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Ecological forecasts are becoming increasingly valuable tools for conservation and management. However, there are few examples of near-real-time forecasting systems that account for the wide range of ecological complexities. We developed a new coral disease ecological forecasting system that explores a suite of ecological relationships and their uncertainty and investigates how forecast skill changes with shorter lead times. The Multi-Factor Coral Disease Risk product introduced here uses a combination of ecological and marine environmental conditions to predict the risk of white syndromes and growth anomalies across reefs in the central and western Pacific and along the east coast of Australia and is available through the US National Oceanic and Atmospheric Administration Coral Reef Watch program. This product produces weekly forecasts for a moving window of 6 months at a resolution of ~5 km based on quantile regression forests. The forecasts show superior skill at predicting disease risk on withheld survey data from 2012 to 2020 compared with predecessor forecast systems, with the biggest improvements shown for predicting disease risk at mid- to high-disease levels. Most of the prediction uncertainty arises from model uncertainty, so prediction accuracy and precision do not improve substantially with shorter lead times. This result arises because many predictor variables cannot be accurately forecasted, which is a common challenge across ecosystems. Weekly forecasts and scenarios can be explored through an online decision support tool and data explorer, co-developed with end-user groups to improve use and understanding of ecological forecasts. The models provide near-real-time disease risk assessments and allow users to refine predictions and assess intervention scenarios. This work advances the field of ecological forecasting with real-world complexities and, in doing so, better supports near-term decision making for coral reef ecosystem managers and stakeholders. Secondarily, we identify clear needs and provide recommendations to further enhance our ability to forecast coral disease risk.

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Globally, coral reefs face increasing disease prevalence and large-scale outbreak events. These outbreaks offer insights into microbial and functional patterns of coral disease, including early indicators of disease that may be present in visually-healthy tissues. Outbreak events also allow investigation of how reef-building corals, typically colonial organisms, respond to disease. We studied Pocillopora damicornis during an acute tissue loss disease outbreak on Guam to determine whether dysbiosis was present in visually-healthy tissues ahead of advancing disease lesions. These data reveal that coral fragments with visual evidence of disease are expectedly dysbiotic with high microbial and metabolomic variability. However, visually-healthy tissues from the same colonies lacked dysbiosis, suggesting disease containment near the affected area. These results challenge the idea of using broad dysbiosis as a pre-visual disease indicator and prompt reevaluation of disease assessment in colonial organisms such as reef-building corals.

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Coral reefs host some of the highest concentrations of biodiversity and economic value in the oceans, yet these ecosystems are under threat due to climate change and other human impacts. Reef monitoring is routinely used to help prioritize reefs for conservation and evaluate the success of intervention efforts. Reef status and health are most frequently characterized using diver-based surveys, but the inherent limitations of these methods mean there is a growing need for advanced, standardized, and automated reef techniques that capture the complex nature of the ecosystem. Here we draw on experiences from our own interdisciplinary research programs to describe advances in in situ diver-based and autonomous reef monitoring. We present our vision for integrating interdisciplinary measurements for select "case-study" reefs worldwide and for learning patterns within the biological, physical, and chemical reef components and their interactions. Ultimately, these efforts could support the development of a scalable and standardized suite of sensors that capture and relay key data to assist in categorizing reef health. This framework has the potential to provide stakeholders with the information necessary to assess reef health during an unprecedented time of reef change as well as restoration and intervention activities.

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The global decline of coral reefs has driven considerable interest in active coral restoration. Despite their importance and dominance on mature reefs, relatively few coral restoration projects use slower growth forms like massive and encrusting coral species. Micro-fragmentation can increase coral cover by orders of magnitude faster than natural growth, which now allows cultivation of slow growing massive forms and shows promise and flexibility for active reef restoration. However, the major causes of variation in growth and survival of outplanted colonies remain poorly understood. Here, we report simple outplanting assays to aid in active reef restoration of slower growing species and increase the likelihood of restoration success. We used two different micro-fragmentation assays. Pyramid assays were used to examine variation associated with fragment size (ranging from ≈1-9 cm2), nursery residence time (for both in-situ and ex-situ nurseries), and 2D vs. 3D measurements of growth. Block assays were used to examine spatial variation among individual performance at outplanting sites in the field. We found 2D and 3D measurements correlated well, so measured survivorship and growth using top-down planar images for two of the main Hawaiian reef building corals, the plating Montipora capitata and the massive Porites compressa. Pyramid assays housed and outplanted from the in-situ nursery showed no effect of residence time or size on overall survivorship or growth for either species. Results from the ex-situ nursery, however, varied by species, with P. compressa again showing no effect of nursery residence time or size on survivorship or growth. In contrast, nursery culture resulted in improved survivorship of small M. capitata fragments, but net growth showed a weak positive effect of nursery time for medium fragments. Small fragments still suffered higher mortality than either medium or large fragments. Due to their lower mortality, medium fragments (≈3 cm2) appear to be the best compromise between growth and survivorship for outplanting. Likewise, given weak positive gains relative to the investment, our results suggest that it could be more cost-effective to simply outplant medium fragments as soon as possible, without intermediate culture in a nursery. Furthermore, the block assay revealed significant differences in survivorship and growth among sites for individuals of both species, emphasizing the importance of considering spatial variation in coral survival and growth following outplanting. These results highlight the value of using short-term micro-fragmentation assays prior to outplanting to assess size, and location specific performance, optimizing the efficiency of active reef restoration activities and maximizing the probability of success for active coral restoration projects.

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Plant microbiomes are shaped by forces working at different spatial scales. Environmental factors determine a pool of potential symbionts while host physiochemical factors influence how those microbes associate with distinct plant tissues. These scales are seldom considered simultaneously, despite their potential to interact. Here, we analyze epiphytic microbes from nine Hibiscus tiliaceus trees across a steep, but short, environmental gradient within a single Hawaiian watershed. At each location, we sampled eight microhabitats: leaves, petioles, axils, stems, roots, and litter from the plant, as well as surrounding air and soil. The composition of bacterial communities is better explained by microhabitat, while location better predicted compositional variance for fungi. Fungal community compositional dissimilarity increased more rapidly along the gradient than did bacterial composition. Additionally, the rates of fungal community compositional dissimilarity along the gradient differed among plant parts, and these differences influenced the distribution patterns and range size of individual taxa. Within plants, microbes were compositionally nested such that aboveground communities contained a subset of the diversity found belowground. Our findings indicate that both environmental context and microhabitat contribute to microbial compositional variance in our study, but that these contributions are influenced by the domain of microbe and the specific microhabitat in question, suggesting a complicated and potentially interacting dynamic.

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The study and conservation of biological communities, such as coral reefs, frequently requires repeated surveys to measure the growth of organisms or the occurrence of ecological processes, such as recruitment, predation, competition, or mortality. In the case of coral reefs, processes influencing coral community structure occur on time scales of days (recruitment, predation), months (seasonal environmental stress), or years (competition for space). In both marine and terrestrial systems, observing the ecology of remote locations at fine temporal scales is made difficult by the high cost or complexity of resurveying the same location at high frequency. These restrictions have produced limited understanding of in-situ ecological processes which occur at fine temporal scales and influence community structure but are easily missed during infrequent surveys. We present a low-cost method for the conversion of consumer cameras into programmable time-lapse platforms, allowing scheduled daily video or photo capture in remote locations for extended time periods. Results of a 1-month deployment with twice-daily photo capture are presented. Total cost to construct and deploy CoralCam in-situ (up to 45 m) is approximately $80 USD, providing a low-cost platform for fine scale data collection where these data are not otherwise logistically or financially possible.

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Ecosystem engineers, organisms that modify the physical environment, are generally thought to increase diversity by facilitating species that benefit from engineered habitats. Recent theoretical work, however, suggests that ecosystem engineering could initiate cascades of trophic interactions that shape community structure in unexpected ways, potentially having negative indirect effects on abundance and diversity in components of the community that do not directly interact with the habitat modifications. We tested the indirect effects of a gall-forming wasp on arthropod communities in surrounding unmodified foliage. We experimentally removed all senesced galls from entire trees during winter and sampled the arthropod community on foliage after budburst. Gall removal resulted in 59% greater herbivore density, 26% greater herbivore richness, and 27% greater arthropod density five weeks after budburst. Gall removal also reduced the differences in community composition among trees (i.e., reduced beta diversity), even when accounting for differences in richness. The community inside galls during winter and through the growing season was dominated by jumping spiders (Salticidae; 0.87 ± 0.12 spiders per gall). We suggest that senesced galls provided habitat for spiders, which suppressed herbivorous arthropods and increased beta diversity by facilitating assembly of unusual arthropod communities. Our results demonstrate that the effects of habitat modification by ecosystem engineers can extend beyond merely providing habitat for specialists; the effects can propagate far enough to influence the structure of communities that do not directly interact with habitat modifications.

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