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Viruses Apr 2024Previous studies have identified diverse bacteriophages that infect strain CB15 ranging from small RNA phages to four genera of jumbo phages. In this study, we focus on...
Previous studies have identified diverse bacteriophages that infect strain CB15 ranging from small RNA phages to four genera of jumbo phages. In this study, we focus on 20 bacteriophages whose genomes range from 40 to 60 kb in length. Genome comparisons indicated that these diverse phages represent six phage genera and one additional genus that includes both and phages. Within species, comparisons revealed that both single base changes and inserted or deleted genetic material cause the genomes of closely related phages to diverge. Among genera, the basic gene order and the orientation of key genes were retained with most of the observed variation occurring at ends of the genomes. We hypothesize that the nucleotide sequences of the ends of these phage genomes are less important than the need to maintain the size of the genome and the stability of the corresponding mRNAs.
Topics: Genome, Viral; Bacteriophages; Caulobacter; Phylogeny; Evolution, Molecular; Gene Order
PubMed: 38675982
DOI: 10.3390/v16040641 -
Frontiers in Microbiology 2024Atopic dermatitis (AD) is one of the most common inflammatory skin diseases. Skin microecological imbalance is an important factor in the pathogenesis of AD, but the...
INTRODUCTION
Atopic dermatitis (AD) is one of the most common inflammatory skin diseases. Skin microecological imbalance is an important factor in the pathogenesis of AD, but the underlying mechanism of its interaction with humans remains unclear.
METHODS
16S rRNA gene sequencing was conducted to reveal the skin microbiota dynamics. Changes in skin metabolites were tracked by LC-MS metabolomics. We then explored the potential mechanism of interaction by analyzing the correlation between skin bacterial communities and metabolites in corresponding skin-associated samples.
RESULTS
Samples from 18 AD patients and 18 healthy volunteers (HVs) were subjected to 16S rRNA gene sequencing and LC-MS metabolomics. AD patients had dysbiosis of the skin bacterial community with decreased species richness and evenness. The relative abundance of the genus increased significantly in AD, while the abundances of the genera and decreased significantly. The relative abundance of the genera in healthy females was significantly higher than those in healthy males, while it showed no difference in AD patients with or without lesions. The effects of AD status, sex and the presence or absence of rashes on the number of differentially abundant metabolites were successively reduced. Multiple metabolites involved in purine metabolism and phenylalanine metabolism pathways (such as xanthosine/xanthine and L-phenylalanine/trans-cinnamate) were increased in AD patients. These trends were much more obvious between female AD patients and female HVs. Spearman correlation analysis revealed that the genus was positively correlated with various compounds involved in phenylalanine metabolism and purine metabolic pathways. The genera and were negatively correlated with various compounds involved in purine metabolism, phenylalanine metabolism and sphingolipid signaling pathways.
DISCUSSION
We suggest that purine metabolism and phenylalanine metabolism pathway disorders may play a certain role in the pathogenic mechanism of in AD. We also found that females are more likely to be colonized by the genus than males. Differentially abundant metabolites involved in purine metabolism and phenylalanine metabolism pathways were more obvious in female. However, we should notice that the metabolites we detected do not necessarily derived from microbes, they may also origin from the host.
PubMed: 38559353
DOI: 10.3389/fmicb.2024.1349674 -
Heliyon Mar 2024In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a...
Unlocking water potential in drylands: Quicklime and fly ash enhance soil microbiome structure, ecological networks and function in acid mine drainage water-irrigated agriculture.
In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a significant knowledge gap exists on the short and long-term effects of treated AMD water on soil health. This study used high-throughput Illumina sequencing and predictive metagenomic profiling to investigate the impact of untreated AMD (AMD), quicklime- (A1Q and A2Q) and quicklime and fly ash-treated AMD water (AFQ) irrigation on soil bacterial diversity, co-occurrence networks and function. Results showed that untreated AMD water significantly increased soil acidity, electrical conductivity (EC), sulfate (SO), and heavy metals (HM), including reduced microbial diversity, disrupted interaction networks, and functional capacity. pH, EC, Cu, and Pb were identified as key environmental factors shaping soil microbial diversity and structure. Predominantly, , , KB913035, , and , known for their adaptability to acidic conditions and metal resistance, were abundant in AMD soils. However, soils irrigated with treated AMD water exhibited significantly reduced acidity (pH > 6.5), HM and SO levels, with an enrichment of a balanced bacterial taxa associated with diverse functions related to soil health and agricultural productivity. These taxa included , , , , , , , , , and Moreover, treated AMD water contributed to higher connectivity and balance within soil bacterial co-occurrence networks compared to untreated AMD water. These results show that quicklime/fly ash treatments can help lessen impacts of AMD water on soil microbiome and health, suggesting its potential for irrigated agriculture in water-scarce regions.
PubMed: 38533070
DOI: 10.1016/j.heliyon.2024.e27985 -
Scientific Reports Mar 2024Health implications of indoor air quality (IAQ) have drawn more attention since the COVID epidemic. There are many different kinds of studies done on how IAQ affects...
Health implications of indoor air quality (IAQ) have drawn more attention since the COVID epidemic. There are many different kinds of studies done on how IAQ affects people's well-being. There hasn't been much research that looks at the microbiological composition of the aerosol in subway transit systems. In this work, for the first time, we examined the aerosol bacterial abundance, diversity, and composition in the microbiome of the Seoul subway and train stations using DNA isolated from the PM samples from each station (three subway and two KTX stations). The average PM mass concentration collected on the respective platform was 41.862 µg/m, with the highest average value of 45.95 µg/m and the lowest of 39.25 µg/m. The bacterial microbiomes mainly constituted bacterial species of soil and environmental origin (e.g., Acinetobacter, Brevundimonas, Lysinibacillus, Clostridiodes) with fewer from human sources (Flaviflexus, Staphylococcus). This study highlights the relationship between microbiome diversity and PM mass concentration contributed by outdoor air and commuters in South Korea's subway and train stations. This study gives insights into the microbiome diversity, the source, and the susceptibility of public transports in disease spreading.
Topics: Humans; Railroads; Particulate Matter; Air Pollutants; Seoul; Environmental Monitoring; Aerosols
PubMed: 38499557
DOI: 10.1038/s41598-023-49848-x -
Scientific Reports Mar 2024As a typical sub-deep reservoir in the upper reaches of the Yangtze River in the southwest region, Zhangjiayan Reservoir is also an important source of drinking water....
As a typical sub-deep reservoir in the upper reaches of the Yangtze River in the southwest region, Zhangjiayan Reservoir is also an important source of drinking water. Exploring the role of microorganisms in the material cycle of water bodies is of great significance for preventing the exacerbation of eutrophication in the reservoir. In this study, water samples from the overlying water of five points in the reservoir were collected four times in spring (April), summer (July), autumn (November), and winter (January) of 2022-2023 using a gas-tight water sampler. Physicochemical factors were measured, and the microbial community structure was analyzed by high-throughput MiSeq sequencing of the V3-V4 hypervariable region of 16S rRNA gene in order to explore the relationship between physicochemical factors and microbial community structure and the dominant microbial populations that affect eutrophication of the reservoir. The following results were obtained through analysis. Among the 20 overlying water samples from Zhangjiayan Reservoir, a total of 66 phyla, 202 classes, 499 orders, 835 families, 1716 genera, and 27,904 ASVs of the bacterial domain were detected. The phyla Proteobacteria and Actinobacteria were dominant in the microbial community of the overlying water in Zhangjiayan Reservoir. At the genus level, hgcI_clade and Actinobacteria had the highest abundance and was the dominant population. The microbial community in the water of Zhangjiayan Reservoir has a high level of diversity. The diversity index ranked by numerical order was winter > autumn > summer > spring. Significant differences were found in the composition and structure of the microbial community between the spring/summer and autumn/winter seasons (p < 0.05). Total phosphorus, dissolved total phosphorus, soluble reactive phosphorus, and dissolved oxygen have a significant impact on the composition and structure of the microbial community (p < 0.01). The bacterial community in the overlying water of Zhangjiayan Reservoir showed a mainly positive correlation. Sphingomonas, Brevundimonas, and Blastomonas were the central populations of the bacterial community in the overlying water of Zhangjiayan Reservoir. This study indicates that environmental factors, such as phosphorus and other nutrients, have a significant impact on the formation of the microbial community structure in different seasons. Sphingomonas, Brevundimonas, and Blastomonas are key populations that may have a significant impact on eutrophication in Zhangjiayan Reservoir.
Topics: Humans; Seasons; RNA, Ribosomal, 16S; Microbiota; Water; Actinobacteria; Caulobacteraceae; Phosphorus
PubMed: 38448523
DOI: 10.1038/s41598-024-55702-5 -
Scientific Reports Mar 2024In the Anthropocene, plastic pollution has become a new environmental biotope, the so-called plastisphere. In the oceans, nano- and micro-sized plastics are omnipresent...
In the Anthropocene, plastic pollution has become a new environmental biotope, the so-called plastisphere. In the oceans, nano- and micro-sized plastics are omnipresent and found in huge quantities throughout the water column and sediment, and their large surface area-to-volume ratio offers an excellent surface to which hydrophobic chemical pollutants (e.g. petrochemicals and POPs) can readily sorb to. Our understanding of the microbial communities that breakdown plastic-sorbed chemical pollutants, however, remains poor. Here, we investigated the formation of 500 nm and 1000 nm polystyrene (PS) agglomerations in natural seawater from a coastal environment, and we applied DNA-based stable isotope probing (DNA-SIP) with the 500 nm PS sorbed with isotopically-labelled phenanthrene to identify the bacterial members in the seawater community capable of degrading the hydrocarbon. Whilst we observed no significant impact of nanoplastic size on the microbial communities associated with agglomerates that formed in these experiments, these communities were, however, significantly different to those in the surrounding seawater. By DNA-SIP, we identified Arcobacteraceae, Brevundimonas, Comamonas, uncultured Comamonadaceae, Delftia, Sphingomonas and Staphylococcus, as well as the first member of the genera Acidiphilum and Pelomonas to degrade phenanthrene, and of the genera Aquabacterium, Paracoccus and Polymorphobacter to degrade a hydrocarbon. This work provides new information that feeds into our growing understanding on the fate of co-pollutants associated with nano- and microplastics in the ocean.
Topics: Microplastics; Plastics; Polystyrenes; Comamonadaceae; DNA Probes; Environmental Pollutants; Isotopes; Microbiota; Phenanthrenes; DNA
PubMed: 38433255
DOI: 10.1038/s41598-024-55825-9 -
Marine Drugs Feb 2024Marine microorganisms have been demonstrated to be an important source for bioactive molecules. In this paper we report the synthesis of Ni nanoparticles (NiSNPs) used...
Marine microorganisms have been demonstrated to be an important source for bioactive molecules. In this paper we report the synthesis of Ni nanoparticles (NiSNPs) used as reducing and capping agents for five bacterial strains isolated from an Antarctic marine consortium: sp. ef1, sp. ef1, sp. ef1, sp. ef1, and sp. ef1. The NiSNPs were characterized by Ultraviolet-visible (UV-vis) spectroscopy, Dynamic Light Scattering (DLS), Transmission Electron Microscopy (TEM), X-ray diffraction (XRD) and Fourier Transform Infrared (FTIR) spectroscopic analysis. The maximum absorbances in the UV-Vis spectra were in the range of 374 nm to 422 nm, corresponding to the Surface plasmon resonance (SPR) of Nickel. DLS revealed NiSNPs with sizes between 40 and 45 nm. All NiSNPs were polycrystalline with a face-centered cubic lattice, as revealed by XRD analyses. The NiSNPs zeta potential values were highly negative. TEM analysis showed that the NiSNPs were either spherical or rod shaped, well segregated, and with a size between 20 and 50 nm. The FTIR spectra revealed peaks of amino acid and protein binding to the NiSNPs. Finally, all the NiSNPs possess significant antimicrobial activity, which may play an important role in the management of infectious diseases affecting human health.
Topics: Humans; Anti-Bacterial Agents; Silver; Nickel; Antarctic Regions; Metal Nanoparticles; X-Ray Diffraction; Spectroscopy, Fourier Transform Infrared; Plant Extracts
PubMed: 38393060
DOI: 10.3390/md22020089 -
BioMed Research International 2024Chlorpyrifos (CP) is a chlorinated organophosphate pesticide. In Kenya, it is commonly used as an acaricide, particularly in dairy farming, leading to soil and water...
Chlorpyrifos (CP) is a chlorinated organophosphate pesticide. In Kenya, it is commonly used as an acaricide, particularly in dairy farming, leading to soil and water contamination. The study is aimed at isolating bacteria with CP-degrading potential and optimizing their growth conditions, including temperature, pH, and CP concentration. The enrichment culture technique was used, with minimal salt medium (MSM) supplemented with commercial grade CP. A multilevel factorial design was used to investigate the interactions of temperature, pH, and CP concentration. According to the findings, seven bacterial strains with potential to degrade CP were characterized and identified as , , , sp. strain , sp. strain , , and clone 99. Growth and biodegradation of bacteria differed significantly among the isolates across pH value, temperature, and concentrations ( ≤ 0.05). The optimum conditions for growth were pH 7, temperature of 25°C, and 25mg/l chlorpyrifos concentration, while optimum degradation conditions were pH 5, temp 25°C, and CP conc. 25mg/l. The Pearson correlation between optimum growth and degradation showed a weak positive relationship ( = 0.1144) for pH and strong positive relationship for temperature and concentration of chlorpyrifos. Other than pH, the study shows that there could be other cofactors facilitating the chlorpyrifos degradation process. The findings show that an efficient consortium, at 25°C and pH 5, can include and sp. as they showed high optical density (OD) values under these conditions. These results indicate the potential for these bacteria to be employed in chlorpyrifos-contaminated ecosystem detoxification efforts upon manipulation of natural growth conditions. The findings of this study offer a potential foundation for future research into the reconstitution of a consortium. Based on the optimum conditions identified, the isolated bacterial strains could be further developed into a consortium to effectively degrade CP in both laboratory and field conditions. Dairy farmers can utilize the isolated strains and the consortia to decontaminate farm soils.
Topics: Chlorpyrifos; Soil; Farms; Kenya; Ecosystem; Bacteria; Biodegradation, Environmental; Pseudomonas; Soil Microbiology; Bacillus
PubMed: 38304346
DOI: 10.1155/2024/1611871 -
Scientific Reports Feb 2024Extensive research has provided a wealth of data on prokaryotes in caves and their role in biogeochemical cycles. Ice caves in carbonate rocks, however, remain enigmatic...
Extensive research has provided a wealth of data on prokaryotes in caves and their role in biogeochemical cycles. Ice caves in carbonate rocks, however, remain enigmatic environments with limited knowledge of their microbial taxonomic composition. In this study, bacterial and archaeal communities of the Obstans Ice Cave (Carnic Alps, Southern Austria) were analyzed by next-generation amplicon sequencing and by cultivation of bacterial strains at 10 °C and studying their metabolism. The most abundant bacterial taxa were uncultured Burkholderiaceae and Brevundimonas spp. in the drip water, Flavobacterium, Alkanindiges and Polaromonas spp. in the ice, Pseudonocardia, Blastocatella spp., uncultured Pyrinomonadaceae and Sphingomonadaceae in carbonate precipitates, and uncultured Gemmatimonadaceae and Longimicrobiaceae in clastic cave sediments. These taxa are psychrotolerant/psychrophilic and chemoorganotrophic bacteria. On a medium with Mg/Ca = 1 at 21 °C and 10 °C, 65% and 35% of the cultivated strains precipitated carbonates, respectively. The first ~ 200 µm-size crystals appeared 2 and 6 weeks after the start of the cultivation experiments at 21 °C and 10 °C, respectively. The crystal structure of these microbially induced carbonate precipitates and their Mg-content are strongly influenced by the Mg/Ca ratio of the culture medium. These results suggest that the high diversity of prokaryotic communities detected in cryogenic subsurface environments actively contributes to carbonate precipitation, despite living at the physical limit of the presence of liquid water.
Topics: Archaea; Bacteria; Calcium Carbonate; Ice; Phylogeny; Extremophiles
PubMed: 38302670
DOI: 10.1038/s41598-024-53131-y -
Frontiers in Microbiology 2023The objective of this study is to examine the impact of various oyster shell soil conditioners, which are primarily composed of oyster shells, on the growth of tomatoes...
The impact of utilizing oyster shell soil conditioner on the growth of tomato plants and the composition of inter-root soil bacterial communities in an acidic soil environment.
INTRODUCTION
The objective of this study is to examine the impact of various oyster shell soil conditioners, which are primarily composed of oyster shells, on the growth of tomatoes in acidic soil. Moreover, the aim of this investigation is to analyze the variety and structure of soil bacterial populations in close proximity to tomato roots while also contributing to the understanding of the physical, chemical, and biological mechanisms of oyster shell soil conditioners.
METHODS
Tomato plants were grown in acidic red soil in three groups: a control group and a treatment group that used two types of oyster shell soil conditioners, OS (oyster shell powder) and OSF (oyster shell powder with organic microbial fertilizer). A range of soil physicochemical properties were measured to study differences in inter-soil physicochemical parameters and the growth of tomato plantings. In addition, this study utilized the CTAB (Cetyltrimethylammonium Bromide) technique to extract DNA from the soil in order to investigate the effects of oyster shell soil conditioner on the composition and diversity of bacterial populations. Utilizing high-throughput sequencing technologies and diversity index analysis, the composition and diversity of bacterial populations in the soil adjacent to plant roots were then evaluated. Ultimately, correlation analysis was used in this study to explore the relationship between environmental factors and the relative abundance of soil bacteria in the inter-root zone of tomato plants.
RESULTS
The findings indicated that the oyster shell soil conditioners were capable of modifying the physicochemical characteristics of the soil. This was evidenced by significant increases in soil total nitrogen (16.2 and 59.9%), soil total carbon (25.8 and 27.7%), pH (56.9 and 55.8%), and electrical conductivity (377.5 and 311.7%) in the OS and OSF groups, respectively, compared to the control group ( < 0.05). Additionally, data pertaining to tomato seed germination and seedling growth biomass demonstrated that both oyster shell soil conditioners facilitated the germination of tomato seeds and the growth of seedlings in an acidic red clay soil (p < 0.05). On the other hand, the application of two oyster shell soil conditioners resulted in a modest reduction in the diversity of inter-root soil bacteria in tomato plants. Specifically, the group treated with OSF exhibited the most substantial fall in the diversity index, which was 13.6% lower compared to the control group. The investigation carried out on the soil between tomato plant roots yielded findings about the identification of the ten most abundant phyla. These phyla together represented 91.00-97.64% of the overall abundance. In the inter-root soil of tomatoes, a study identified four major phyla, namely , and , which collectively accounted for up to 85% of the total abundance. At the general level, the relative abundance of increased by 2.18 and 7.93%, by 5.43 and 3.01%, and by 3.12 and 7.49% in the OS and OSF groups, respectively, compared to the control group. However, the pathogenic bacteria decreased by 5.76 and 5.05%, respectively. The correlation analysis yielded conclusive evidence indicating that, which involved the use of CCA (Canonical Correlation Analysis) graphs and Spearman correlation coefficients, pH exhibited a positive correlation ( < 0.05) with and a negative correlation ( < 0.05) with . The relative abundance of and exhibited a positive correlation with the levels of total soil nitrogen.
DISCUSSION
The utilization of oyster shell soil conditioner on acidic red soil resulted in several positive effects. Firstly, it raised the pH level of the inter-root soil of tomato plants, which is typically acidic. This pH adjustment facilitated the germination of tomato seeds and promoted the growth of seedlings. In addition, the application of oyster shell soil conditioner resulted in changes in the structure of the bacterial community in the inter-root soil, leading to an increase in the relative abundance of and and a decrease in the relative abundance of . Furthermore, this treatment fostered the proliferation of genera of beneficial bacteria like , , and , ultimately enhancing the fertility of the red soil.
PubMed: 38293555
DOI: 10.3389/fmicb.2023.1276656