Geographical location and habitat predict variation in prokaryotic community composition of Suberites diversicolor

Purpose: Marine lakes are unique habitats that house diverse assemblages of benthic and planktonic organisms including endemic species. In this study, we aimed to assess to what extent geographical location (Berau versus Papua) and the degree of marine lake connectivity (relatively open versus closed) to the surrounding marine environment structures the prokaryotic community composition of the sponge species Suberites diversicolor. Methods: Sponge specimens were sampled in five marine lakes in Borneo and Papua and one open sea habitat in Taiwan. Result: Prokaryotic communities of S. diversicolor were dominated by members assigned to the Proteobacteria (particularly Alphaproteobacteria and Gammaproteobacteria) and Cyanobacteria, which together made up from 78 to 87% of sequences in all samples. The dominant operational taxonomic units (OTUs) in most samples, OTUs 1 and 3, were both assigned to the alphaproteobacterial order Rhodospirillales with OTU-1 dominant in the marine lakes of Berau and Papua and OTU-3 in Taiwan. OTU-3 was also largely absent from Papuan samples but present in all Berau samples. Compositionally, S. diversicolor samples clustered according to geographical location with the main axis of variation separating marine lake samples collected in Berau from those collected in Papua and the second axis of variation separating open sea samples collected in Taiwan from all marine lake samples. In addition, our results suggest that the degree of lake connectivity to the open sea also influences prokaryotic composition. Conclusion: Although previous studies have shown that sponge-associated microbial communities tend to be stable across different geographical and environmental gradients, in the present study, both geography and local environmental conditions were significant predictors of variation in prokaryotic community composition of S. diversicolor.publishe

Bacterial composition and putative functions associated with sponges, sediment and seawater from the Tioman coral reef system, Peninsular Malaysia

Microbial communities associated with sponges play important roles in sponge health, defence and nutrient dynamics in coral reef systems. Here, we used a 16S rRNA gene high-throughput sequencing approach in order to test for differences in bacterial composition and predictive functional differences among two LMA (low microbial abundance) (Stylissa carteri and Stylissa massa), one well-known HMA (high microbial abundance) (Xestospongia testudinaria), one putative HMA (Aaptos lobata) sponge species, sediment and seawater in a coral reef ecosystem surrounding Tioman Island. Our results showed that biotope (sponge species, sediment and seawater) was a significant predictor of composition and abundance of bacterial communities. Proteobacteria was the dominant phylum in S. carteri, seawater, sediment and A. lobata, whilst bacterial communities of S. massa and X. testudinaria were dominated by Cyanobacteria and Chloroflexi, respectively. The predicted metagenome revealed differentially enriched pathways in HMA and LMA sponges. Differentially enriched subcategories in HMA sponges included ‘Signaling Molecules and Interaction’, ‘Carbohydrate Metabolism’ and ‘Excretory System’. Subcategories enriched in LMA sponges included ‘Replication and Repair’, ‘Energy Metabolism’, ‘Metabolism of Cofactors and Vitamins’ and ‘Environmental Adaptation’. Overall, the predicted functional analysis suggests that, although HMA and LMA associated bacterial communities shared core functional features, they use different strategies to defend against pathogens, obtain energy or cope with stress

Compositional analysis of bacterial communities in seawater, sediment, and sponges in the Misool coral reef system, Indonesia

Sponge species have been deemed high microbial abundance (HMA) or low microbial abundance (LMA) based on the composition and abundance of their microbial symbionts. In the present study, we evaluated the richness and composition of bacterial communities associated with one HMA sponge (Xestospongia testudinaria; Demospongiae: Haplosclerida: Petrosiidae), one LMA sponge (Stylissa carteri; Demospongiae: Scopalinida - Scopalinidae), and one sponge with a hitherto unknown microbial community (Aaptos suberitoides; Demospongiae: Suberitida: Suberitidae) inhabiting the Misool coral reef system in the West Papua province of Indonesia. The bacterial communities of these sponge species were also compared with seawater and sediment bacterial communities from the same coastal coral reef habitat. Using a 16S rRNA gene barcoded pyrosequencing approach, we showed that the most abundant phylum overall was Proteobacteria. The biotope (sponge species, sediment or seawater) explained almost 84% of the variation in bacterial composition with highly significant differences in composition among biotopes and a clear separation between bacterial communities from seawater and S. carteri; X. testudinaria and A. suberitoides and sediment. The Chloroflexi classes SAR202 and Anaerolineae were most abundant in A. suberitoides and X. testudinaria and both of these species shared several OTUs that were largely absent in the remaining biotopes. This suggests that A. suberitoides is a HMA sponge. Although similar, the bacterial communities of S. carteri and seawater were compositionally distinct. These results confirm compositional differences between sponge and non-sponge biotopes and between HMA and LMA sponges.publishe

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Ragworm fatty acid profiles reveals habitat and trophic interactions with halophytes and with mercury

The present study aimed to assess if ragworm fatty acids (FA) profiles could be used to discriminate their spatial distribution in an historically mercury-contaminated estuarine environment, i.e., if it was possible to differentiate ragworms present in salt marsh sediments surrounding plant roots and rhizomes (rhizosediment) from adjacent unvegetated sediment. Additionally, we also tried to determine if ragworms differed in mercury content and if these values could also be used to identify the habitat they occur in. Results show that, within the same area, ragworms can be distinguished using FA profiles and that in halophyte rhizosediment ragworms display more than twice the levels of alpha-linolenic acid (18:3n-3). The ratio cis-vaccenic/oleic acids (18:1n-7/18:ln-9) in ragworms suggests higher carnivory in unvegetated sediments. Our study indicates that ragworm FA profiles can be used to identify their habitat, their trophic interaction with halophytes and reveal a spatially contrasting feeding behaviour, which also reflects mercury accumulation.publishe

Bacterial composition of sponges, sediment and seawater in enclosed and open marine lakes in Ha Long Bay Vietnam

Marine lakes are landlocked bodies of seawater, isolated to varying degrees from the surrounding marine habitat. Isolated lakes generally have lower pH values, salinities and higher temperatures than more open lakes. We used a 16S rRNA gene barcoded pyrosequencing approach to study the bacterial communities of two sponge species, sediment and seawater in one enclosed and two open marine lakes. Bacterial communities of the sponge Spheciospongia solida mainly consisted of Proteobacteria, Cyanobacteria and Bacteroidetes. In contrast, Proteobacteria, Chloroflexi and Acidobacteria dominated the bacterial communities of the sponge Spongia ceylonensis. Although only a limited amount of samples were collected, both water and S. ceylonensis sponge had higher relative abundances of Cyanobacteria in the enclosed lake, which mainly consisted of OTUs assigned to the genus Synechococcus. This is in line with a number of previous studies, which have shown that environmental conditions found within low pH environments such as marine lakes benefit the growth of Synechococcus spp. Future studies should address the mechanism by which Synechococcus spp. may help host sponges and their bacterial communities adapt to low pH conditions in isolated marine lakes and other low-pH environments.publishe

Habitat and water quality variables as predictors of community composition in an Indonesian coral reef: a multi-taxon study in the Spermonde Archipelago

Assemblages of corals, sponges, foraminifera, sediment bacteria and sediment archaea were assessed at two depths in the Spermonde Archipelago. Our goal was to assess to what extent variation in composition could be explained by habitat and water quality variables. The habitat variables consisted of depth, substrate type and scleractinian coral coverwhile water quality variableswere derived from ocean color satellite imagery, including the colored dissolved organic matter index (CDOM), chlorophyll-a (Chlor-a) and remote sensing reflectance at 645 nm (Rrs_645). Together, habitat and water quality variables explained from 31% (sediment bacteria) to 80% (forams) of the variation in composition. The variation in composition of corals, sponges, forams and sediment archaea was primarily related to habitat variables, while the variation in composition of sediment bacteria was primarily related towater quality variables.Habitat andwater quality variables explained similaramounts of variation in the composition of corals and sediment bacteria. CDOM (sponges, sediment bacteria and sediment archaea), Chlor-a (corals and forams) and Rrs_645 (sponges and forams) proved significant predictors of variation in composition for the studied taxa. In addition to water quality variables, all taxa responded to a range of habitat variables including depth and the percentage cover of various benthic life forms including coral cover variables, rubble and sand. Sand coverwas themost important habitat variable for corals, sponges, sediment bacteria and sediment archaea. Coral life forms including the cover of branching and tabular corals were important habitat variables for sponges and forams. These results show marked differences in how various taxa respond to variation in habitat andwater quality in the Spermonde Archipelago.Moreover, our results indicate that variables estimated from ocean color satellite imagery proved to be better predictors of variation in marine community composition than commonly-used proxies such as the distance offshore or distance to the nearest river

Compositional analysis of archaeal communities in high and low microbial abundance sponges in the Misool coral reef system, Indonesia

The high/low microbial abundance (HMA/LMA) dichotomy in sponges has been the subject of several studies over recent years, but few studies have analysed this dichotomy in terms of the sponge archaeal community and function. Using a 16S rRNA gene barcoded pyrosequencing approach and predictive functional analysis (PICRUSt) we compared the archaeal composition, richness and predicted function of one HMA sponge (Xestospongia testudinaria), one LMA sponge (Stylissa carteri) and one sponge species of unknown microbial abundance (Aaptos lobata). Although most of the archaeal sequences were assigned to the Crenarchaeota phylum, S. carteri had the highest percentage of sequences assigned to the Euryarchaeota phylum. Variation among sponge species explained >85% of the variation in archaeal operational taxonomic unit (OTU) composition with each sponge species forming a distinct cluster. There were significant differences in predicted PICRUSt profiles among sponge species, suggesting that archaeal communities present in the studied sponge species may perform different functions. X. testudinaria and A. lobata were similar both in terms of OTU and KEGG orthologues composition, which may indicate that A. lobata is a HMA sponge. Additionally, some of the most enriched functions seem to be related to traits associated with high and low microbial abundance sponges.publishe