Diversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes.

IMPORTANCE: Salt marshes are known for their significant carbon storage capacity, and sulfur cycling is closely linked with the ecosystem-scale carbon cycling in these ecosystems. Sulfate reducers are key for the decomposition of organic matter, and sulfur oxidizers remove toxic sulfide, supporting the productivity of marsh plants. To date, the complexity of coastal environments, heterogeneity of the rhizosphere, high microbial diversity, and uncultured majority hindered our understanding of the genomic diversity of sulfur-cycling microbes in salt marshes. Here, we use comparative genomics to overcome these challenges and provide an in-depth characterization of sulfur-cycling microbial diversity in salt marshes. We characterize communities across distinct sites and plant species and uncover extensive genomic diversity at the taxon level and specific genomic features present in MAGs affiliated with uncultivated sulfur-cycling lineages. Our work provides insights into the partnerships in salt marshes and a roadmap for multiscale analyses of diversity in complex biological systems.

Predator dispersal influences predator distribution but not prey diversity in pitcher plant microbial metacommunities.

The spatial distribution of predators can affect both the distribution and diversity of their prey. Therefore, differences in predator dispersal ability that affect their spatial distribution, could also affect prey communities. Here, we use the microbial communities within pitcher plant leaves as a model system to test the relationship between predator (protozoa) dispersal ability and distribution, and its consequences for prey (bacteria) diversity and composition. We hypothesized that limited predator dispersal results in clustered distributions and heterogeneous patches for prey species, whereas wide predator dispersal and distribution could homogenize prey metacommunities. We analyzed the distribution of two prominent bacterivore protozoans from a 2-year survey of an intact field of Sarracenia purpurea pitcher plants, and found a clustered distribution of Tetrahymena and homogeneous distribution of Poterioochromonas. We manipulated the sources of protozoan colonists and recorded protozoan recruitment and bacterial diversity in target leaves in a field experiment. We found the large ciliate, Tetrahymena, was dispersal limited and occupied few leaves, whereas the small flagellate Poterioochromonas was widely dispersed. However, the bacterial communities these protozoans feed on was unaffected by clustering of Tetrahymena, but likely influenced by Poterioochromonas and other bacterivores dispersing in the field. We propose that bacterial communities in this system are structured by a combination of well dispersed bacterivores, bacterial dispersal, and bottom-up mechanisms. Clustered predators could become strong drivers of prey communities if they were specialists or keystone predators, or if they exerted a dominant influence on other predators in top-down controlled systems. Linking dispersal ability within trophic levels and its consequences for trophic dynamics can lead to a more robust perspective on trophic metacommunities.

Metagenomics and metatranscriptomics reveal broadly distributed, active, novel methanotrophs in the Gulf of Mexico hypoxic zone and in the marine water column.

The northern Gulf of Mexico (nGOM) hypoxic zone is a shallow water environment where methane, a potent greenhouse gas, fluxes from sediments to bottom water and remains trapped due to summertime stratification. When the water column is destratified, an active planktonic methanotrophic community could mitigate the efflux of methane, which accumulates to high concentrations, to the atmosphere. To investigate the possibility of such a biofilter in the nGOM hypoxic zone we performed metagenome assembly, and metagenomic and metatranscriptomic read mapping. Methane monooxygenase (pmoA) was an abundant transcript, yet few canonical methanotrophs have been reported in this environment, suggesting a role for non-canonical methanotrophs. To determine the identity of these methanotrophs, we reconstructed six novel metagenome-assembled genomes (MAGs) in the Planctomycetota, Verrucomicrobiota and one putative Latescibacterota, each with at least one pmoA gene copy. Based on ribosomal protein phylogeny, closely related microbes (mostly from Tara Oceans) and isolate genomes were selected and co-analyzed with the nGOM MAGs. Gene annotation and read mapping suggested that there is a large, diverse and unrecognized community of active aerobic methanotrophs in the nGOM hypoxic zone and in the global ocean that could mitigate methane flux to the atmosphere.

Bacterial communities vary across populations and tissue type in red mangroves (Rhizophora mangle, Rhizophoraceae) along an expanding front.

Plant-associated microbial communities may be important sources of functional diversity and genetic variation that influence host evolution. Bacteria provide benefits for their hosts, yet in most plant systems we know little about their taxonomic composition or variation across tissues and host range. Red Mangrove (Rhizophora mangle L.) is a vital coastal plant species that is currently expanding poleward and with it, perhaps, its microbiome. We explored variability in bacterial communities across tissues, individuals, and populations. We collected samples from six sample types from 5 to 10 individuals at each of three populations and used 16S rRNA gene (iTag) sequencing to describe their bacterial communities. Core community members and dominant bacterial classes were determined for each sample type. Pairwise PERMANOVA of Bray-Curtis dissimilarity and Indicator Species Analysis revealed significant differences in bacterial communities between sample types and populations. We described the previously unexplored microbiome of the reproductive tissues of R. mangle. Populations and most sample types were associated with distinct communities. Bacterial communities associated with R. mangle are influenced by host geography and sample type. Our study provides a foundation for future work exploring the functional roles of these microbes and their relevance to biogeochemical cycling.

Effects of Community Richness and Competitive Asymmetry on Protozoa Evolution in Sarracenia purpurea Leaves.

AbstractPredicting evolution in natural systems will require understanding how selection operates in multispecies communities. We predicted that the amount that traits evolve in multispecies mixtures would be less than the amount that would be predicted from the additive contributions of the pairwise interactions and that subordinate species will be more likely to evolve in competitive systems than dominant species. We conducted an experimental test of these predictions using a guild of protozoans found in the water-filled leaves of the pitcher plant Sarracenia purpurea. The response to selection did not significantly change as we increased richness from monocultures to two- and four-species mixtures. In accordance with our second prediction, subordinate species demonstrated greater growth in competition after selection than before, while dominant species generally showed no response to selection. Monod-type experiments to determine minimum resource levels found that the dominant species had much higher resource requirements than the subordinate species and that the minimum resource requirements evolved to be higher in the subordinate species. Importantly, these results suggest that subordinate species evolve to become more similar to dominant species, which may involve resource use convergence. Our findings and other recent works suggest that community diversity can affect evolution in surprising ways that warrant further investigation.

Metagenomic analysis of microbial communities across a transect from low to highly hydrocarbon-contaminated soils in King George Island, Maritime Antarctica.

Soil samples from a transect from low to highly hydrocarbon-contaminated soils were collected around the Brazilian Antarctic Station Comandante Ferraz (EACF), located at King George Island, Antarctica. Quantitative PCR (qPCR) analysis of bacterial 16S rRNA genes, 16S rRNA gene (iTag), and shotgun metagenomic sequencing were used to characterize microbial community structure and the potential for petroleum degradation by indigenous microbes. Hydrocarbon contamination did not affect bacterial abundance in EACF soils (bacterial 16S rRNA gene qPCR). However, analysis of 16S rRNA gene sequences revealed a successive change in the microbial community along the pollution gradient. Microbial richness and diversity decreased with the increase of hydrocarbon concentration in EACF soils. The abundance of Cytophaga, Methyloversatilis, Polaromonas, and Williamsia was positively correlated (p-value = <.05) with the concentration of total petroleum hydrocarbons (TPH) and/or polycyclic aromatic hydrocarbons (PAH). Annotation of metagenomic data revealed that the most abundant hydrocarbon degradation pathway in EACF soils was related to alkyl derivative-PAH degradation (mainly methylnaphthalenes) via the CYP450 enzyme family. The abundance of genes related to nitrogen fixation increased in EACF soils as the concentration of hydrocarbons increased. The results obtained here are valuable for the future of bioremediation of petroleum hydrocarbon-contaminated soils in polar environments.

Correction: Host and environmental determinants of microbial community structure in the marine phyllosphere.

[This corrects the article DOI: 10.1371/journal.pone.0235441.].

Composition of seagrass phyllosphere microbial communities suggests rapid environmental regulation of community structure.

Recent studies have revealed that seagrass blade surfaces, also known as the phyllosphere, are rich habitats for microbes; however, the primary drivers of composition and structure in these microbial communities are largely unknown. This study utilized a reciprocal transplant approach between two sites with different environmental conditions combined with 16S rRNA gene sequencing (iTag) to examine the relative influence of environmental conditions and host plant on phyllosphere community composition of the seagrass Thalassia testudinum. After 30 days, identity of phyllosphere microbial community members was more similar within the transplant sites than between despite differences in the source of host plant. Additionally, the diversity and evenness of these communities was significantly different between the two sites. These results indicated that local environmental conditions can be a primary driver in structuring seagrass phyllosphere microbial communities over relatively short time scales. Composition of microbial community members in this study also deviated from those in previous seagrass phyllosphere studies with a higher representation of candidate bacterial phyla and archaea than previously observed. The capacity for seagrass phyllosphere microbial communities to shift dramatically with environmental conditions, including ecosystem perturbations, could significantly affect seagrass-microbe interactions in ways that may influence the health of the seagrass host.

Characteristics and attitudes of first round invitees in the Irish National Colorectal Cancer Screening Programme.

Background/objective: Colorectal cancer (CRC) screening is proven to reduce CRC-related mortality. Faecal immunochemical testing (FIT)-positive clients in the Irish National CRC Screening Programme underwent colonoscopy. Round 1 uptake was 40.2%. We sought to identify barriers to participation by assessing knowledge of CRC screening and examining attitudes towards FIT test and colonoscopy. Methods: Questionnaires based on a modified Champion's Health Belief Model were mailed to 3500 invitees: 1000 FIT-positive, 1000 FIT-negative and 1500 non-participants. 44% responded: 550 (46%) FIT-positive, 577 (48%) FIT-negative and 69 (6%) non-responders (NR). Results: 25% of respondents (n=286) did not perceive a personal risk of cancer, did not perceive CRC to be a serious disease and did not perceive benefits to screening. These opinions were more likely to be expressed by men (p=0.035). One-fifth (n=251) found screening stressful. Fear of cancer diagnosis and test results were associated with stress. FIT-positive clients, women and those with social medical insurance were more likely to experience stress. Conclusions: The CRC screening process causes stress to one-fifth of participants. Greater use of media and involvement of healthcare professionals in disseminating information on the benefits of screening may lead to higher uptake in round 2.

Enrichment of potential pathogens in marine microbiomes with different degrees of anthropogenic activity.

Anthropogenic activities in coastal marine ecosystems can lead to an increase in the abundance of potentially harmful microorganisms in the marine environment. To understand anthropogenic impacts on the marine microbiome, we first used publicly available microbial phylogenetic and functional data to establish a dataset of bacterial genera potentially related to pathogens that cause diseases (BGPRD) in marine organisms. Representatives of low-, medium- and highly impacted marine coastal environments were selected, and the abundance and composition of their microbial communities were determined by quantitative PCR and 16 S rRNA gene sequencing. In total, 72 BGPRD were cataloged, and 11, 36 and 37 BGPRD were found in low-, medium- and highly human-impacted ecosystems, respectively. The absolute abundance of BGPRD and the co-occurrence of antibiotic resistance genes (AGR) increased with the degree of anthropogenic perturbation in these ecosystems. Anthropogenically impacted coastal microbiomes were compositionally and functionally distinct from those of less impacted sites, presenting features that may contribute to adverse outcomes for marine macrobiota in the Anthropocene era.

Tissue sodium stores in peritoneal dialysis and hemodialysis patients determined by 23-sodium magnetic resonance imaging.

BACKGROUND: Tissue sodium content in patients on maintenance hemodialysis (MHD) and peritoneal dialysis (PD) were previously explored using 23Sodium magnetic resonance imaging (23NaMRI). Larger studies would provide a better understanding of sodium stores in patients on dialysis as well as the factors influencing this sodium accumulation. METHODS: In this cross-sectional study, we quantified the calf muscle and skin sodium content in 162 subjects (10 PD, 33 MHD patients, and 119 controls) using 23NaMRI. Plasma levels of interleukin-6 (IL-6) and high-sensitivity C-reactive protein (hsCRP) were measured to assess systemic inflammation. Sixty-four subjects had repeat 23NaMRI scans that were analyzed to assess the repeatability of the 23NaMRI measurements. RESULTS: Patients on MHD and PD exhibited significantly higher muscle and skin sodium accumulation compared to controls. African American patients on dialysis exhibited greater muscle and skin sodium content compared to non-African Americans. Multivariable analysis showed that older age was associated with both higher muscle and skin sodium. Male sex was also associated with increased skin sodium deposition. Greater ultrafiltration was associated with lower skin sodium in patients on PD (Spearman's rho=-0.68, P = 0.035). Higher plasma IL-6 and hsCRP levels correlated with increased muscle and skin sodium content in the overall study population. Patients with higher baseline tissue sodium content exhibited greater variability in tissue sodium stores on repeat measurements. CONCLUSIONS: Our findings highlight greater muscle and skin sodium content in dialysis patients compared to controls without kidney disease. Tissue sodium deposition and systemic inflammation seen in dialysis patients might influence one another bidirectionally.

Effects of long-term intradialytic oral nutrition and exercise on muscle protein homeostasis and markers of mitochondrial content in patients on hemodialysis.

Patients with end-stage kidney disease on maintenance hemodialysis commonly develop protein-energy wasting, a syndrome characterized by nutritional and metabolic abnormalities. Nutritional supplementation and exercise are recommended to prevent protein-energy wasting. In a 6-mo prospective randomized, open-label, clinical trial, we reported that the combination of resistance exercise and nutritional supplementation does not have an additive effect on lean body mass measured by dual-energy X-ray absorptiometry. To provide more mechanistic data, we performed a secondary analysis where we hypothesized that the combination of nutritional supplementation and resistance exercise would have additive effects on muscle protein accretion by stable isotope protein kinetic experiments, muscle mass by MRI, and mitochondrial content markers in muscle. We found that 6 mo of nutritional supplementation during hemodialysis increased muscle protein net balance [baseline: 2.5 (-17.8, 13.0) µg·100 mL-1·min-1 vs. 6 mo: 43.7 (13.0, 98.5) µg·100 mL-1·min-1, median (interquartile range), P = 0.04] and mid-thigh fat area [baseline: 162.3 (104.7, 226.6) cm2 vs. 6 mo: 181.9 (126.3, 279.2) cm2, median (interquartile range), P = 0.04]. Three months of nutritional supplementation also increased markers of mitochondrial content in muscle. Although the study is underpowered to detected differences, the combination of nutritional supplementation and exercise failed to show further benefit in protein accretion or muscle cross-sectional area. We conclude that long-term nutritional supplementation increases the skeletal muscle anabolic effect, the fat cross-sectional area of the thigh, and markers of mitochondrial content in skeletal muscle.

Host and environmental determinants of microbial community structure in the marine phyllosphere.

Although seagrasses are economically and ecologically critical species, little is known about their blade surface microbial communities and how these communities relate to the plant host. To determine microbial community composition and diversity on seagrass blade surfaces and in the surrounding seawater,16S rRNA gene sequencing (iTag) was used for samples collected at five sites along a gradient of freshwater input in the northern Gulf of Mexico on three separate sampling dates. Additionally, seagrass surveys were performed and environmental parameters were measured to characterize host characteristics and the abiotic conditions at each site. Results showed that Thalassia testudinum (turtle grass) blades hosted unique microbial communities that were distinct in composition and diversity from the water column. Environmental conditions, including water depth, salinity, and temperature, influenced community structure as blade surface microbial communities varied among sites and sampling dates in correlation with changes in environmental parameters. Microbial community composition also correlated with seagrass host characteristics, including growth rates and blade nutrient composition. There is some evidence for a core community for T. testudinum as 21 microorganisms from five phyla (Cyanobacteria, Proteobacteria, Planctomycetes, Chloroflexi, and Bacteroidetes) were present in all blade surface samples. This study provides new insights and understanding of the processes that influence the structure of marine phyllosphere communities, how these microbial communities relate to their host, and their role as a part of the seagrass holobiont, which is an important contribution given the current decline of seagrass coverage worldwide.

Investigating promising substrates for promoting 1,4-dioxane biodegradation: effects of ethane and tetrahydrofuran on microbial consortia.

Cometabolic biodegradation of 1,4-dioxane (dioxane) in the presence of primary substrates is a promising strategy for treating dioxane at environmentally relevant concentrations. Seven aqueous amendments (i.e., tetrahydrofuran (THF), butanone, acetone, 1-butanol, 2-butanol, phenol and acetate) and five gaseous amendments (i.e., C1-C4 alkanes and ethylene) were evaluated as the primary substrates for dioxane degradation by mixed microbial consortia. The aqueous amendments were tested in microcosm bottles and the gaseous amendments were tested in a continuous-flow membrane biofilm reactor with hollow fibers pressurized by the gaseous amendments. Ethane was found to be the most effective gaseous substrate and THF was the only aqueous substrate that promoted dioxane degradation. A diverse microbial community consisting of several putative dioxane degraders-Mycobacterium, Flavobacterium and Bradyrhizobiaceae-were enriched in the presence of ethane. This is the first study showing that ethane was the most effective substrate among the short-chain alkanes and it promoted dioxane degradation by enriching dioxane-degraders that did not harbor the well-known dioxane/tetrahydrofuran monooxygenase.

Religion, Spirituality, and Risk of End-Stage Kidney Disease Among Adults of Low Socioeconomic Status in the Southeastern United States.

BACKGROUND: Religiosity, encompassing spirituality and religious practices, is associated with reduced disease incidence among individuals of low socioeconomic status and who self-identify as Black. We hypothesized that religiosity associates with reduced end-stage kidney disease (ESKD) risk among Black but not White adults of low socioeconomic status. DESIGN: Cox models of religiosity and ESKD risk in 76,443 adults. RESULTS: Black adults reporting high spirituality had reduced ESKD risk after adjusting for demographic characteristics [Hazard Ratio (HR) .82 (95% Confidence Interval (CI)) (.69-.98)], depressive symptoms, social support, and tobacco use [HR .81 (CI .68-.96)]. When clinical covariates were added, associations between spirituality and ESKD were slightly attenuated and lost significance [HR .85 (CI .68-1.06)]. Associations were not demonstrated among White adults. CONCLUSIONS: Spirituality associates with reduced ESKD risk among Black adults of low socioeconomic status independent of demographic, psychosocial, and behavioral characteristics. Effect modification by race was not statistically significant.

Fetal growth trajectories and their association with maternal and child characteristics.

Background: The growth of the fetus is a complex process, influenced by genetic and environmental factors. Longitudinal patterns of fetal growth are required to fully understand this process, however to date, a paucity of data exists in this area.Objective: To identify fetal growth trajectories in-utero and to assess their association with maternal and child characteristics up to 5 years postnatal.Methods: Data from 781 mother-child pairs from the ROLO longitudinal birth cohort study were analyzed. The ROLO study was a randomized control trial of a low glycemic index diet in pregnancy to prevent recurrence of macrosomia. Fetal ultrasound measurements were recorded at 20 and 34 weeks gestation, and birth weight was recorded. Abdominal circumference (AC), weight (fetal weight, or birth weight), a standardized proxy for length (femur length or birth length, individually standardized), and AC:length ratio were examined for trajectory classes using latent class trajectory mixture models. Two-, three-, four-, and five-class models were evaluated for fit, using a linear (first order) trajectory over three time-points. ANOVA and chi-square tests were applied to test associations between trajectory membership and maternal and child characteristics up to age 5.Results: For AC, two fetal growth trajectories were identified, with 29% of participants on a "slow" trajectory and 71% on a "fast" trajectory. Those on a fast trajectory had higher rates of maternal impaired glucose tolerance (28.7 versus 16.5%, p<.001) and higher rates of mean child 5-year body mass index (BMI) centiles (64th versus 58th centile, p<.05) compared to those on the slow trajectory. For estimated fetal weight, four trajectories were identified, with 4% on a "very-slow" trajectory, 63% in a "moderate-slow" trajectory, 30% in a "moderate-fast" trajectory and 3% on a "very-fast" trajectory. Mothers with a fetus on the fastest trajectory had higher antenatal serum glucose levels (p<.05), and were more likely to deliver by cesarean section (59.1 versus 20%, p<.001). At 5 years of age, children on the fastest growth trajectory had the highest mean BMI centile (86th versus 60th centile, p<.05).Conclusions: This study shows that specific fetal growth trajectories may be associated with maternal serum glucose concentrations during pregnancy, mode of delivery and child BMI at 5 years of age. Diet and lifestyle measures that target maternal glucose levels during pregnancy may have lifelong benefits for children's BMI. Identifying those on an accelerated growth trajectory during fetal life provides a unique opportunity for antenatal and infant interventions that may have long-lasting health benefits.

Serious Illness Treatment Preferences for Older Adults with Advanced CKD.

BACKGROUND: Patient-centered care for older adults with CKD requires communication about patient's values, goals of care, and treatment preferences. Eliciting this information requires tools that patients understand and that enable effective communication about their care preferences. METHODS: Nephrology clinic patients age ≥60 years with stage 4 or 5 nondialysis-dependent CKD selected one of four responses to the question, "If you had a serious illness, what would be important to you?" Condensed versions of the options were, "Live as long as possible;" "Try treatments, but do not suffer;" "Focus on comfort;" or "Unsure." Patients also completed a validated health outcome prioritization tool and an instrument determining the acceptability of end-of-life scenarios. Patient responses to the three tools were compared. RESULTS: Of the 382 participants, 35% (n=134) selected "Try treatments, but do not suffer;" 33% (n=126) chose "Focus on comfort;" 20% (n=75) opted for "Live as long as possible;" and 12% (n=47) selected "Unsure." Answers were associated with patients' first health outcome priority and acceptability of end-of-life scenarios. One third of patients with a preference to "Focus on comfort" reported that a life on dialysis would not be worth living compared with 5% of those who chose "Live as long as possible" (P<0.001). About 90% of patients agreed to share their preferences with their providers. CONCLUSIONS: Older adults with advanced CKD have diverse treatment preferences and want to share them. A single treatment preference question correlated well with longer, validated health preference tools and may provide a point of entry for discussions about patient's treatment goals.

Venous thromboembolism incidence in the Ireland east hospital group: a retrospective 22-month observational study.

OBJECTIVES: To determine the incidence of venous thromboembolism (VTE) and the incidence of hospital-acquired VTE (HA-VTE) arising within the population served by the Ireland East Hospital Group (IEHG). DESIGN: /home/user/Documents/Sathish Kumar G/RFO/June/21-06-2019/bmjopen_iss_9_7_20190621_1/ A retrospective observational study was conducted using hospital discharge data obtained from the hospital inpatient enquiry data reporting system. In this system, VTE events recorded as 'primary diagnosis' represented the reason for initial hospital admission, whereas VTE recorded as a 'secondary diagnosis' occurred following admission and were therefore used as an approximation of HA-VTE. These data were used to estimate the overall incidence of VTE and the proportion of these events which were hospital-acquired. SETTING: The IEHG is the largest hospital group in the Irish healthcare system and serves a population of over 1 million individuals. PARTICIPANTS: Data were generated from records pertaining to the 2727 patient admission episodes where a diagnosis of VTE was made during the 22-month study period. RESULTS: During the study period, 2727 VTE events were recorded within the IEHG (which serves a population of 1 036 279) corresponding to an incidence of 1.44 (95% CI 1.36 to 1.51) per 1000 per annum. 1273 (47%) of VTE events were recorded as secondary VTE. The incidence of VTE was highest among individuals over 85 years of age (16.03 per 1000;95% CI 12.81 to 19.26) and was more common following emergency hospital admission. CONCLUSION: These data suggest that HA-VTE accounts for at least 47% of all VTE events arising within a hospital group serving a population of over 1 million individuals within the Ireland. Given that HA-VTE is a well-recognised source of (potentially preventable) hospital deaths, these findings provide a compelling argument for prioritising strategies directed at reducing the risk of VTE among hospital patients served by the IEHG and within the Ireland as a whole.

Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure.

Rich geochemical datasets generated over the past 30 years have provided fine-scale resolution on the northern Gulf of Mexico (nGOM) coastal hypoxic (≤ 2 mg of O2 L-1) zone. In contrast, little is known about microbial community structure and activity in the hypoxic zone despite the implication that microbial respiration is responsible for forming low dissolved oxygen (DO) conditions. Here, we hypothesized that the extent of the hypoxic zone is a driver in determining microbial community structure, and in particular, the abundance of ammonia-oxidizing archaea (AOA). Samples collected across the shelf for two consecutive hypoxic seasons in July 2013 and 2014 were analyzed using 16S rRNA gene sequencing, oligotyping, microbial co-occurrence analysis, and quantification of thaumarchaeal 16S rRNA and archaeal ammonia-monooxygenase (amoA) genes. In 2014 Thaumarchaeota were enriched and inversely correlated with DO while Cyanobacteria, Acidimicrobiia, and Proteobacteria where more abundant in oxic samples compared to hypoxic. Oligotyping analysis of Nitrosopumilus 16S rRNA gene sequences revealed that one oligotype was significantly inversely correlated with DO in both years. Oligotyping analysis revealed single nucleotide variation among all Nitrosopumilaceae, including Nitrosopumilus 16S rRNA gene sequences, with one oligotype possibly being better adapted to hypoxia. We further provide evidence that in the hypoxic zone of both year 2013 and 2014, low DO concentrations and high Thaumarchaeota abundances influenced microbial co-occurrence patterns. Taken together, the data demonstrated that the extent of hypoxic conditions could potentially drive patterns in microbial community structure, with two years of data revealing the annual nGOM hypoxic zone to be emerging as a low DO adapted AOA hotspot.

Discrimination between recent and non-recent HIV infections using routine diagnostic serological assays.

The suitability of routine diagnostic HIV assays to accurately discriminate between recent and non-recent HIV infections has not been fully investigated. The aim of this study was to compare an established HIV recency assay, the Sedia limiting antigen HIV avidity assay (LAg), with the diagnostic assays; Abbott ARCHITECT HIV Ag/Ab Combo and INNO-LIA HIV line assays. Samples from all new HIV diagnoses in Ireland from January to December 2016 (n = 455) were tested. An extended logistic regression model, the Spiegelhalter-Knill-Jones method, was utilised to establish a scoring system to predict recency of HIV infection. As proof of concept, 50 well-characterised samples were obtained from the CEPHIA repository whose stage of infection was blinded to the authors, which were tested and analysed. The proportion of samples that were determined as recent was 18.1% for LAg, 6.4% with the ARCHITECT, and 14.5% in the INNO-LIA assay. There was a significant correlation between the ARCHITECT S/CO values and the LAg results, r = 0.717, p < 0.001. ROC analysis revealed that an ARCHITECT S/CO < 250 had a sensitivity and specificity of 90.32% and 89.83%, respectively. Combining the Abbott ARCHITECT HIV Ag/Ab Combo assay and INNO-LIA HIV assays resulted in an observed risk of being recent of 100%. Analysis of the CEPHIA samples revealed a strong agreement between the LAg assay and the combination of routine assays (κ = 0.908, p < 0.001). Our findings provide evidence that assays routinely employed to diagnose and confirm HIV infection may be utilised to determine the recency of HIV infection.