bed communities

It has recently been proposed that many communities are structured by a hierarchy of interactions in which facilitation by foundation species is of primary importance. We conducted the first explicit experimental test of this hypothesis by investigating the organization of positive interactions on New England cobblestone beaches. In this midintertidal community, wave-generated substrate instability and solar stress largely limit marine organisms to the shelter of cordgrass beds. Cordgrass, which can establish and persist without the aid of other foundation species, facilitates a dense assemblage of inhabitants (e.g., mussels, snails, seaweeds) with roots/rhizomes that stabilize substrate and a dense canopy that baffles waves and provides shade. Within the cordgrass bed community, ribbed mussels further enhance physical conditions and densities of other species (e.g., amphipods, barnacles) by providing crevice space and hard substrate. We conclude that cordgrass bed communities are hierarchically organized: secondary interactions (e.g., facilitation by ribbed mussels) play a key role within an assemblage dependent on primary facilitation by the independently successful foundation species cordgrass. Our results identify emergent indirect positive interactions in the form of facilitation cascades, have broad implications for conservation, and help unify existing models of community organization that were developed without considering the fundamental role of positive interactions.

The impact of exploiting grazers (Scaridae) on the dynamics of Caribbean coral reefs

Coral reefs provide a number of ecosystem services including coastal defense from storms, the generation of building materials, and fisheries. It is increasingly clear that the management of reef resources requires an ecosystem approach in which extractive activities are weighed against the needs of the ecosystem and its functions rather than solely those of the fishery. Here, I use a spatially explicit simulation model of a Caribbean coral reef to examine the ecosystem requirements for grazing which is primarily conducted by parrotfishes (Scaridae). The model allows the impact of fishing grazers to be assessed in the wider context of other ecosystem processes including coral-algal competition, hurricanes, and mass extinction of the herbivorous urchin Diadema antillarum. Using a new analytical model of scarid grazing, it is estimated that parrotfishes can only maintain between 10% and 30% of a structurally complex forereef in a grazed state. Predictions from this grazing model were then incorporated into a broader simulation model of the ecosystem. Simulations predict that scarid grazing is unable to maintain high levels of coral cover (> or = 30%) when severe hurricanes occur on a decadal basis, such as occurs in parts of the northern Caribbean. However, reefs can withstand such intense disturbance when grazing is undertaken by both scarids and the urchin Diadema. Scarid grazing is predicted to allow recovery from hurricanes when their incidence falls to 20 years or less (e.g., most of Central and South America). Sensitivity analyses revealed that scarid grazing had the most acute impact on model behavior, and depletion led to the emergence of a stable, algal-dominated community state. Under conditions of heavy grazer depletion, coral cover was predicted to decline rapidly from an initial level of 30% to less than 1% within 40 years, even when hurricane frequency was low at 60 years. Depleted grazers caused a population bottleneck in juvenile corals in which algal overgrowth caused elevated levels of postsettlement mortality and resulted in a bimodal distribution of coral sizes. Several new hypotheses were generated including a region-wide change in the spatial heterogeneity of coral reefs following extinction of Diadema. The management of parrotfishes on Caribbean reefs is usually approached implicitly through no-take marine reserves. The model predicts that depletion of grazers in nonreserve areas can severely limit coral accretion. Other studies have shown that low coral accretion can reduce the structural complexity and therefore quality of the reef habitat for many organisms. A speculative yet rational inference from the model is that failure to manage scarid populations outside reserves will have a profoundly negative impact on the functioning of the reserve system and status of non-reserve reefs.

CONSEQUENCES OF PATCH REEF SPACING FOR DENSITY-DEPENDENT MORTALITY OF CORAL-REEF FISHES

The spatial configuration of habitat patches can profoundly affect a number of ecological interactions, including those between predators and prey. I examined the effects of reef spacing on predator-prey interactions within coral-reef fish assemblages in the Bahamas. Using manipulative field experiments, I determined that reef spacing influences whether and how density-dependent predation occurs. Mortality rates of juveniles of two ecologically dissimilar species (beaugregory damselfish and yellowhead wrasse) were similarly affected by reef spacing; for both species, mortality was density dependent on reef patches that were spatially isolated (separated by 50 m), and density independent on reef patches that were aggregated (separated by 5 m). A subsequent experiment with the damselfish demonstrated that a common resident predator (coney) caused a substantial proportion of the observed mortality, independent of reef spacing. Compared to isolated reefs, aggregated reefs were much more likely to be visited by transient predators (mostly yellowtail snappers), regardless of prey density, and on these reefs, mortality rates approached 100% for both prey species. Transient predators exhibited neither an aggregative response nor a type 3 functional response, and consequently were not the source of density dependence observed on the isolated reefs. These patterns suggest that resident predators caused density-dependent mortality in their prey through type 3 functional responses on all reefs, but on aggregated reefs, this density dependence was overwhelmed by high, density-independent mortality caused by transient predators. Thus, the spatial configuration of reef habitat affected both the magnitude of total predation and the existence of density-dependent mortality. The combined effects of the increasing fragmentation of coral reef habitats at numerous scales and global declines in predatory fish may have important consequences for the regulation of resident fish populations.

Assessing the magnitude of intra- and interspecific competition in two coral reef fishes

Many field experiments have tested for effects of competition in nature, but relatively few have used designs allowing simultaneous assessment of the influence of intra- and interspecific competition. Using a response surface design and a press manipulation of densities, we tested effects of competition within and between two species of coral reef fishes (Coryphopterus glaucofraneum and Gnatholepis thompsoni). By tracking individually tagged fishes, we showed that the per-capita effect of intraspecific competitors on individual growth was at least twice as great as the effect of interspecific competitors. Growth rate was better predicted by measures of density that incorporated body size, rather than numerical density, suggesting interference competition. Individuals of both species interacted aggressively with conspecifics at least twice as often as with heterospecifics. Individuals of both species also covered more area while foraging and spent less time in shelter when crowded than when at lower densities. In combination, these behaviours suggest that increased metabolic costs at high density contribute to competitive effects on growth. These competitive interactions occurred among adult fishes, so reduced growth may translate to reduced fecundity as well as reduced survival, and so contribute to population regulation.