Abstract
Coral reefs harbor the most diverse assemblages in the ocean, however, a large proportion of the diversity is cryptic and, therefore, undetected by standard visual census techniques. Cryptic and exposed communities differ considerably in species composition and ecological function. This study compares three different coral reef assessment protocols: i) visual benthic reef surveys: ii) visual census of Autonomous Reef Monitoring Structures (ARMS) plates; and iii) metabarcoding techniques of the ARMS (including sessile, 106–500 μm and 500–2000 μm size fractions), that target the cryptic and exposed communities of three reefs in the central Red Sea. Visual census showed a dominance of Cnidaria (Anthozoa) and Rhodophyta on the reef substrate, while Porifera, Bryozoa and Rhodophyta were the most abundant groups on the ARMS plates. Metabarcoding, targeting the 18S rRNA gene, significantly increased estimates of the species diversity (p < 0.001); revealing that Annelida were generally the dominant phyla (in terms of reads) of all fractions and reefs. Furthermore, metabarcoding detected microbial eukaryotic groups such as Syndiniophyceae, Mamiellophyceae and Bacillariophyceae as relevant components of the sessile fraction. ANOSIM analysis showed that the three reef sites showed no differences based on the visual census data. Metabarcoding showed a higher sensitivity for identifying differences between reef communities at smaller geographic scales than standard visual census techniques as significant differences in the assemblages were observed amongst the reefs. Comparison of the techniques showed no similar patterns for the visual techniques while the metabarcoding of the ARMS showed similar patterns amongst fractions. Establishing ARMS as a standard tool in reef monitoring will not only advance our understanding of local processes and ecological community response to environmental changes, as different faunal components will provide complementary information but also improve the estimates of biodiversity in coral reef benthic communities. This study lays the foundations for further studies looking at integrating traditional reef survey methodologies with complementary approaches, such as metabarcoding, which investigate other components of the reef community.
Highlights
It has been estimated that one billion people benefit directly from coral reefs through a variety of services, including fisheries and tourism (Hughes et al, 2007)
In the current scenario of environmental change due to natural and anthropogenic pressures, it is vital to have a sound understanding of biodiversity patterns across multiple spatial and temporal scales
Identification keys for the Red Sea are often inadequate, and taxonomic expertise is limited, sometimes it is hard to distinguish between some groups like Porifera, Ascidiacea and Bryozoa
Summary
It has been estimated that one billion people benefit directly from coral reefs through a variety of services, including fisheries and tourism (Hughes et al, 2007). Coral reefs have been termed the “rainforests of the sea” (Reaka-Kudla 1997), as they are believed to host 25% to 33% of marine biodiversity (Plaisance et al 2011). Small cavities within the coral limestone in which organisms can inhabit, has been estimated at 30 – 75% of the reef habitat (Ginsburg 1983; Scheffers et al, 2003). Exploration of these cryptic spaces has been achieved by using techniques that employ endoscopy of cavities in the limestone revealing, for example, abundant sponge communities in Red Sea coral reefs (Richter et al, 2001). A large cohort of biodiversity nested within coral reefs may remain unreported
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