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Dramatic changes in populations of fishes living on coral reefs have been documented globally and, in response, the research community has initiated efforts to assess and monitor reef fish assemblages. A variety of visual census techniques are employed, however results are often incomparable due to differential methodological performance. Although comparability of data may promote improved assessment of fish populations, and thus management of often critically important nearshore fisheries, to date no standardized and agreed-upon survey method has emerged. This study describes the use of methods across the research community and identifies potential drivers of method selection. An online survey was distributed to researchers from academic, governmental, and non-governmental organizations internationally. Although many methods were identified, 89% of survey-based projects employed one of three methods-belt transect, stationary point count, and some variation of the timed swim method. The selection of survey method was independent of the research design (i.e., assessment goal) and region of study, but was related to the researcher's home institution. While some researchers expressed willingness to modify their current survey protocols to more standardized protocols (76%), their willingness decreased when methodologies were tied to long-term datasets spanning five or more years. Willingness to modify current methodologies was also less common among academic researchers than resource managers. By understanding both the current application of methods and the reported motivations for method selection, we hope to focus discussions towards increasing the comparability of quantitative reef fish survey data.

Effective conservation requires rigorous baselines of pristine conditions to assess the impacts of human activities and to evaluate the efficacy of management. Most coral reefs are moderately to severely degraded by local human activities such as fishing and pollution as well as global change, hence it is difficult to separate local from global effects. To this end, we surveyed coral reefs on uninhabited atolls in the northern Line Islands to provide a baseline of reef community structure, and on increasingly populated atolls to document changes associated with human activities. We found that top predators and reef-building organisms dominated unpopulated Kingman and Palmyra, while small planktivorous fishes and fleshy algae dominated the populated atolls of Tabuaeran and Kiritimati. Sharks and other top predators overwhelmed the fish assemblages on Kingman and Palmyra so that the biomass pyramid was inverted (top-heavy). In contrast, the biomass pyramid at Tabuaeran and Kiritimati exhibited the typical bottom-heavy pattern. Reefs without people exhibited less coral disease and greater coral recruitment relative to more inhabited reefs. Thus, protection from overfishing and pollution appears to increase the resilience of reef ecosystems to the effects of global warming.

Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated ( approximately 5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems worldwide.

Recent advances in food-web ecology highlight that most real food webs (1) represent an interplay between producer- and detritus-based webs and (2) are governed by consumers which are rampant omnivores; feeding on varied prey across trophic levels and resource channels. A possible avenue to unify these advances comes from models demonstrating that predators feeding on distinctly different channels may stabilize food webs. Empirical studies suggest many consumers engage in such behavior by feeding on prey items from both living-autotroph (green) and detritus-based (brown) webs, what we term \"multichannel feeding,\" yet we know little about how common such feeding is across systems and trophic levels, or its effect on system stability. Considering 23 empirical webs, we find that multichannel feeding is equally common across terrestrial, freshwater, and marine systems, with >50% of consumers classified as multichannel consumers. Multichannel feeding occurred most often at the first consumer level, indicating that most taxa at the herbivore/detritivore level are more aptly described as multichannel consumers, and that such feeding is not restricted to predators. We next developed a simple four-compartment nutrient cycling model for consumers eating both autotrophs and detritus with separate parameter sets to represent aquatic vs. terrestrial ecosystems. Modeling results showed that, across terrestrial and aquatic ecosystems, multichannel feeding is stabilizing at low attack rates on autotrophs or when attack rates are asymmetric (moderate on autotrophs while low on detritus), but destabilizing at high attack rates on autotrophs, compared to herbivory- or detritivory-only models. The set of conditions with stable webs with multichannel consumers is narrower, however, for aquatic systems, suggesting that multichannel feeding may generally be more stabilizing in terrestrial systems. Together, our results demonstrate that multichannel feeding is common across ecosystems and may be a stabilizing force in real webs that have consumers with low or asymmetric attack rates.

Human impacts can homogenize and simplify ecosystems, favoring communities that are no longer naturally coupled with (or reflective of) the background environmental regimes in which they are found. Such a process of biophysical decoupling has been explored little in the marine environment due to a lack of replication across the intact-to-degraded ecosystem spectrum. Coral reefs lacking local human impacts provide critical baseline scenarios in which to explore natural biophysical relationships, and provide a template against which to test for their human-induced decoupling. Using 39 Pacific islands, 24 unpopulated (relatively free from local human impacts) and 15 populated (with local human impacts present), spanning 45° of latitude and 65° of longitude, we ask, what are ‘natural’ biophysical relationships on coral reefs and do we see evidence for their human-induced decoupling? Estimates of the percent cover of benthic groups were related to multiple physical environmental drivers (sea surface temperature, irradiance, chlorophyll-a, and wave energy) using mixed-effects models and island mean condition as the unit of replication. Models across unpopulated islands had high explanatory power, identifying key physical environmental drivers of variations in benthic cover in the absence of local human impacts. These same models performed poorly and lost explanatory power when fitted anew to populated (human impacted) islands; biophysical decoupling was clearly evident. Furthermore, key biophysical relationships at populated islands (i.e. those relationships driving benthic variation across space in conjunction with chronic human impact) bore little resemblance to the baseline scenarios identified from unpopulated islands. Our results highlight the ability of local human impacts to decouple biophysical relationships in the marine environment and fundamentally restructure the natural rules of nature.

Holobionts are species-specific associations between macro- and microorganisms. On coral reefs, the benthic coverage of coral and algal holobionts varies due to natural and anthropogenic forcings. Different benthic macroorganisms are predicted to have specific microbiomes. In contrast, local environmental factors are predicted to select for specific metabolic pathways in microbes. To reconcile these two predictions, we hypothesized that adaptation of microbiomes to local conditions is facilitated by the horizontal transfer of genes responsible for specific metabolic capabilities. To test this hypothesis, microbial metagenomes were sequenced from 22 coral reefs at 11 Line Islands in the central Pacific that together span a wide range of biogeochemical and anthropogenic influences. Consistent with our hypothesis, the percent cover of major benthic functional groups significantly correlated with particular microbial taxa. Reefs with higher coral cover had a coral microbiome with higher abundances of Alphaproteobacteria (such as Rhodobacterales and Sphingomonadales), whereas microbiomes of algae-dominated reefs had higher abundances of Gammaproteobacteria (such as Alteromonadales, Pseudomonadales, and Vibrionales), Betaproteobacteria, and Bacteriodetes. In contrast to taxa, geography was the strongest predictor of microbial community metabolism. Microbial communities on reefs with higher nutrient availability (e.g., equatorial upwelling zones) were enriched in genes involved in nutrient-related metabolisms (e.g., nitrate and nitrite ammonification, Ton/Tol transport, etc.). On reefs further from the equator, microbes had more genes encoding chlorophyll biosynthesis and photosystems I/II. These results support the hypothesis that core microbiomes are determined by holobiont macroorganisms, and that those core taxa adapt to local conditions by selecting for advantageous metabolic genes.

It is now clear that fished populations can fluctuate more than unharvested stocks. However, it is not clear why. Here we distinguish among three major competing mechanisms for this phenomenon, by using the 50-year California Cooperative Oceanic Fisheries Investigations (CalCOFI) larval fish record. First, variable fishing pressure directly increases variability in exploited populations. Second, commercial fishing can decrease the average body size and age of a stock, causing the truncated population to track environmental fluctuations directly. Third, age-truncated or juvenescent populations have increasingly unstable population dynamics because of changing demographic parameters such as intrinsic growth rates. We find no evidence for the first hypothesis, limited evidence for the second and strong evidence for the third. Therefore, in California Current fisheries, increased temporal variability in the population does not arise from variable exploitation, nor does it reflect direct environmental tracking. More fundamentally, it arises from increased instability in dynamics. This finding has implications for resource management as an empirical example of how selective harvesting can alter the basic dynamics of exploited populations, and lead to unstable booms and busts that can precede systematic declines in stock levels. Why fishing threatens fish Ecologists have long suspected that the reason why the abundance of harvested fish stocks fluctuates more than that of unharvested stocks is linked to the fact that they are harvested. Three main hypotheses have been put forward in explanation. The first is that variable fishing pressure itself directly increases stock variability. The other two hypotheses relate to the age truncation effect: either the loss of mature fish makes the more juvenile population more susceptible to environmental change, or it causes unstable population dynamics by altering factors such as intrinsic growth rates. A 50-year record of larval fish populations in the California Current fisheries has been used to distinguish between these possibilities. There was no evidence for the first hypothesis and little support for the second. It is the third option that finds support: fishing increases the dynamic instability of populations and can lead to booms and busts followed by systematic declines in stock levels. This means that, without harvest policies to restrict stock depletion, many economically important fisheries can be expected to collapse. Increased volatility of exploited fish stocks is due to amplified nonlinear behaviour caused by fishing. This paper shows how selective harvesting can alter the basic dynamics of exploited populations, and lead to unstable booms and busts that can precede systematic declines in stock levels.

Population distributions are affected by a variety of spatial processes, including dispersal, intraspecific dynamics and habitat selection. Within reef‐building coral communities, these processes are especially important during the earliest life stages when reproduction provides mobility among sessile organisms and populations experience the greatest mortality bottlenecks both before and immediately after settlement. Here, we used large‐area imaging to create photomosaics that allowed us to identify and map the location of 4681 juvenile (1–5 cm diameter) and 25 902 adult (>5 cm diameter) coral colonies from eight 100‐m2 plots across the forereef of Palmyra Atoll. Using metrics of density, percent cover and the relative location of each colony within each plot, we examined abundance and spatial relationships between juvenile and adult coral taxa. Within coral taxa, juvenile density was generally positively related to the numerical density and percent cover of adults. Nearest neighbor analyses showed aggregation of juveniles near adults of the same taxon for two of the focal taxa (Pocillopora and Fungiids), while all other taxa showed random spatial patterning relative to adults. Three taxa had clustered distributions of juveniles overall. Additionally, we found that on a colony level, juveniles for five of nine focal taxa (accounting for >98% of all identified juveniles) associated with a specific habitat type, with four of those five taxa favoring unconsolidated (e.g. rubble) over consolidated substrata. The general lack of clustering in juvenile corals contrasts with consistent clustering patterns seen in adult corals, suggesting that adult spatial patterns are largely driven by processes occurring after maturity such as partial colony mortality, including fission and fragmentation. The association of many taxa with unconsolidated habitat also suggests that corals may play an important role in colonizing natural rubble patches that could contribute to reef stabilization over time.

Coral reef ecosystems are exposed to a range of environmental forcings that vary on daily to decadal time scales and across spatial scales spanning from reefs to archipelagos. Environmental variability is a major determinant of reef ecosystem structure and function, including coral reef extent and growth rates, and the abundance, diversity, and morphology of reef organisms. Proper characterization of environmental forcings on coral reef ecosystems is critical if we are to understand the dynamics and implications of abiotic-biotic interactions on reef ecosystems. This study combines high-resolution bathymetric information with remotely sensed sea surface temperature, chlorophyll-a and irradiance data, and modeled wave data to quantify environmental forcings on coral reefs. We present a methodological approach to develop spatially constrained, island- and atoll-scale metrics that quantify climatological range limits and anomalous environmental forcings across U.S. Pacific coral reef ecosystems. Our results indicate considerable spatial heterogeneity in climatological ranges and anomalies across 41 islands and atolls, with emergent spatial patterns specific to each environmental forcing. For example, wave energy was greatest at northern latitudes and generally decreased with latitude. In contrast, chlorophyll-a was greatest at reef ecosystems proximate to the equator and northern-most locations, showing little synchrony with latitude. In addition, we find that the reef ecosystems with the highest chlorophyll-a concentrations; Jarvis, Howland, Baker, Palmyra and Kingman are each uninhabited and are characterized by high hard coral cover and large numbers of predatory fishes. Finally, we find that scaling environmental data to the spatial footprint of individual islands and atolls is more likely to capture local environmental forcings, as chlorophyll-a concentrations decreased at relatively short distances (>7 km) from 85% of our study locations. These metrics will help identify reef ecosystems most exposed to environmental stress as well as systems that may be more resistant or resilient to future climate change.

An increase in the intensity and frequency of extreme environmental conditions due to anthropogenic climate change impacts coral reefs through myriad stressors, from elevated sea-surface temperatures to increased storm activity. A reef’s response to these disturbances can be influenced by factors including taxonomic composition, life history strategies, or spatial patterning of the reef community members. We explored the disturbance-specific responses of coral reefs by following changes in benthic cover of major functional groups, community assemblage, and the response of common coral taxa at six islands across the central Pacific over the course of two years. We observed a decrease in average coral cover at four of the six islands, with differing underlying shifts in assemblage structure. Reefs with the highest pre-disturbance benthic coverage of Montipora spp. displayed significant increases in average hard coral cover compared to those where Acropora spp. was in the highest abundance; Acropora -dominated reefs showed significant declines in coral cover especially when exposed to the physical stress associated with a cyclone. Change in total coral cover was variable between islands within the same region, even among adjacent islands facing similar disturbance. These results highlight the importance of assemblage composition in influencing how benthic communities respond to major disturbance events such as thermal stress or cyclones. Improving our understanding of the drivers of differential community responses to disturbance will be important in predicting future changes in reef structure under changing ocean conditions.