title: Please mind the gap - Visual census and cryptic biodiversity assessment at central Red Sea coral reefs.
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.
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia. Electronic address: john.pearman@kaust.edu.sa.
authors.forename: John K
authors.initials: JK
authors.lastname: Pearman
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Holger
authors.initials: H
authors.lastname: Anlauf
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Xabier
authors.initials: X
authors.lastname: Irigoien
authors.affiliation: King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Susana
authors.initials: S
authors.lastname: Carvalho
mesh_terms: D000818:Animals; D037421:Anthozoa / Q000145:classification* / Q000254:growth & development; D044822:Biodiversity; D058448:Biota; D019352:Censuses; D057894:Coral Reefs; D004784:Environmental Monitoring / Q000379:methods*; D019156:Indian Ocean
keywords: Autonomous reef monitoring structures; Benthos; Biodiversity surveys; Coral reefs; Marine ecology; Metabarcoding; Monitoring; Red Sea