On the use of visual survey methods for estimating reef fish standing stocks

Surveys, Reef fish, Stock assessment

Nature and origins of unique high diversity reef faunas in the Bay of Tomini, Central Sulawesi: the ultimate "Centre of Diversity"?

The staghorn corals (Acropora spp.) of the Bay of Tomini in eastern Central Sulawesi may typify the maximal marine biodiversity associated with the idea of a "centre of diversity" in the central Indo-Pacific: other faunal groups have variable diversity, but unexpected species composition. Faunal assemblages from several phyla in this bay were assessed against phylogenetic and biogeographic data and biotic and environmental parameters in order to compare several hypotheses about the origins of the unusual species composition. It was found that the Togian Islands within the bay support a fauna with strong affinities to sites in the western equatorial Pacific, in all the studied groups except Stomatopoda. Both species composition and distribution of ecological functional groups is influenced by unusually calm and oligotrophic conditions in the islands and populations within the islands have various levels of genetic connectively to populations in other parts of Sulawesi, including complete isolation of some populations. It is proposed that these islands represent lagoonal refugia from Pleistocene lowstands, with affinities to similar refugia in the western Pacific. Additionally, the bay is possibly influenced by larval distributions from the Pacific through-flow current and there is little or no influence from the Indian Ocean

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Cryptofauna of the epilithic algal matrix on an inshore coral reef, Great Barrier Reef

Composed of a collection of algae, detritus, sediment and invertebrates, the epilithic algal matrix (EAM) is an abundant and ubiquitous feature of coral reefs. Despite its prevalence, there is a paucity of information regarding its associated invertebrate fauna. The cryptofaunal invertebrate community of the EAM was quantitatively investigated in Pioneer Bay on Orpheus Island, Great Barrier Reef. Using a vacuum collection method, a diversity of organisms representing 10 different phyla were identified. Crustacea dominated the samples, with harpacticoid copepods being particularly abundant (2025 ± 132 100 cm⁻²; mean density ± SE). The volume of coarse particulate matter in the EAM was strongly correlated with the abundance of harpacticoid copepods. The estimated biomass of harpacticoid copepods (0.48 ± 0.05 g m⁻²; wet weight) suggests that this group is likely to be important for reef trophodynamics and nutrient cycling

Benthic Crustacea on coral reefs: a quantitative survey

Benthic crustaceans are an important component of the coral reef fauna, yet our understanding of their ecological significance is incomplete. To determine the community structure, abundance, biomass and productivity of benthic Crustacea at Lizard Island, a mid-shelf reef on the Great Barrier Reef, Australia, we investigated 5 major microhabitats: dead coral, coral rubble, sand, epilithic algal matrix (EAM) and fine-branching live coral. Crustacean communities differed significantly among habitats, with the exception of dead coral and coral rubble. Dead coral was the most important microhabitat type in terms of crustacean abundance (7838 ± 628 ind. 100 cm-2, mean ± SE), biomass (0.75 ± 0.13 g m-2, wet weight) and estimated productivity (0.17 ± 0.043 g 100 cm-2 yr-1 ash free dry weight). These values were 2 to 3 orders of magnitude greater than those for the least important habitats (EAM and fine-branching live coral). Despite their abundance, the average crustacean body length was just 0.79 ± 0.32 mm, largely due to the dominance of harpacticoid copepods. In contrast, decapods exhibited very low abundances, but yielded the greatest biomass and productivity and were particularly abundant in dead coral and coral rubble. The results highlight the importance of small crustaceans and dead coral microhabitats as valuable contributors to the trophic structure of coral reefs

Large‐scale spatial variation in epilithic algal matrix cryptofaunal assemblages on the Great Barrier Reef

Spatial variation in the epilithic algal matrix (EAM) cryptofauna was investigated at three locations on the Great Barrier Reef: two inner shelf—Orpheus Island and the Turtle Island group—and a mid-shelf location, Lizard Island. Although the EAM appears to be a relatively simple and consistent habitat, significant differences in cryptofaunal assemblages were found between locations. EAM assemblages from Orpheus Island were markedly different. This appears to be a function of the sediment profile characteristics (grain size >60 μm) at Orpheus Island, as many cryptofaunal taxa displayed positive relationships with sediment volume. However, sediment volumes did not differ significantly between the three locations, highlighting the possibility of cyclonic activity affecting the sediment profile at Orpheus Island in the months preceding the study, in addition to the nutrient input from major terrigenous sources. The results of this study show that EAM cryptofaunal assemblages are not uniform across the Great Barrier Reef and suggest that dissolved nutrients, sediment loads and distance from river systems may be significant drivers of cryptobenthic faunal compositions

The trophic importance of algal turfs for coral reef fishes: the crustacean link

On coral reefs, the epilithic algal matrix (EAM) is widely recognised as an important resource for herbivorous and detritivorous fishes. In comparison, little is known of the interaction between benthic carnivores and the EAM, despite the abundance of Crustacea within the EAM. The trophic importance of the EAM to fishes was investigated in Pioneer Bay, Orpheus Island, Great Barrier Reef. Fish densities were quantified using visual and clove oil censuses, and gut content analyses conducted on abundant fish species. Crustaceans were found to be an important dietary category, contributing between 49.5 and 100 % of the gut contents, with harpacticoid copepods being the dominant component. Of the benthic carnivores, the goby Eviota zebrina was found to consume the most harpacticoids with a mean of 249 copepods m−2 day−1. This represents approximately 0.1 % of the available harpacticoid population in the EAM. In a striking comparison, herbivorous parrotfishes were estimated to consume over 12,000 harpacticoids m−2 day−1, over 27 times more than all benthic carnivores surveyed, representing approximately 5.3 % of the available harpacticoid copepod population each day. The high consumption of harpacticoid copepods by benthic carnivores and parrotfishes indicates that harpacticoids form an important trophic link between the EAM and higher trophic levels on coral reefs

Emergent fauna from hard surfaces on the Great Barrier Reef, Australia

The community composition of a coral reef emergent fauna was quantified on Orpheus Island, Great Barrier Reef. Emergence traps deployed over hard surfaces revealed a wide diversity of organisms, spanning eight different phyla, of which Crustacea were particularly abundant. Within the Crustacea, harpacticoid copepods were the most common (24 ± 2 ind. 100 cm–2, mean ± s.e.). The composition of the emergent fauna differed markedly from previous descriptions of the cryptofauna in the epilithic algal matrix. Furthermore, the emergent fauna was two orders of magnitude less abundant than their benthic counterparts. Our results point to a limited trophic link between the benthos and the overlying nocturnal plankton assemblage