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Abstract Larval settlement and recruitment of sessile organisms are key ecological processes for population recovery and maintenance that occur at scales invisible to the human eye. Accordingly, proxies of recruitment have commonly been quantified using artificial substrata such as settlement tiles made of diverse materials and shapes, which are typically transported to the laboratory for examination. However, it is unknown how much bias is introduced with this sampling strategy and how recruitment quantified on tiles relates to recruitment on nearby natural substrata. Here, we applied techniques that combine macrophotography with photogrammetry (macrophotogrammetry) underwater to monitor benthic communities at submillimetre scale. This application allows the investigation of recruitment and community succession of the earliest life‐history stages in situ and on natural substrata. We tested the use of four different imaging systems, varying in costs from US$ 1400 to US$ 5440. While the most expensive SONY αRiv system provided the best visual output and ground resolution (up to 5 μm/pixel with a + 4 close‐up lens); regardless of systems, 3D models always had a ground resolution ≤23 μm/pixel and errors in planar measurements of submillimetre features were similar among systems. This level of resolution compares well with stereomicroscopy in the range of 5:1 to 10:1 magnification, while providing detailed 3D digital records through time. Using a coral reef example, we apply this approach to demonstrate how it can be used to monitor small reef areas (~300–600 cm2) through time, including the quantification of biophysical metrics such as cover of small facilitative and competitive organisms and microhabitat complexity. We further show that organisms as small 0.5 mm in size, such as 2‐month‐old coral settlers, can be located accurately within the 3D models and measured with a good level of confidence. This method can be readily applied to other benthic environments to elucidate drivers of early recruitment and recovery of benthic organisms following disturbance impacts at very fine scales, directly on natural substrata, to avoid biases inherent with laboratory‐based analyses of artificial surfaces.

Abstract Ocean warming and acidification caused by increases of atmospheric carbon dioxide are now thought to be major threats to coral reefs on a global scale. Here we evaluated the environmental conditions and benthic community structures in semi-closed Nikko Bay at the inner reef area in Palau, which has high pCO2 and seawater temperature conditions with high zooxanthellate coral coverage. Nikko Bay is a highly sheltered system with organisms showing low connectivity with surrounding environments, making this bay a unique site for evaluating adaptation and acclimatization responses of organisms to warmed and acidified environments. Seawater pCO2/Ωarag showed strong gradation ranging from 380 to 982 µatm (Ωarag: 1.79–3.66), and benthic coverage, including soft corals and turf algae, changed along with Ωarag while hard coral coverage did not change. In contrast to previous studies, net calcification was maintained in Nikko Bay even under very low mean Ωarag (2.44). Reciprocal transplantation of the dominant coral Porites cylindrica showed that the calcification rate of corals from Nikko Bay did not change when transplanted to a reference site, while calcification of reference site corals decreased when transplanted to Nikko Bay. Corals transplanted out of their origin sites also showed the highest interactive respiration (R) and lower gross photosynthesis (Pg) to respiration (Pg:R), indicating higher energy acquirement of corals at their origin site. The results of this study give important insights about the potential local acclimatization and adaptation capacity of corals to different environmental conditions including pCO2 and temperature.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Palau has a rich heritage of conservation that has evolved from the traditional moratoria on fishing, or "bul", to more western Marine Protected Areas (MPAs), while still retaining elements of customary management and tenure. In 2003, the Palau Protected Areas Network (PAN) was created to conserve Palau's unique biodiversity and culture, and is the country's mechanism for achieving the goals of the Micronesia Challenge (MC), an initiative to conserve ≥30% of near-shore marine resources within the region by 2020. The PAN comprises a network of numerous MPAs within Palau that vary in age, size, level of management, and habitat, which provide an excellent opportunity to test hypotheses concerning MPA design and function using multiple discreet sampling units. Our sampling design provided a robust space for time comparison to evaluate the relative influence of potential drivers of MPA efficacy. Our results showed that no-take MPAs had, on average, nearly twice the biomass of resource fishes (i.e. those important commercially, culturally, or for subsistence) compared to nearby unprotected areas. Biomass of non-resource fishes showed no differences between no-take areas and areas open to fishing. The most striking difference between no-take MPAs and unprotected areas was the more than 5-fold greater biomass of piscivorous fishes in the MPAs compared to fished areas. The most important determinates of no-take MPA success in conserving resource fish biomass were MPA size and years of protection. Habitat and distance from shore had little effect on resource fish biomass. The extensive network of MPAs in Palau likely provides important conservation and tourism benefits to the Republic, and may also provide fisheries benefits by protecting spawning aggregation sites, and potentially through adult spillover.