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CO 2 fixation (i.e. primary production) is a key function of all ecosystems, providing the carbon and energy that fuel the entire food web. It also plays an important role in mitigating climate change as CO 2 is the most important greenhouse gas. While photosynthesis is regarded as the most important carbon fixation pathway, prokaryotes able to fix carbon in the absence of light (chemolithoautotrophs) can also be a significant source of energy in a light-limited ecosystem. Boreal lakes, notoriously colored and stratified with respect to oxygen and nutrients, present ideal conditions for this so-called dark carbon fixation by the chemolithoautotrophs. However, the prevalence of dark carbon fixation in boreal lakes remains unknown. Here, we measured dark carbon fixation in Swedish lakes from the boreal and boreo-nemoral zones, during summer stratification. We detected dark carbon fixation in 16 out of the 17 lakes studied, and concluded that dark fixation is a widespread phenomenon in boreal lakes. Moreover, the average dark primary production ranged from 18.5 % in the epilimnion to 81.4 % in the hypolimnion of all tested lakes. Our data further suggests that chemolithoautotrophic activity is mostly driven by iron-oxidizing bacteria. The chemolithoautotrophic guild is diverse and seems to be composed of both ubiquitous bacteria, like Gallionellaceae or Chromatiaceae, and endemic taxa, such as Ferrovaceae, which appears to be favored by a low pH. These results are particularly exciting as they suggest that dark carbon fixation could partly compensate for the low photosynthetic capacity in lakes with dark-colored water., (Copyright © 2024. Published by Elsevier B.V.)

Background: The occurrence of colorectal cancer (CRC) is increasing among young adults, but the etiology is still largely unknown. In addition to germline monogenetic variants also polygenic risk scores (PRS) have been proven to correctly estimate the risk of CRC., Case Description: We present a 24-year-old male with disseminated colon cancer who carried a germline duplication on chromosome 1 spanning 200 kb and covering CD101, TTF2, MIR942, TRIM45, and parts of PTGFRN and VTCN1 . The duplication was located in tandem. A similar duplication was previously reported in a family with CRC among two brothers aged 52 and 61 years old at diagnosis. Particularly, MIR942 was an interesting finding as it is involved in the regulation of the Wnt signaling pathway. Disruption of the Wnt pathway is known to cause CRC. However, in our case the duplication did not segregate with disease in the family. Calculation of a PRS in our patient found an average PRS for CRC., Conclusions: Our findings do not support that this duplication is a monogenetic cause of CRC, nor did a PRS point towards an increased risk in this 24-year-old male. Whether the duplication is a risk factor in combination with other genetic and non-genetic risk factors requires further studies., Competing Interests: Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://jgo.amegroups.com/article/view/10.21037/jgo-24-148/coif). K.W. reports a speaking engagement at Seagen Denmark ApS for which she received payment. The other authors have no conflicts of interest to declare., (2024 AME Publishing Company. All rights reserved.)

Arctic soil microbial communities may shift with increasing temperatures and water availability from climate change. We examined temperature and volumetric liquid water content (VWC) in the upper 80 cm of permafrost-affected soil over 2 years (2018-2019) at the Bayelva monitoring station, Ny Ålesund, Svalbard. We show VWC increases with depth, whereas in situ temperature is more stable vertically, ranging from -5°C to 5 °C seasonally. Prokaryotic metagenome-assembled genomes (MAGs) were obtained at 2-4 cm vertical resolution collected while frozen in April 2018 and at 10 cm vertical resolution collected while thawed in September 2019. The most abundant MAGs were Acidobacteriota, Actinomycetota, and Chloroflexota. Actinomycetota and Chloroflexota increase with depth, while Acidobacteriota classes Thermoanaerobaculia Gp7-AA8, Blastocatellia UBA7656, and Vicinamibacteria Vicinamibacterales are found above 6 cm, below 6 cm, and below 20 cm, respectively. All MAGs have diverse carbon-degrading genes, and Actinomycetota and Chloroflexota have autotrophic genes. Genes encoding β -glucosidase, N-acetyl-β-D-glucosaminidase, and xylosidase increase with depth, indicating a greater potential for organic matter degradation with higher VWC. Acidobacteriota dominate the top 6 cm with their classes segregating by depth, whereas Actinomycetota and Chloroflexota dominate below ∼6 cm. This suggests that Acidobacteriota classes adapt to lower VWC at the surface, while Actinomycetota and Chloroflexota persist below 6 cm with higher VWC. This indicates that VWC may be as important as temperature in microbial climate change responses in Arctic mineral soils. Here we describe MAG-based Seqcode type species in the Acidobacteriota, Onstottus arcticum, Onstottus frigus, and Gilichinskyi gelida and in the Actinobacteriota, Mayfieldus profundus., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier GmbH.)

Ecology and evolution are often viewed as distinct processes, which interact on contemporary time scales in microbiomes. To observe these processes in a natural system, we collected a two-decade, 471-sample freshwater lake time series, creating the longest metagenome dataset to date. Among 2,855 species-representative genomes, diverse species and strains followed cyclical seasonal patterns, and one in five species experienced decadal shifts in strain composition. The most globally abundant freshwater bacterium had constant species-level abundance, but environmental extremes appeared to trigger a shift in strain composition and positive selection of amino acid and nucleic acid metabolism genes. These genes identify organic nitrogen compounds as potential drivers of freshwater responses to global change. Seasonal and long-term strain dynamics could be regarded as ecological processes or equivalently as evolutionary change. Rather than as distinct processes that interact, we propose a conceptualization where ecology and evolution converge along a continuum to better describe change in diverse microbial communities., Competing Interests: Competing interests Authors declare that they have no competing interests.

Aims/hypotheses: Glucagon and glucagon-like peptide-1 (GLP-1) are derived from the same precursor; proglucagon, and dual agonists of their receptors are currently being explored for the treatment of obesity and metabolic dysfunction-associated steatotic liver disease (MASLD). Elevated levels of endogenous glucagon (hyperglucagonaemia) have been linked with hyperglycaemia in individuals with type 2 diabetes but are also observed in individuals with obesity and MASLD. GLP-1 levels have been reported to be largely unaffected or even reduced in similar conditions. We investigated potential determinants of plasma proglucagon and associations of glucagon receptor signalling with metabolic diseases based on data from the UK Biobank., Methods: We used exome sequencing data from the UK Biobank for ~410,000 white participants to identify glucagon receptor variants and grouped them based on their known or predicted signalling. Data on plasma levels of proglucagon estimated using Olink technology were available for a subset of the cohort (~40,000). We determined associations of glucagon receptor variants and proglucagon with BMI, type 2 diabetes and liver fat (quantified by liver MRI) and performed survival analyses to investigate if elevated proglucagon predicts type 2 diabetes development., Results: Obesity, MASLD and type 2 diabetes were associated with elevated plasma levels of proglucagon independently of each other. Baseline proglucagon levels were associated with the risk of type 2 diabetes development over a 14 year follow-up period (HR 1.13; 95% CI 1.09, 1.17; n=1562; p=1.3×10 -12 ). This association was of the same magnitude across strata of BMI. Carriers of glucagon receptor variants with reduced cAMP signalling had elevated levels of proglucagon (β 0.847; 95% CI 0.04, 1.66; n=17; p=0.04), and carriers of variants with a predicted frameshift mutation had higher levels of liver fat compared with the wild-type reference group (β 0.504; 95% CI 0.03, 0.98; n=11; p=0.04)., Conclusions/interpretation: Our findings support the suggestion that glucagon receptor signalling is involved in MASLD, that plasma levels of proglucagon are linked to the risk of type 2 diabetes development, and that proglucagon levels are influenced by genetic variation in the glucagon receptor, obesity, type 2 diabetes and MASLD. Determining the molecular signalling pathways downstream of glucagon receptor activation may guide the development of biased GLP-1/glucagon co-agonist with improved metabolic benefits., Data Availability: All coding is available through https://github.com/nicwin98/UK-Biobank-GCG., (© 2024. The Author(s).)

Bacteria form groups comprised of cells and a secreted polymeric matrix that controls their spatial organization. These groups - termed biofilms - can act as refuges from environmental disturbances and from biotic threats, including phages. Despite the ubiquity of temperate phages and bacterial biofilms, live propagation of temperate phages within biofilms has never been characterized on cellular spatial scales. Here, we leverage several approaches to track temperate phages and distinguish between lytic and lysogenic host infections. We determine that lysogeny within E. coli biofilms initially occurs within a predictable region of cell group packing architecture on the biofilm periphery. Because lysogens are generally found on the periphery of large cell groups, where lytic viral infections also reduce local biofilm cell packing density, lysogens are predisposed to disperse into the passing liquid and are over-represented in biofilms formed from the dispersal pool of the original biofilm-phage system. Comparing our results with those for virulent phages reveals that temperate phages have previously unknown advantages in propagating over long spatial and time scales within and among bacterial biofilms.

The candidate phyla radiation (CPR) represents a distinct monophyletic clade and constitutes a major portion of the tree of life. Extensive efforts have focused on deciphering the functional diversity of its members, primarily using sequencing-based techniques. However, cultivation success remains scarce, presenting a significant challenge, particularly in CPR-dominated groundwater microbiomes characterized by low biomass. Here, we employ an advanced high-throughput droplet microfluidics technique to enrich CPR taxa from groundwater. Utilizing a low-volume filtration approach, we successfully harvested a microbiome resembling the original groundwater microbial community. We assessed CPR enrichment in droplet and aqueous bulk cultivation for 30 days using a novel CPR-specific primer to rapidly track the CPR fraction through the cultivation attempts. The combination of soil extract and microbial-derived necromass provided the most supportive conditions for CPR enrichment. Employing these supplemented conditions, droplet cultivation proved superior to bulk cultivation, resulting in up to a 13-fold CPR enrichment compared to a 1- to 2-fold increase in bulk cultivation. Amplicon sequencing revealed 10 significantly enriched CPR orders. The highest enrichment in CPRs was observed for some unknown members of the Parcubacteria order, Cand . Jorgensenbacteria, and unclassified UBA9983. Furthermore, we identified co-enriched putative host taxa, which may guide more targeted CPR isolation approaches in subsequent investigations., Competing Interests: There are no conflicts to declare., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Implications of geographic separation and temporal dynamics on the evolution of free-living bacterial species are widely unclear. However, the vast amount of metagenome sequencing data generated during the last decades from various habitats around the world provides an unprecedented opportunity for such investigations. Here, we exploited publicly available and new freshwater metagenomes in combination with the genomes of abundant freshwater bacteria to reveal geographic and temporal population structure. We focused on species that were detected across broad geographic ranges at high enough sequence coverage for meaningful population genomic analyses, associated with the predominant freshwater taxa acI, LD12, Polynucleobacter, and Candidatus Methylopumilus. Despite the broad geographic ranges, each species appeared as a sequence-discrete cluster, in contrast to abundant marine taxa, for which continuous diversity structures were reported on a global scale. Population differentiation increased significantly with spatial distance in all species, but notable dispersal barriers (e.g. oceanic) were not apparent. Yet, the different species showed contrasting rates of geographic divergence and strikingly different intra-population dynamics in time series within individual habitats. The change in an LD12 population over 7 years was minor (FST = 0.04) compared to differentiation between lakes, whereas a Polynucleobacter population displayed strong changes within merely 2 months (FST up to 0.54), similar in scale to differentiation between populations separated by thousands of kilometers. The slowly and steadily evolving LD12 population showed high strain diversity, whereas the dynamic Polynucleobacter population exhibited alternating clonal expansions of mostly two strains only. Based on the contrasting population structures, we propose distinct models of speciation., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Background: The accurate etiological diagnosis of lower respiratory tract infections (LRTI) is essential for their effective clinical management. The extensive use of molecular methods during the COVID-19 pandemic has enabled massive data acquisition on viral lower respiratory tract infections. The current study aims to identify clinical features associated with eight viral agents among children presenting severe LRTI., Methods: retrospective cohort study of data from the Brazilian Influenza Epidemiological Surveillance Information System. Patients under 20 years-old who had severe LRTI with etiological confirmation through RT-PCR between 2020 and 2022 were included. Binary logistic regressions were used to examine associations between pathogens and symptoms., Results: 60,657 cases were assessed. The main viral agents detected were Sars-CoV-2 (COV2) (41.2%), Respiratory Syncytial Virus (29.1%), Human Rhinovirus (HRV) (12.1%), and Influenza (FLU) (5.5%). A general mortality rate of 4.3% was observed. The multivariate analysis evidenced that COV2 less likely presented with cough (OR: 0.34; 95%CI: 0.32-0.36), respiratory discomfort (Adjusted Odds Ratio (aOR): 0.61; 95%Confidence Interval (CI): 0.59-0.64), and desaturation (aOR: 0.71; 95%CI: 0.69-0.75). RSV strongly associated with cough (aOR: 2.59; 95%CI: 2.45-2.75) and respiratory discomfort (aOR: 1.54; 95%CI: 1.46-1.62), whereas FLU was linked to fever (aOR: 2.27; 95%CI: 2.06-2.50) and sore throat (aOR: 1.48; 95%CI: 1.34-1.64)., Conclusions: The viral agents responsible for severe LRTI have distinct associations with clinical features in children., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Background: Removal of trace organic chemicals (TOrCs) in aquatic environments has been intensively studied. Some members of natural microbial communities play a vital role in transforming chemical contaminants, however, complex microbial interactions impede us from gaining adequate understanding of TOrC biotransformation mechanisms. To simplify, in this study, we propose a strategy of establishing reduced-richness model communities capable of removing diverse TOrCs via pre-adaptation and dilution-to-extinction., Results: Microbial communities were adapted from tap water, soil, sand, sediment deep and sediment surface to changing concentrations of 27 TOrCs mixture. After adaptation, the communities were further diluted to reduce diversity into 96 deep well plates for high-throughput cultivation. After characterizing microbial structure and TOrC removal performance, thirty taxonomically non-redundant model communities with different removal abilities were obtained. The pre-adaptation process was found to reduce the microbial richness but to increase the evenness and phylogenetic diversity of resulting model communities. Moreover, phylogenetic diversity showed a positive effect on the number of TOrCs that can be transformed simultaneously. Pre-adaptation also improved the overall TOrC removal rates, which was found to be positively correlated with the growth rates of model communities., Conclusions: This is the first study that investigated a wide range of TOrC biotransformation based on different model communities derived from varying natural microbial systems. This study provides a standardized workflow of establishing model communities for different metabolic purposes with changeable inoculum and substrates. The obtained model communities can be further used to find the driving agents of TOrC biotransformation at the enzyme/gene level., (© 2023. The Author(s).)

Microbial communities drive global biogeochemical cycles and shape the health of plants and animals-including humans. Their structure and function are determined by ecological and environmental interactions that govern the assembly, stability and evolution of microbial communities. A widely held view is that antagonistic interactions such as competition predominate in microbial communities and are ecologically more important than synergistic interactions-for example, mutualism or commensalism. Over the past decade, however, a more nuanced picture has emerged, wherein bacteria, archaea and fungi exist within interactive networks in which they exchange essential and non-essential metabolites. These metabolic interactions profoundly impact not only the physiology, ecology and evolution of the strains involved, but are also central to the functioning of many, if not all, microbiomes. Therefore, we advocate for a balanced view of microbiome ecology that encompasses both synergistic and antagonistic interactions as key forces driving the structure and dynamics within microbial communities., (© 2023. Springer Nature Limited.)

Urban lakes provide multiple benefits to society while influencing life quality. Moreover, lakes and their microbiomes are sentinels of anthropogenic impact and can be used for natural resource management and planning. Here, we release original metagenomic data from several well-characterized and anthropogenically impacted eutrophic lakes in the vicinity of Stockholm (Sweden). Our goal was to collect representative microbial community samples and use shotgun sequencing to provide a broad view on microbial diversity of productive urban lakes. Our dataset has an emphasis on Lake Mälaren as a major drinking water reservoir under anthropogenic impact. This dataset includes short-read sequence data and metagenome assemblies from each of 17 samples collected from eutrophic lakes near the greater Stockholm area. We used genome-resolved metagenomics and obtained 2378 metagenome assembled genomes that de-replicated into 514 species representative genomes. This dataset adds new datapoints to previously sequenced lakes and it includes the first sequenced set of metagenomes from Lake Mälaren. Our dataset serves as a baseline for future monitoring of drinking water reservoirs and urban lakes., (© 2023. The Author(s).)

Gut microbes play important roles for their hosts. Previous studies suggest that host-microbial systems can form long-term associations over evolutionary time and the dynamic changes of the intestinal system may represent major driving forces and contribute to insect dietary diversification and speciation. Our study system includes a set of six closely related leaf beetle species (Galerucella spp.) and our study aims to separate the roles of host phylogeny and ecology in determining the gut microbial community and to identify eventual relationship between host insects and gut bacteria. We collected adult beetles from their respective host plants and quantified their microbial community using 16S rRNA sequencing. The results showed that the gut bacteria community composition was structured by host beetle phylogeny, where more or less host-specific gut bacteria interact with the different Galerucella species. For example, the endosymbiotic bacteria Wolbachia was found almost exclusively in G. nymphaea and G. sagittariae. Diversity indicators also suggested that α- and β-diversities of gut bacteria communities varied among host beetle species. Overall, our results suggest a phylogenetically controlled co-occurrence pattern between the six closely related Galerucella beetles and their gut bacteria, indicating the potential of co-evolutionary processes occurring between hosts and their gut bacterial communities., (© 2023. The Author(s).)

Testicular cancer is predominantly curable, but the long-term side effects of chemotherapy have a severe impact on life quality. In this research study, we focus on hearing loss as a part of overall chemotherapy-induced ototoxicity. This is a unique approach where we combine clinical data from the acclaimed nationwide Danish Testicular Cancer (DaTeCa)-Late database. Clinical and genetic data on 433 patients were collected from hospital files in October 2014. Hearing loss was classified according to the FACT/GOG-Ntx-11 version 4 self-reported Ntx6. Machine learning models combining a genome-wide association study within a nested cross-validated logistic regression were applied to identify patients at high risk of hearing loss. The model comprising clinical and genetic data identified 67% of the patients with hearing loss; however, this was with a false discovery rate of 49%. For the non-affected patients, the model identified 66% of the patients with a false omission rate of 19%. An area under the receiver operating characteristic (ROC-AUC) curve of 0.73 (95% CI, 0.71-0.74) was obtained, and the model suggests genes SOD2 and MGST3 as important in improving prediction over the clinical-only model with a ROC-AUC of 0.66 (95% CI, 0.65-0.66). Such prediction models may be used to allow earlier detection and prevention of hearing loss. We suggest a possible biological mechanism for cisplatin-induced hearing loss development. On confirmation in larger studies, such models can help balance treatment in clinical practice.

While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems., (© 2023. The Author(s).)

Food waste (FW) generation has become one of the largest environmental concerns for human society. Thanks to its chemical features and its high biodegradability, FW can be used as starting platform to produce biocommodities. Lactic acid (LA) is one of those chemicals that is gaining the attention of industry and research for its important role in polylactic acids production. To exploit better the organic content of FW, several FW pretreatments have been proposed in the literature, though none of them were aimed at influencing LA fermentation. Thermal and ultrasonic pretreatment effects on solubilization rates and LA production yields have been investigated in this batch study. The highest solubilization rate was achieved with 30 minutes ultrasonic pretreated FW resulting in a 15% increment in soluble COD (sCOD). The highest LA yield was obtained after 90-minute thermal pretreatment at 80 and 100°C at a yield of 0.49 g LA•g COD -1 . This study shows that ultrasonic pretreatment generally performed better than thermal pretreatment when considering the increase in sCOD but caused a reduction in LA concentrations and yields after fermentation with high production of ethanol. The opposite trend was recorded in the thermal pretreated incubations, in which LA was present for 50% of the sCOD with higher LA concentrations of 2.90 g COD•L -1 .

Introduction: The COVID-19 pandemic resulted in tremendous physical and psychological pressure on healthcare professionals, especially on those working in intensive care units (ICUs) and Emergency Departments (EDs). The present study intended to characterize the profile of these professionals which is associated with burnout and determine the potential predictors of such condition., Methods: A Prospective cohort study was carried out in a tertiary hospital between March 2020 and March 2021, in Salvador, Brazil. A standardized and validated version of the Oldenburg Burnout inventory (OLBI) was applied to assess risk of burnout together with data forms designed to collect information on sociodemographic characteristics and religious beliefs. ICU and ED healthcare professionals were evaluated during off-hours at two distinct periods of the COVID-19 pandemic, in 2020 and in 2021. Differences in the results obtained from each study participant between the timepoints were compared. A binary logistic regression analysis was performed to identify the predictors of burnout development independent of other confounding factors., Results: Seventy-seven healthcare professionals with a median age of 33 (interquartile range [IQR]: 31-37.5) years and predominantly female (72.7%; n  = 56) were enrolled. There were 62 professionals at risk of developing burnout through the OLBI. Those had a median age of 33 (IQR: 31-37) and female predominance (71%, n  = 44). Disengagement and burnout were the only features which frequencies significantly changed over time, with increasing detection at the latest timepoint. Alcohol consumption was found to be an important risk factor for burnout development [adjusted odds ratio (aOR): 10.8 (95% CI: 1.8-64.2)]. Importantly, working in the ICU [aOR: 0.04 (95%CI: 0.01-0.32)] and the habit of praying daily [aOR: 0.07 (95%CI: 0.01-0.41)] were characteristics linked to reduced odds of burnout., Discussion: Disengagement substantially increased during the COVID-19 pandemic in healthcare professionals. Alcohol consumption favors the onset of burnout whereas habit of praying daily and working in the ICU are protective against such outcome. Institutional policies aimed at minimizing etilism may positively impact mental health of these professionals., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Silva, Menezes, Garcia, Pustilnik, Ferreira, Aguiar, Filgueiras Filho, Araújo-Pereira and Andrade.)

Viral infections modulate bacterial metabolism and ecology. Here, we investigated the hypothesis that viruses influence the ecology of purple and green sulfur bacteria in anoxic and sulfidic lakes, analogs of euxinic oceans in the geologic past. By screening metagenomes from lake sediments and water column, in addition to publicly-available genomes of cultured purple and green sulfur bacteria, we identified almost 300 high and medium-quality viral genomes. Viruses carrying the gene psbA , encoding the small subunit of photosystem II protein D1, were ubiquitous, suggesting viral interference with the light reactions of sulfur oxidizing autotrophs. Viruses predicted to infect these autotrophs also encoded auxiliary metabolic genes for reductive sulfur assimilation as cysteine, pigment production, and carbon fixation. These observations show that viruses have the genomic potential to modulate the production of metabolic markers of phototrophic sulfur bacteria that are used to identify photic zone euxinia in the geologic past., Competing Interests: Competing interestsThe authors declare no competing interests., (© The Author(s) 2023.)

Background: Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities potentially changing the diversity of functional genes and its associated metabolic processes. In this study, we investigated spatial variability and how environmental variables structure the diversity and composition of benthic functional genes and metabolic pathways across various fundamental environmental gradients. We analyzed metagenomic data from sediment samples, measured related abiotic data (e.g., salinity, oxygen and carbon content), covering 59 stations spanning 1,145 km across the Baltic Sea., Results: The composition of genes and microbial communities were mainly structured by salinity plus oxygen, and the carbon to nitrogen (C:N) ratio for specific metabolic pathways related to nutrient transport and carbon metabolism. Multivariate analyses indicated that the compositional change in functional genes was more prominent across environmental gradients compared to changes in microbial taxonomy even at genus level, and indicate functional diversity adaptation to local environments. Oxygen deficient areas (i.e., dead zones) were more different in gene composition when compared to oxic sediments., Conclusions: This study highlights how benthic functional genes are structured over spatial distances and by environmental gradients and resource availability, and suggests that changes in, e.g., oxygenation, salinity, and carbon plus nitrogen content will influence functional metabolic pathways in benthic habitats. Video Abstract., (© 2022. The Author(s).)

Background and Aim: Genome wide association studies have scaled up both in terms of sample size and range of complex disorders investigated, but these have explained relatively little phenotypic variance. Of the several reasons, phenotypic heterogeneity seems to be a likely contributor for missing out genetic associations of large effects. Ayurveda, the traditional Indian system of medicine is one such tool which adopts a holistic deep phenotyping approach and classifies individuals based on their body constitution/prakriti. We hypothesized that Ayurveda based phenotypic stratification of healthy and diseased individuals will allow us to achieve much desired homogeneous cohorts which would facilitate detection of genetic association of large effects. In this proof of concept study, we performed a genome wide association testing of clinically diagnosed rheumatoid arthritis patients and healthy controls, who were re-phenotyped into Vata, Pitta and Kapha predominant prakriti sub-groups., Experimental Procedure: Genotypes of rheumatoid arthritis cases (Vata = 49; Pitta = 117; Kapha = 78) and controls (Vata = 33; Pitta = 175; Kapha = 85) were retrieved from the total genotype data, used in a recent genome-wide association study performed in our laboratory. A total of 528461 SNPs were included after quality control. Prakriti-wise genome-wide association analysis was employed., Results and Conclusion: This study identified (i) prakriti-specific novel disease risk genes of high effect sizes; (ii) putative candidates of novel therapeutic potential; and (iii) a good correlation between genetic findings and clinical knowledge in Ayurveda. Adopting Ayurveda based deep phenotyping may facilitate explaining hitherto undiscovered heritability in complex traits and may propel much needed progress in personalized medicine., Competing Interests: Conflict of interest None., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

Our view of genome size in Archaea and Bacteria has remained skewed as the data has been dominated by genomes of microorganisms that have been cultivated under laboratory settings. However, the continuous effort to catalog Earth's microbiomes, specifically propelled by recent extensive work on uncultivated microorganisms, provides an opportunity to revise our perspective on genome size distribution. We present a meta-analysis that includes 26,101 representative genomes from 3 published genomic databases; metagenomic assembled genomes (MAGs) from GEMs and stratfreshDB, and isolates from GTDB. Aquatic and host-associated microbial genomes present on average the smallest estimated genome sizes (3.1 and 3.0 Mbp, respectively). These are followed by terrestrial microbial genomes (average 3.7 Mbp), and genomes from isolated microorganisms (average 4.3 Mbp). On the one hand, aquatic and host-associated ecosystems present smaller genomes sizes in genera of phyla with genome sizes above 3 Mbp. On the other hand, estimated genome size in phyla with genomes under 3 Mbp showed no difference between ecosystems. Moreover, we observed that when using 95% average nucleotide identity (ANI) as an estimator for genetic units, only 3% of MAGs cluster together with genomes from isolated microorganisms. Although there are potential methodological limitations when assembling and binning MAGs, we found that in genome clusters containing both environmental MAGs and isolate genomes, MAGs were estimated only an average 3.7% smaller than isolate genomes. Even when assembly and binning methods introduce biases, estimated genome size of MAGs and isolates are very similar. Finally, to better understand the ecological drivers of genome size, we discuss on the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Rodríguez-Gijón, Nuy, Mehrshad, Buck, Schulz, Woyke and Garcia.)

Objective: An indeterminate thyroid nodule fine-needle aspiration (FNA) presents a unique dilemma. We evaluated our institution's experience with Bethesda III thyroid nodules, including the risk of malignancy (ROM) of these nodules removed for diagnostic lobectomy and radiologic and clinical risk factors for malignancy., Study Design: Retrospective chart review., Setting: San Antonio Military Medical Center (SAMMC; 483 bed Military Treatment Facility and Level 1 Trauma Center)., Methods: We identified all patients with a Bethesda III thyroid FNA at our institution from 2010 to 2018 and determined which nodules were removed. The final histological diagnosis was recorded. Whether or not age, gender, body mass index (BMI), race, nodule size, margin regularity, rate of nodule growth, vascularity, internal calcifications, family history of thyroid cancer, personal history of radiation, and history of repeated AUS/FLUS on FNA had a significant impact on malignancy risk was evaluated with chi square and rank sum Wilcoxon tests., Results: 492 patients had 1 or more AUS result. 52% (258/492) underwent repeat FNA. This resulted in Bethesda II or III in 90% (232/258). In 10% (26/258), the repeat FNA resulted in a higher Bethesda grade. 183 lobectomies were performed on the side containing an AUS nodule. The malignancy percentage was 38.3% (70/183). Age less than 30 was the only variable showing statistical significance for increased risk of malignancy ( P  = .04)., Conclusion: The ROM of nodules characterized as AUS/FLUS on FNA may be higher than expected. Age may be a better predictor of malignancy than repeat FNA.

Boreal lakes and ponds produce two-thirds of the total natural methane emissions above the latitude of 50° North. These lake emissions are regulated by methanotrophs which can oxidize up to 99% of the methane produced in the sediments and the water column. Despite their importance, the diversity and distribution of the methanotrophs in lakes are still poorly understood. Here, we used shotgun metagenomic data to explore the diversity and distribution of methanotrophs in 40 oxygen-stratified water bodies in boreal and subarctic areas in Europe and North America. In our data, gammaproteobacterial methanotrophs (order Methylococcales ) generally dominated the methanotrophic communities throughout the water columns. A recently discovered lineage of Methylococcales , Candidatus Methylumidiphilus, was present in all the studied water bodies and dominated the methanotrophic community in lakes with a high relative abundance of methanotrophs. Alphaproteobacterial methanotrophs were the second most abundant group of methanotrophs. In the top layer of the lakes, characterized by low CH 4 concentration, their abundance could surpass that of the gammaproteobacterial methanotrophs. These results support the theory that the alphaproteobacterial methanotrophs have a high affinity for CH 4 and can be considered stress-tolerant strategists. In contrast, the gammaproteobacterial methanotrophs are competitive strategists. In addition, relative abundances of anaerobic methanotrophs, Candidatus Methanoperedenaceae and Candidatus Methylomirabilis, were strongly correlated, suggesting possible co-metabolism. Our data also suggest that these anaerobic methanotrophs could be active even in the oxic layers. In non-metric multidimensional scaling, alpha- and gammaproteobacterial methanotrophs formed separate clusters based on their abundances in the samples, except for the gammaproteobacterial Candidatus Methylumidiphilus, which was separated from these two clusters. This may reflect similarities in the niche and environmental requirements of the different genera within alpha- and gammaproteobacterial methanotrophs. Our study confirms the importance of O 2 and CH 4 in shaping the methanotrophic communities and suggests that one variable cannot explain the diversity and distribution of the methanotrophs across lakes. Instead, we suggest that the diversity and distribution of freshwater methanotrophs are regulated by lake-specific factors., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Martin, Rissanen, Garcia, Mehrshad, Buck and Peura.)

Nitrous acid (HONO) is a toxic household pollutant and a major source of indoor OH radicals. The high surface-to-volume ratio and diverse lighting conditions make the indoor photochemistry of HONO complex. This study demonstrates surface uptake of NO 2 and gaseous HNO 3 followed by gas-phase HONO generation on gypsum surfaces, model system for drywall, under reaction conditions appropriate for an indoor air environment. Tens of parts per billion of steady-state HONO are detected under these experimental conditions. Mechanistic insight into this heterogeneous photochemistry is obtained by exploring the roles of material compositions, relative humidities, and light sources. NO 2 and HNO 3 are adsorbed onto drywall surfaces, which can generate HONO under illumination and under dark conditions. Photoenhanced HONO generation is observed for illumination with a solar simulator as well as with the common indoor light sources such as compact fluorescence light and incandescent light bulbs. Incandescent light sources release more HONO and NO 2 near the light source compared to the solar radiation. Overall, HONO production on the gypsum surface increases with the increase of RH up to 70% relative humidity; above that, the gaseous HONO level decreases due to surface loss. Heterogeneous hydrolysis of NO 2 is predicted to be the dominant HONO generation channel, where NO 2 is produced through the photolysis of surface-adsorbed nitrates. This hydrolysis reaction predominantly occurs in the first layer of surface-adsorbed water.

Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.

Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi ) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or "species"). Of the 71 mOTUs, 57 were classified within the genus Chlorobium , and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium -associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia -associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs., (Copyright © 2021 Garcia et al.)

Aerosols impact climate, human health, and the chemistry of the atmosphere, and aerosol pH plays a major role in the physicochemical properties of the aerosol. However, there remains uncertainty as to whether aerosols are acidic, neutral, or basic. In this research, we show that the pH of freshly emitted (nascent) sea spray aerosols is significantly lower than that of sea water (approximately four pH units, with pH being a log scale value) and that smaller aerosol particles below 1 μm in diameter have pH values that are even lower. These measurements of nascent sea spray aerosol pH, performed in a unique ocean-atmosphere facility, provide convincing data to show that acidification occurs "across the interface" within minutes, when aerosols formed from ocean surface waters become airborne. We also show there is a correlation between aerosol acidity and dissolved carbon dioxide but no correlation with marine biology within the seawater. We discuss the mechanisms and contributing factors to this acidity and its implications on atmospheric chemistry., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

Background: The nonlesional skin of children with atopic dermatitis (AD) with peanut allergy (PA) is associated with increased transepidermal water loss; low urocanic acid (UCA) and pyrrolidone carboxylic acid (PCA), both of which are filaggrin breakdown products; and a reduced ratio of esterified ω-hydroxy fatty acid sphingosine ceramides (EOS-CERs) to nonhydroxy fatty acid sphingosine ceramides (NS-CERs) in the skin. The skin barrier of subjects with PA without AD (AD - PA + ) has not been studied., Objective: Our aim was to explore whether AD - PA + is associated with skin barrier abnormalities., Methods: A total of 33 participants were enrolled, including 13 AD - PA + , 9 AD + PA + , and 11 nonatopic (NA) participants., Results: The PCA content in the stratum corneum of AD - PA + subjects was significantly reduced versus that in NA subjects (median level, 67 vs 97 μg/mg protein [P = .028]). The ratio between cis- and trans-UCA decreased significantly from being highest in the NA group (1.62) to lowest in AD + PA + group (0.07 [P < .001 vs in the NA group; P = .006 vs in the AD - PA + group]), with the AD - PA + group having an intermediate cis/trans-UCA ratio (1.17 [P = .024 vs in the NA group]). The TEWL in AD - PA + subjects did not differ from that in the group with NA skin. Interestingly, AD - PA + subjects had an increased EOS/NS-CER ratio versus that in the group of subjects with NA skin (1.9 vs 1.3 [P = .008]), whereas the AD + PA + group had a decreased proportion of EOS-CERs (0.8 [P = .001] vs in the AD - PA + group)., Conclusion: Our data demonstrate that irrespective of AD, PA is associated with decreased skin cis-UCA and PCA content. An increase in skin EOS-CER/NS-CER ratio separates the AD - PA + group from the AD + PA + and NA groups., (Copyright © 2020 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.)

Diet is an important component in weight management strategies, but heterogeneous responses to the same diet make it difficult to foresee individual weight-loss outcomes. Omics-based technologies now allow for analysis of multiple factors for weight loss prediction at the individual level. Here, we classify weight loss responders (N = 106) and non-responders (N = 97) of overweight non-diabetic middle-aged Danes to two earlier reported dietary trials over 8 weeks. Random forest models integrated gut microbiome, host genetics, urine metabolome, measures of physiology and anthropometrics measured prior to any dietary intervention to identify individual predisposing features of weight loss in combination with diet. The most predictive models for weight loss included features of diet, gut bacterial species and urine metabolites (ROC-AUC: 0.84-0.88) compared to a diet-only model (ROC-AUC: 0.62). A model ensemble integrating multi-omics identified 64% of the non-responders with 80% confidence. Such models will be useful to assist in selecting appropriate weight management strategies, as individual predisposition to diet response varies.

While fastidious microbes can be abundant and ubiquitous in their natural communities, many fail to grow axenically in laboratories due to auxotrophies or other dependencies. To overcome auxotrophies, these microbes rely on their surrounding cohort. A cohort may consist of kin (ecotypes) or more distantly related organisms (community) with the cooperation being reciprocal or nonreciprocal and expensive (Black Queen hypothesis) or costless (by-product). These metabolic partnerships (whether at single species population or community level) enable dominance by and coexistence of these lineages in nature. Here we examine the relevance of these cooperation models to explain the abundance and ubiquity of the dominant fastidious bacterioplankton of a dimictic mesotrophic freshwater lake. Using both culture-dependent (dilution mixed cultures) and culture-independent (small subunit [SSU] rRNA gene time series and environmental metagenomics) methods, we independently identified the primary cohorts of actinobacterial genera " Candidatus Planktophila" (acI-A) and " Candidatus Nanopelagicus" (acI-B) and the proteobacterial genus " Candidatus Fonsibacter" (LD12). While " Ca Planktophila" and " Ca. Fonsibacter" had no correlation in their natural habitat, they have the potential to be complementary in laboratory settings. We also investigated the bifunctional catalase-peroxidase enzyme KatG (a common good which " Ca Planktophila" is dependent upon) and its most likely providers in the lake. Further, we found that while ecotype and community cooperation combined may explain " Ca Planktophila" population abundance, the success of " Ca. Nanopelagicus" and " Ca. Fonsibacter" is better explained as a community by-product. Ecotype differentiation of " Ca. Fonsibacter" as a means of escaping predation was supported but not for overcoming auxotrophies. IMPORTANCE This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: " Ca Planktophila" (acI-A), " Ca. Nanopelagicus" (acI-B), and " Ca. Fonsibacter" (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing clades of bacteria can coexist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied., (Copyright © 2020 Mondav et al.)

The genotype of a single SNP, rs12913832, is the primary predictor of blue and brown eye colours. The genotypes rs12913832:AA and rs12913832:GA are most often observed in individuals with brown eye colours, whereas rs12913832:GG is most often observed in individuals with blue eye colours. However, approximately 3% of Europeans with the rs12913832:GG genotype have brown eye colours. The purpose of the study presented here was to identify variants that explain brown eye colour formation in individuals with the rs12913832:GG genotype. Genes and regulatory regions surrounding SLC24A4, TYRP1, SLC24A5, IRF4, TYR, and SLC45A2, as well as the upstream region of OCA2 within the HERC2 gene were sequenced in a study comprising 40 individuals with the rs12913832:GG genotype. Of these, 24 individuals were considered to have blue eye colours and 16 individuals were considered to have brown eye colours. We identified 211 variants within the SLC24A4, TYRP1, IRF4, and TYR target regions associated with eye colour. Based on in silico analyses of predicted variant effects we recognized four variants, TYRP1 rs35866166:C, TYRP1 rs62538956:C, SLC24A4 rs1289469:C, and TYR rs1126809:G, to be the most promising candidates for explanation of brown eye colour in individuals with the rs12913832:GG genotype. Of the 16 individuals with brown eye colours, 14 individuals had four alleles, whereas the alleles were rare in the blue eyed individuals. rs35866166, rs62538956, and rs1289469 were for the first time found to be associated with pigmentary traits, whilst rs1126809 was previously found to be associated with pigmentary variation. To improve prediction of eye colours we suggest that future eye colour prediction models should include rs35866166, rs62538956, rs1289469, and rs1126809., Competing Interests: The authors have declared that no competing interests exist.

Background: Cisplatin-based chemotherapy may induce nephrotoxicity. This study presents a random forest predictive model that identifies testicular cancer patients at risk of nephrotoxicity before treatment., Methods: Clinical data and DNA from saliva samples were collected for 433 patients. These were genotyped on Illumina HumanOmniExpressExome-8 v1.2 (964 193 markers). Clinical and genomics-based random forest models generated a risk score for each individual to develop nephrotoxicity defined as a 20% drop in isotopic glomerular filtration rate during chemotherapy. The area under the receiver operating characteristic curve was the primary measure to evaluate models. Sensitivity, specificity, and positive and negative predictive values were used to discuss model clinical utility., Results: Of 433 patients assessed in this study, 26.8% developed nephrotoxicity after bleomycin-etoposide-cisplatin treatment. Genomic markers found to be associated with nephrotoxicity were located at NAT1 , NAT2 , and the intergenic region of CNTN6 and CNTN4 . These, in addition to previously associated markers located at ERCC1 , ERCC2 , and SLC22A2 , were found to improve predictions in a clinical feature-trained random forest model. Using only clinical data for training the model, an area under the receiver operating characteristic curve of 0.635 (95% confidence interval [CI] = 0.629 to 0.640) was obtained. Retraining the classifier by adding genomics markers increased performance to 0.731 (95% CI = 0.726 to 0.736) and 0.692 (95% CI = 0.688 to 0.696) on the holdout set., Conclusions: A clinical and genomics-based machine learning algorithm improved the ability to identify patients at risk of nephrotoxicity compared with using clinical variables alone. Novel genetics associations with cisplatin-induced nephrotoxicity were found for NAT1 , NAT2 , CNTN6 , and CNTN4 that require replication in larger studies before application to clinical practice., (© The Author(s) 2020. Published by Oxford University Press.)

Climate change scenarios anticipate decreased spring snow cover in boreal and subarctic regions. Forest lakes are abundant in these regions and substantial contributors of methane emissions. To investigate the effect of reduced snow cover, we experimentally removed snow from an anoxic frozen lake. We observed that the removal of snow increased light penetration through the ice, increasing water temperature and modifying microbial composition in the different depths. Chlorophyll a and b concentrations increased in the upper water column, suggesting activation of algal primary producers. At the same time, Chlorobiaceae , one of the key photosynthetic bacterial families in anoxic lakes, shifted to lower depths. Moreover, a decrease in the relative abundance of methanotrophs within the bacterial family Methylococcaceae was detected, concurrent with an increase in methane concentration in the water column. These results indicate that decreased snow cover impacts both primary production and methane production and/or consumption, which may ultimately lead to increased methane emissions after spring ice off. IMPORTANCE Small lakes are an important source of greenhouse gases in the boreal zone. These lakes are severely impacted by the winter season, when ice and snow cover obstruct gas exchange between the lake and the atmosphere and diminish light availability in the water column. Currently, climate change is resulting in reduced spring snow cover. A short-term removal of the snow from the ice stimulated algal primary producers and subsequently heterotrophic bacteria. Concurrently, the relative abundance of methanotrophic bacteria decreased and methane concentrations increased. Our results increase the general knowledge of microbial life under ice and, specifically, the understanding of the potential impact of climate change on boreal lakes., (Copyright © 2019 Garcia et al.)

Freshwater lakes harbor complex microbial communities, but these ecosystems are often dominated by acI Actinobacteria Members of this cosmopolitan lineage are proposed to bolster heterotrophic growth using phototrophy because their genomes encode actino-opsins ( actR ). This model has been difficult to validate experimentally because acI Actinobacteria are not consistently culturable. Based primarily on genomes from single cells and metagenomes, we provide a detailed biosynthetic route for members of acI clades A and B to synthesize retinal and its carotenoid precursors. Consequently, acI cells should be able to natively assemble light-driven actinorhodopsins (holo-ActR) to pump protons, unlike many bacteria that encode opsins but may need to exogenously obtain retinal because they lack retinal machinery. Moreover, we show that all acI clades contain genes for a secondary branch of the carotenoid pathway, implying synthesis of a complex carotenoid. Transcription analysis of acI Actinobacteria in a eutrophic lake shows that all retinal and carotenoid pathway operons are transcribed and that actR is among the most highly transcribed of all acI genes. Furthermore, heterologous expression of acI retinal pathway genes showed that lycopene, retinal, and ActR can be made using the genes encoded in these organisms. Model cells producing ActR and the key acI retinal-producing β-carotene oxygenase formed holo-ActR and acidified solution during illumination. Taken together, our results prove that acI Actinobacteria containing both ActR and acI retinal production machinery have the capacity to natively synthesize a green light-dependent outward proton-pumping rhodopsin. IMPORTANCE Microbes play critical roles in determining the quality of freshwater ecosystems, which are vital to human civilization. Because acI Actinobacteria are ubiquitous and abundant in freshwater lakes, clarifying their ecophysiology is a major step in determining the contributions that they make to nitrogen and carbon cycling. Without accurate knowledge of these cycles, freshwater systems cannot be incorporated into climate change models, ecosystem imbalances cannot be predicted, and policy for service disruption cannot be planned. Our work fills major gaps in microbial light utilization, secondary metabolite production, and energy cycling in freshwater habitats., (Copyright © 2018 American Society for Microbiology.)

Introduction: Occupational noise threatens U.S. worker health and safety and commands a significant financial burden on state and federal government worker compensation programs. Previous studies suggest that hearing conservation programs have contributed to reduced occupational hearing loss for noise-exposed workers. Many military personnel are overexposed to noise and are provided hearing conservation services. Select military branches require all active duty personnel to follow hearing conservation program guidelines, regardless of individual noise exposure. We evaluated the cost-effectiveness of a military hearing conservation program, relative to no intervention, in relation to cases of hearing loss prevented., Methods: We employed cost-effectiveness analytic methods to compare the costs and effectiveness, in terms of hearing loss cases prevented, of a military hearing conservation program relative to no program. We used costs and probability estimates available in the literature and publicly available sources. The effectiveness of the interventions was analyzed based on whether hearing loss occurred over a 20-yr time frame., Results: The incremental cost-effectiveness ratio of the hearing conservation program compared with no intervention was $10,657 per case of hearing loss prevented. Workers were 28% less likely to sustain hearing loss in our model when they received the hearing conservation program compared with no intervention, which reflected the greater effectiveness of the hearing conservation program. Cost-effectiveness results were sensitive to estimated values for the probability of acquiring hearing loss from both interventions and the cost of hearing protection. We performed a Monte Carlo probabilistic sensitivity analysis where we simultaneously varied all the model parameters to their extreme plausible bounds. When we ran 10,000 Monte Carlo iterations, we observed that the hearing conservation program was more cost-effective in 99% of cases when decision makers were willing to pay $64,172 per case of hearing loss prevented., Conclusions: Conceding a lifetime cost for service-related compensation for hearing loss per individual of $64,172, the Department of Defense Hearing Conservation Program is an economically reasonable program relative to no intervention, if a case of hearing loss avoided costs $10,657. Considering the net difference of the costs and comparative benefits of both treatment strategies, providing a hearing conservation program for all active duty military workers may be a cost-effective intervention for the Department of Defense., (© Association of Military Surgeons of the United States 2018. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members., (Copyright © 2018 Garcia et al.)

To understand the forces driving differentiation and diversification in wild bacterial populations, we must be able to delineate and track ecologically relevant units through space and time. Mapping metagenomic sequences to reference genomes derived from the same environment can reveal genetic heterogeneity within populations, and in some cases, be used to identify boundaries between genetically similar, but ecologically distinct, populations. Here we examine population-level heterogeneity within abundant and ubiquitous freshwater bacterial groups such as the acI Actinobacteria and LD12 Alphaproteobacteria (the freshwater sister clade to the marine SAR11) using 33 single-cell genomes and a 5-year metagenomic time series. The single-cell genomes grouped into 15 monophyletic clusters (termed "tribes") that share at least 97.9% 16S rRNA identity. Distinct populations were identified within most tribes based on the patterns of metagenomic read recruitments to single-cell genomes representing these tribes. Genetically distinct populations within tribes of the acI Actinobacterial lineage living in the same lake had different seasonal abundance patterns, suggesting these populations were also ecologically distinct. In contrast, sympatric LD12 populations were less genetically differentiated. This suggests that within one lake, some freshwater lineages harbor genetically discrete (but still closely related) and ecologically distinct populations, while other lineages are composed of less differentiated populations with overlapping niches. Our results point at an interplay of evolutionary and ecological forces acting on these communities that can be observed in real time.

An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the "seed set framework," which computes the set of compounds that an organism must acquire from its environment (E. Borenstein, M. Kupiec, M. W. Feldman, and E. Ruppin, Proc Natl Acad Sci U S A 105:14482-14487, 2008, https://doi.org/10.1073/pnas.0806162105), enables computational analysis of metabolic reconstructions while providing new insights into a microbe's metabolic capabilities, such as nutrient use and auxotrophies. We apply this framework to members of the ubiquitous freshwater actinobacterial lineage acI, confirming and extending previous experimental and genomic observations implying that acI bacteria are heterotrophs reliant on peptides and saccharides. We also present the first metatranscriptomic study of the acI lineage, revealing high expression of transport proteins and the light-harvesting protein actinorhodopsin. Putative transport proteins complement predictions of nutrients and essential metabolites while providing additional support of the hypothesis that members of the acI are photoheterotrophs. IMPORTANCE The metabolic activity of uncultivated microorganisms contributes to numerous ecosystem processes, ranging from nutrient cycling in the environment to influencing human health and disease. Advances in sequencing technology have enabled the assembly of genomes for these microorganisms, but our ability to generate reference genomes far outstrips our ability to analyze them. Common approaches to analyzing microbial metabolism require reconstructing the entirety of an organism's metabolic pathways or performing targeted searches for genes involved in a specific process. This paper presents a third approach, in which draft metabolic reconstructions are used to identify compounds through which an organism may interact with its environment. These compounds can then guide more-intensive metabolic reconstruction efforts and can also provide new hypotheses about the specific contributions that microbes make to ecosystem-scale metabolic processes.

Background: We developed a DVD training tool to educate physicians evaluating emergency residents on accurate Standardized Direct Observation Assessment Tool (SDOT) application., Objective: Our goal was to assess whether this training video improved attendings' and senior residents' SDOT use., Methods: Participants voluntarily completed SDOT evaluations based on a scripted "test" video. A DVD with "positive" and "negative" scenarios of proper SDOT use was viewed. It included education on appropriate recording of 26 behaviors. The test scenario was viewed again and follow-up SDOTs submitted. Performances by attendings and residents on the pre- and post-test SDOTs were compared., Results: Twenty-six attendings and 26 senior residents participated. Prior SDOT experience was noted for 8 attendings and 11 residents. For 20 anchors, participants recorded observed behaviors with statistically significant difference on one each of the pretest (no. 20; p = 0.034) and post-test (no. 14; p = 0.041) SDOTs. On global competency assessments, pretest medical knowledge (p = 0.016) differed significantly between groups. The training intervention changed one anchor (no. 5; p = 0.035) and one global assessment (systems-based practice; p = 0.031) more negatively for residents. Recording SDOTs with exact agreement occurred 48.73% for attendings pretest and 54.41% post-test; resident scores were 45.86% and 49.55%, respectively. DVD exposure slightly raised attending scores (p = 0.289) and significantly lowered resident scores (p = 0.046)., Conclusions: Exposure to an independently developed SDOT training video tended to raise attending scores, though without significance, while at the same time lowered senior resident scores statistically significantly. Emergency attendings' and senior residents' SDOT scoring rarely differed with significance; about half of anchor behaviors were recorded with exact agreement. This suggests senior residents, with appropriate education, may participate in SDOT assessment., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Azithromycin is a commonly prescribed antibiotic but is not considered a common etiologic agent for Stevens-Johnson syndrome (SJS). SJS is a dermatologic emergency that occurs within a spectrum of severity and can result in severe morbidity and mortality.

Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to 'social' interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring 'interactomes' and to overcome our inability to isolate and grow the microbes dominating in nature., (© 2015 John Wiley & Sons Ltd.)

Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di- and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.