Environmental DNA metabarcoding for biodiversity monitoring of a highly-diverse tropical fish community in a coral-reef lagoon: Estimation of species richness and detection of habitat segregation

An environmental DNA (eDNA) metabarcoding approach has been widely used for biodiversity monitoring of fishes, although it has rarely been applied to tropical and subtropical aquatic ecosystems, where species diversity is remarkably high. This study examined the extent to which species richness can be estimated in a small coral reef lagoon (1500 × 900 m) near Okinawa Island, southern Japan, where the surrounding waters are likely to harbor more than 1500 species of fish. During 2015–2017, a total of 16 capture-based surveys were conducted to create a faunal list of fish species, followed by eDNA metabarcoding based on seawater samples taken from 11 sites in the lagoon on a day in May 2019. We also tested whether eDNA metabarcoding could detect differences between adjacent fish communities inhabiting the offshore reef edge and shore-side seagrass beds within the lagoon. A total of 217 fish species were confirmed by the capture-based samplings, while 291 fish species were detected by eDNA metabarcoding, identifying a total of 410 species distributed across 119 families and 193 genera. Of these 410 species, only 96 (24% of the total) were commonly identified by both methods, indicating that capture-based surveys failed to collect a number of species detected by eDNA metabarcoding. Interestingly, two different approaches to estimate species richness based on eDNA data yielded values close to the 410 species, including one that suggested an additional three or more eDNA surveys from 11 sites (36 samples) would detect 90% of the 410 species. In addition, non-metric multi-dimensional scaling for fish assemblages clearly distinguished between the fish communities of the offshore reef edge and those of the shore-side seagrass beds.

An Experimental Study of Wave-Induced Set-Up Over a Horizontal Reef With an Idealized Ridge

Wave action has been the primary focus of near-shore hydrodynamic studies over decades. The wave-induced set-up due to wave breaking is one of the important factors to consider in determining both water level and mass transport above the reef-top, which has ecological as well as engineering significance. Previous investigations into reef hydrodynamics (including laboratory experiments, field investigations, theoretical analysis and numerical simulations) focused mainly on wave-induced set-up on reefs with a horizontal reef-top (Gourlay, 1996. J. Coastal Eng. 27:161–193). It has been observed that a ridge (reef crest) may be present at the reef edge, but so far we are not aware of any published studies on the effects of this type of ridge on the wave-induced set-up over the reef-top. To understand the role of the ridge in wave-breaking mechanism and wave-induced set-up over the reef, a series of experiments were carried out in a wave flume of 36m long and 0.55m wide, with idealized reef-ridge models being installed at the reef edge to simulate fringing reefs with rectangle ridges. The surface elevations at four locations over the reef were measured with Ultralab sensors (General Acoustics), revealing the variation of wave-induced set-up along the reef. Experimental results are reported for two water depths and eighteen regular wave conditions. Also discussed are the effects of the ridge width on the wave-induced set-up. The focus of this paper will be given to the comparison of wave-induced set-ups with and without the rectangular ridges. Preliminary analysis shows that the ridge controls the water level above the reef-top in a way similar to that a broad crest weir controls the water level in open channel flows. Furthermore, the presence of the ridge is found to alter significantly the wave transformation process near the reef edge, especially the strength of the reflected waves and the locations of breakers. Experiments also show that the wave-induced set-up over reef-top with a ridge is generally much larger than that without a ridge. Finally, an attempt is made to introduce a new dimensionless parameter in order to take the ridge configuration into consideration and achieve a better agreement between experiments and predictions when ridges are present.

Fragmentation and genotypic diversity of the scleractinian coral Montipora capitata in Kaneohe Bay, Hawaii

The fragmentation and genotypic diversity of Montipora capitata was determined in Kaneohe Bay, Hawaii, using field investigations and allozyme electrophoresis. Two stations were established in the Bay, one in the centre (exposed reef edge, EXPO) and the other at the south end (sheltered lagoonal reef, SHEL). Although the number and mean per cent cover of attached colonies did not differ significantly between the two habitats, number and cover of unattached colonies (fragments) were significantly higher at the sheltered habitat. Thirty-seven genotypes were detected in 176 samples using two or three enzyme loci. Although mean genet number did not differ significantly between the two habitats (mean±SE, 8.2±1.2 and 12.2±1.7 in exposed and sheltered reefs, respectively), lower genetic diversity was detected at SHEL (mean NG:N±SE, 0.75±0.08 and 0.50±0.06 for EXPO and SHEL, respectively). There was no evidence of strong clonal structure, i.e. many colonies, but few genets. Sexually produced new genets may account for the high genotypic diversity in M. capitata at these two habitats.

THE SUCCESSFUL TRANSPLANTATION OF ACROPORA MICROPHTHALMA AT BARRANG LOMPO REEF EDGE< SOUTH SULAWESI

Research on transplantation of Acropora microphthalma was conducted at Barrang Lompo Island reef edge of South Sulawesi from September to December 2002. The aim of this research was to know the successful rate of several coral transplantation methods for rehabilitation of coral reefs, covering the survival and growth rates. The methods used were framework earthenware (FE), iron stake (IS), dead coral tying (DCT), where the mother colony (MC) was used as control. These transplantation techniques were applied at five meter depth in two stations, north and south sites of the island. The survival rate for each method FE, IS, DCT and MC at the northern station was 85.71; 42.86; 85.71; 57.14%, while for southern station was 85.71; 85.71; 71.43 and 85.71%, respectively. The growth rates observed for each method at the first station were 2.18; 2.02; 1.40; 1.05 cm, and for the second station were 2.56; 2.21; 1.61; 1.04 cm, respectively.

Growth, sexual dimorphism, and population biology of the olive sea snake, Aipysurus laevis, on the Great Barrier Reef of Australia

The olive sea snake, Aipysurus laevis (Lacépède) grows at a rate of 0.22-0.95 cm/month, with young animals growing faster than older ones. Males reach sexual maturity in their third year and females in their fourth or fifth year. There is sexual dimorphism in size, with females larger than males; at snout-vent lengths greater than 80 cm, females are heavier than males of equivalent length. Small snakes were uncommon. Apparent sexratio favours males in winter but moves toward equality or even a preponderance of females in summer, probably reflecting changes in reproductive behaviour. Numbers of snakes are approximately 0.70-0.86 snakes per metre of reef edge. Olive sea snakes live to about 15 years or older.