Coral Reefs at the Northernmost Tip of Borneo: An Assessment of Scleractinian Species Richness Patterns and Benthic Reef Assemblages

Two centuries of sponges (phylum Porifera) taxonomic studies in Indonesia (1820-2021): checklist and bibliography

Sponges in Indonesia have been studied since the 19th century during several historical expeditions and international collaborations. Hundreds of new species were reported from various locations, e.g., Ambon, Ternate, Sulawesi, Aru, and Kei Islands. This study aimed to create a sponge (Porifera: Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha) species checklist from Indonesia based on World Porifera Database. With a total of 731 species, our checklist comprises approximately 45 species of Calcarea, 566 species of Demospongiae, 115 species of Hexactinellida, and five species of Homoscleromorpha. The number of species are recorded from 12 marine ecoregions across the Indonesian Archipelago and freshwater habitats (Spongillida) between 1820-2021. The species composition indicates higher regional endemism or poorly studied since no other report after the original description. However, several marine ecoregions of Indonesia remain highly overlooked (e.g., Northeast Sulawesi, Papua, Southern Java, Western Sumatra), including freshwater habitats. Therefore, a taxonomic biodiversity baseline study, particularly on Porifera, is necessary to better understand the aquatic and marine biodiversity in the Indonesia Archipelago.

Coral diversity matches marine park zonation but not economic value of coral reef sites at St. Eustatius, eastern Caribbean

Stony corals play a key role in the marine biodiversity of many tropical coastal areas as suppliers of substrate, food and shelter for other reef organisms. Therefore, it is remarkable that coral diversity usually does not play a role in the planning of protected areas in coral reef areas. In the present study we examine how stony coral diversity patterns relate to marine park zonation and the economic value of reefs around St. Eustatius, a small island in the eastern Caribbean, with fisheries and tourism as important sources of income. The marine park contains two no-take reserves. A biodiversity survey was performed at 39 sites, 24 inside the reserves and 15 outside; 22 had a maximum depth >18 m and 17 were shallower. Data on economic value per site were obtained from the literature. Corals were photographed for the verification of identifications made in the field. Coral species richness (n = 49) was highest in the no-take reserves and species composition was mainly affected by maximum depth. No distinct relation is observed between coral diversity and fishery value or total economic value. Based on the outcome of this study we suggest that in future designs of marine park zonation in reef areas, coral diversity should be taken into consideration. This is best served by including reef areas with a continuous depth gradient from shallow flats to deep slopes.

Scleractinian coral (Cnidaria, Hexacorallia, Scleractinia) diversity of the Mersing Islands, Peninsular Malaysia

We present a comprehensive checklist of scleractinian (hard) corals for the Mersing Islands, Malaysia based on surveys conducted at 24 reefs across protected and unprotected marine areas. A total of 261 species of corals from 16 families and one incertae sedis (Pachyseris spp.) were recorded, along with ten records that are new for the east coast of Peninsular Malaysia. Compared against the IUCN Red List, 46.7% of coral species found in the Mersing Islands were of Least Concern (LC), 29.5% as Near Threatened (NT) and 16.4% Vulnerable (V). Only one recorded species, Pectiniamaxima (Moll & Best, 1984), was listed as Endangered (EN). Baseline species diversity data are essential for the monitoring and management of marine biodiversity, especially within marine protected areas. With both protected and unprotected coral reef areas in the vicinity of the widely scattered Mersing Islands, the diversity and distribution of coral species can be used as the basis for area-based conservation and management strategies. The diversity and abundance of scleractinian corals of each island or area should be surveyed periodically to ensure the appropriate level of protection is afforded to retain scleractinian biodiversity in this region.

A New Species of Sea Whip Gorgonian-Associated Zoantharian (Cnidaria: Anthozoa: Hexacorallia: Parazoanthidae) from the Ryukyu Islands, Japan, with Subgeneric Subdivision of Genus Umimayanthus

Symbioses between invertebrates are common in the ocean although usually the diversity and specificity of their interactions are not well understood. Parazoanthidae (Cnidaria: Anthozoa: Zoantharia) is one of the most diverse zoantharian families in terms of numbers of genera and species. Species in this family are commonly associated with various other invertebrates that they utilize as their substrate. Previous studies have re-organized the taxonomy of Parazoanthidae and revealed a strong specificity between many parazoanthid species and genera and their substrates. However, our understanding of the species diversity of Parazoanthidae is far from complete, as parazoanthids are often overlooked in sampling surveys. In this study, we establish three subgenera under the genus Umimayanthus Montenegro, Sinniger, and Reimer, 2015; the nominotypical Umimayanthus, Paraumimayanthus subgen nov., and Gorgoniazoanthus subgen. nov., based on the finding of a new species, Umimayanthus (Gorgoniazoanthus) kanabou sp. nov., associated with the sea-whip gorgonian Ellisella sp. from approximately 30 m depth in shallow mesophotic coral reef communities in Oura Bay on Okinawajima Island and in Oshima Strait near Amami-Oshima Island, in the Ryukyu Islands, southern Japan. We additionally report on gastropods and crustaceans observed in association with U. kanabou, and these species are thought to potentially prey upon the zoantharians or on gorgonian polyps. Umimayanthus kanabou is phylogenetically closely related to congeneric sponge-associated Umimayanthus spp., further supporting the recent hypothesis that substrate preferences may change during the evolutionary history of zoantharians.

A first phylogenetic study on stoloniferous octocorals off the coast of Kota Kinabalu, Sabah, Malaysia, with the description of two new genera and five new species

Sabah, Malaysia, is well known for its extensive and diverse coral reefs. It is located on the northwestern edge of the Coral Triangle, the region with the highest marine biodiversity. Much of the marine fauna here is still unknown, especially inconspicuous animals, such as small stoloniferous octocorals, which are common on coral reefs. Here, we describe two new monospecific genera of the family Arulidae found off the coast of Kota Kinabalu, Sabah, East Malaysia; Bunga payung gen. nov. et sp. nov. and Laeta waheedae gen. nov. et sp. nov. As well, the stoloniferan genus Phenganax Alderslade & McFadden, 2011 belonging to the family Clavulariidae is expanded with three new species, P. marumi sp. nov., P. subtilis sp. nov., and P. stokvisi sp. nov., which are all sclerite-free. Additionally, we report a possibly undescribed species, closely related to the clavulariid genera Azoriella Lopez-Gonzalez & Gili, 2001 and Cervera Lopez-Gonzalez et al., 1995. As this and other recent studies have shown, discoveries of small stoloniferous octocorals are helping to fill gaps in our knowledge of the overall systematics of Octocorallia.

Borneo coral reefs subject to high sediment loads show evidence of resilience to various environmental stressors

For reefs in South East Asia the synergistic effects of rapid land development, insufficient environmental policies and a lack of enforcement has led to poor water quality and compromised coral health from increased sediment and pollution. Those inshore turbid coral reefs, subject to significant sediment inputs, may also inherit some resilience to the effects of thermal stress and coral bleaching. We studied the inshore turbid reefs near Miri, in northwest Borneo through a comprehensive assessment of coral cover and health in addition to quantifying sediment-related parameters. Although Miri’s Reefs had comparatively low coral species diversity, dominated by massive and encrusting forms of Diploastrea, Porites, Montipora, Favites, Dipsastrea and Pachyseris, they were characterized by a healthy cover ranging from 22 to 39%. We found a strong inshore to offshore gradient in hard coral cover, diversity and community composition as a direct result of spatial differences in sediment at distances <10 km. As well as distance to shore, we included other environmental variables like reef depth and sediment trap accumulation and particle size that explained 62.5% of variation in benthic composition among sites. Miri’s reefs showed little evidence of coral disease and relatively low prevalence of compromised health signs including bleaching (6.7%), bioerosion (6.6%), pigmentation response (2.2%), scars (1.1%) and excessive mucus production (0.5%). Tagged colonies of Diploastrea and Pachyseris suffering partial bleaching in 2016 had fully (90–100%) recovered the following year. There were, however, seasonal differences in bioerosion rates, which increased five-fold after the 2017 wet season. Differences in measures of coral physiology, like that of symbiont density and chlorophyll a for Montipora, Pachyseris and Acropora, were not detected among sites. We conclude that Miri’s reefs may be in a temporally stable state given minimal recently dead coral and a limited decline in coral cover over the last two decades. This study provides further evidence that turbid coral reefs exposed to seasonally elevated sediment loads can exhibit relatively high coral cover and be resilient to disease and elevated sea surface temperatures.

Morphological and phylogenetic diversity of Waminoa and similar flatworms (Acoelomorpha) in the western Pacific Ocean

The genus Waminoa currently contains two described species, which each contains two types of endosymbiotic algae. Waminoa individuals are basically brown in body color, derived from these algal symbionts, and their body shape has been described as "discoid to obcordate". They have been found as associates of various anthozoans (Cnidaria) in the Indo-Pacific Ocean and the Red Sea. In order to reveal the diversity of the genus Waminoa and their hosts, we conducted phylogenetic and morphological analyses on acoelomate flatworms specimens collected from Japan, Palau and Indonesia. At least 18 Waminoa morphotypes were found on at least 20 anthozoan host species, and two specimens were found on species of two sea stars. Overall, there were two main body shapes of specimens; obcordate, as seen in W. litus and W. brickneri, and the other molar-like with an elongated body. These two body shapes each represented a separate clade in 18S rDNA and mitochondrial cytochrome c oxidase subunit 1 (COI) phylogenetic trees, with W. brickneri included in the obcordate subclade. Automatic Barcode Gap Discovery (ABGD) analyses on COI sequences of our specimens revealed the presence of at least five operational taxonomic units (OTUs). These five OTUs consisted of one large group of all obcordate animals, three OTUs consisting of one specimen each within the molar-like clade, and one large group of the remaining molar-like specimens. Both clades contain numerous morphotypes and were associated with a variety of hosts. Finally, based on genetic distances, the molar-like specimens are considered as an unnamed genus group separate from Waminoa, which needs to be clarified in future studies.

The Role of Maximum Shelf Depth versus Distance from Shore in Explaining a Diversity Gradient of Mushroom Corals (Fungiidae) off Jakarta

Many coral reef systems are shelf-based and consist of reefs that are arranged in rows parallel to the coastline. They usually show an increase in species richness in the offshore direction, coinciding with decreasing terrigenous impact and a deeper seafloor. These two conditions usually concur, which makes it less easy to distinguish how each of them influences coral diversity separately. Since reefs off Jakarta (in the Thousand Islands archipelago) are arranged in an 80 km long string perpendicular to the coastline in south-to-north direction, with a maximum shelf depth halfway along (instead of at the end of) the string, this archipelago is very suitable for studies on inshore–offshore gradients. In the present study, mushroom corals (Fungiidae; n = 31) were used to examine diversity patterns on 38 reef sites along such a gradient, involving species richness over their entire depth range from reef flat to reef base (2–30 m) and separately at shallow depths (2–6 m). Total species diversity was highest in the central part of the archipelago, with unique species occurring in deep habitats. Diversity at shallow depths was only slightly higher here than at reefs located more nearshore and offshore, which both had less clear water. Therefore, shelf depth and distance from the mainland can be considered separate determinants of coral diversity off Jakarta.

Molecular diversity of benthic ctenophores (Coeloplanidae)

Coeloplanidae, the largest family of benthic ctenophores, comprises 33 species, all described based on traditional morphological characteristics, such as coloration, length, and number of aboral papillae, which are highly variable and can be affected by fixation methods and environmental conditions. Thus, there is a need for reliable genetic markers to complement the morphological identifications at the species level. Here, we analyzed 95 specimens from 11 morphologically distinct species of benthic ctenophores from the Red Sea and Sulu Sea, and tested selected regions of four genetic markers (ITS1, 18S rRNA, 28S rRNA and COI) for their ability to differentiate between species. We show that the barcoding region of the mitochondrial gene, cytochrome oxidase subunit I (COI), is highly variable among species of Coeloplanidae, and effectively discriminates between species in this family. The average Kimura-2-parameter (K2P) distance between species-level clades was 10%, while intraspecific variation was ~30 times lower (0.36%). COI-based phylogeny supported the delineation of four recently described new species from the Red Sea. The other nuclear markers tested were found to be too conserved in order to separate between species. We conclude that COI is a potential molecular barcode for the family Coeloplanidae and suggest to test it in pelagic ctenophores.

Scleractinian corals (Fungiidae, Agariciidae and Euphylliidae) of Pulau Layang-Layang, Spratly Islands, with a note on Pavonamaldivensis (Gardiner, 1905)

Layang-Layang is a small island part of an oceanic atoll in the Spratly Islands off Sabah, Malaysia. As the reef coral fauna in this part of the South China Sea is poorly known, a survey was carried out in 2013 to study the species composition of the scleractinian coral families Fungiidae, Agariciidae and Euphylliidae. A total of 56 species was recorded. The addition of three previously reported coral species brings the total to 59, consisting of 32 Fungiidae, 22 Agariciidae, and five Euphylliidae. Of these, 32 species are new records for Layang-Layang, which include five rarely reported species, i.e., the fungiids Lithophyllonranjithi, Podabaciasinai, Sandalolithaboucheti, and the agariciids Leptoseriskalayaanensis and Leptoseristroglodyta. The coral fauna of Layang-Layang is poor compared to other areas in Sabah, which may be related to its recovery from a crown-of-thorns seastar outbreak in 2010, and its low habitat diversity, which is dominated by reef slopes consisting of steep outer walls. Based on integrative molecular and morphological analyses, a Pavona variety with small and extremely thin coralla was revealed as Pavonamaldivensis. Since specimens from Sabah previously identified as Pavonamaldivensis were found to belong to Pavonaexplanulata, the affinities and distinctions of Pavonamaldivensis and Pavonaexplanulata are discussed.