Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient

Background Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion Overall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance

Marine biodiversity research in the Ryukyu Islands, Japan: current status and trends

Marine biodiversity and derived ecosystem services are critical to the healthy functioning of marine ecosystems, and to human economic and societal well-being. Thus, an understanding of marine biodiversity in different ecosystems is necessary for their conservation and management. Coral reefs in particular are noted for their high levels of biodiversity, and among the world’s coral reefs, the subtropical Ryukyu Islands (RYS; also known as the Nansei Islands) in Japan have been shown to harbor very high levels of marine biodiversity. This study provides an overview of the state of marine biodiversity research in the RYS. First, we examined the amount of English language scientific literature in the Web of Science (WoS; 1995–2017) on six selected representative taxa spanning protists to vertebrates across six geographic sub-regions in the RYS. Our results show clear taxonomic and sub-region bias, with research on Pisces, Cnidaria, and Crustacea to be much more common than on Dinoflagellata, Echinodermata, and Mollusca. Such research was more commonly conducted in sub-regions with larger human populations (Okinawa, Yaeyama). Additional analyses with the Ocean Biogeographic Information System (OBIS) records show that within sub-regions, records are concentrated in areas directly around marine research stations and institutes (if present), further showing geographical bias within sub-regions. While not surprising, the results indicate a need to address ‘understudied’ taxa in ‘understudied sub-regions’ (Tokara, Miyako, Yakutane, Amami Oshima), particularly sub-regions away from marine research stations. Second, we compared the numbers of English language scientific papers on eight ecological topics for the RYS with numbers from selected major coral reef regions of the world; the Caribbean (CAR), Great Barrier Reef (GBR), and the Red Sea (RES). As expected, the numbers for all topics in the RYS were well below numbers from all other regions, yet within this disparity, research in the RYS on ‘marine protected areas’ and ‘herbivory’ was an order of magnitude lower than numbers in other regions. Additionally, while manuscript numbers on the RYS have increased from 1995 to 2016, the rate of increase (4.0 times) was seen to be lower than those in the CAR, RES, and GBR (4.6–8.4 times). Coral reefs in the RYS feature high levels of both endemism and anthropogenic threats, and subsequently they contain a concentration of some of the world’s most critically endangered marine species. To protect these threatened species and coral reef ecosystems, more data are needed to fill the research gaps identified in this study

Anionic polysaccharides for stabilization and sustained release of antimicrobial peptides

Chemical and enzymatic in vivo degradation of antimicrobial peptides represents a major challenge for their therapeutic use to treat bacterial infections. In this work, anionic polysaccharides were investigated for their ability to increase the chemical stability and achieve sustained release of such peptides. The investigated formulations comprised a combination of antimicrobial peptides (vancomycin (VAN) and daptomycin (DAP)) and anionic polysaccharides (xanthan gum (XA), hyaluronic acid (HA), propylene glycol alginate (PGA) and alginic acid (ALG)). VAN dissolved in buffer of pH 7.4 and incubated at 37 °C showed first order degradation kinetics with a reaction rate constant k obs of 5.5 × 10 -2 day -1 corresponding with a half-life of 13.9 days. However, once VAN was present in a XA, HA or PGA-based hydrogel, k obs decreased to (2.1-2.3) × 10 -2 day -1 while k obs was not affected in an alginate hydrogel and a dextran solution (5.4 × 10 -2 and 4.4 × 10 -2 day -1). Under the same conditions, XA and PGA also effectively decreased k obs for DAP (5.6 × 10 -2 day -1), whereas ALG had no effect and HA even increased the degradation rate. These results demonstrate that the investigated polysaccharides (except ALG for both peptides and HA for DAP) slowed down the degradation of VAN and DAP. DSC analysis was used to investigate on polysaccharide ability to bind water molecules. Rheological analysis highlighted that the polysaccharides containing VAN displayed an increase in G' of their formulations, pointing that the peptides interaction act as crosslinker of the polymer chains. The obtained results suggest that the mechanism of stabilization of VAN and DAP against hydrolytic degradation is conferred by electrostatic interactions between the ionizable amine groups of the drugs and the anionic carboxylate groups of the polysaccharides. This, in turn, results in a close proximity of the drugs to the polysaccharide chain, where the water molecules have a lower mobility and, therefore, a lower thermodynamic activity

The DICA Endoscopic Classification for Diverticular Disease of the Colon Shows a Significant Interobserver Agreement among Community Endoscopists: an International Study

Background & Aims: The Diverticular Inflammation and Complication Assessment (DICA) endoscopic classification of diverticulosis and diverticular disease (DD) is currently available. It scores severity of the disease as DICA 1, DICA 2 and DICA 3. Our aim was to assess the agreement on this classification in an international endoscopists community setting. Methods: A total of 96 doctors (82.9% endoscopists) independently scored a set of DD endoscopic videos. The percentages of overall agreement on DICA score and a free-marginal multirater kappa (kappa) coefficient were reported as statistical measures of interrater agreement. Results: Overall agreement in using DICA was 91.8% with a free-marginal kappa of 88% (95% CI 80-95). The overall agreement levels were: DICA 1, 85.2%; DICA 2, 96.5%; DICA 3, 99.5%. The free marginal. was: DICA 1 = 0.753, DICA 2 = 0.958, DICA 3 = 0.919. The agreement about the main endoscopic items was 83.4% (k 67%) for diverticular extension, 62.6% (k 65%) for number of diverticula for each district, 86.8% (k 82%) for presence of inflammation, and 98.5 (k 98%) for presence of complications. Conclusions: The overall interrater agreement in this study ranges from good to very good. DICA score is a simple and reproducible endoscopic scoring system for diverticulosis and DD

International Consensus on Diverticulosis and Diverticular Disease. Statements from the 3rd International Symposium on Diverticular Disease

The statements produced by the Chairmen and Speakers of the 3rd International Symposium on Diverticular Disease, held in Madrid on April 11th-13th 2019, are reported. Topics such as current and evolving concepts on the pathogenesis, the course of the disease, the news in diagnosing, hot topics in medical and surgical treatments, and finally, critical issues on the disease were reviewed by the Chairmen who proposed 39 statements graded according to level of evidence and strength of recommendation. Each topic was explored focusing on the more relevant clinical questions. The vote was conducted on a 6-point scale and consensus was defined a priori as 67% agreement of the participants. The voting group consisted of 124 physicians from 18 countries, and agreement with all statements was provided. Comments were added explaining some controversial areas

サンゴ被度とサンゴ礫内在・間隙微小動物相による造礁サンゴ移植評価に関する研究

博士(理学)琉球大

Coral cover and rubble cryptofauna abundance and diversity at outplanted reefs in Okinawa, Japan

Global climate change is leading to damage and loss of coral reef ecosystems. On subtropical Okinawa Island in southwestern Japan, the prefectural government is working on coral reef restoration by outplanting coral colonies from family Acroporidae back to reefs after initially farming colonies inside protected nurseries. In order to establish a baseline for future comparisons, in this study we documented the current status of reefs undergoing outplanting at Okinawa Island, and nearby locations where no human manipulation has occurred. We examined three sites on the coast of Onna Village on the west coast of the island; each site included an outplanted and control location. We used (1) coral rubble sampling to measure and compare abundance and diversity of rubble cryptofauna; and (2) coral reef monitoring using Line Intercept Transects to track live coral coverage. Results showed that rubble shape had a positive correlation with the numbers of animals found within rubble themselves and may therefore constitute a reliable abundance predictor. Each outplanted location did not show differences with the corresponding control location in terms of rubble cryptofauna abundance, but outplanted locations had significantly lower coral coverage. Overall, differences between sites (Maeganeku1, Maeganeku2 and Manza, each including both outplanted and control locations) were significant, for both rubble cryptofauna and coral coverage. We recommend (1) to outplant colonies from more stress-resistant genera in place of Acropora, and (2) to conduct regular surveys to monitor the situation closely. With a lack of baseline data preceding impacts, rigorous monitoring over time can highlight trends towards increases or decreases in evaluated variables, allowing to obtain a clearer idea of the effects of transplants and on the trajectory of impacts due to climate change and local stressors . Finally, we also recommend (3) to establish conservation and sustainable practices that could aid the ongoing restoration efforts such as installing anchoring buoys to reduce impacts from anchoring, which could reduce coral mortality of both outplanted and native coral colonies

Three new species and the molecular phylogeny of Antipathozoanthus from the Indo-Pacific Ocean (Anthozoa, Hexacorallia, Zoantharia)

Volume: 725Start Page: 97End Page: 12