Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea

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.

Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.

Composition, uniqueness and connectivity across tropical coastal lagoon habitats in the Red Sea

Background

Tropical habitats and their associated environmental characteristics play a critical role in shaping macroinvertebrate communities. Assessing patterns of diversity over space and time and investigating the factors that control and generate those patterns is critical for conservation efforts. However, these factors are still poorly understood in sub-tropical and tropical regions. The present study applied a combination of uni- and multivariate techniques to test whether patterns of biodiversity, composition, and structure of macrobenthic assemblages change across different lagoon habitats (two mangrove sites; two seagrass meadows with varying levels of vegetation cover; and an unvegetated subtidal area) and between seasons and years.

Results

In total, 4771 invertebrates were identified belonging to 272 operational taxonomic units (OTUs). We observed that macrobenthic lagoon assemblages are diverse, heterogeneous and that the most evident biological pattern was spatial rather than temporal. To investigate whether macrofaunal patterns within the lagoon habitats (mangrove, seagrass, unvegetated area) changed through the time, we analysed each habitat separately. The results showed high seasonal and inter-annual variability in the macrofaunal patterns. However, the seagrass beds that are characterized by variable vegetation cover, through time, showed comparatively higher stability (with the lowest values of inter-annual variability and a high number of resident taxa). These results support the theory that seagrass habitat complexity promotes diversity and density of macrobenthic assemblages. Despite the structural and functional importance of seagrass beds documented in this study, the results also highlighted the small-scale heterogeneity of tropical habitats that may serve as biodiversity repositories.

Conclusions

Comprehensive approaches at the “seascape” level are required for improved ecosystem management and to maintain connectivity patterns amongst habitats. This is particularly true along the Saudi Arabian coast of the Red Sea, which is currently experiencing rapid coastal development. Also, considering the high temporal variability (seasonal and inter-annual) of tropical shallow-water habitats, monitoring and management plans must include temporal scales.

Natural Products Repertoire of the Red Sea

Marine natural products have achieved great success as an important source of new lead compounds for drug discovery. The Red Sea provides enormous diversity on the biological scale in all domains of life including micro- and macro-organisms. In this review, which covers the literature to the end of 2019, we summarize the diversity of bioactive secondary metabolites derived from Red Sea micro- and macro-organisms, and discuss their biological potential whenever applicable. Moreover, the diversity of the Red Sea organisms is highlighted as well as their genomic potential. This review is a comprehensive study that compares the natural products recovered from the Red Sea in terms of ecological role and pharmacological activities.

Marine environmental DNA: Approaches, applications, and opportunities

Environmental DNA (eDNA) is increasingly being used to document species distributions and habitat use in marine systems, with much of the recent effort focused on leveraging advances in next-generation DNA sequencing to assess and track biodiversity across taxonomic groups. Environmental DNA offers a number of important advantages over traditional survey techniques, including non-invasive sampling, sampling where traditional approaches are impractical or inefficient (e.g. deep oceans), reduced cost, and increased detection sensitivity. However, eDNA applications are currently limited because of an insufficient understanding of the influence of sample source, analytical approach, and marker type on eDNA detections. Because approaches vary considerably among eDNA studies, we present a summary of the current state of the field and emerging best practices. The impact of observed variation in rates of eDNA production, persistence, and transport are also discussed and future research needs are highlighted with the goal of expanding eDNA applications, including the development of statistical models to improve the predictability of eDNA detection and quantification.

Coupled effects of land use pattern and hydrological regime on composition and diversity of riverine eukaryotic community in a coastal watershed of Southeast China

The coupled effects of land use pattern and hydrological regime on composition and diversity of riverine eukaryotic community are needed for understanding riverine ecosystem health and algal blooming mechanism. In-situ monitoring and 18S rRNA gene sequencing were used to investigate spatiotemporal variations of eukaryotic community in three types of watershed with different dominant land use type (i.e. urban, forest, and natural) during three seasons (i.e. dry, transition, and wet seasons) in a coastal watershed of Southeast China. Results showed that agricultural and urban watersheds had significantly higher diversity in dry and transition seasons, and higher richness in transition and wet seasons than those in forest watershed. The non-metric multidimensional scaling analysis further verified great spatiotemporal variations of eukaryotic community. Stramenopiles, Alveolata, Animalia, and Eukaryota, dominated the sequences reads for all sampling sites in three seasons. Agricultural watershed had the highest relative abundant of Animalia, whereas Eukaryota was the most abundant in urban watershed and forest watershed had the highest relative abundance of Stramenopiles and Alveolata. The RDA ordination showed that Builtup and streamflow were two most important factors for moderate taxa and abundant taxa, respectively. Variation partitioning revealed that land use pattern and hydrological regime together explained 54.4%, 61% and 67.2% variances of the composition of eukaryotic community. Among three sampling seasons, the relative contribution of land use pattern was higher than that of hydrological regime. The results of this investigation demonstrated how land use pattern and hydrological regime affected the composition and diversity of riverine eukaryotic community. The findings can provide a useful insight into the riverine eukaryotic communities and their underlying ecological mechanisms in coastal China watersheds.

Lessons from photo analyses of Autonomous Reef Monitoring Structures as tools to detect (bio-)geographical, spatial, and environmental effects

We investigated the validity of Autonomous Reef Monitoring Structures (ARMS) as monitoring tools for hard bottoms across a wide geographic and environmental range. We deployed 36 ARMS in the northeast Atlantic, northwest Mediterranean, Adriatic and Red Sea at 7-17 m depth. After 12-16 months, community composition was inferred from photographs, in six plate-faces for each ARMS. Overall, we found a highly significant effect of sea region, site (within seas), and plate-face on community composition. Plate-faces thus represent distinct micro-habitats and provide pseudo-replicates, increasing statistical power. Within each sea region taken individually, there was also a highly significant effect of site and plate-face. Because strong effects were obtained despite the fusion of taxonomic categories at high taxonomic ranks (to ensure comparability among biogeographic provinces), ARMS photo-analysis appears a promising monitoring tool for each sea region. We recommend keeping three ARMS per site and analyzing more numerous sites within a sea region to investigate environmental effects.