LncRNA PAPAS promotes hepatocellular carcinoma by interacting with miR-188-5p.

It has been observed that long noncoding RNA (lncRNA) PAPAS regulates rRNA synthesis, but its role in human diseases is unclear. Our study was carried out to investigate the role of PAPAS in hepatocellular carcinoma (HCC). In the present study, we found that PAPAS was upregulated both in plasma from patients with HCC and tumors compared with plasma from healthy people and tumor-adjacent healthy tissues. Expression levels of PAPAS in tumor tissues and plasma of patients with HCC were significantly and positively correlated. Plasma levels of PAPAS effectively distinguished stage I patients from healthy controls. MicroRNA (miR)-188-5p was downregulated in tumor tissues than in tumor-adjacent healthy tissues of patients with HCC, and was inversely correlated with PAPAS in tumor tissues but not in adjacent healthy tissues. PAPAS and miR-188-5p downregulated each other. PAPAS overexpression promoted, while miR-188-5p overexpression inhibited the HCC cell proliferation. Rescue experiment showed that miR-34a overexpression attenuated the effects of PAPAS overexpression. However, PAPAS overexpression failed to affect significantly cancer cell migration and invasion. Therefore, lncRNA PAPAS promotes HCC by interacting with miR-188-5p.

Exploring links between water quality and E. coli O157:H7 survival potential in well waters from a rural area of southern Changchun City, China.

Waterborne infectious disease outbreak associated with well water contamination is a worldwide public health issue, especially for rural areas in developing countries. In the current study, we characterized 20 well water samples collected from a rural area of southern Changchun city, China, and investigated the survival potential of Escherichia coli O157:H7 in those water samples. The results showed that nitrate and ammonia concentrations in some well water samples exceed the corresponding China drinking water standards, indicating potential contamination by local agricultural farms. Our results also revealed that the average survival time (ttd) of E. coli O157:H7 in all well water samples was 30.09 days, with shortest and longest ttd being 17.95 and 58.10 days, respectively. The ttds were significantly correlated with pH and the ratio of total nitrogen to total phosphorus. In addition, it was found that the shape parameter (p) and first decimal reduction parameter (δ) were negatively (P < 0.05) and positively (P < 0.05) correlated to ttd, respectively. Our study showed that E. coli O157:H7 could survive up to two months in well water, suggesting that this pathogen could constitute a great public health risk.

The Adsorption and Desorption of Pb(2+) and Cd(2+) in Freeze-Thaw Treated Soils.

Adsorption and desorption are important processes that influence the potential toxicity and bioavailability of heavy metals in soils. However, information regarding adsorption and desorption behavior of heavy metals in soils subjected to freeze-thaw cycles is poorly understood. In the current study, the effect of freeze-thaw cycles with different freezing temperature (-15, -25, -35°C) on soil properties was investigated. Then the adsorption and desorption behavior of Pb(2+) and Cd(2+) in freeze-thaw treated soils was studied. The adsorption amounts of Pb(2+) and Cd(2+) in freeze-thaw treated soils were smaller than those in unfrozen soils (p < 0.05), due to the fact that pH, cation exchange capacity, organic matter content, free iron oxide content, and CaCO3 content in freeze-thaw treated soils were smaller than those in unfrozen soils. The adsorption amounts of Pb(2+) and Cd(2+) in soils treated with lower freezing temperatures were higher than those in soils treated with higher freezing temperatures. Desorption percentages of Pb(2+) and Cd(2+) in unfrozen soils were smaller than those in freeze-thaw treated soils (p < 0.05). The desorption percentages of Pb(2+) and Cd(2+) were smaller in soils treated with lower freezing temperatures than those in soils treated with higher freezing temperatures. The results obtained highlight the change of the adsorption and desorption behavior of typical heavy metals in freeze-thaw treated soils located in seasonal frozen soils zone in northeast China.

Shotgun proteomic analysis unveils survival and detoxification strategies by Caulobacter crescentus during exposure to uranium, chromium, and cadmium.

The ubiquitous bacterium Caulobacter crescentus holds promise to be used in bioremediation applications due to its ability to mineralize U(VI) under aerobic conditions. Here, cell free extracts of C. crescentus grown in the presence of uranyl nitrate [U(VI)], potassium chromate [Cr(VI)], or cadmium sulfate [Cd(II)] were used for label-free proteomic analysis. Proteins involved in two-component signaling and amino acid metabolism were up-regulated in response to all three metals, and proteins involved in aerobic oxidative phosphorylation and chemotaxis were down-regulated under these conditions. Clustering analysis of proteomic enrichment revealed that the three metals also induce distinct patterns of up- or down-regulated expression among different functional classes of proteins. Under U(VI) exposure, a phytase enzyme and an ABC transporter were up-regulated. Heat shock and outer membrane responses were found associated with Cr(VI), while efflux pumps and oxidative stress proteins were up-regulated with Cd(II). Experimental validations were performed on select proteins. We found that a phytase plays a role in U(VI) and Cr(VI) resistance and detoxification and that a Cd(II)-specific transporter confers Cd(II) resistance. Interestingly, analysis of promoter regions in genes associated with differentially expressed proteins suggests that U(VI) exposure affects cell cycle progression.

Microbial community functional structure in response to micro-aerobic conditions in sulfate-reducing sulfur-producing bioreactor.

Limited oxygen supply to anaerobic wastewater treatment systems had been demonstrated as an effective strategy to improve elemental sulfur (S(0)) recovery, coupling sulfate reduction and sulfide oxidation. However, little is known about the impact of dissolved oxygen (DO) on the microbial functional structures in these systems. We used a high throughput tool (GeoChip) to evaluate the microbial community structures in a biological desulfurization reactor under micro-aerobic conditions (DO: 0.02-0.33 mg/L). The results indicated that the microbial community functional compositions and structures were dramatically altered with elevated DO levels. The abundances of dsrA/B genes involved in sulfate reduction processes significantly decreased (p < 0.05, LSD test) at relatively high DO concentration (DO: 0.33 mg/L). The abundances of sox and fccA/B genes involved in sulfur/sulfide oxidation processes significantly increased (p < 0.05, LSD test) in low DO concentration conditions (DO: 0.09 mg/L) and then gradually decreased with continuously elevated DO levels. Their abundances coincided with the change of sulfate removal efficiencies and elemental sulfur (S(0)) conversion efficiencies in the bioreactor. In addition, the abundance of carbon degradation genes increased with the raising of DO levels, showing that the heterotrophic microorganisms (e.g., fermentative microorganisms) were thriving under micro-aerobic condition. This study provides new insights into the impacts of micro-aerobic conditions on the microbial functional structure of sulfate-reducing sulfur-producing bioreactors, and revealed the potential linkage between functional microbial communities and reactor performance.

GeoChip-based analysis of the microbial community functional structures in simultaneous desulfurization and denitrification process.

The elemental sulfur (S°) recovery was evaluated in the presence of nitrate in two development models of simultaneous desulfurization and denitrification (SDD) process. At the loading rates of 0.9 kg S/(m³·day) for sulfide and 0.4 kg N/(m³·day) for nitrate, S° conversion rate was 91.1% in denitrifying sulfide removal (DSR) model which was higher than in integrated simultaneous desulfurization and denitrification (ISDD) model (25.6%). A comprehensive analysis of functional diversity, structure and metabolic potential of microbial communities was examined in two models by using functional gene array (GeoChip 2.0). GeoChip data indicated that diversity indices, community structure, and abundance of functional genes were distinct between two models. Diversity indices (Simpson's diversity index (1/D) and Shannon-Weaver index (H')) of all detected genes showed that with elevated influent loading rate, the functional diversity decreased in ISDD model but increased in DSR model. In contrast to ISDD model, the overall abundance of dsr genes was lower in DSR model, while some functional genes targeting from nitrate-reducing sulfide-oxidizing bacteria (NR-SOB), such as Thiobacillus denitrificans, Sulfurimonas denitrificans, and Paracoccus pantotrophus were more abundant in DSR model which were highly associated with the change of S(0) conversion rate obtained in two models. The results obtained in this study provide additional insights into the microbial metabolic mechanisms involved in ISDD and DSR models, which in turn will improve the overall performance of SDD process.

E. coli cotransport with composite colloid in unsaturated porous media: Multi-risk on migration and biomolecular response.

The diversity of colloidal types and the differences in the composite ratios in porous media are important factors governing the migration and biological risk of pathogenic microorganisms in the subsurface environment. In this study, E. coli O157:H7 was subjected to co-migration experiments with different compositions of the composite colloid montmorillonite (MMT)-Fe2O3, and the biomolecular response of E. coli under the action of colloids was analyzed by Raman spectroscopy to quantify the risk of E. coli under the action of composite colloids based on both. The results showed that Fe2O3 colloids inhibited E. coli migration mainly by electrostatic adsorption and reduced E. coli metabolism. MMT colloid inhibited E. coli migration mainly by blockage, and E. coli metabolism increased, and surface macromolecules decreased to reduce E. coli adhesion. MMT-Fe2O3 complex colloids inhibited migration through electrostatic attraction between the two and formation of cohesive colloids, with reduced E. coli metabolism and insignificant biomolecular response. It was briefly assessed that the composite colloids reduced E. coli risk less strongly than single colloids, stemming from the difference in the mechanism of influence and the actual need to consider colloid interactions. This conclusion can inform the management and control of pathogen risk in porous media environments.

Arsenic methylation in soils and its relationship with microbial arsM abundance and diversity, and as speciation in rice.

Methylation of arsenic in soil influences its environmental behavior and accumulation by plants, but little is known about the factors affecting As methylation. As speciation was determined in the pore waters of six soils from diverse geographical locations over 54 days of incubation under flooded conditions. The concentration of methylated As (monomethylarsonic acid, MMA, and dimethylarsinic acid, DMA) varied from 0 to 85 µg L(-1) (0 - 69% of the total As in pore water). Two Bangladeshi paddy soils contaminated by irrigation of As-laden groundwater produced large concentrations of inorganic As but relatively little methylated As. Two contaminated paddy soils from China produced a transient peak of DMA during the early phase of incubation. Methylated As represented considerable proportions of the total soluble As in the two uncontaminated soils from the UK and U.S. The copy number of the microbial arsenite methyltransferase gene (arsM) correlated positively with soil pH. However, pore-water methylated As correlated negatively with pH or arsM copy number, and positively with dissolved organic C. GeoChip assay revealed considerable arsM diversity among the six soils, with 27-35 out of 66 sequences in the microarray being detected. As speciation in rice plants grown in the soils generally mirrored that in the pore water. The results suggest that methylated As species in plants originated from the soil and As methylation in soil was influenced strongly by the soil conditions.

Migration risk of Escherichia coli O157:H7 in unsaturated porous media in response to different colloid types and compositions.

The vadose zone is a critical zone for microbial entry into the subsurface environment, and various types of inorganic and organic colloids can affect the migration of pathogenic bacteria. In the study, we explored the migration behavior of Escherichia coli O157:H7 with humic acids (HA), iron oxides (Fe2O3) or their mixture, uncovering their migration mechanisms in the vadose zone. The effect of complex colloids on the physiological properties of E. coli O157:H7 was analyzed based on the measured particle size, zeta potential and contact angle. HA colloids significantly promoted the migration of E. coli O157:H7, where Fe2O3 was opposite. The migration mechanism of E. coli O157:H7 with HA and Fe2O3 is obviously different. Multiple colloids dominated by organic colloid will further highlight its promoting effect on E. coli O157:H7 under the guidance of electrostatic repulsion due to the influence of colloidal stability. Multiple colloids dominated by metallic colloid will inhibit the migration of E. coli O157:H7 under the control of capillary force due to the restriction of contact angle. The risk of secondary release of E. coli O157:H7 can be effectively reduced when the ratio of HA/Fe2O3 is ≥ 1. Combining this conclusion with the distribution characteristics of soil in China, an attempt was made to analyse the migration risk of E. coli O157:H7 on a national scale. In China, from north to south, the migration capacity of E. coli O157:H7 gradually decreased, and the risk of secondary release gradually increased. These results provide ideas for the subsequent study of the effect of other factors on the migration of pathogenic bacteria on a national scale and provide risk information about soil colloids for the construction of pathogen risk assessment model under comprehensive conditions in the future.

Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land.

Livestock manure, dairy lagoon effluent, and treated wastewater are known reservoirs of antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and virulence factor genes (VFGs), and their application to agricultural farmland could be a serious public health threat. However, their dissemination to agricultural lands and impact on important geochemical pathways such as the nitrogen (N) cycle have not been jointly explored. In this study, shotgun metagenomic sequencing and analyses were performed to examine the diversity and composition of microbial communities, ARGs, VFGs, and N cycling genes in different livestock manure/lagoon and treated wastewater collected from concentrated animal feeding operations (CAFOs) and a municipal wastewater treatment plant along the west coast of the United States. Multivariate analysis showed that diversity indices of bacterial taxa from the different microbiomes were not significantly different based on InvSimpson (P = 0.05), but differences in ARG mechanisms were observed between swine manure and other microbiome sources. Comparative resistome profiling showed that ARGs in microbiome samples belonged to four core resistance classes: aminoglycosides (40-55 %), tetracyclines (30-45 %), beta-lactam-resistance (20-35 %), macrolides (18-30 %), and >50 % of the VFGs that the 24 microbiomes harbored were phyletically affiliated with two bacteria, Bacteroidetes fragilis and Enterobacter aerogenes. Network analysis based on Spearman correlation showed co-occurrence patterns between several genes such as transporter-gene and regulator, efflux pump and involved-in-polymyxin- resistance, aminoglycoside, beta-lactam, and macrolide with VFGs and bacterial taxa such as Firmicutes, Candidatus Themoplasmatota, Actinobacteria, and Bacteroidetes. Metabolic reconstruction of metagenome-assembled genome (MAGs) analysis showed that the most prevalent drug resistance mechanisms were associated with carbapenem resistance, multidrug resistance (MDR), and efflux pump. Bacteroidales was the main taxa involved in dissimilatory nitrate reduction (DNRA) in dairy lagoon effluent. This study demonstrates that the dissemination of waste from these sources can increase the spread of ARGs, ARB, and VFGs into agricultural lands, negatively impacting both soil and human health.

Persistence of Escherichia coli O157:H7 in major leafy green producing soils.

Persistence of Escherichia coli O157:H7 in 32 (16 organically managed and 16 conventionally managed) soils from California (CA) and Arizona (AZ) was investigated. Results showed that the longest survival (ttd, time needed to reach detection limit, 100 CFU g(-1) dry soil) of E. coli O157:H7 was observed in the soils from Salinas Valley, CA and in organically managed soils from AZ. Detrended correspondence analysis revealed that the survival profiles in organically managed soils in Yuma, AZ were different from the ones in conventionally managed soils from the same site. Principal component analysis and stepwise regression analysis showed that E. coli O157:H7 survival in soils was negatively correlated with salinity (EC) (P < 0.001), while positively correlated with assimilable organic carbon (AOC) and total nitrogen (TN) (P < 0.01). Pearson correlation analysis revealed that a greater ttd was associated with a larger δ (time needed for first decimal reduction in E. coli population). EC was negatively correlated and TN was positively correlated (P < 0.05) with δ, suggesting that EC and TN likely have a direct impact on ttd. On the other hand, AOC showed a close correlation with p (the shape parameter) that was not directly related to ttd, indicating that AOC might have an indirect effect in the overall survival of E. coli O157:H7 in soils. Our data showed that AOC and EC significantly affected the survival of E. coli O157:H7 in leafy green producing soils and the development of good agricultural practices (manure/composting/irrigation water source management) in the preharvest environment must be followed to minimize foodborne bacterial contamination on fresh produce.

Persistence of E. coli O157:H7 in urban recreational waters from Spring and Autumn: a comparison analysis.

People might get infected by pathogens found in urban recreational waters during water-contact activities, such as swimming, boating, bathing, and yachting. However, the persistence of pathogenic bacteria in those waters was not well documented. In this study, persistence of E. coli O157:H7 (EcO157) in 48 water samples (24 Spring samples and 24 Autumn samples) from the 3 urban recreational waters was investigated. Multivariate statistical analysis was performed to correlate survival data with water physicochemical properties and bacterial communities. Our data showed that EcO157 survived longer in Spring samples than in Autumn samples regardless of the lakes. Results revealed that recreational water physicochemical properties and bacterial community in Spring samples were different from those in Autumn samples. Mantel and Partial Mantel tests, as well as co-occurrence network analysis illustrated that EC salinity, TOC, and bacterial community were correlated with survival time (ttd) (p < 0.05). Variation partition analysis (VPA) indicated that bacterial community, EC, TOC, and TN explained about 64.81% of overall ttd variation in Spring samples, and bacterial community, EC, pH, and TP accounted for about 56.59% of overall ttd variation in Autumn samples. Structural equation model (SEM) illustrated that EC indirectly positively affected ttd through bacterial community. The correlation between bacterial community and ttd was negative in Spring samples and positive in Autumn samples. TN appeared a direct positive effect on ttd in Spring samples. TP displayed a direct negative effect on ttd in Autumn samples. Our results concluded that there was seasonal variation in environmental factors that directly or indirectly affected the survival of EcO157 in urban recreational waters.

Commensal effect of pectate lyases secreted from Dickeya dadantii on proliferation of Escherichia coli O157:H7 EDL933 on lettuce leaves.

The outbreaks caused by enterohemorrhagic Escherichia coli O157:H7 on leafy greens have raised serious and immediate food safety concerns. It has been suggested that several phytopathogens aid in the persistence and proliferation of the human enteropathogens in the phyllosphere. In this work, we examined the influence of virulence mechanisms of Dickeya dadantii 3937, a broad-host-range phytopathogen, on the proliferation of the human pathogen E. coli O157:H7 EDL933 (EDL933) on postharvest lettuce by coinoculation of EDL933 with D. dadantii 3937 derivatives that have mutations in virulence-related genes. A type II secretion system (T2SS)-deficient mutant of D. dadantii 3937, A1919 (ΔoutC), lost the capability to promote the multiplication of EDL933, whereas Ech159 (ΔrpoS), a stress-responsive σ factor RpoS-deficient mutant, increased EDL933 proliferation on lettuce leaves. A spectrophotometric enzyme activity assay revealed that A1919 (ΔoutC) was completely deficient in the secretion of pectate lyases (Pels), which play a major role in plant tissue maceration. In contrast to A1919 (ΔoutC), Ech159 (ΔrpoS) showed more than 2-fold-greater Pel activity than the wild-type D. dadantii 3937. Increased expression of pelD (encodes an endo-pectate lyase) was observed in Ech159 (ΔrpoS) in planta. These results suggest that the pectinolytic activity of D. dadantii 3937 is the dominant determinant of enhanced EDL933 proliferation on the lettuce leaves. In addition, RpoS, the general stress response σ factor involved in cell survival in suboptimal conditions, plays a role in EDL933 proliferation by controlling the production of pectate lyases in D. dadantii 3937.

Soil salinity, pH, and indigenous bacterial community interactively influence the survival of E. coli O157:H7 revealed by multivariate statistics.

Complexities of biotic-abiotic interactions in soils result in the lack of integrated understanding of environmental variables that restrict the survival of shiga toxin-producing E. coli O157:H7. Herein, we reanalyzed previously published data and highlighted the influence of soil abiotic factors on E. coli O157:H7 survivability and elucidated how these factors took effect indirectly through affecting indigenous bacterial community. Interaction network analysis indicated salinity and pH decreased the relative abundances of some bacterial taxa (e.g., Acidobacteria_Gp4, Acidobacteria_Gp6, and Deltaproteobacteria) which were positively correlated with the survival of E. coli O157:H7 in soils, and vice versa (e.g., Gammaproteobacteria and Flavobacteria) (P < 0.05). An array of multivariate statistical approaches including partial Mantel test, variation partition analysis (VPA), and structural equation model (SEM) further confirmed that biotic and abiotic factors interactively shaped the survival profile of E. coli O157:H7. This study revealed that some bacterial taxa were correlated with survival of E. coli O157:H7 directly, and salinity and pH could affect E. coli O157:H7 survival through changing these bacterial taxa. These findings suggest that salinity in soil might benefit the control of fecal pathogenic E. coli invasion, while soil acidification caused by anthropogenic influences could potentially increase the persistence of E. coli O157:H7 in agro-ecosystem.

Persistence of Salmonella Typhimurium in apple-pear (Pyrus bretschneideri Rehd.) orchard soils influenced by bacterial communities and soil properties.

2In this study, we investigated the persistence of Salmonella Typhimurium in 26 soil samples from apple-pear orchards in Yanji, Longjing and Helong in northeastern China. The time to reach detection limit (ttds) of Salmonella Typhimurium in soils varied from 20 to 120 days. Redundancy analysis and variation partition analysis elucidated that bacterial communities, clay content, pH, electrical conductivity (EC) salinity, and NO3--N could explain more than 85% of overall variation of the persistence behaviors. Results of structural equation models and Mantel tests revealed that clay content and EC displayed both direct and indirect effect on ttds, while NO3--N and pH exhibited direct and indirect effect on the survival patterns, respectively. Furthermore, Actinobacteria, Acidobacteria and Deltaproteobacteria at class level showed highly close correlations with ttds. Our results revealed that certain biotic and abiotic factors could greatly contribute to the overall persistence of Salmonella in apple-pear orchard soils.

Soil characteristics and microbial community response in rare earth mining areas in southern Jiangxi Province, China.

The microbial community and functional flora in rare earth mining areas are correlated, but the characteristics and metabolic pathways of pollutant in such mining areas are still poorly known. The heavy metals, rare earth elements, and microorganisms present after mining of rare earth mine sites were analyzed. After mining, all sampling sites exhibited low pH and low total organic carbon levels, accompanied by high iron and aluminum concentrations. The development of vegetation is closely related to the development of microorganisms. In the complex environment of rare earth mining areas, Proteobacteria exhibit an absolute competitive advantage. During mine environmental recovery, the relative abundances of Acidobacteria and Chloroflexi will increase markedly, and with further restoration the relative abundance of Firmicutes will gradually decrease. Many genera of bacteria related to the N cycle and heavy metal metabolism were detected in the study area, indicating the important metabolic pathways for ammonia nitrogen and heavy metals in rare earth mining areas. Bacterial genera that promote plant nitrogen fixation also occur in the area, further revealing the nitrogen cycle. This research is important for health assessment and recovery of rare earth mines.

Disentangling survival of Escherichia coli O157:H7 in soils: From a subpopulation perspective.

Soil physicochemical properties and microbial community have been proved to be correlated to survival behaviors of Shiga toxin-producing Escherichia coli O157:H7, but the roles of biotic and abiotic factors in the different stages of inactivation process remain unclear. Here, fruit producing soils were collected, and soils physicochemical properties, bacterial and fungal community structure were characterized. Survival experiments were performed by inoculating E. coli O157:H7 in soils. Double Weibull survival model was found to better fit the experimental data, and two subpopulations with different capability on resistance to stress were identified. The sensitive subpopulation with smaller δ (time needed for first decimal reduction) (i.e., δ1) died off faster compared to the more resistant subpopulation with greater δ (i.e., δ2). Partial Mantel test revealed that ttd (time needed to reach detection limit) was jointly influenced by physical factors, chemical factors, and bacterial composition (P < 0.05); δ1 was shaped by physical factors (P < 0.01) and additional bacterial composition (P < 0.05); and δ2 was strongly steered by bacterial community (P < 0.001). Bacterial co-occurrence network analysis revealed that samples with lower δ2 were coupled with higher network complexity and closer taxa relationship (e.g. higher average (weighted) degree, higher network diameter, higher graph density, and lower modularity), and vice versa. Taken together, the sensitive subpopulation had difficulty in adapting to coarse particles conditions, while resistant subpopulation might eventually succumb to the robust biodiversity. This study provides novel insights into the E. coli O157:H7 survival mechanism through subpopulation perspective and sheds light on the reduction of edaphic colonization by pathogens via agricultural management strategy.

Interaction between Fungal Communities, Soil Properties, and the Survival of Invading E. coli O157:H7 in Soils.

Pathogens that invade into the soil cancontaminate food and water, andinfect animals and human beings. It is well documented that individual bacterial phyla are well correlated with the survival of E. coliO157 (EcO157), while the interaction betweenthe fungal communities and EcO157 survival remains largely unknown. In this study, soil samples from Tongliao, Siping, and Yanji in northeast China were collected and characterized. Total DNA was extracted for fungal and bacterial community characterization. EcO157 cells were spiked into the soils, and their survival behavior was investigated. Results showed that both fungal and bacterial communities were significantly correlated (p < 0.01) with the survival of EcO157 in soils, and the relative abundances of fungal groups (Dothideomycetes and Sordariomycetes) and some bacterial phyla (Acidobacteria, Firmicutes, gamma- and delta-Proteobacteria)weresignificantly correlated with ttds (p < 0.01). Soil pH, EC (electric conductance) salinity, and water-soluble nitrate nitrogen were significantly correlated with survival time (time to reach the detection limit, ttd) (p < 0.05). The structural equation model indicated that fungal communities could directly influence ttds, and soil properties could indirectly influence the ttds through fungal communities. The first log reduction time (δ) was mainly correlated with soil properties, while the shape parameter (p) was largely correlated with fungal communities. Our data indicated that both fungal and bacterial communities were closely correlated (p < 0.05)with the survival of EcO157 in soils, and different fungal and bacterial groups might play different roles. Fungal communities and bacterial communities explained 5.87% and 17.32% of the overall variation of survival parameters, respectively. Soil properties explained about one-third of the overall variation of survival parameters. These findings expand our current understanding of the environmental behavior of human pathogens in soils.

Functional relationships between aboveground and belowground spinach (Spinacia oleracea L., cv. Racoon) microbiomes impacted by salinity and drought.

Salinity is a major problem facing agriculture in arid and semiarid regions of the world. This problem may vary among seasons affecting both above- and belowground plant microbiomes. However, very few studies have been conducted to examine the influence of salinity and drought on microbiomes and on their functional relationships. The objective for the study was to examine the effects of salinity and drought on above- and belowground spinach microbiomes and evaluate seasonal changes in their bacterial community composition and diversity. Furthermore, potential consequences for community functioning were assessed based on 16S V4 rRNA gene profiles by indirectly inferring the abundance of functional genes based on results obtained with Piphillin. The experiment was repeated three times from early fall to late spring in sand tanks planted with spinach (Spinacia oleracea L., cv. Racoon) grown with saline water of different concentrations and provided at different amounts. Proteobacteria, Cyanobacteria, and Bacteroidetes accounted for 77.1% of taxa detected in the rhizosphere; Proteobacteria, Bacteroidetes, and Actinobacteria accounted for 55.1% of taxa detected in soil, while Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria accounted for 55.35% of taxa detected in the phyllosphere. Salinity significantly affected root microbiome beta-diversity according to weighted abundances (p = 0.032) but had no significant effect on the relative abundances of microbial taxa (p = 0.568). Pathways and functional genes analysis of soil, rhizosphere, and phyllosphere showed that the most abundant functional genes were mapped to membrane transport, DNA repair and recombination, signal transduction, purine metabolism, translation-related protein processing, oxidative phosphorylation, bacterial motility protein secretion, and membrane receptor proteins. Monoterpenoid biosynthesis was the most significantly enriched pathway in rhizosphere samples when compared to the soil samples. Overall, the predictive abundances indicate that, functionally, the rhizosphere bacteria had the highest gene abundances and that salinity and drought affected the above- and belowground microbiomes differently.

Role of menaquinone biosynthesis genes in selenate reduction by Enterobacter cloacae SLD1a-1 and Escherichia coli K12.

In this study, we investigated the role of menaquinone biosynthesis genes in selenate reduction by Enterobacter cloacae SLD1a-1 and Escherichia coli K12. A mini-Tn5 transposon mutant of E. cloacae SLD1a-1, designated as 4E6, was isolated that had lost the ability to reduce Se(VI) to Se(0). Genetic analysis of mutant strain 4E6 showed that the transposon was inserted within a menD gene among a menFDHBCE gene cluster that encodes for proteins required for menaquinone biosynthesis. A group of E. coli K12 strains with single mutations in the menF, menD, menC and menE genes were tested for loss of selenate reduction activity. The results showed that E. coli K12 carrying a deletion of either the menD, menC or menE gene was unable to reduce selenate. Complementation using wild-type sequences of the E. cloacae SLD1a-1 menFDHBCE sequence successfully restored the selenate reduction activity in mutant strain 4E6, and E. coli K12 menD and menE mutants. Selenate reduction activity in 4E6 was also restored by chemical complementation using the menaquinone precursor compound 1,4-dihydroxy-2-nathphoic acid. The results of this work suggest that menaquinones are an important source of electrons for the selenate reductase, and are required for selenate reduction activity in E. cloacae SLD1a-1 and E. coli K12.