Responses of the coral reef cryptobiome to environmental gradients in the Red Sea.

An essential component of the coral reef animal diversity is the species hidden in crevices within the reef matrix, referred to as the cryptobiome. These organisms play an important role in nutrient cycling and provide an abundant food source for higher trophic levels, yet they have been largely overlooked. Here, we analyzed the distribution patterns of the mobile cryptobiome (>2000 µm) along the latitudinal gradient of the Saudi Arabian coast of the Red Sea. Analysis was conducted based on 54 Autonomous Reef Monitoring Structures. We retrieved a total of 5273 organisms, from which 2583 DNA sequences from the mitochondrially encoded cytochrome c oxidase I were generated through sanger sequencing. We found that the cryptobiome community is variable over short geographical distances within the basin. Regression tree models identified sea surface temperature (SST), percentage cover of hard coral and turf algae as determinant for the number of operational taxonomic units present per Autonomous Reef Monitoring Structures (ARMS). Our results also show that the community structure of the cryptobiome is associated with the energy available (measured as photosynthetic active radiation), sea surface temperature, and nearby reef habitat characteristics (namely hard corals, turf and macroalgae). Given that temperature and reef benthic characteristics affect the cryptobiome, current scenarios of intensive climate change are likely to modify this fundamental biological component of coral reef functioning. However, the trajectory of change is unknow and can be site specific, as for example, diversity is expected to increase above SST of 28.5°C, and with decreasing hard coral and turf cover. This study provides a baseline of the cryptobenthic community prior to major coastal developments in the Red Sea to be used for future biodiversity studies and monitoring projects. It can also contribute to better understand patterns of reef biodiversity in a period where Marine Protected Areas are being discussed in the region.

Biodiversity patterns of the coral reef cryptobiota around the Arabian Peninsula.

The Arabian Peninsula accounts for approximately 6% of the world's coral reefs. Some thrive in extreme environments of temperature and salinity. Using 51 Autonomous Reef Monitoring Structure (ARMS), a standardized non-destructive monitoring device, we investigated the spatial patterns of coral reef cryptobenthic diversity in four ecoregions around the Arabian Peninsula and analyzed how geographical and/or environmental drivers shape those patterns. The mitochondrial cytochrome c oxidase subunit I (COI) gene was used to identify Amplicon Sequence Variants and assign taxonomy of the cryptobenthic organisms collected from the sessile and mobile fractions of each ARMS. Cryptobenthic communities sampled from the two ecoregions in the Red Sea showed to be more diverse than those inhabiting the Arabian (Persian) Gulf and the Gulf of Oman. Geographic distance revealed a stronger relationship with beta diversity in the Mantel partial correlation than environmental distance. However, the two mobile fractions (106-500 µm and 500-2000 µm) also had a significant correlation between environmental distance and beta diversity. In our study, dispersal limitations explained the beta diversity patterns in the selected reefs, supporting the neutral theory of ecology. Still, increasing differences in environmental variables (environmental filtering) also had an effect on the distribution patterns of assemblages inhabiting reefs within short geographic distances. The influence of geographical distance in the cryptofauna assemblages makes these relevant, yet usually ignored, communities in reef functioning vulnerable to large scale coastal development and should be considered in ecosystem management of such projects.

Global mesozooplankton communities show lower connectivity in deep oceanic layers.

Mesozooplankton is a key component of the ocean, regulating global processes such as the carbon pump, and ensuring energy transfer from lower to higher trophic levels. Yet, knowledge on mesozooplankton diversity, distribution and connectivity at global scale is still fragmented. To fill this gap, we applied DNA metabarcoding to mesozooplankton samples collected during the Malaspina-2010 circumnavigation expedition across the Atlantic, Indian and Pacific oceans from the surface to bathypelagic depths. We highlight the still scarce knowledge on global mesozooplankton diversity and identify the Indian Ocean and the deep sea as the oceanic regions with the highest proportion of hidden diversity. We report no consistent alpha-diversity patterns for mesozooplankton at a global scale, neither across vertical nor horizontal gradients. However, beta-diversity analysis suggests horizontal and vertical structuring of mesozooplankton communities mostly attributed to turnover and reveals an increase in mesozooplankton beta-diversity with depth, indicating reduced connectivity at deeper layers. Additionally, we identify a water mass type-mediated structuring of mesozooplankton bathypelagic communities instead of an oceanic basin-mediated as observed at upper layers. This suggests limited dispersal at deep ocean layers, most likely due to weaker currents and lower mixing of water mass types, thus reinforcing the importance of oceanic currents and barriers to dispersal in shaping global plankton communities.

Hurdles and opportunities in implementing marine biosecurity systems in data-poor regions.

Managing marine nonindigenous species (mNIS) is challenging, because marine environments are highly connected, allowing the dispersal of species across large spatial scales, including geopolitical borders. Cross-border inconsistencies in biosecurity management can promote the spread of mNIS across geopolitical borders, and incursions often go unnoticed or unreported. Collaborative surveillance programs can enhance the early detection of mNIS, when response may still be possible, and can foster capacity building around a common threat. Regional or international databases curated for mNIS can inform local monitoring programs and can foster real-time information exchange on mNIS of concern. When combined, local species reference libraries, publicly available mNIS databases, and predictive modeling can facilitate the development of biosecurity programs in regions lacking baseline data. Biosecurity programs should be practical, feasible, cost-effective, mainly focused on prevention and early detection, and be built on the collaboration and coordination of government, nongovernment organizations, stakeholders, and local citizens for a rapid response.

Widespread diversity deficits of coral reef sharks and rays.

A global survey of coral reefs reveals that overfishing is driving resident shark species toward extinction, causing diversity deficits in reef elasmobranch (shark and ray) assemblages. Our species-level analysis revealed global declines of 60 to 73% for five common resident reef shark species and that individual shark species were not detected at 34 to 47% of surveyed reefs. As reefs become more shark-depleted, rays begin to dominate assemblages. Shark-dominated assemblages persist in wealthy nations with strong governance and in highly protected areas, whereas poverty, weak governance, and a lack of shark management are associated with depauperate assemblages mainly composed of rays. Without action to address these diversity deficits, loss of ecological function and ecosystem services will increasingly affect human communities.

Interaction effects of crude oil and nutrient exposure on settlement of coral reef benthos.

Anthropogenic stressors increasingly cause ecosystem-level changes to sensitive marine habitats such as coral reefs. Intensification of coastal development and shipping traffic can increase nutrient and oil pollution on coral reefs, yet these two stressors have not been studied in conjunction. Here, we simulate a disturbance scenario exposing carbonate settlement tiles to nutrient and oil pollution in a full-factorial design with four treatments: control, nutrients, oil, and combination to examine community structure and net primary productivity (NPP) of pioneer communities throughout 28 weeks. Compared to the control treatment oil pollution decreased overall settlement and NPP, while nutrients increased turf algae and NPP. However, the combination of these two stressors resulted in similar community composition and NPP as the control. These results indicate that pioneer communities may experience shifts due to nutrient enrichment, and/or oil pollution. However, the timing and duration of an event will influence recovery trajectories requiring further study.

A portfolio of climate-tailored approaches to advance the design of marine protected areas in the Red Sea.

Intensified coastal development is compromising the health and functioning of marine ecosystems. A key example of this is the Red Sea, a biodiversity hotspot subjected to increasing local human pressures. While some marine-protected areas (MPAs) were placed to alleviate these stressors, it is unclear whether these MPAs are managed or enforced, thus providing limited protection. Yet, most importantly, MPAs in the Red Sea were not designed using climate considerations, likely diminishing their effectiveness against global stressors. Here, we propose to tailor the design of MPAs in the Red Sea by integrating approaches to enhance climate change mitigation and adaptation. First, including coral bleaching susceptibility could produce a more resilient network of MPAs by safeguarding reefs from different thermal regions that vary in spatiotemporal bleaching responses, reducing the risk that all protected reefs will bleach simultaneously. Second, preserving the basin-wide genetic connectivity patterns that are assisted by mesoscale eddies could further ensure recovery of sensitive populations and maintain species potential to adapt to environmental changes. Finally, protecting mangrove forests in the northern and southern Red Sea that act as major carbon sinks could help offset greenhouse gas emissions. If implemented with multinational cooperation and concerted effort among stakeholders, our portfolio of climate-tailored approaches may help build a network of MPAs in the Red Sea that protects more effectively its coastal resources against escalating coastal development and climate instability. Beyond the Red Sea, we anticipate this study to serve as an example of how to improve the utility of tropical MPAs as climate-informed conservation tools.

A step towards the validation of bacteria biotic indices using DNA metabarcoding for benthic monitoring.

Environmental genomics is a promising field for monitoring biodiversity in a timely fashion. Efforts have increasingly been dedicated to the use of bacteria DNA derived data to develop biotic indices for benthic monitoring. However, a substantial debate exists about whether bacteria-derived data using DNA metabarcoding should follow, for example, a taxonomy-based or a taxonomy-free approach to marine bioassessments. Here, we showcase the value of DNA-based monitoring using the impact of fish farming as an example of anthropogenic disturbances in coastal areas and compare the performance of taxonomy-based and taxonomy-free approaches in detecting environmental alterations. We analysed samples collected near to the farm cages and along distance gradients from two aquaculture installations, and at control sites, to evaluate the effect of this activity on bacterial assemblages. Using the putative response of bacterial taxa to stress we calculated the taxonomy-based biotic index microgAMBI. The distribution of individual amplicon sequence variants (ASVs), as a function of a gradient in sediment acid volatile sulphides, was then used to derive a taxonomy-free bacterial biotic index specific for this data set using a de novo approach based on quantile regression splines. Our results show that microgAMBI revealed a organically enriched environment along the gradient. However, the de novo biotic index outperformed microgAMBI by providing a higher discriminatory power in detecting changes in abiotic factors directly related to fish production, whilst allowing the identification of new ASVs bioindicators. The de novo strategy applied here represents a robust method to define new bioindicators in regions or habitats where no previous information about the response of bacteria to environmental stressors exists.

Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap.

A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.

Pan-regional marine benthic cryptobiome biodiversity patterns revealed by metabarcoding Autonomous Reef Monitoring Structures.

Autonomous Reef Monitoring Structures (ARMS) have been applied worldwide to characterize the critical yet frequently overlooked biodiversity patterns of marine benthic organisms. In order to disentangle the relevance of environmental factors in benthic patterns, here, through standardized metabarcoding protocols, we analyse sessile and mobile (<2 mm) organisms collected using ARMS deployed across six regions with different environmental conditions (3 sites × 3 replicates per region): Baltic, Western Mediterranean, Adriatic, Black and Red Seas, and the Bay of Biscay. A total of 27,473 Amplicon Sequence Variants (ASVs) were observed ranging from 1,404 in the Black Sea to 9,958 in the Red Sea. No ASVs were shared among all regions. The highest number of shared ASVs was between the Western Mediterranean and the Adriatic Sea (116) and Bay of Biscay (115). Relatively high numbers of ASVs (103), mostly associated with the genus Amphibalanus, were also shared between the lower salinity seas (Baltic and Black Seas). We found that compositional differences in spatial patterns of rocky-shore benthos are determined slightly more by dispersal limitation than environmental filtering. Dispersal limitation was similar between sessile and mobile groups, while the sessile group had a larger environmental niche breadth than the mobile group. Further, our study can provide a foundation for future evaluations of biodiversity patterns in the cryptobiome, which can contribute up to 70% of the local biodiversity.

Translational Molecular Ecology in practice: Linking DNA-based methods to actionable marine environmental management.

Molecular-based approaches can provide timely biodiversity assessments, showing an immense potential to facilitate decision-making in marine environmental management. However, the uptake of molecular data into environmental policy remains minimal. Here, we showcase a selection of local to global scale studies applying molecular-based methodologies for environmental management at various stages of implementation. Drawing upon lessons learned from these case-studies, we provide a roadmap to facilitate applications of DNA-based methods to marine policies and to overcome the existing challenges. The main impediment identified is the need for standardized protocols to guarantee data comparison across spatial and temporal scales. Adoption of Translational Molecular Ecology - the sustained collaboration between molecular ecologists and stakeholders, will enhance consensus with regards to the objectives, methods, and outcomes of environmental management projects. Establishing a sustained dialogue among stakeholders is key to accelerating the adoption of molecular-based approaches for marine monitoring and assessment.

Disentangling the complex microbial community of coral reefs using standardized Autonomous Reef Monitoring Structures (ARMS).

Autonomous Reef Monitoring Structures (ARMS) have been applied worldwide to describe eukaryotic cryptic reef fauna. Conversely, bacterial communities, which are critical components of coral reef ecosystem functioning, remain largely overlooked. Here we deployed 56 ARMS across the 2,000-km spread of the Red Sea to assay biodiversity, composition and inferred underlying functions of coral reef-associated bacterial communities via 16S rRNA gene sequencing. We found that bacterial community structure and diversity aligned with environmental differences. Indeed, sea surface temperature and macroalgae cover were key in explaining bacterial relative abundance. Importantly, taxonomic and functional alpha diversity decreased under more extreme environmental conditions (e.g., higher temperatures) in the southern Red Sea. This may imply a link between bacterial community diversity and functional capabilities, with implications for conservation management. Our study demonstrates the utility of ARMS to investigate the response of coral reef-associated bacterial communities to environmental change.

Beyond the visual: using metabarcoding to characterize the hidden reef cryptobiome.

In an era of coral reef degradation, our knowledge of ecological patterns in reefs is biased towards large conspicuous organisms. The majority of biodiversity, however, inhabits small cryptic spaces within the framework of the reef. To assess this biodiverse community, which we term the 'reef cryptobiome', we deployed 87 autonomous reef monitoring structures (ARMS), on 22 reefs across 16 degrees latitude of the Red Sea. Combining ARMS with metabarcoding of the mitochondrial cytochrome oxidase I gene, we reveal a rich community, including the identification of 14 metazoan phyla within 10 416 operational taxonomic units (OTUs). While mobile and sessile subsets were similarly structured along the basin, the main environmental driver was different (particulate organic matter and sea surface temperature, respectively). Distribution patterns of OTUs showed that only 1.5% were present in all reefs, while over half were present in a single reef. On both local and regional scales, the majority of OTUs were rare. The high heterogeneity in community patterns of the reef cryptobiome has implications for reef conservation. Understanding the biodiversity patterns of this critical component of reef functioning will enable a sound knowledge of how coral reefs will respond to future anthropogenic impacts.

A bacterial community-based index to assess the ecological status of estuarine and coastal environments.

Biotic indices for monitoring marine ecosystems are mostly based on the analysis of benthic macroinvertebrate communities. Due to their high sensitivity to pollution and fast response to environmental changes, bacterial assemblages could complement the information provided by benthic metazoan communities as indicators of human-induced impacts, but so far, this biological component has not been well explored for this purpose. Here we performed 16S rRNA gene amplicon sequencing to analyze the bacterial assemblage composition of 51 estuarine and coastal stations characterized by different environmental conditions and human-derived pressures. Using the relative abundance of putative indicator bacterial taxa, we developed a biotic index that is significantly correlated with a sediment quality index calculated on the basis of organic and inorganic compound concentrations. This new index based on bacterial assemblage composition can be a sensitive tool for providing a fast environmental assessment and allow a more comprehensive integrative ecosystem approach for environmental management.

Analysis of Illumina MiSeq Metabarcoding Data: Application to Benthic Indices for Environmental Monitoring.

This protocol details the analysis of Illumina MiSeq amplicon libraries derived from marine benthic macroinvertebrate samples and based on two barcodes of the mitochondrial cytochrome oxidase 1 (CO1) gene: a "short region," covered by overlapping forward and reverse reads and a "long region" for which forward and reverse reads do not overlap. Aside from providing guidelines for analyzing both types of amplicons, we show how amplicon reads can be used for the calculation of benthic indices for environmental monitoring.

Environmental status assessment using DNA metabarcoding: towards a genetics based Marine Biotic Index (gAMBI).

Marine ecosystem protection and conservation initiatives rely on the assessment of ecological integrity and health status of marine environments. The AZTI's Marine Biotic Index (AMBI), which consists on using macroinvertebrate diversity as indicator of ecosystem health, is used worldwide for this purpose. Yet, this index requires taxonomic assignment of specimens, which typically involves a time and resource consuming visual identification of each sample. DNA barcoding or metabarcoding are potential harmonized, faster and cheaper alternatives for species identification, although the suitability of these methods for easing the implementation of the AMBI is yet to be evaluated. Here, we analyze the requirements for the implementation of a genetics based AMBI (gAMBI), and show, using available sequence data, that information about presence/absence of the most frequently occurring species provides accurate AMBI values. Our results set the basics for the implementation of the gAMBI, which has direct implications for a faster and cheaper marine monitoring and health status assessment.