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Underwater photogrammetry presents unique challenges due to the optical properties of water that, if not correctly taken into account, might affect the quality of the survey and the related 2D and 3D products. It is recognized nowadays the importance to train newcomers to underwater surveying, and extend and consolidate the knowledge of best practices for underwater data acquisition. Starting from this consideration, we propose the development of POSER, a 3D simulation framework designed to facilitate the teaching of underwater imaging principles. The project, an ISPRS Educational and Capacity Building Initiative, is built upon the open-source platform Blender, incorporating realistic modelling of the physical properties of water, including light refraction, scattering, and absorption phenomena, to simulate underwater surveying conditions. We foster a learning-by-doing approach, providing users with ready-to-use application scenarios inspired by real-life case studies. They will cover a range of application fields, from marine ecology to archaeology and subsea metrology, and allow users to address the complexities of underwater surveying practices. This paper introduces POSER to the community, presenting its educational vocation and describing its constituent components. [ABSTRACT FROM AUTHOR]

Nous présentons ici les relations longueur-poids (LWR) pour 11 espèces de poissons de récif corallien de huit îles de Polyné- sie française. Au total, 1930 poissons ont été collectés dans cinq îles de l’archipel de la Société (Moorea, Tahiti, Raiatea, Huahine, Tetiaroa) et dans trois atolls de l’archipel des Tuamotu (Takapoto, Tikehau et Rangiroa). Ces poissons couvrent plusieurs niveaux trophiques, avec des planctonophages, des herbivores et des carni- vores, et sont parmi les espèces les plus abondantes de la région. Les estimations comprennent des LWR pour des espèces qui n’ont jamais été publiées auparavant ou qui ne sont pas disponibles dans la littérature ou les bases de données accessibles. Les mesures de longueur totale (TL : précision de 0,1 cm) et de poids total (P : pré- cision de 0,01 g) ont été effectuées. Ces estimations augmentent le nombre de LWR disponibles et robustes pour les poissons des récifs coralliens, ce qui permet de mieux comprendre la croissance de ces espèces. Avec un focus plus particulier sur les espèces de petite taille, parmi les plus abondantes observées lors des compta- ges visuels sous-marins, ces estimations permettront aux gestion- naires des ressources marines et aux scientifiques locaux de carac- tériser les biomasses de poissons en Polynésie française avec une plus grande précision [ABSTRACT FROM AUTHOR]

Tropical reef communities contain spatial patterns at multiple scales, observable from microscope and satellite alike. Many of the smaller-scale patterns are generated physiologically (e.g., skeletal structures of corals at <1-m scale), while some of the larger patterns have been attributed to scale-dependent feedbacks (e.g., spur and groove reefs at 10–100-m scales). In describing the spatial patterning of reef benthic communities at landscape levels, we uncovered unique spatial patterning among living marine algae. Populations of the calcifying green alga Halimeda were observed to form a consistent polygonal pattern at a characteristic scale of 3–4 m. The pattern showed no clear evidence of having been formed through biologically created shifts in hydrodynamical conditions or related mechanisms. In considering the specifics of Halimeda growth patterns, a model of self-organization involving separation and patterned extension is proposed, a mechanism revealed in some geological pattern formation. This observation reinforces the diversity of pathways by which striking spatial patterns can occur in ecosystems. [ABSTRACT FROM AUTHOR]

The Hawaiian Archipelago experienced a moderate bleaching event in 2019—the third major bleaching event over a 6-year period to impact the islands. In response, the Hawai'i Coral Bleaching Collaborative (HCBC) conducted 2,177 coral bleaching surveys across the Hawaiian Archipelago. The HCBC was established to coordinate bleaching monitoring efforts across the state between academic institutions, non-governmental organizations, and governmental agencies to facilitate data sharing and provide management recommendations. In 2019, the goals of this unique partnership were to: 1) assess the spatial and temporal patterns of thermal stress; 2) examine taxa-level patterns in bleaching susceptibility; 3) quantify spatial variation in bleaching extent; 4) compare 2019 patterns to those of prior bleaching events; 5) identify predictors of bleaching in 2019; and 6) explore site-specific management strategies to mitigate future bleaching events. Both acute thermal stress and bleaching in 2019 were less severe overall compared to the last major marine heatwave events in 2014 and 2015. Bleaching observed was highly site- and taxon-specific, driven by the susceptibility of remaining coral assemblages whose structure was likely shaped by previous bleaching and subsequent mortality. A suite of environmental and anthropogenic predictors was significantly correlated with observed bleaching in 2019. Acute environmental stressors, such as temperature and surface light, were equally important as previous conditions (e.g. historical thermal stress and historical bleaching) in accounting for variation in bleaching during the 2019 event. We found little evidence for acclimation by reefs to thermal stress in the main Hawaiian Islands. Moreover, our findings illustrate how detrimental effects of local anthropogenic stressors, such as tourism and urban run-off, may be exacerbated under high thermal stress. In light of the forecasted increase in severity and frequency of bleaching events, future mitigation of both local and global stressors is a high priority for the future of corals in Hawai'i. [ABSTRACT FROM AUTHOR]

Although parasites are ubiquitous in marine ecosystems, predicting the abundance of parasites present within marine ecosystems has proven challenging due to the unknown effects of multiple interacting environmental gradients and stressors. Furthermore, parasites often are considered as a uniform group within ecosystems despite their significant diversity.We aim to determine the potential importance of multiple predictors of parasite abundance in coral reef ecosystems, including reef area, island area, human population density, chlorophyll‐a, host diversity, coral cover, host abundance and island isolation.Using a model selection approach within a database of more than 1,200 individual fish hosts and their parasites from 11 islands within the Pacific Line Islands archipelago, we reveal that geographic gradients, including island area and island isolation, emerged as the best predictors of parasite abundance.Life history moderated the relationship; parasites with complex life cycles increased in abundance with increasing island isolation, while parasites with direct life cycles decreased with increasing isolation. Direct life cycle parasites increased in abundance with increasing island area, although complex life cycle parasite abundance was not associated with island area.This novel analysis of a unique dataset indicates that parasite abundance in marine systems cannot be predicted precisely without accounting for the independent and interactive effects of each parasite's life history and environmental conditions. [ABSTRACT FROM AUTHOR]

Detecting acoustic transients by signal-to-noise ratio (SNR) becomes problematic in nonstationary ambient noise environments characteristic of coral reefs. An alternate approach presented here uses signal directionality to automatically detect and localize transient impulsive sounds collected on underwater vector sensors spaced tens of meters apart. The procedure, which does not require precise time synchronization, first constructs time-frequency representations of both the squared acoustic pressure (spectrogram) and dominant directionality of the active intensity (azigram) on each sensor. Within each azigram, sets of time-frequency cells associated with transient energy arriving from a consistent azimuthal sector are identified. Binary image processing techniques then link sets that share similar duration and bandwidth between different sensors, after which the algorithm triangulates the source location. Unlike most passive acoustic detectors, the threshold criterion for this algorithm is bandwidth instead of pressure magnitude. Data collected from shallow coral reef environments demonstrate the algorithm's ability to detect SCUBA bubble plumes and consistent spatial distributions of somniferous fish activity. Analytical estimates and direct evaluations both yield false transient localization rates from 3% to 6% in a coral reef environment. The SNR distribution of localized pulses off Hawaii has a median of 7.7 dB and interquartile range of 7.1 dB. [ABSTRACT FROM AUTHOR]

Aim: Identification of the processes that generate and maintain species diversity within the same region can provide insight into biogeographic patterns at broader spatiotemporal scales. Hawkfishes in the genus Paracirrhites are a unique taxon to explore with respect to niche differentiation, exhibiting diagnostic differences in coloration, and an apparent center of distribution outside of the Indo–Malay–Philippine (IMP) biodiversity hotspot for coral reef fishes. Our aim is to use next‐generation sequencing methods to leverage samples of a taxon at their center of maximum diversity to explore phylogenetic relationships and a possible mechanism of coexistence. Location: Flint Island, Southern Line Islands, Republic of Kiribati. Methods: A comprehensive review of museum records, the primary literature, and unpublished field survey records was undertaken to determine ranges for four "arc‐eye" hawkfish species in the Paracirrhites species complex and a potential hybrid. Fish from four Paracirrhites species were collected from Flint Island in the Southern Line Islands, Republic of Kiribati. Hindgut contents were sequenced, and subsequent metagenomic analyses were used to assess the phylogenetic relatedness of the host fish, the microbiome community structure, and prey remains for each species. Results: Phylogenetic analyses conducted with recovered mitochondrial genomes revealed clustering of P. bicolor with P. arcatus and P. xanthus with P. nisus, which were unexpected on the basis of previous morphological work in this species complex. Differences in taxonomic composition of gut microbial communities and presumed prey remains indicate likely separation of foraging niches. Main Conclusions: Our findings point toward previously unidentified relationships in this cryptic species complex at its proposed center of distribution. The three species endemic to the Polynesian province (P. nisus, P. xanthus, and P. bicolor) cluster separately from the more broadly distributed P. arcatus on the basis of relative abundance of metazoan sequences in the gut (presumed prey remains). Discordance between gut microbial communities and phylogeny of the host fish further reinforce the hypothesis of niche separation. [ABSTRACT FROM AUTHOR]

Upwelling is an important source of inorganic nutrients in marine systems, yet little is known about how gradients in upwelling affect primary producers on coral reefs. The Southern Line Islands span a natural gradient of inorganic nutrient concentrations across the equatorial upwelling region in the central Pacific. We used this gradient to test the hypothesis that benthic autotroph ecophysiology is enhanced on nutrient-enriched reefs. We measured metabolism and photophysiology of common benthic taxa, including the algae Porolithon, Avrainvillea, and Halimeda, and the corals Pocillopora and Montipora. We found that temperature (27.2–28.7°C) was inversely related to dissolved inorganic nitrogen (0.46–4.63 μM) and surface chlorophyll a concentrations (0.108–0.147 mg m-3), which increased near the equator. Contrary to our prediction, ecophysiology did not consistently track these patterns in all taxa. Though metabolic rates were generally variable, Porolithon and Avrainvillea photosynthesis was highest at the most productive and equatorial island (northernmost). Porolithon photosynthetic rates also generally increased with proximity to the equator. Photophysiology (maximum quantum yield) increased near the equator and was highest at northern islands in all taxa. Photosynthetic pigments also were variable, but chlorophyll a and carotenoids in Avrainvillea and Montipora were highest at the northern islands. Phycobilin pigments of Porolithon responded most consistently across the upwelling gradient, with higher phycoerythrin concentrations closer to the equator. Our findings demonstrate that the effects of in situ nutrient enrichment on benthic autotrophs may be more complex than laboratory experiments indicate. While upwelling is an important feature in some reef ecosystems, ancillary factors may regulate the associated consequences of nutrient enrichment on benthic reef organisms. [ABSTRACT FROM AUTHOR]

Abstract: Human impacts on ecosystems can decouple the fundamental ecological relationships that create patterns of diversity in free‐living species. Despite the abundance, ubiquity, and ecological importance of parasites, it is unknown whether the same decoupling effects occur for parasitic species. We investigated the influence of fishing on the relationship between host diversity and parasite diversity for parasites of coral reef fishes on three fished and three unfished islands in the central equatorial Pacific. Fishing was associated with a shallowing of the positive host‐diversity–parasite‐diversity relationship. This occurred primarily through negative impacts of fishing on the presence of complex life‐cycle parasites, which created a biologically impoverished parasite fauna of directly transmitted parasites resilient to changes in host biodiversity. Parasite diversity appears to be decoupled from host diversity by fishing impacts in this coral reef ecosystem, which suggests that such decoupling might also occur for parasites in other ecosystems affected by environmental change. [ABSTRACT FROM AUTHOR]

For sessile organisms such as reef-building corals, differences in the degree of dispersion of individuals across a landscape may result from important differences in life-history strategies or may reflect patterns of habitat availability. Descriptions of spatial patterns can thus be useful not only for the identification of key biological and physical mechanisms structuring an ecosystem, but also by providing the data necessary to generate and test ecological theory. Here, we used an in situ imaging technique to create large-area photomosaics of 16 plots at Palmyra Atoll, central Pacific, each covering 100 m of benthic habitat. We mapped the location of 44,008 coral colonies and identified each to the lowest taxonomic level possible. Using metrics of spatial dispersion, we tested for departures from spatial randomness. We also used targeted model fitting to explore candidate processes leading to differences in spatial patterns among taxa. Most taxa were clustered and the degree of clustering varied by taxon. A small number of taxa did not significantly depart from randomness and none revealed evidence of spatial uniformity. Importantly, taxa that readily fragment or tolerate stress through partial mortality were more clustered. With little exception, clustering patterns were consistent with models of fragmentation and dispersal limitation. In some taxa, dispersion was linearly related to abundance, suggesting density dependence of spatial patterning. The spatial patterns of stony corals are non-random and reflect fundamental life-history characteristics of the taxa, suggesting that the reef landscape may, in many cases, have important elements of spatial predictability. [ABSTRACT FROM AUTHOR]

Fisheries exploitation represents a considerable threat to coral reef fish resources because even modest levels of extraction can alter ecological dynamics via shifts of stock size, species composition, and size-structure of the fish assemblage. Although species occupying higher trophic groups are known to suffer the majority of exploitative effects, changes in composition among lower trophic groups may be major, though are not frequently explored. Using size-based biomass spectrum analysis, we investigate the effects of fishing on the size-structure of coral reef fish assemblages spanning four geopolitical regions and determine if patterns of exploitation vary across trophic groups. Our analyses reveal striking evidence for the variety of effects fisheries exploitation can have on coral reef fish assemblages. When examining biomass spectra across the entire fish assemblage we found consistent evidence of size-specific exploitation, in which large-bodied individuals experience disproportionate reductions. The pattern was paralleled by and likely driven by, strongly size-specific reductions among top predators. In contrast, evidence of exploitation patterns was variable among lower trophic groups, in many cases including evidence of reductions across all size classes. The breadth of size classes and trophic groups that showed evidence of exploitation related positively to local human population density and diversity of fishing methods employed. Our findings highlight the complexity of coral reef fisheries and that the effects of exploitation on coral reefs can be realized throughout the entire fish assemblage, across multiple trophic groups and not solely restricted to large-bodied top-predators. Size-specific changes among fishes of lower trophic groups likely lead to altered ecological functioning of heavily exploited coral reefs. Together these findings reinforce the value of taking a multi-trophic group approach to monitoring and managing coral reef fisheries. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The majority of the world's coral reefs are in various stages of decline. While a suite of disturbances (overfishing, eutrophication, and global climate change) have been identified, the mechanism(s) of reef system decline remain elusive. Increased microbial and viral loading with higher percentages of opportunistic and specific microbial pathogens have been identified as potentially unifying features of coral reefs in decline. Due to their relative size and high per cell activity, a small change in microbial biomass may signal a large reallocation of available energy in an ecosystem; that is the microbialization of the coral reef. Our hypothesis was that human activities alter the energy budget of the reef system, specifically by altering the allocation of metabolic energy between microbes and macrobes. To determine if this is occurring on a regional scale, we calculated the basal metabolic rates for the fish and microbial communities at 99 sites on twenty-nine coral islands throughout the Pacific Ocean using previously established scaling relationships. From these metabolic rate predictions, we derived a new metric for assessing and comparing reef health called the microbialization score. The microbialization score represents the percentage of the combined fish and microbial predicted metabolic rate that is microbial. Our results demonstrate a strong positive correlation between reef microbialization scores and human impact. In contrast, microbialization scores did not significantly correlate with ocean net primary production, local chla concentrations, or the combined metabolic rate of the fish and microbial communities. These findings support the hypothesis that human activities are shifting energy to the microbes, at the expense of the macrobes. Regardless of oceanographic context, the microbialization score is a powerful metric for assessing the level of human impact a reef system is experiencing. [ABSTRACT FROM AUTHOR]

Fishes at Isla del Coco National Park, Costa Rica, were surveyed as part of a larger scientific expedition to the area in September 2009. The average total biomass of nearshore fishes was 7.8 tonnes per ha, among the largest observed in the tropics, with apex predators such as sharks, jacks, and groupers accounting for nearly 40% of the total biomass. The abundance of reef and pelagic sharks, particularly large aggregations of threatened species such as the scalloped hammerhead shark (up to 42 hammerheads ha-1) and large schools of jacks and snappers show the capacity for high biomass in unfished ecosystems in the Eastern Tropical Pacific. However, the abundance of hammerhead and reef whitetip sharks appears to have been declining since the late 1990s, and likely causes may include increasing fishing pressure on sharks in the region and illegal fishing inside the Park. One Galapagos shark tagged on September 20, 2009 in the Isla del Coco National Park moved 255km southeast towards Malpelo Island in Colombia, when it stopped transmitting. These results contribute to the evidence that sharks conduct large-scale movements between marine protected areas (Isla del Coco, Malpelo, Galápagos) in the Eastern tropical Pacific and emphasize the need for regional-scale management. More than half of the species and 90% of the individuals observed were endemic to the tropical eastern Pacific. These high biomass and endemicity values highlight the uniqueness of the fish assemblage at Isla del Coco and its importance as a global biodiversity hotspot. [ABSTRACT FROM AUTHOR]

The article discusses a survey which can be used to assess populations of coral reef fishes in which a pair of SCUBA divers maneuver towboard dive plans and record of large-bodied reef fishes while being towed at slow speed behind a small boat. It cites the main objectives in sampling coral reef fish communities. According to the authors, the towed-diver method provides managers and scientists with a tool to assess the distribution and status of reef fish stocks.

Comparable information on the status of natural resources across large geographic and human impact scales provides invaluable context to ecosystem-based management and insights into processes driving differences among areas. Data on fish assemblages at 39 US flag coral reef-areas distributed across the Pacific are presented. Total reef fish biomass varied by more than an order of magnitude: lowest at densely-populated islands and highest on reefs distant from human populations. Remote reefs (<50 people within 100 km) averaged ∼4 times the biomass of "all fishes" and 15 times the biomass of piscivores compared to reefs near populated areas. Greatest within-archipelagic differences were found in Hawaiian and Mariana Archipelagos, where differences were consistent with, but likely not exclusively driven by, higher fishing pressure around populated areas. Results highlight the importance of the extremely remote reefs now contained within the system of Pacific Marine National Monuments as ecological reference areas. [ABSTRACT FROM AUTHOR]

A series of surveys were carried out to characterize the physical and biological parameters of the Millennium Atoll lagoon during a research expedition in April of 2009. Millennium is a remote coral atoll in the Central Pacific belonging to the Republic of Kiribati, and a member of the Southern Line Islands chain. The atoll is among the few remaining coral reef ecosystems that are relatively pristine. The lagoon is highly enclosed, and was characterized by reticulate patch and line reefs throughout the center of the lagoon as well as perimeter reefs around the rim of the atoll. The depth reached a maximum of 33.3 m in the central region of the lagoon, and averaged between 8.8 and 13.7 m in most of the pools. The deepest areas were found to harbor large platforms of Favia matthaii, which presumably provided a base upon which the dominant corals (Acropora spp.) grew to form the reticulate reef structure. The benthic algal communities consisted mainly of crustose coralline algae (CCA), microfilamentous turf algae and isolated patches of Halimeda spp. and Caulerpa spp. Fish species richness in the lagoon was half of that observed on the adjacent fore reef. The lagoon is likely an important nursery habitat for a number of important fisheries species including the blacktip reef shark and Napoleon wrasse, which are heavily exploited elsewhere around the world but were common in the lagoon at Millennium. The lagoon also supports an abundance of giant clams (Tridacna maxima). Millennium lagoon provides an excellent reference of a relatively undisturbed coral atoll. As with most coral reefs around the world, the lagoon communities of Millennium may be threatened by climate change and associated warming, acidification and sea level rise, as well as sporadic local resource exploitation which is difficult to monitor and enforce because of the atoll's remote location. While the remote nature of Millennium has allowed it to remain one of the few nearly pristine coral reef ecosystems in the world, it is imperative that this ecosystem receives protection so that it may survive for future generations. [ABSTRACT FROM AUTHOR]

Human impacts to terrestrial and marine communities are widespread and typically begin with the local extirpation of large- bodied animals. In the marine environment, few pristine areas relatively free of human impact remain to provide baselines of ecosystem function and goals for restoration efforts. Recent comparisons of remote and/or protected coral reefs versus impacted sites suggest remote systems are dominated by apex predators, yet in these systems the ecological role of non-predatory, large-bodied, highly vulnerable species such as the giant bumphead parrotfish (Bolbometopon muricatum) has received less attention. Overfishing of Bolbometopon has lead to precipitous declines in population density and avoidance of humans throughout its range, contributing to its status as a candidate species under the U. S. Endangered Species Act and limiting opportunities to study unexploited populations. Here we show that extraordinary ecological processes, such as violent headbutting contests by the world’s largest parrotfish, can be revealed by studying unexploited ecosystems, such as the coral reefs of Wake Atoll where we studied an abundant population of Bolbometopon. Bolbometopon is among the largest of coral reef fishes and is a well known, charismatic species, yet to our knowledge, no scientific documentation of ritualized headbutting exists for marine fishes. Our observations of aggressive headbutting by Bolbometopon underscore that remote locations and marine reserves, by inhibiting negative responses to human observers and by allowing the persistence of historical conditions, can provide valuable opportunities to study ecosystems in their natural state, thereby facilitating the discovery, conservation, and interpretation of a range of sometimes remarkable behavioral and ecological processes. [ABSTRACT FROM AUTHOR]

Summary Mixotrophy is among the most successful nutritional strategies in terrestrial and marine ecosystems. The ability of organisms to supplement primary nutritional modes along continua of autotrophy and heterotrophy fosters trophic flexibility that can sustain metabolic demands under variable or stressful conditions. Symbiotic, reef-building corals are among the most broadly distributed and ecologically important mixotrophs, yet we lack a basic understanding of how they modify their use of autotrophy and heterotrophy across gradients of food availability. Here, we evaluate how one coral species, Pocillopora meandrina , supplements autotrophic nutrition through heterotrophy within an archipelago and test whether this pattern holds across species globally. Using stable isotope analysis (δ13C) and satellite-derived estimates of nearshore primary production (chlorophyll- a , as a proxy for food availability), we show that P. meandrina incorporates a greater proportion of carbon via heterotrophy when more food is available across five central Pacific islands. We then show that this pattern is consistent globally using data from 15 coral species across 16 locations spanning the Caribbean Sea and the Indian and Pacific Oceans. Globally, surface chlorophyll- a explains 77% of the variation in coral heterotrophic nutrition, 86% for one genus across 10 islands, and 94% when controlling for coral taxonomy within archipelagos. These results demonstrate, for the first time, that satellite-derived estimates of nearshore primary production provide a globally relevant proxy for resource availability that can explain variation in coral trophic ecology. Thus, our model provides a pivotal step toward resolving the biophysical couplings between mixotrophic organisms and spatial patterns of resource availability in the coastal oceans. Highlights • Variation in primary production can reshape coral trophic ecology across scales • A common coral increased heterotrophy at shallow depths on more productive islands • Corals are more heterotrophic in regions of higher nearshore primary production • Coral persistence may be linked to patterns of oceanic primary production How mixotrophic corals balance autotrophic and heterotrophic nutrition in relation to food availability is unknown. Fox et al. demonstrate that satellite estimates of nearshore primary production predict the trophic ecology of reef-building corals at regional and global scales. In more productive regions, some corals are consistently more heterotrophic. [ABSTRACT FROM AUTHOR]

As coral reef ecosystems experience unprecedented change, effective monitoring of reef features supports management, conservation, and intervention efforts. Omic techniques show promise in quantifying key components of reef ecosystems including dissolved metabolites and microorganisms that may serve as invisible sensors for reef ecosystem dynamics. Dissolved metabolites are released by reef organisms and transferred among microorganisms, acting as chemical currencies and contributing to nutrient cycling and signaling on reefs. Here, we applied four omic techniques (taxonomic microbiome via amplicon sequencing, functional microbiome via shotgun metagenomics, targeted metabolomics, and untargeted metabolomics) to waters overlying Florida's Coral Reef, as well as microbiome profiling on individual coral colonies from these reefs to understand how microbes and dissolved metabolites reflect biogeographical, benthic, and nutrient properties of this 500-km barrier reef. We show that the microbial and metabolite omic approaches each differentiated reef habitats based on geographic zone. Further, seawater microbiome profiling and targeted metabolomics were significantly related to more reef habitat characteristics, such as amount of hard and soft coral, compared to metagenomic sequencing and untargeted metabolomics. Across five coral species, microbiomes were also significantly related to reef zone, followed by species and disease status, suggesting that the geographic water circulation patterns in Florida also impact the microbiomes of reef builders. A combination of differential abundance and indicator species analyses revealed metabolite and microbial signatures of specific reef zones, which demonstrates the utility of these techniques to provide new insights into reef microbial and metabolite features that reflect broader ecosystem processes., (© The Author(s) 2023. Published by Oxford University Press on behalf of National Academy of Sciences.)

Islands support unique plants, animals, and human societies found nowhere else on the Earth. Local and global stressors threaten the persistence of island ecosystems, with invasive species being among the most damaging, yet solvable, stressors. While the threat of invasive terrestrial mammals on island flora and fauna is well recognized, recent studies have begun to illustrate their extended and destructive impacts on adjacent marine environments. Eradication of invasive mammals and restoration of native biota are promising tools to address both island and ocean management goals. The magnitude of the marine benefits of island restoration, however, is unlikely to be consistent across the globe. We propose a list of six environmental characteristics most likely to affect the strength of land-sea linkages: precipitation, elevation, vegetation cover, soil hydrology, oceanographic productivity, and wave energy. Global databases allow for the calculation of comparable metrics describing each environmental character across islands. Such metrics can be used today to evaluate relative potential for coupled land-sea conservation efforts and, with sustained investment in monitoring on land and sea, can be used in the future to refine science-based planning tools for integrated land-sea management. As conservation practitioners work to address the effects of climate change, ocean stressors, and biodiversity crises, it is essential that we maximize returns from our management investments. Linking efforts on land, including eradication of island invasive mammals, with marine restoration and protection should offer multiplied benefits to achieve concurrent global conservation goals.

The giant bumphead parrotfish (Bolbometopon muricatum) has experienced precipitous population declines throughout its range due to its importance as a highly-prized fishery target and cultural resource. Because of its diet, Bolbometopon may serve as a keystone species on Indo-Pacific coral reefs, yet comprehensive descriptions of its reproductive ecology do not exist. We used a variety of underwater visual census (UVC) methods to study an intact population of Bolbometopon at Wake Atoll, a remote and protected coral atoll in the west Pacific. Key observations include spawning activities in the morning around the full and last quarter moon, with possible spawning extending to the new moon. We observed peaks in aggregation size just prior to and following the full and last quarter moon, respectively, and observed a distinct break in spawning at the site that persisted for four days; individuals returned to the aggregation site one day prior to the last quarter moon and resumed spawning the following day. The mating system was lek-based, characterized by early male arrival at the spawning site followed by vigorous defense (including head-butting between large males) of small territories. These territories were apparently used to attract females that arrived later in large schools, causing substantial changes in the sex ratio on the aggregation site at any given time during the morning spawning period. Aggression between males and courtship of females led to pair spawning within the upper water column. Mating interference was not witnessed but we noted instances suggesting that sperm competition might occur. Densities of Bolbometopon on the aggregation site averaged 10.07(±3.24 SE) fish per hectare (ha) with maximum densities of 51.5 fish per ha. By comparing our observations to the results of biennial surveys conducted by the National Oceanic and Atmospheric Administration (NOAA) Coral Reef Ecosystem Division (CRED), we confirmed spatial consistency of the aggregation across years as well as a temporal break in spawning activity and aggregation that occurred during the lunar phase. We estimated the area encompassed by the spawning aggregation to be 0.72 ha, suggesting that spawning site closures and temporal closures centered around the full to the new moon might form one component of a management and conservation plan for this species. Our study of the mating system and spawning aggregation behavior of Bolbometopon from the protected, relatively pristine population at Wake Atoll provides crucial baselines of population density, sex ratio composition, and productivity of a spawning aggregation site from an oceanic atoll. Such information is key for conservation efforts and provides a basic platform for the design of marine protected areas for this threatened iconic coral reef fish, as well as for species with similar ecological and life history characteristics.

Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.