Fate of enteric viruses during leafy greens (romaine lettuce) production using treated municipal wastewater and AP205 bacteriophage as a surrogate.

Water reuse programs are being explored to close the gap between supply and demand for irrigation in agriculture. However, these sources could contain hazardous microbial contaminants, and pose risks to public health. This study aimed to grow and irrigate romaine lettuce with inoculated wastewater effluent to track AP205 bacteriophage prevalence through cultivation and post-harvest storage. AP205 is a bacteriophage and was used as a surrogate for enteric viruses. Low and high dosages (mean ± standard deviation) of AP205 at 4.8 ± 0.4 log PFU/mL and 6.6 ± 0.2 log PFU/mL; respectively, were prepared to examine viral load influence on contamination levels. Foliage, leachate, and soil contamination levels were directly related to AP205 concentrations in the effluent. AP205 concentrations increased throughout cultivation for foliage and leachate, suggesting bacteriophage accumulation. During post-harvest storage (14 day at 4 °C), there was a significant decrease in AP205 concentration on the foliage. Results show that wastewater effluents usage for leafy greens cultivation can pose risks to humans and additional steps are required to safely apply wastewater effluents to soils and crops.

Escherichia coli Concentration as a Function of Stream Order and Watershed Size.

This research examines the relationship of concentrations to stream order and watershed size and considers the implications on water quality standards. To assess geospatial effects, data were obtained from 743 monitoring stations in the Central Great Plains, Cross Timbers, and South Central Plains ecoregions of Texas and Oklahoma. Median and geometric mean concentrations were analyzed for correlation with stream order and watershed size at each site. Comparison of the three ecoregions revealed concentrations were highest in the westernmost Central Great Plains and lowest in the easternmost South Central Plains. Similarly, the strength of 's correlation with stream order and watershed area decreased with ecoregion moving west to east. Thus, incorporating ecoregion approaches when defining stream water quality standards is supported. Analysis showed no significant relationship of stream order or watershed size to concentrations in least-impacted watersheds (i.e., watersheds with minimal wastewater discharge and urbanization). Conversely, analysis of data from all sites showed a weak negative relationship between concentration and stream order and watershed size, with concentration generally decreasing with increasing stream order and watershed size. However, variability in smaller watersheds and lower-order streams supports continued use of site-specific studies to determine appropriate standards. Three-parameter exponential models provided an approach to estimate concentrations using Shreve stream order and watershed area and identify outlier streams potentially affected by anthropogenic activities where further investigation or remediation may be warranted.

Within-House Spatial Distribution of Fecal Indicator Bacteria in Poultry Litter.

Land application of poultry litter is often considered to be a major source of water pollutants in poultry-producing regions. However, reported levels of fecal indicator microorganisms in litter vary widely, with considerable variation possible within houses and across farms, depending on management practices. Therefore, a study was conducted to determine the levels and distribution of indicator microorganisms within 12 broiler farms representing three companies. Within each house, litter samples were collected from around the feed line, water line, north wall, cool pad end, middle, and fan end. Litter moisture content was significantly different within the houses, with the litter being driest around the feed line (19.8%) and wettest around the water line (40.7%). Mean levels of total coliforms, , enterococci, and were 3.7, 3.3, 6.4, and 4.0 log colony-forming units g dry litter, respectively. Levels of total coliforms, , and were positively correlated with litter moisture content, but enterococci levels were not. Consequently, levels of total coliforms, , and , as well as enterococci, were highest around the water line and lowest around the feed line. These results indicate that areas with higher litter water content are more likely to contain higher levels of most fecal indicator microorganisms. Approaches to reduce litter water content in these areas would not only benefit the microbial quality of litter for land application but would also likely improve in-house disease control.

Impacts of Heronries on Water Quality as Evaluated through Escherichia coli and Fecal Sterol Analyses.

The authors used fecal sterol analysis to determine the potential contribution of E. coli from heronries to waterbodies in east-central Texas. They analyzed E. coli and fecal sterol concentrations in samples from four heronries during the breeding seasons in 2011-2013. The highest E. coli concentrations were in water samples from the two largest heronries established directly over water. The main sterols in fecal samples were cholesterol and stigmasterol, and in water, cholesterol, coprostanol, and cholestanol. Total sterols ranged 979 to 5838 ng/g dry weight in fecal samples, and 13 to 600 ng/L in water samples. There was a positive correlation between E. coli and the sum of bird sterols in water exposed directly to fecal deposition, but not in water surrounding the heronries. The authors found a strong association between E. coli and stigmasterol, suggesting that the presence of stigmasterol in water could be used for predicting E. coli sources from heronries nesting close to waterbodies.

Effects of field storage method on E. coli concentrations measured in storm water runoff.

Storm water runoff is increasingly assessed for fecal indicator organisms (e.g., Escherichia coli, E. coli) and its impact on contact recreation. Concurrently, use of autosamplers along with logistic, economic, technical, and personnel barriers is challenging conventional protocols for sample holding times and storage conditions in the field. A common holding time limit for E. coli is 8 h with a 10 °C storage temperature, but several research studies support longer hold time thresholds. The use of autosamplers to collect E. coli water samples has received little field research attention; thus, this study was implemented to compare refrigerated and unrefrigerated autosamplers and evaluate potential E. coli concentration differences due to field storage temperature (storms with holding times ≤24 h) and due to field storage time and temperature (storms >24 h). Data from 85 runoff events on four diverse watersheds showed that field storage times and temperatures had minor effects on mean and median E. coli concentrations. Graphs and error values did, however, indicate a weak tendency for higher concentrations in the refrigerated samplers, but it is unknown to what extent differing die-off and/or regrowth rates, heterogeneity in concentrations within samples, and laboratory analysis uncertainty contributed to the results. The minimal differences in measured E. coli concentrations cast doubt on the need for utilizing the rigid conventional protocols for field holding time and storage temperature. This is not to say that proper quality assurance and quality control is not important but to emphasize the need to consider the balance between data quality and practical constraints related to logistics, funding, travel time, and autosampler use in storm water studies.

Microbiome analysis revealed distinct microbial communities occupying different sized nodules in field-grown peanut.

Legume nodulation is the powerhouse of biological nitrogen fixation (BNF) where host-specific rhizobia dominate the nodule microbiome. However, other rhizobial or non-rhizobial inhabitants can also colonize legume nodules, and it is unclear how these bacteria interact, compete, or combinedly function in the nodule microbiome. Under such context, to test this hypothesis, we conducted 16S-rRNA based nodule microbiome sequencing to characterize microbial communities in two distinct sized nodules from field-grown peanuts inoculated with a commercial inoculum. We found that microbial communities diverged drastically in the two types of peanut nodules (big and small). Core microbial analysis revealed that the big nodules were inhabited by Bradyrhizobium, which dominated composition (>99%) throughout the plant life cycle. Surprisingly, we observed that in addition to Bradyrhizobium, the small nodules harbored a diverse set of bacteria (~31%) that were not present in big nodules. Notably, these initially less dominant bacteria gradually dominated in small nodules during the later plant growth phases, which suggested that native microbial communities competed with the commercial inoculum in the small nodules only. Conversely, negligible or no competition was observed in the big nodules. Based on the prediction of KEGG pathway analysis for N and P cycling genes and the presence of diverse genera in the small nodules, we foresee great potential of future studies of these microbial communities which may be crucial for peanut growth and development and/or protecting host plants from various biotic and abiotic stresses.

Isolation and Characterization of Bacterial Endophytes from Small Nodules of Field-Grown Peanut.

It is evident that legume root nodules can accommodate rhizobial and non-rhizobial bacterial endophytes. Our recent nodule microbiome study in peanuts described that small nodules can harbor diverse bacterial endophytes. To understand their functional role, we isolated 87 indigenous endophytes from small nodules of field-grown peanut roots and characterized them at molecular, biochemical, and physiological levels. The amplified 16S rRNA genes and phylogenetic analysis of these isolates revealed a wide variety of microorganisms related to the genera Bacillus, Burkholderia, Enterobacter, Herbaspirillum, Mistsuaria, Pantoea, Pseudomonas, and Rhizobia. It was observed that 37% (100% identity) and 56% (>99% identity) of the isolates matched with the amplified sequence variants (ASVs) from our previous microbiome study. All of these isolates were tested for stress tolerance (high temperature, salinity, acidic pH) and phosphate (P) solubilization along with ammonia (NH3), indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate deaminase (ACCD), and siderophore production. The majority (78%) of the isolates were found to be halotolerant, thermotolerant, and acidophilic, and a few of them showed a significant positive response to the production of IAA, NH3, siderophore, ACCD, and P-solubilization. To evaluate the plant growth promotion (PGP) activity, plant and nodulation assays were performed in the growth chamber conditions for the selected isolates from both the non-rhizobial and rhizobial groups. However, these isolates appeared to be non-nodulating in the tested conditions. Nonetheless, the isolates 2 (Pantoea), 17 (Burkholderia), 21 (Herbaspirillum), 33o (Pseudomonas), and 77 (Rhizobium sp.) showed significant PGP activity in terms of biomass production. Our findings indicate that these isolates have potential for future biotechnological applications through the development of biologicals for sustainable crop improvement.

Hurricane Harvey Impacts on Water Quality and Microbial Communities in Houston, TX Waterbodies.

Extreme weather events can temporarily alter the structure of coastal systems and generate floodwaters that are contaminated with fecal indicator bacteria (FIB); however, every coastal system is unique, so identification of trends and commonalities in these episodic events is challenging. To improve our understanding of the resilience of coastal systems to the disturbance of extreme weather events, we monitored water quality, FIB at three stations within Clear Lake, an estuary between Houston and Galveston, and three stations in bayous that feed into the estuary. Water samples were collected immediately before and after Hurricane Harvey (HH) and then throughout the fall of 2017. FIB levels were monitored by culturing E. coli and Enterococci. Microbial community structure was profiled by high throughput sequencing of PCR-amplified 16S rRNA gene fragments. Water quality and FIB data were also compared to historical data for these water body segments. Before HH, salinity within Clear Lake ranged from 9 to 11 practical salinity units (PSU). Immediately after the storm, salinity dropped to < 1 PSU and then gradually increased to historical levels over 2 months. Dissolved inorganic nutrient levels were also relatively low immediately after HH and returned, within a couple of months, to historical levels. FIB levels were elevated immediately after the storm; however, after 1 week, E. coli levels had decreased to what would be acceptable levels for freshwater. Enterococci levels collected several weeks after the storm were within the range of historical levels. Microbial community structure shifted from a system dominated by Cyanobacteria sp. before HH to a system dominated by Proteobacteria and Bacteroidetes immediately after. Several sequences observed only in floodwater showed similarity to sequences previously reported for samples collected following Hurricane Irene. These changes in beta diversity corresponded to salinity and nitrate/nitrite concentrations. Differential abundance analysis of metabolic pathways, predicted from 16S sequences, suggested that pathways associated with virulence and antibiotic resistance were elevated in floodwater. Overall, these results suggest that floodwater generated from these extreme events may have high levels of fecal contamination, antibiotic resistant bacteria and bacteria rarely observed in other systems.

Dynamics of microbial community composition and function during in situ bioremediation of a uranium-contaminated aquifer.

A pilot-scale system was established to examine the feasibility of in situ U(VI) immobilization at a highly contaminated aquifer (U.S. DOE Integrated Field Research Challenge site, Oak Ridge, TN). Ethanol was injected intermittently as an electron donor to stimulate microbial U(VI) reduction, and U(VI) concentrations fell to below the Environmental Protection Agency drinking water standard (0.03 mg liter(-1)). Microbial communities from three monitoring wells were examined during active U(VI) reduction and maintenance phases with GeoChip, a high-density, comprehensive functional gene array. The overall microbial community structure exhibited a considerable shift over the remediation phases examined. GeoChip-based analysis revealed that Fe(III)-reducing bacterial (FeRB), nitrate-reducing bacterial (NRB), and sulfate-reducing bacterial (SRB) functional populations reached their highest levels during the active U(VI) reduction phase (days 137 to 370), in which denitrification and Fe(III) and sulfate reduction occurred sequentially. A gradual decrease in these functional populations occurred when reduction reactions stabilized, suggesting that these functional populations could play an important role in both active U(VI) reduction and maintenance of the stability of reduced U(IV). These results suggest that addition of electron donors stimulated the microbial community to create biogeochemical conditions favorable to U(VI) reduction and prevent the reduced U(IV) from reoxidation and that functional FeRB, SRB, and NRB populations within this system played key roles in this process.

Water management impacts on arsenic speciation and iron-reducing bacteria in contrasting rice-rhizosphere compartments.

Rice cultivated on arsenic (As) contaminated-soils will accumulate variable grain-As concentrations, as impacted by varietal differences, soil variables, and crop management. A field-scale experiment was conducted to study the impact of intermittent and continuous flooding on As speciation and microbial populations in rice rhizosphere compartments of soils that were either historically amended with As pesticide or unamended with As. Rhizosphere-soil, root-plaque, pore-water and grain As were quantified and speciated, and microbial populations in rhizosphere soil and root-plaque were characterized. Total-As concentrations in rhizosphere and grain were significantly lower in intermittently flooded compared to the continuously flooded plots (86% lower in pore-water, 55% lower in root-plaque and 41% lower in grain samples). iAs(V), iAs(III), and DMAs(V) were the predominant As species detected in rhizosphere-soil and root-plaque, pore-water and grain samples, respectively. Relative proportions of Archaea and iron-reducing bacteria (FeRB) were higher in rhizosphere soil compared to root-plaque. In rhizosphere soil, the relative abundance of FeRB was lower in intermittently flooded compared to continuously flooded plots, but there were no differences between root-plaque samples. This study has demonstrated that reductions in dissolved As concentrations in the rhizosphere and subsequent decreases in grain-As concentration can be attained through water management.

Niche Differentiation of Arsenic-Transforming Microbial Groups in the Rice Rhizosphere Compartments as Impacted by Water Management and Soil-Arsenic Concentrations.

Arsenic (As) bioavailability in the rice rhizosphere is influenced by many microbial interactions, particularly by metal-transforming functional groups at the root-soil interface. This study was conducted to examine As-transforming microbes and As-speciation in the rice rhizosphere compartments, in response to two different water management practices (continuous and intermittently flooded), established on fields with high to low soil-As concentration. Microbial functional gene composition in the rhizosphere and root-plaque compartments were characterized using the GeoChip 4.0 microarray. Arsenic speciation and concentrations were analyzed in the rhizosphere soil, root-plaque, pore water, and grain samples. Results confirmed several As-biotransformation processes in the rice rhizosphere compartments, and distinct assemblage of As-reducing and methylating bacteria was observed between the root-plaque and rhizosphere. Results confirmed higher potential for microbial As-reduction and As-methylation in continuously flooded, long term As-contaminated fields, which accumulated highest concentrations of AsIII and methyl-As concentrations in pore water and rice grains. Water management treatment significantly altered As-speciation in the rhizosphere, and intermittent flooding reduced methyl-As and AsIII concentrations in the pore water, root-plaque and rice grain. Ordination and taxonomic analysis of detected gene-probes indicated that root-plaque and rhizosphere assembled significantly different microbial functional groups demonstrating niche separation. Taxonomic non-redundancy was evident, suggesting that As-reduction, -oxidation and -methylation processes were performed by different microbial functional groups. It was also evident that As transformation was coupled to different biogeochemical cycling processes (nutrient assimilation, carbon metabolism etc.) in the compartments and between treatments, revealing functional non-redundancy of rice-rhizosphere microbiome in response to local biogeochemical conditions and As contamination. This study provided novel insights on As-biotransformation processes and their implications on As-chemistry at the root-soil interface and their responses to water management, which could be applied for mitigating As-bioavailability and accumulation in rice grains.

Increased Antimicrobial and Multidrug Resistance Downstream of Wastewater Treatment Plants in an Urban Watershed.

Development and spread of antimicrobial resistance (AMR) and multidrug resistance (MDR) through propagation of antibiotic resistance genes (ARG) in various environments is a global emerging public health concern. The role of wastewater treatment plants (WWTPs) as hot spots for the dissemination of AMR and MDR has been widely pointed out by the scientific community. In this study, we collected surface water samples from sites upstream and downstream of two WWTP discharge points in an urban watershed in the Bryan-College Station (BCS), Texas area, over a period of nine months. E. coli isolates were tested for resistance to ampicillin, tetracycline, sulfamethoxazole, ciprofloxacin, cephalothin, cefoperazone, gentamycin, and imipenem using the Kirby-Bauer disc diffusion method. Antimicrobial resistant heterotrophic bacteria were cultured on R2A media amended with ampicillin, ciprofloxacin, tetracycline, and sulfamethoxazole for analyzing heterotrophic bacteria capable of growth on antibiotic-containing media. In addition, quantitative real-time polymerase chain reaction (qPCR) method was used to measure eight ARG - tetA, tetW, aacA, ampC, mecA, ermA, blaTEM, and intI1 in the surface water collected at each time point. Significant associations (p < 0.05) were observed between the locations of sampling sites relative to WWTP discharge points and the rate of E. coli isolate resistance to tetracycline, ampicillin, cefoperazone, ciprofloxacin, and sulfamethoxazole together with an increased rate of isolate MDR. The abundance of antibiotic-resistant heterotrophs was significantly greater (p < 0.05) downstream of WWTPs compared to upstream locations for all tested antibiotics. Consistent with the results from the culture-based methods, the concentrations of all ARG were substantially higher in the downstream sites compared to the upstream sites, particularly in the site immediately downstream of the WWTP effluent discharges (except mecA). In addition, the Class I integron (intI1) genes were detected in high amounts at all sites and all sampling points, and were about ∼20 times higher in the downstream sites (2.5 × 107 copies/100 mL surface water) compared to the upstream sites (1.2 × 106 copies/100 mL surface water). Results suggest that the treated WWTP effluent discharges into surface waters can potentially contribute to the occurrence and prevalence of AMR in urban watersheds. In addition to detecting increased ARG in the downstream sites by qPCR, findings from this study also report an increase in viable AMR (HPC) and MDR (E. coli) in these sites. This data will benefit establishment of improved environmental regulations and practices to help manage AMR/MDR and ARG discharges into the environment, and to develop mitigation strategies and effective treatment of wastewater.

Elevated Incidences of Antimicrobial Resistance and Multidrug Resistance in the Maumee River (Ohio, USA), a Major Tributary of Lake Erie.

Maumee River, the major tributary in the western basin of Lake Erie, serves as one of major sources of freshwater in the area, supplying potable, recreational, and industrial water. In this study we collected water samples from four sites in the Maumee River Bay between 2016-2017 and E. coli was isolated, enumerated, and analyzed for antimicrobial resistance (AMR) and multidrug resistance (MDR). Strikingly, 95% of the total isolates were found to be resistant to at least one antibiotic. A very high resistance to the drugs cephalothin (95.3%), ampicillin (38.3%), tetracycline (8.8%), gentamicin (8.2%), ciprofloxacin (4.2%), cefoperazone (4%), and sulfamethoxazole (1.5%) was observed within isolates from all four sampling sites. Percentages of AMR and MDR was consistently very high in the summer and fall months, whereas it was observed to be lowest in the winter. A remarkably high number of the isolates were detected to be MDR-95% resistant to ≥1 antibiotic, 43% resistant to ≥2 antibiotics, 15% resistant to ≥3 antibiotics, 4.9% resistant to ≥4 antibiotic and 1.2% resistant to ≥5 antibiotics. This data will serve in better understanding the environmental occurrence and dissemination of AMR/MDR in the area and assist in improving and establishing control measures.

Prevalence of Escherichia coli and Antibiotic-Resistant Bacteria During Fresh Produce Production (Romaine Lettuce) Using Municipal Wastewater Effluents.

High demand for food and water encourages the exploration of new water reuse programs, including treated municipal wastewater usage. However, these sources could contain high contaminant levels posing risks to public health. The objective of this study was to grow and irrigate a leafy green (romaine lettuce) with treated wastewater from a municipal wastewater treatment plant to track Escherichia coli and antibiotic-resistant microorganisms through cultivation and post-harvest storage to assess their fate and prevalence. Contamination levels found in the foliage, leachate, and soil were directly (p < 0.05) related to E. coli concentrations in the irrigation water. Wastewater concentrations from 177 to 423 CFU ml-1 resulted in 15-25% retention in the foliage. Leachate and soil presented means of 231 and 116% retention, respectively. E. coli accumulation on the foliage was observed (p < 0.05) and increased by over 400% during 14-day storage (4°C). From randomly selected E. coli colonies, in all four biomass types, 81 and 34% showed resistance to ampicillin and cephalothin, respectively. Reclaimed wastewater usage for leafy greens cultivation could pose potential health risks, especially considering the bacteria found have a high probability of being antibiotic resistance. Successful reuse of wastewater in agriculture will depend on appropriate mitigation and management strategies to guarantee an inexpensive, efficient, and safe water supply.

Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.

Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 µM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.

Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production.

The carboxylate platform utilizes a mixed microbial community to convert lignocellulosic biomass into chemicals and fuels. While much of the platform is well understood, little is known about its microbiology. Mesophilic (40 degrees C) and thermophilic (55 degrees C) fermentations employing a sorghum feedstock and marine sediment inoculum were profiled using 16S rRNA tag-pyrosequencing over the course of a 30-day incubation. The contrasting fermentation temperatures converted similar amounts of biomass, but the mesophilic community was significantly more productive, and the two temperatures differed significantly with respect to propionic and butyric acid production. Pyrotag sequencing revealed the presence of dynamic communities that responded rapidly to temperature and changed substantially over time. Both temperatures were dominated by bacteria resembling Clostridia, but they shared few taxa in common. The species-rich mesophilic community harbored a variety of Bacteroidetes, Actinobacteria, and gamma-Proteobacteria, whereas the thermophilic community was composed mainly of Clostridia and Bacilli. Despite differences in composition and productivity, similar patterns of functional class dynamics were observed. Over time, organisms resembling known cellulose degraders decreased in abundance, while organisms resembling known xylose degraders increased. Improved understanding of the carboxylate platform's microbiology will help refine platform performance and contribute to our growing knowledge regarding biomass conversion and biofuel production processes.

Whole genome sequence analysis reveals high genetic variation of newly isolated Acidithiobacillus ferrooxidans IO-2C.

Acidithiobacillus ferrooxidans, a chemolithoautotrophic bacterium, is well known for its mineral oxidizing properties. The current study combines experimental and whole genome sequencing approaches to investigate an iron oxidizing, extreme acidophilic bacterium, A. ferrooxidans isolate (IO-2C) from an acid seep area near Carlos, TX, USA. Strain IO-2C was capable of oxidizing iron i.e. iron sulphate and iron ammonium sulphate yielding shwertmannite and jarosite minerals. Further, the bacterium's genome was sequenced, assembled and annotated to study its general features, structure and functions. To determine genetic heterogeneity, it was compared with the genomes of other published A. ferrooxidans strains. Pan-genome analysis displayed low gene conservation and significant genetic diversity in A. ferrooxidans species comprising of 6926 protein coding sequences with 23.04% (1596) core genes, 46.13% (3195) unique and 30.82% (2135) accessory genes. Variant analysis showed >75,000 variants, 287 of them with a predicted high impact, in A. ferrooxidans IO-2C genome compared to the reference strain, resulting in abandonment of some important functional key genes. The genome contains numerous functional genes for iron and sulphur metabolism, nitrogen fixation, secondary metabolites, degradation of aromatic compounds, and multidrug and heavy metal resistance. This study demonstrated the bio-oxidation of iron by newly isolated A. ferrooxidans IO-2C under acidic conditions, which was further supported by genomic analysis. Genomic analysis of this strain provided valuable information about the complement of genes responsible for the utilization of iron and tolerance of other metals.

Fungal Community Structural and Microbial Functional Pattern Changes After Soil Amendments by Oilseed Meals of Jatropha curcas and Camelina sativa: A Microcosm Study.

The meals after oil extraction from many oilseed crops have nutrition and biofumigation potential for land application. Oilseed meal (SM) from the dedicated bioenergy crop Jatropha curcas were implicated to contain compounds that have antibacterial properties on some soil pathogens. However, little is known about its effect on non-targeted soil microbial community, especially on fungi. SM from Camelina sativa contains moderate level of glucosinolates (GLS) and was under studied. To investigate soil fungal community responses to jatropha and camelina SMs, we conducted a lab based microcosm study, amending soil with 1% SMs of jatropha, camelina, flax, and biomass of wheat straw. Fungal community abundance and structure were analyzed based on the ITS region using qPCR and tag-pyrosequencing. Microbial functional changes were examined by community level physiological profile (CLPP) using Biolog assay. Both SMs from jatropha and camelina showed biofumigant properties and inhibited fungal proliferation. Jatropha SM significantly altered soil fungal community structures with lower fungal biodiversity and higher Chaetomium composition. Camelina SM amended soil promoted Fusarium proliferation. CLPP indicated sequential hierarchy for C metabolism in the oilseed-amended microcosms was generally complex C > phosphate-associated C > carboxylic acids > carbohydrates > amines > amino acids. No significant difference in CLPP was detected due to the type of SM treatment. Our data indicate that both SMs of jatropha and camelina have biofumigant properties and can differentially impact soil microbial communities, and the changes were relatively persistent over time. Microbial functional patterns on the other side were not impacted by SM type. Our study revealed biofumigant and nutritional influence of SMs from dedicated biofuel plants on soil microbial community. This information will help properly using jatropha and camelina SMs for pathogen control while minimizing their negative impacts on non-target microorganisms. However, further studies in the field are demanded to investigate their influences in real practice.

Diesel degrading bacterial endophytes with plant growth promoting potential isolated from a petroleum storage facility.

Thirteen (13) endophytic bacterial strains were isolated from Echinochloa crus-galli (Cockspur grass) and Cynodon dactylon (Bermuda grass) growing in an oil-contaminated site at a petroleum storage and transportation facility. Of the 13 strains assessed for their potential to degrade monoaromatic compounds (phenol, toluene, and xylene) and diesel and for their plant growth promoting (PGP) ability (phosphate solubilization, siderophores and 1-aminocyclopropane-1-carboxylate (ACC) deaminase production), isolate J10 (identified as Pseudomonas sp. by 16S rRNA gene sequencing) was found to the best diesel biodegrader with the best PGP traits. The Monod model used for Pseudomonas sp. J10 growth kinetics on diesel fuel as the sole carbon source showed that the maximum specific bacterial growth rate was 0.0644 h- 1 and the half velocity constant (K s ) was estimated as 4570 mg L- 1. The overall growth yield coefficient and apparent growth yield were determined to be 0.271 g h- 1 and 0.127 g cells/g substrate, respectively. Pseudomonas sp. J10 removed 69% diesel in four days as determined by gas chromatographic (GC) analysis. These findings could assist in developing an endophyte assisted efficient diesel biodegradation system using Pseudomonas sp. J10 isolated from Echinochloa crus-galli.

Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels.

Microbial enumeration, 16S rRNA gene clone libraries, and chemical analysis were used to evaluate the in situ biological reduction and immobilization of uranium(VI) in a long-term experiment (more than 2 years) conducted at a highly uranium-contaminated site (up to 60 mg/liter and 800 mg/kg solids) of the U.S. Department of Energy in Oak Ridge, TN. Bioreduction was achieved by conditioning groundwater above ground and then stimulating growth of denitrifying, Fe(III)-reducing, and sulfate-reducing bacteria in situ through weekly injection of ethanol into the subsurface. After nearly 2 years of intermittent injection of ethanol, aqueous U levels fell below the U.S. Environmental Protection Agency maximum contaminant level for drinking water and groundwater (<30 microg/liter or 0.126 microM). Sediment microbial communities from the treatment zone were compared with those from a control well without biostimulation. Most-probable-number estimations indicated that microorganisms implicated in bioremediation accumulated in the sediments of the treatment zone but were either absent or in very low numbers in an untreated control area. Organisms belonging to genera known to include U(VI) reducers were detected, including Desulfovibrio, Geobacter, Anaeromyxobacter, Desulfosporosinus, and Acidovorax spp. The predominant sulfate-reducing bacterial species were Desulfovibrio spp., while the iron reducers were represented by Ferribacterium spp. and Geothrix spp. Diversity-based clustering revealed differences between treated and untreated zones and also within samples of the treated area. Spatial differences in community structure within the treatment zone were likely related to the hydraulic pathway and to electron donor metabolism during biostimulation.