RESUMEN
In shotgun metagenomics (SM), the state-of-the-art bioinformatic workflows are referred to as high-resolution shotgun metagenomics (HRSM) and require intensive computing and disk storage resources. While the increase in data output of the latest iteration of high-throughput DNA sequencing systems can allow for unprecedented sequencing depth at a minimal cost, adjustments in HRSM workflows will be needed to properly process these ever-increasing sequence datasets. One potential adaptation is to generate so-called shallow SM datasets that contain fewer sequencing data per sample as compared with the more classic high coverage sequencing. While shallow sequencing is a promising avenue for SM data analysis, detailed benchmarks using real-data are lacking. In this case study, we took four public SM datasets, one massive and the others moderate in size and subsampled each dataset at various levels to mimic shallow sequencing datasets of various sequencing depths. Our results suggest that shallow SM sequencing is a viable avenue to obtain sound results regarding microbial community structures and that high-depth sequencing does not bring additional elements for ecological interpretation. More specifically, results obtained by subsampling as little as 0.5 M sequencing clusters per sample were similar to the results obtained with the largest subsampled dataset for human gut and agricultural soil datasets. For an Antarctic dataset, which contained only a few samples, 4 M sequencing clusters per sample was found to generate comparable results to the full dataset. One area where ultra-deep sequencing and maximizing the usage of all data was undeniably beneficial was in the generation of metagenome-assembled genomes.
Asunto(s)
Metagenómica , Microbiota , Humanos , Análisis de Secuencia de ADN/métodos , Metagenómica/métodos , Metagenoma , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Microbiota/genéticaRESUMEN
In 1999, a tidal wetland located along the St. Lawrence River close to Ste. Croix de Lotbinière (Quebec, Eastern Canada) was the site of an experimental oil spill. Test plots were established and subjected to an experimental crude oil spill to evaluate natural attenuation, nutrient amendment and vegetation cropping as countermeasures. In 2020, this study re-visited the test plots to investigate residual oil and habitat recovery. Only concentrations of mid-chain length n-alkanes (C10-C36), but not of polycyclic aromatic hydrocarbons (PAHs), were significantly above detection limit, and were detected in both test plot and control sediments. Hydrocarbon, total organic carbon, nitrogen and phosphate contents did not differ significantly between test plot and control sediments. Microbial analyses did not detect significant differences in microbial load, microbial diversity or microbial community composition between test plot and control sediments. Key genes for the aerobic and anaerobic degradation of n-alkanes as well as for the aerobic degradation of PAHs were detected in all sediment samples. Associated gene abundances did not differ significantly between test plot and control sediments. This study shows that oil-exposed test plot sediments of the Ste. Croix wetland can be considered completely recovered after 21 years irrespective of the performed countermeasure.
Asunto(s)
Microbiota , Contaminación por Petróleo , Petróleo , Hidrocarburos Policíclicos Aromáticos , Contaminantes Químicos del Agua , Contaminación por Petróleo/análisis , Ríos , Humedales , Petróleo/análisis , Sedimentos Geológicos/análisis , Contaminantes Químicos del Agua/análisis , Hidrocarburos Policíclicos Aromáticos/análisis , Alcanos/análisis , Monitoreo del AmbienteRESUMEN
With an on-going disproportional warming of the Arctic Ocean and the reduction of the sea ice cover, the risk of an accidental oil spill from ships or future oil exploration is increasing. It is hence important to know how crude oil weathers in this environment and what factors affect oil biodegradation in the Arctic. However, this topic is currently poorly studied. In the 1980s, the Baffin Island Oil Spill (BIOS) project carried out a series of simulated oil spills in the backshore zone of beaches located on Baffin Island in the Canadian High Arctic. In this study two BIOS sites were re-visited, offering the unique opportunity to study the long-term weathering of crude oil under Arctic conditions. Here we show that residual oil remains present at these sites even after almost four decades since the original oiling. Oil at both BIOS sites appears to have attenuated very slowly with estimated loss rates of 1.8-2.7% per year. The presence of residual oil continues to significantly affect sediment microbial communities at the sites as manifested by a significantly decreased diversity, differences in the abundance of microorganisms and an enrichment of putative oil-degrading bacteria in oiled sediments. Reconstructed genomes of putative oil degraders suggest that only a subset is specifically adapted for growth under psychrothermic conditions, further reducing the time for biodegradation during the already short Arctic summers. Altogether, this study shows that crude oil spilled in the Arctic can persist and significantly affect the Arctic ecosystem for a long time, in the order of several decades.
Asunto(s)
Contaminación por Petróleo , Petróleo , Petróleo/metabolismo , Ecosistema , Canadá , Regiones Árticas , Biodegradación AmbientalRESUMEN
BACKGROUND: An increasing proportion of patients are undergoing total hip arthroplasty (THA) for osteonecrosis (ON). Comorbid conditions and surgical risk factors are known to be greater in ON patients compared with patients who have osteoarthritis (OA) alone. The purpose of our study was to quantify the specific in-hospital complications and resource utilization associated with patients undergoing THA for ON versus OA. METHODS: A large national database was queried to identify patients undergoing primary THA from January 1, 2016 to December 31, 2019. A total of 1,383,880 OA, 21,080 primary ON, and 54,335 secondary ON patients were identified. Demographics, in-hospital complications, costs, lengths of stay, and discharge dispositions for primary and secondary ON cohorts were compared to OA only. Age, race, ethnicity, comorbidities, Medicaid, and income status were controlled with binary logistic regression analyses. RESULTS: The ON patients were often younger, African American or Hispanic, and had more comorbidities. Those undergoing THA for primary and secondary ON had a significantly higher risk of perioperative complications, including myocardial infarction, postoperative blood transfusion, and intraoperative bleeding. Total hospital costs and lengths of stay were significantly higher for both primary ON and secondary ON and both cohorts were less likely to be discharged home. CONCLUSION: While rates of most complications have decreased over recent decades in ON patients undergoing THA, the ON patients still have worse outcomes even when controlling for comorbidity differences. Bundled payment systems and perioperative management strategies for these different patient cohorts should be considered separately.
Asunto(s)
Artroplastia de Reemplazo de Cadera , Osteoartritis , Osteonecrosis , Estados Unidos/epidemiología , Humanos , Artroplastia de Reemplazo de Cadera/efectos adversos , Osteoartritis/cirugía , Comorbilidad , Factores de Riesgo , Hospitales , Osteonecrosis/epidemiología , Osteonecrosis/etiología , Osteonecrosis/cirugía , Complicaciones Posoperatorias/epidemiología , Complicaciones Posoperatorias/etiología , Complicaciones Posoperatorias/cirugía , Tiempo de Internación , Estudios RetrospectivosRESUMEN
The global increase in marine transportation of dilbit (diluted bitumen) can increase the risk of spills, and the application of chemical dispersants remains a common response practice in spill events. To reliably evaluate dispersant effects on dilbit biodegradation over time, we set large-scale (1,500 mL) microcosms without nutrient addition using a low dilbit concentration (30 ppm). Shotgun metagenomics and metatranscriptomics were deployed to investigate microbial community responses to naturally and chemically dispersed dilbit. We found that the large-scale microcosms could produce more reproducible community trajectories than small-scale (250 mL) ones based on the 16S rRNA gene amplicon sequencing. In the early-stage large-scale microcosms, multiple genera were involved in the biodegradation of dilbit, while dispersant addition enriched primarily Alteromonas and competed for the utilization of dilbit, causing depressed degradation of aromatics. The metatranscriptomic-based metagenome-assembled genomes (MAG) further elucidated early-stage microbial antioxidation mechanism, which showed that dispersant addition triggered the increased expression of the antioxidation process genes of Alteromonas species. Differently, in the late stage, the microbial communities showed high diversity and richness and similar compositions and metabolic functions regardless of dispersant addition, indicating that the biotransformation of remaining compounds can occur within the post-oil communities. These findings can guide future microcosm studies and the application of chemical dispersants for responding to a marine dilbit spill. IMPORTANCE In this study, we employed microcosms to study the effects of marine dilbit spill and dispersant application on microbial community dynamics over time. We evaluated the impacts of microcosm scale and found that increasing the scale is beneficial for reducing community stochasticity, especially in the late stage of biodegradation. We observed that dispersant application suppressed aromatics biodegradation in the early stage (6 days), whereas exerting insignificant effects in the late stage (50 days), from both substance removal and metagenomic/metatranscriptomic perspectives. We further found that Alteromonas species are vital for the early-stage chemically dispersed oil biodegradation and clarified their degradation and antioxidation mechanisms. These findings help us to better understand microcosm studies and microbial roles for biodegrading dilbit and chemically dispersed dilbit and suggest that dispersant evaluation in large-scale systems and even through field trails would be more realistic after marine oil spill response.
Asunto(s)
Contaminación por Petróleo , Petróleo , Contaminantes Químicos del Agua , Biodegradación Ambiental , Metagenoma , Metagenómica , Petróleo/metabolismo , Contaminación por Petróleo/análisis , ARN Ribosómico 16S/genética , Agua de Mar/química , Contaminantes Químicos del Agua/análisisRESUMEN
AIMS: This study evaluated changes in epiphytic microbial population of alfalfa (Medicago sativa) during the growing season. First cut forage was harvested to study the effects of an inoculant combining two obligate heterofermentative lactic acid bacteria strains on the bacterial and fungal communities and the fermentation of alfalfa silage. METHODS AND RESULTS: The epiphytic microbiome of alfalfa was evaluated 10-times during the growing season. Alfalfa wilted to 395.0 g/kg was treated with water (Control) or with a combination of L. buchneri NCIMB 40788 and L. hilgardii CNCM-I-4785 (LBLH). Mini-silos were opened after 1, 4, 8, 16, 32, and 64 days of ensiling. The relative abundance (RA) of the epiphytic bacterial and fungal families varied during the growing season. After 1 day, Weissella was the most abundant genus and present at similar RA in the two treatments (average 80.4%). Compared with Control, LBLH had a higher RA of Lactobacillus at day 1, 16, 32, and 64, and a lower RA of Weissella from day 8 to 64. Control contained more bacteria belonging to the Enterobacteriales than LBLH up to day 16. Inoculated silage had more acetate than Control at day 32 and 64. The fungal population were similar between treatments. The enhanced development and dominance of Lactobacillus in inoculated silage led to greater accumulation of acetate and propionate, which reduced the numbers of culturable yeasts but did not markedly affect the fungal community structure. CONCLUSIONS: The bacterial community composition of alfalfa stands in the filed changed over time and was affected by cutting. For the ensiling trial, inoculation modified the composition of the bacterial community of alfalfa, increasing the RA of Lactobacillus while reducing the RA of Weissella and of Enterobacteriaceae. SIGNIFICANCE AND IMPACT OF STUDY: Inoculation increased the RA of Lactobacillus, hampering the dominance of Weissella in the early stages of ensiling, improving antifungal compounds production and reducing the numbers of culturable yeasts.
Asunto(s)
Medicago sativa , Microbiota , Antifúngicos , Bacterias/genética , Fermentación , Humanos , Lactobacillus , Medicago sativa/microbiología , Propionatos , Estaciones del Año , Ensilaje/microbiología , Agua , LevadurasRESUMEN
Rhizodegradation is a promising cleanup technology where microorganisms degrade soil contaminants in the rhizosphere. A symbiotic relationship is expected to occur between plant roots and soil microorganisms in contaminated soils that enhances natural microbial degradation. However, little is known about how different initial microbiotas influence the rhizodegradation outcome. Recent studies have hinted that soil initial diversity has a determining effect on the outcome of contaminant degradation. To test this, we either planted (P) or not (NP) balsam poplars (Populus balsamifera) in two soils of contrasting diversity (agricultural and forest) that were contaminated or not with 50 mg kg-1 of phenanthrene (PHE). The DNA from the rhizosphere of the P and the bulk soil of the NP pots was extracted and the bacterial genes encoding the 16S rRNA, the PAH ring-hydroxylating dioxygenase alpha subunits (PAH-RHDα) of Gram-positive and Gram-negative bacteria, and the fungal ITS region were sequenced to characterize the microbial communities. The abundances of the PAH-RHDα genes were quantified by real-time quantitative PCR. Plant presence had a significant effect on PHE degradation only in the forest soil, whereas both NP and P agricultural soils degraded the same amount of PHE. Fungal communities were mainly affected by plant presence, whereas bacterial communities were principally affected by the soil type, and upon contamination the dominant PAH-degrading community was similarly constrained by soil type. Our results highlight the crucial importance of soil microbial and physicochemical characteristics in the outcome of rhizoremediation.IMPORTANCE Polycyclic aromatic hydrocarbons (PAH) are a group of organic contaminants that pose a risk to ecosystems' health. Phytoremediation is a promising biotechnology with the potential to restore PAH-contaminated soils. However, some limitations prevent it from becoming the remediation technology of reference, despite being environmentally friendlier than mainstream physicochemical alternatives. Recent reports suggest that the original soil microbial diversity is the key to harnessing the potential of phytoremediation. Therefore, this study focused on determining the effect of two different soil types in the fate of phenanthrene (a polycyclic aromatic hydrocarbon) under balsam poplar remediation. Poplar increased the degradation of phenanthrene in forest, but not in agricultural soil. The fungi were affected by poplars, whereas total bacteria and specific PAH-degrading bacteria were constrained by soil type, leading to different degradation patterns between soils. These results highlight the importance of performing preliminary microbiological studies of contaminated soils to determine whether plant presence could improve remediation rates or not.
Asunto(s)
Fenantrenos/metabolismo , Populus , Rizosfera , Microbiología del Suelo , Contaminantes del Suelo/metabolismo , Agricultura , Bacterias/genética , Biodegradación Ambiental , Bosques , Hongos/genética , Microbiota/genética , ARN Ribosómico 16S/genética , Suelo/químicaRESUMEN
Microbial communities are an important aspect of overall riverine ecology; however, appreciation of the effects of anthropogenic activities on unique riverine microbial niches, and how the collection of these samples affects the observed diversity and community profile is lacking. We analyzed prokaryotic and eukaryotic communities from surface water, biofilms, and suspended load niches along a gradient of oil sands-related contamination in the Athabasca River (Alberta, Canada), with suspended load or particle-associated communities collected either via Kenney Sampler or centrifugation manifold. At the phylum level, different niche communities were highly similar to each other and across locations. However, there were significant differences in the abundance of specific genera among the different niches and across sampling locations. A generalized linear model revealed that use of the Kenney Sampler resulted in more diverse bacterial and eukaryotic suspended load community than centrifugal collection, though suspended load communities collected by any means remained stably diverse across locations. Although there was an influence of water quality parameters on community composition, all sampled sites support diverse bacterial and eukaryotic communities regardless of the degree of contamination, highlighting the need to look beyond ecological diversity as a means of assessing ecological perturbations, and consider collecting samples from multiple niche environments.
Asunto(s)
Ríos , Contaminantes Químicos del Agua , Alberta , Monitoreo del Ambiente , Eucariontes/genética , Minería , Yacimiento de Petróleo y Gas , Contaminantes Químicos del Agua/análisisRESUMEN
Soil microorganisms play a critical role in the biosphere, and the influence of cropland fertilization on the evolution of soil as a living entity is being actively documented. In this study, we used a shotgun metagenomics approach to globally expose the effects of 50-year N and P fertilization of wheat on soil microbial community structure and function, and their potential involvement in overall N cycling. Nitrogen (N) fertilization increased alpha diversity in archaea and fungi while reducing it in bacteria. Beta diversity of archaea, bacteria and fungi, as well as soil function, were also mainly driven by N fertilization. The abundance of archaea was negatively impacted by N fertilization while bacterial and fungal abundance was increased. The responses of N metabolism-related genes to fertilization differed in archaea, bacteria and fungi. All archaeal N metabolic processes were decreased by N fertilization, while denitrification, assimilatory nitrate reduction and organic-N metabolism were highly increased by N fertilization in bacteria. Nitrate assimilation was the main contribution of fungi to N cycling. Thaumarchaeota and Halobacteria in archaea; Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria in bacteria; and Sordariomycetes in fungi participated dominantly and widely in soil N metabolic processes.
Asunto(s)
Microbiota/efectos de los fármacos , Nitrógeno/farmacología , Fósforo/farmacología , Microbiología del Suelo , Triticum/microbiología , Archaea/efectos de los fármacos , Archaea/fisiología , Fenómenos Fisiológicos Bacterianos/efectos de los fármacos , Biodiversidad , Fertilizantes , Hongos/efectos de los fármacos , Hongos/fisiología , Estudios Longitudinales , Suelo/química , Triticum/crecimiento & desarrolloRESUMEN
Oil biodegradation has been extensively studied in the wake of the deepwater horizon spill, but the application of dispersant to oil spills in marine environments remains controversial. Here, we report metagenomic (MG) and metatranscriptomic (MT) data mining from microcosm experiments investigating the oil degrading potential of Canadian west and east coasts to estimate the gene abundance and activity of oil degrading bacteria in the presence of dispersant. We found that the addition of dispersant to crude oil mainly favours the abundance of Thalassolituus in the summer and Oleispira in the winter, two key natural oil degrading bacteria. We found a high abundance of genes related not only to n-alkane and aromatics degradation but also associated with transporters, two-component systems, bacterial motility, secretion systems and bacterial chemotaxis.
Asunto(s)
Biodegradación Ambiental , Oceanospirillaceae/genética , Oceanospirillaceae/metabolismo , Contaminación por Petróleo/análisis , Petróleo/metabolismo , Alcanos/metabolismo , Canadá , Metagenoma/genética , Agua de Mar/microbiología , Contaminantes Químicos del Agua/metabolismoRESUMEN
Western Canada produces large amounts of bitumen, a heavy, highly weathered crude oil. Douglas Channel and Hecate Strait on the coast of British Columbia are two water bodies that may be impacted by a proposed pipeline and marine shipping route for diluted bitumen (dilbit). This study investigated the potential of microbial communities from these waters to mitigate the impacts of a potential dilbit spill. Microcosm experiments were set up with water samples representing different seasons, years, sampling stations, and dilbit blends. While the alkane fraction of the tested dilbit blends was almost completely degraded after 28 days, the majority of the polycyclic aromatic hydrocarbons (PAHs) remained. The addition of the dispersant Corexit 9500A most often had either no effect or an enhancing effect on dilbit degradation. Dilbit-degrading microbial communities were highly variable between seasons, years, and stations, with dilbit type having little impact on community trajectories. Potential oil-degrading genera showed a clear succession pattern and were for the most part recruited from the "rare biosphere." At the community level, dispersant appeared to stimulate an accelerated enrichment of genera typically associated with hydrocarbon degradation, even in dilbit-free controls. This suggests that dispersant-induced growth of hydrocarbon degraders (and not only increased bioavailability of oil-associated hydrocarbons) contributes to the degradation-enhancing effect previously reported for Corexit 9500A.IMPORTANCE Western Canada hosts large petroleum deposits, which ultimately enter the market in the form of dilbit. Tanker-based shipping represents the primary means to transport dilbit to international markets. With anticipated increases in production to meet global energy needs, the risk of a dilbit spill is expected to increase. This study investigated the potential of microbial communities naturally present in the waters of a potential dilbit shipping lane to mitigate the effects of a spill. Here we show that microbial degradation of dilbit was mostly limited to n-alkanes, while the overall concentration of polycyclic aromatic hydrocarbons, which represent the most toxic fraction of dilbit, decreased only slightly within the time frame of our experiments. We further investigated the effect of the oil dispersant Corexit 9500A on microbial dilbit degradation. Our results highlight the fact that dispersant-associated growth stimulation, and not only increased bioavailability of hydrocarbons and inhibition of specific genera, contributes to the overall effect of dispersant addition.
Asunto(s)
Bacterias/metabolismo , Hidrocarburos/análisis , Contaminación por Petróleo/análisis , Contaminantes Químicos del Agua/análisis , Biodegradación Ambiental , Colombia Británica , Agua de Mar/análisisRESUMEN
Serratia marcescens is an environmental bacterium that is commonly associated with outbreaks in neonatal intensive care units (NICUs). Investigations of S. marcescens outbreaks require efficient recovery and typing of clinical and environmental isolates. In this study, we investigated how the use of next-generation sequencing applications, such as bacterial whole-genome sequencing (WGS) and bacterial community profiling, could improve S. marcescens outbreak investigations. Phylogenomic links and potential antibiotic resistance genes and plasmids in S. marcescens isolates were investigated using WGS, while bacterial communities and relative abundances of Serratia in environmental samples were assessed using sequencing of bacterial phylogenetic marker genes (16S rRNA and gyrB genes). Typing results obtained using WGS for the 10 S. marcescens isolates recovered during a NICU outbreak investigation were highly consistent with those obtained using pulsed-field gel electrophoresis (PFGE), the current standard typing method for this bacterium. WGS also allowed the identification of genes associated with antibiotic resistance in all isolates, while no plasmids were detected. Sequencing of the 16S rRNA and gyrB genes both showed greater relative abundances of Serratia at environmental sampling sites that were in close contact with infected babies. Much lower relative abundances of Serratia were observed following disinfection of a room, indicating that the protocol used was efficient. Variations in the bacterial community composition and structure following room disinfection and among sampling sites were also identified through 16S rRNA gene sequencing. Together, results from this study highlight the potential for next-generation sequencing tools to improve and to facilitate outbreak investigations.
Asunto(s)
Infección Hospitalaria/epidemiología , Infección Hospitalaria/microbiología , Brotes de Enfermedades , Técnicas de Diagnóstico Molecular/métodos , Infecciones por Serratia/epidemiología , Infecciones por Serratia/microbiología , Serratia marcescens/aislamiento & purificación , ADN Bacteriano/genética , Electroforesis en Gel de Campo Pulsado/normas , Femenino , Marcadores Genéticos/genética , Genoma Bacteriano/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Lactante , Recién Nacido , Unidades de Cuidado Intensivo Neonatal , Masculino , Quebec/epidemiología , Análisis de Secuencia de ADN , Serratia marcescens/clasificación , Serratia marcescens/genéticaRESUMEN
Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation. Colonization of the root occurs despite a sophisticated plant immune system, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments from both soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plant-microbe interactions derived from complex soil communities.
Asunto(s)
Arabidopsis/microbiología , Endófitos/clasificación , Endófitos/aislamiento & purificación , Metagenoma , Raíces de Plantas/microbiología , Microbiología del Suelo , Actinobacteria/genética , Actinobacteria/aislamiento & purificación , Arabidopsis/clasificación , Arabidopsis/crecimiento & desarrollo , Endófitos/genética , Genotipo , Hibridación Fluorescente in Situ , Raíces de Plantas/clasificación , Raíces de Plantas/crecimiento & desarrollo , Proteobacteria/genética , Proteobacteria/aislamiento & purificación , ARN Ribosómico 16S/genética , ARN Ribosómico 16S/aislamiento & purificación , Rizosfera , Ribotipificación , Análisis de Secuencia de ADN , SimbiosisRESUMEN
The enrichment of H2-oxidizing bacteria (HOB) by H2 generated by nitrogen-fixing nodules has been shown to have a fertilization effect on several different crops. The benefit of HOB is attributed to their production of plant growth-promoting factors, yet their interactions with other members of soil microbial communities have received little attention. Here we report that the energy potential of H2, when supplied to soil, alters ecological niche partitioning of bacteria and fungi, with multifaceted consequences for both generalist and specialist microbial functions. We used dynamic microcosms to expose soil to the typical atmospheric H2 mixing ratio (0.5 ppmv) permeating soils, as well as mixing ratios comparable to those found at the soil-nodule interface (10,000 ppmv). Elevated H2 exposure exerted direct effects on two HOB subpopulations distinguished by their affinity for H2 while enhancing community level carbon substrate utilization potential and lowering CH4 uptake activity in soil. We found that H2 triggered changes in the abundance of microorganisms that were reproducible yet inconsistent across soils at the taxonomic level and even among HOB. Overall, H2 exposure altered microbial process rates at an intensity that depends upon soil abiotic and biotic features. We argue that further examination of direct and indirect effects of H2 on soil microbial communities will lead to a better understanding of the H2 fertilization effect and soil biogeochemical processes.IMPORTANCE An innovative dynamic microcosm chamber system was used to demonstrate that H2 diffusing in soil triggers changes in the distribution of HOB and non-HOB. Although the response was uneven at the taxonomic level, an unexpected coordinated response of microbial functions was observed, including abatement of CH4 oxidation activity and stimulation of carbon turnover. Our work suggests that elevated H2 rewires soil biogeochemical structure through a combination of direct effects on the growth and persistence of HOB and indirect effects on a variety of microbial processes involving HOB and non-HOB.
Asunto(s)
Bacterias/metabolismo , Biodiversidad , Hongos/aislamiento & purificación , Hidrógeno/metabolismo , Microbiología del Suelo , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Hongos/clasificación , Hongos/genética , Hongos/metabolismo , Nitrógeno/metabolismo , Oxidación-Reducción , Filogenia , Suelo/químicaRESUMEN
The aim of this study is to obtain a systems-level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of Dehalococcoides was upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions.IMPORTANCE The key chloroethene-dechlorinating bacterium Dehalococcoides mccartyi is a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions between Dehalococcoides and the corrinoid-providing microorganisms in a community. This study provides systems-level information, i.e., taxonomic and functional compositions and dynamics of the supportive microorganisms in dechlorinating communities under different cobalamin conditions. The findings shed light on the important roles of Veillonellaceae species in the communities compared to other coexisting community members in producing and providing corrinoids for Dehalococcoides species under cobalamin-limited conditions.
Asunto(s)
Chloroflexi/genética , Chloroflexi/metabolismo , Perfilación de la Expresión Génica , Metagenómica , Consorcios Microbianos , Vitamina B 12/metabolismo , Bacterias/metabolismo , Biodegradación Ambiental , Vías Biosintéticas/genética , Chloroflexi/efectos de los fármacos , Corrinoides/metabolismo , Genoma Bacteriano , Halogenación , Consorcios Microbianos/efectos de los fármacos , Consorcios Microbianos/genética , Tricloroetileno/metabolismo , Veillonellaceae/genética , Veillonellaceae/metabolismo , Vitamina B 12/farmacologíaRESUMEN
Introduction: Social determinants of health (SDOH) are fundamental causes of poor cardiovascular health, yet cardiovascular disease (CVD) risk assessment tools exclude SDOH. Our objective was to determine whether SDOH are independently associated with CVD risk in US adults. Methods: Utilizing the National Health and Nutrition Examination Survey (NHANES), we combined years 1999-2018 and included participants aged 40-79 without history of CVD and with information to calculate CVD risk (n = 21,694). Ten-year risk of atherosclerotic CVD (ASCVD) was calculated using the American Heart Association/American College of Cardiology (AHA/ACC) pooled cohort equations. We used linear regression models to estimate the association between SDOH and ASCVD risk, after adjusting for demographic factors. All analyses accounted for the complex survey design. Results: Mean age was 54.7 years, with 52.7 % female, 73.8 % non-Hispanic White, 9.4 % non-Hispanic Black, and 10.7 % Hispanic. From adjusted models, compared with an income of ≥ $75 K, ASCVD risk was greater by 3.06 (95 % CI: 2.65, 3.47) among those with income < $25 K, by 1.55 (95 % CI: 1.21, 1.89) among those with income $25 K-<$55 K, and by 1.20 (95 % CI: 0.84, 1.56) among those with income $55 K-<$75 K. Compared to college graduates, ASCVD risk was greater by 3.09 (95 % CI: 2.56, 3.62) among those with less than a high school education, by 1.65 (95 % CI: 1.31, 200) among those who were high school graduates, and by 1.41 (95 % CI: 1.11, 1.72) among those with some college education. Conclusion: We found strong graded associations between lower income and lower educational attainment with greater CVD risk.
RESUMEN
Microorganisms can improve plant resistance to drought through various mechanisms, such as the production of plant hormones, osmolytes, antioxidants, and exopolysaccharides. It is, however, unclear how previous exposure to water stress affects the functional capacity of the soil microbial community to help plants resist drought. We compared two soils that had either a continuous or intermittent water stress history (WSH) for almost 40 years. We grew wheat in these soils and subjected it to water stress, after which we collected the rhizosphere soil and shotgun sequenced its metagenome. Wheat growing in soil with an intermittent WSH maintained a higher biomass when subjected to water stress. Genes related to indole-acetic acid and osmolyte production were more abundant in the metagenome of the soil with an intermittent WSH as compared to the soil with a continuous WSH. We suggest that an intermittent WSH selects traits beneficial for life under water stress.
RESUMEN
INTRODUCTION: Among certain immigrant groups, length of time spent living in the United States (LOT) is associated with poor cardiometabolic health. We aimed to evaluate the association between LOT and cardiometabolic outcomes among US Black adults. METHODS: The National Health Interview Survey is an annual representative survey of non-institutionalized US civilians. We combined 2016-2018 data and included all Black adults (N = 10,034). LOT was defined as the number of years lived in the US, if foreign-born. Obesity, hypertension, diabetes, and high cholesterol were each self-reported. We used logistic regression models to determine whether LOT was associated with cardiometabolic health factors overall and by origin subgroups-US-born non-Hispanic, Hispanic, African-born, and Caribbean/Central American (CA)-born groups. RESULTS: Our study population was 81% US-born non-Hispanic, 5% Hispanic (both foreign- and US-born), 6% African-born, and 6% Caribbean/CA-born groups. Among Black adults, compared with the US-born, being foreign-born with < 15 years in the US was associated with lower odds of obesity (OR: 0.31, 95%CI: 0.23-0.42) and hypertension (OR: 0.35, 95%CI: 0.24-0.49). In subgroup analyses, Caribbean/CA-born individuals with < 15 years in the US had 64% lower odds of obesity (OR: 0.36, 95%CI 0.15-0.84) and 63% lower odds of hypertension (OR: 0.37, 95%CI 0.15-0.88) compared with those with ≥ 15 years. CONCLUSION: Shorter LOT was associated with more favorable cardiometabolic health, with differential associations among foreign-born Black adults based on origin. This heterogeneity suggests a need to examine the implications of acculturation in the context of the specific population of interest.
RESUMEN
In this announcement, we present the set of putative terpene synthase (TS) gene fragments detected in a subseafloor sediment sample collected off Shimokita Peninsula, Japan. This data set contains sequences with 72 to 100% identity to TS from actinobacteria and cyanobacteria.