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Successful recruitment of invertebrate larvae to reef substrates is essential to the health of tropical coral reef ecosystems and to their capacity to recover from disturbances. Crustose calcifying red algae (CCRA) are a species rich group of seaweeds that have been identified as important recruitment substrates for scleractinian corals. Most studies on the settlement preference of coral larvae on CCRA use morphological species identifications that can lead to unreliable species identification and do not allow for examining species-specific interactions between coral larvae and CCRA. Accurate identifications of CCRA species is important for coral reef restoration and management to assess CCRA community composition and to detect CCRA species that are favored as coral recruitment substrates. In this study, DNA sequence analysis, was used to identify CCRA species to (1) investigate the species richness and community composition of CCRA on experimental coral recruitment tiles and (2) assess if the coral Acropora surculosa preferred any of these CCRA species as recruitment substrates. The CCRA community assemblages on the coral recruitment tiles was species-rich, comprising 27 distinct CCRA species of the orders Corallinales and Peyssonneliales which constitute new species records for Guam. Lithophylloideae sp. 1 (Corallinales) was the CCRA species that was significantly favored by coral larvae as a recruitment substrate. Lithophylloideae sp. 1 showed to hold a valuable ecological role for coral larval recruitment preference. Lithophylloideae sp. 1 had the highest benthic cover on the recruitment tiles and contained most A. surculosa recruits. DNA barcoding revealed a high taxonomic diversity of CCRA species on a microhabitat scale and provided detailed insight into the species-specific ecological interactions between CCRA and corals. With a steady decline in coral cover, detailed information on species interactions that drive reef recovery is valuable for the planning of marine management actions and restoration efforts. [ABSTRACT FROM AUTHOR]

Evidence-based environmental management is urgently required to enable progress towards global conservation commitments. To fill large-scale biodiversity knowledge gaps, governments, organisations and communities must adopt innovative ecological monitoring techniques. The emergence of environmental DNA (eDNA) survey methods, as well as the increased availability of in situ ocean observation and satellite remote sensing data, offers opportunities to overcome significant logistic and financial challenges previously associated with traditional biodiversity monitoring. Here, a 1.5 year-long eDNA survey reveals the spatial and temporal presence of 'critically endangered' scalloped hammerhead sharks (Sphyrna lewini) in Apra Harbor, Guam. The survey confirms the presence of S. lewini in the region, and shows eDNA detections are most frequent at the beginning of the dry season, in January. Combined analysis of eDNA results with open (freely available) ecological data identifies that S. lewini presence is associated with increases in water velocity, turbidity and wind direction, as well as decreases in temperature and wind speed. Additionally, the data indicate S. lewini are most frequent at sampling sites characterised by high turbidity, shallow depths, and large distances from the harbor entrance. Information on local distribution and habitat preferences generated here is fundamental to the establishment of management protocols that aim to minimise negative anthropogenic impacts on S. lewini in Apra Harbor. The work provides an example of contemporary marine monitoring for the efficient generation of biodiversity data; an approach that will enable informed management decisions and help to reduce the risk and rate of species extinctions throughout the next decade. [Display omitted] • 1.5-year long eDNA survey for critically endangered scalloped hammerhead sharks. • Results provide previously unobtainable species distribution data for Micronesia. • Freely available data for 13 environmental variables permits ecological inference. • Spatial and temporal presence data enable compliance with protective legislation. • The utility of innovative and efficient monitoring techniques is demonstrated. [ABSTRACT FROM AUTHOR]

• Novel eDNA survey for detecting critically endangered scalloped hammerhead sharks. • Enables the first detection of scalloped hammerheads in Guam since 1971. • A single-day eDNA sampling effort outperforms five decades of visual surveys. • The eDNA survey method is non-invasive, cost-effective, and user friendly. • Survey application allows for rapid data generation for science-based conservation. Among the hammerhead sharks, scalloped hammerheads (Sphyrna lewini) have undergone the steepest population declines worldwide. Due to their high susceptibility to exploitation, the species is now classified as 'critically endangered', the most threatened category listed by the International Union for Conservation of Nature. There is an urgent need for data on the distribution of S. lewini to inform the design and implementation of effective conservation management strategies, and mitigate the risk of global extinction. Environmental DNA (eDNA) is emerging as a powerful method to monitor the geographic distribution, population trends, and habitat usage of rare and endangered species. In comparison to traditional survey methods, eDNA methods offer lower cost, higher detection rates, and are non-invasive. At present, there is no targeted eDNA assay for the detection of S. lewini and existing methods to assess their distribution are either fisheries-dependent, leading to bias, or costly and laborious, leading to impracticality in regions of low or unknown abundance. Here we present an optimised workflow for the detection of S. lewini presence using eDNA methods, and apply these to successfully detect scalloped hammerhead sharks in Guam, of the western Pacific Ocean, where their presence has not been scientifically reported since the 1970s. The detection of S. lewini by eDNA survey methods was achieved from a single-day sampling effort, demonstrating the efficacy of the technique and workflow. If implemented, the eDNA survey methods developed here will enable the rapid generation of information on the distribution of scalloped hammerhead sharks in the western Pacific, and likely globally, and assist in the accurate placement of no-take reserves to best enable the species' recovery. [ABSTRACT FROM AUTHOR]