Rhizosphere Microbiomes of Potato Cultivated under Bacillus subtilis Treatment Influence the Quality of Potato Tubers.

Plants serve as a niche for the growth and proliferation of a diversity of microorganisms. Soil microorganisms, which closely interact with plants, are increasingly being recognized as factors important to plant health. In this study, we explored the use of high-throughput DNA sequencing of the fungal ITS and bacterial 16S for characterization of the fungal and bacterial microbiomes following biocontrol treatment (DT) with Bacillus subtilis strain Bv17 relative to treatments without biocontrol (DC) during the potato growth cycle at three time points. A total of 5631 operational taxonomic units (OTUs) were identified from the 16S data, and 2236 OTUs were identified from the ITS data. The number of bacterial and fungal OTU in DT was higher than in DC and gradually increased during potato growth. In addition, indices such as Ace, Chao, Shannon, and Simpson were higher in DT than in DC, indicating greater richness and community diversity in soil following the biocontrol treatment. Additionally, the potato tuber yields improved without a measurable change in the bacterial communities following the B. subtilis strain Bv17 treatment. These results suggest that soil microbial communities in the rhizosphere are differentially affected by the biocontrol treatment while improving potato yield, providing a strong basis for biocontrol utilization in crop production.

Comparison of bacterial and archaeal communities in two fertilizer doses and soil compartments under continuous cultivation system of garlic.

Soil microbial communities are affected by interactions between agricultural management (e.g., fertilizer) and soil compartment, but few studies have considered combinations of these factors. We compared the microbial abundance, diversity and community structure in two fertilizer dose (high vs. low NPK) and soil compartment (rhizosphere vs. bulk soils) under 6-year fertilization regimes in a continuous garlic cropping system in China. The soil contents of NO3- and available K were significantly higher in bulk soil in the high-NPK. The 16S rRNA gene-based bacterial and archaeal abundances were positively affected by both the fertilizer dose and soil compartment, and were higher in the high-NPK fertilization and rhizosphere samples. High-NPK fertilization increased the Shannon index and decreased bacterial and archaeal richness, whereas the evenness was marginally positively affected by both the fertilizer dose and soil compartment. Soil compartment exerted a greater effect on the bacterial and archaeal community structure than did the fertilization dose, as demonstrated by both the nonmetric multidimensional scaling and redundancy analysis results. We found that rhizosphere effects significantly distinguished 12 dominant classes of bacterial and archaeal communities, whereas the fertilizer dose significantly identified four dominant classes. In particular, a Linear Effect Size analysis showed that some taxa, including Alphaproteobacteria, Rhizobiales, Xanthomonadaceae and Flavobacterium, were enriched in the garlic rhizosphere of the high-NPK fertilizer samples. Overall, the fertilizer dose interacted with soil compartment to shape the bacterial and archaeal community composition, abundance, and biodiversity in the garlic rhizosphere. These results provide an important basis for further understanding adaptive garlic-microbe feedback, reframing roots as a significant moderating influence in agricultural management and shaping the microbial community.

Deciphering the associated risk on soil microbes upon use of biopesticides in rice ecosystem.

Plant species, viz Cleistanthus collinus, Lantana camara, and Strychnos nux-vomica are being traditionally used for pest management in rice. However, limited investigation has been carried out to understand the toxic effect of these materials on soil microbes. Hot water extracts of these plants were evaluated for their effects on soil microbial population and enzyme activities along with neem oil and chlorpyrifos as check. Soil microbial population, viz bacteria, fungi, phosphate-solubilizing bacteria (PSB), and asymbiotic nitrogen fixers were unchanged after application of plant extracts. Maximum population of bacteria including PSB and asymbiotic nitrogen fixers were observed in control, whereas, S. nux-vomica, and C. collinus-treated soil had higher number of actinomycetes and fungal population, respectively. Soil microbial biomass did not vary differently among the plant extracts. Application of plant extracts did not alter dehydrogenase, ß-glycosidase, acid phosphatase, alkaline phosphatase, and urease content in soil. Secondary metabolites present in these plant extracts may be responsible for variable effects on soil microbes. Chlorpyrifos had a fleeting negative effect on soil microbes and enzymes in comparison to plant extracts. All the three plants did not have any negative effect on soil microbes and enzymes and can be safely recommended in rice pest management.

Soil nutrients status affected by simple and enriched biochar application under salinity conditions.

In order to study the effect of biochar application as simple and enriched, on the soil nutrients status in the salinity conditions, a research was conducted as a factorial arrangement based on completely randomized design (CRD) with three replicates. The biochar (grape pruning residues) was applied in three levels (0, 2% biochar, and 2% enriched biochar by rock phosphate and cow manure). Also, the salinity treatment was considered in three levels (2, 4.5, and 9 dSm-1). After treating the soil, it was incubated in polyethylene containers for a 70-day period at 25 °C and 70% field capacity moisture regime. The results showed that salinity significantly affected the soil pH, electrical conductivity (EC), calcium, magnesium, sodium, basal respiration, and nitrifying bacteria frequency (P < 0.001) and chloride concentration (P < 0.01). Also, the biochar significantly affected the pH, organic carbon, concentration of total nitrogen, phosphorous, solution potassium, sodium, iron, zinc, copper, basal respiration, and nitrifying bacteria frequency (P < 0.001) of the soil. The interaction effect of biochar and salinity levels was significant on soil sodium concentration (P < 0.01) and pH (P < 0.05). In comparison with the control treatment, the enriched biochar, decreased soil pH (about 1.4%) and increased the phosphorous, iron, and zinc up to 36%, 29%, and 36%, respectively and simple biochar increased the Nitrogen and Potassium up to 46% and 48%, respectively. In general, it was concluded that both types of the biochars lowered the sodium concentration of the soil in different salinity levels due to high potential of biochar for sodium absorption which this ability may be considered in saline soils remediation.

Municipal solid wastes as a resource for environmental recovery: Impact of water treatment residuals and compost on the microbial and biochemical features of As and trace metal-polluted soils.

In this study we evaluated the microbiological and biochemical impact of iron-based water treatment residuals (Fe-WTRs) and municipal solid waste compost (MSWC), alone and combined, on three different soils co-contaminated with arsenic (As) and trace-metals (TM), i.e. Pb, Cu and Zn. Overall, all the amendments considered significantly increased the abundance of culturable heterotrophic bacteria, with MSWC showing the greatest impact across all soils (up to a 24% increase). In most of treated soils this was accompanied by a significant reduction of both the (culturable) fungal/bacterial ratio, and the proportion of culturable As(V)- and As(III)-resistant bacteria with respect to total bacterial population. The catabolic potential and versatility of the resident microbial communities (assessed by community level physiological profile) was highly soil-dependent and substantial increases of both parameters were observed in the amended soils with the higher total As concentration (from approx. 749 to 22,600 mg kg-1). Moreover, both carbon source utilisation profile and 16S rRNA soil metagenome sequencing indicated a significant impact of MSWC and Fe-WTRs on the structure and diversity of soil microbial communities, with Proteobacteria, Actinobacteria and Firmicutes being the most affected taxa. The assessment of selected soil enzyme activities (dehydrogenase, urease and ß-glucosidase) indicated an increase of metabolic functioning especially in soils treated with MSWC (e.g. dehydrogenase activity increased up to 19.5-fold in the most contaminated soil treated with MSWC). Finally, the microbial and biochemical features of treated (and untreated) contaminated soils (i.e. total bacterial counts, catabolic potential and versatility and soil enzyme activities) were highly correlated with the concentrations of labile As and TM in these latter soils and supported a clear role of the tested amendments (especially MSWC) as As- and TM-immobilising agents.

Negative effect of copper nanoparticles on the conjugation frequency of conjugative catabolic plasmids.

Due to their antimicrobial properties, copper nanoparticles (CuNPs) have been proposed to be used in agriculture for pest control. Pesticides removal is mainly done by microorganisms, whose genes usually are found in conjugative catabolic plasmids (CCP). The aim of this work was to evaluate if CuNPs at subinhibitory concentrations modify the conjugation frequency (CF) of two CCP (pJP4 and pADP1). CuNPs were characterized by scanning electron microscopy with an X-ray detector, dynamic light scattering and X-ray diffraction. Mating assays were done in LB broth supplemented with CuNPs (10, 20, 50 and 100 µg mL-1) or equivalent concentrations of CuSO4. Interestingly, we observed that in LB, Cu+2 release from CuNPs is fast as evaluated by atomic absorption spectrophotometry. Donor and recipient strains were able to grow in all copper concentrations assayed, but CF of mating pairs was reduced to 10% in the presence of copper at 20 or 50 µg Cu mL-1 compared to control. Thus, our results indicated that both copper forms, CuNPs or CuSO4, negatively affected the transfer of catabolic plasmids by conjugation. Since dissemination of degradative genes by conjugation contribute to degradation of pesticides by microorganisms, this work improves our understanding of the risks of using copper in agriculture soils, which could affect the biodegradative potential of microbial communities.

Continuous cropping of endangered therapeutic plants via electron beam soil-treatment and neutron tomography.

Various medicinal plants are threatened with extinction owing to their over-exploitation and the prevalence of soil borne pathogens. In this study, soils infected with root-rot pathogens, which prevent continuous-cropping, were treated with an electron beam. The level of soil-borne fungus was reduced to ≤0.01% by soil electron beam treatment without appreciable effects on the levels of antagonistic microorganism or on the physicochemical properties of the soil. The survival rate of 4-year-old plant was higher in electron beam-treated soil (81.0%) than in fumigated (62.5%), virgin (78%), or untreated-replanting soil (0%). Additionally, under various soils conditions, neutron tomography permitted the monitoring of plant health and the detection of root pathological changes over a period of 4-6 years by quantitatively measuring root water content in situ. These methods allow continual cropping on the same soil without pesticide treatment. This is a major step toward the environmentally friendly production of endangered therapeutic herbs.

Impact of the Fenton-like treatment on the microbial community of a diesel-contaminated soil.

Fenton-like treatment (FLT) is an ISCO technique relying on the iron-induced H2O2 activation in the presence of additives aimed at increasing the oxidant lifetime and maximizing iron solubility under natural soil pH conditions. The efficacy of FLT in the clean-up of hydrocarbon-contaminated soils is well established at the field-scale. However, a better assessment of the impact of the FLT on density, diversity and activity of the indigenous soil microbiota, might provide further insights into an optimal combination between FLT and in-situ bioremediation (ISB). The aim of this work was to assess the impacts of FLT on the microbial community of a diesel-contaminated soil collected nearby a gasoline station. Different FLT conditions were tested by varying either the H2O2 concentrations (2 and 6%) or the oxidant application mode (single or double dosage). The impact of these treatments on the indigenous microbial community was assessed immediately after the Fenton-like treatment and after 30, 60 and 90 d and compared with enhanced natural attenuation (ENA). After FLT, a dramatic decrease in bacterial density, diversity and functionality was evident. Although in microcosms with double dosing at 2% H2O2 a delayed recovery of the indigenous microbiota was observed as compared to those subjected to single oxidant dose, after 60 d incubation the respiration rate increased from 0.036 to 0.256 µg CCO2 g-1soil h-1. Irrespective of the oxidant dose, best degradation results after 90 d incubation (around 80%) were observed with combined FLT, relying on double oxidant addition, and bioremediation.

Distribution of ion contents and microorganisms during the electro-bioremediation of petroleum-contaminated saline soil.

This study investigated the distribution of ion contents and microorganisms during the electro-bioremediation (EK-Bio) of petroleum-contaminated saline soil. The results showed that soil ions tend to accumulate around the electrodes, and the concentration was correlated with the distance from the electrodes. The average soil ion content was 7.92 g/kg around the electrodes (site A) and 0.55 g/kg at the furthest distance from the electrodes (site B) after 112 days of treatment, while the initial average content was 3.92 g/kg. Smooth linear (R2 = 0.98) loss of soil ions was observed at site C, which was closer to the electrodes than site B, and had a final average soil ion content of 1.96 g/kg. The dehydrogenase activity was much higher in EK-Bio test soil than in the Bio test soil after 28 days of treatment, and followed the order: site C > site B > site A. However, the soil dehydrogenase activity dropped continuously when the soil ion reached very high and low concentrations at sites A and B. The soil microbial community varied in sample sites that had different ion contents, and the soil microbial diversity followed the order: site C > site B > site A. The applied electric field clearly enhanced the biodegradation efficiency for soil petroleum contaminants. However, the biodegradation promotion effects were weakening in soils where the ion contents were extremely high and low (sites A and B). These results can provide useful information for EK-Bioremediation of organic-contaminated saline soil.

Soil-transmitted helminthiasis: the relationship between prevalence and classes of intensity of infection.

BACKGROUND: Recently, WHO has developed a predictive model to evaluate the impact of preventive chemotherapy programs to control the morbidity of soil-transmitted helminths (STHs). To make predictions, this model needs baseline information about the proportion of infections classified as low, moderate and high intensity, for each of the three STH species. However, epidemiological data available are often limited to prevalence estimates. METHODS: We reanalyzed available data from 19 surveys in 10 countries and parameterized the relationship between prevalence of STH infections and the proportion of moderate and heavy intensity infections. RESULTS: The equations derived allow feeding the WHO model with estimates of the proportion of the different classes of infection intensity when only prevalence data is available. CONCLUSIONS: The prediction capacities of the STH model using the equations developed in the present study, should be tested by comparing it with the changes on STH epidemiological data observed in control programs operating for several years.

A framework for developing research protocols for evaluation of microbial hazards and controls during production that pertain to the application of untreated soil amendments of animal origin on land used to grow produce that may be consumed raw.

Application of manure or soil amendments of animal origin (untreated soil amendments; UTSAs) to agricultural land has been a long-standing practice to maintain or improve soil quality through addition of organic matter, nitrogen, and phosphorus. Much smaller quantities of these types of UTSAs are applied to land used for food crops than to land used for animal grain and forage. UTSAs can harbor zoonotic enteric pathogens that may survive for extended periods after application. Additional studies are needed to enhance our understanding of preharvest microbial food safety hazards and control measures pertaining to the application of UTSAs especially for land used to grow produce that may be consumed raw. This document is intended to provide an approach to study design and a framework for defining the scope and type of data required. This document also provides a tool for evaluating the strength of existing data and thus can aid the produce industry and regulatory authorities in identifying additional research needs. Ultimately, this framework provides a means by which researchers can increase consistency among and between studies and facilitates direct comparison of hazards and efficacy of controls applied to different regions, conditions, and practices.

Effect of nitrogen amendment on respiration and respiratory quotient (RQ) in three hydrocarbon contaminated soils of different type.

Three soil types (sandy gravel, silty clay and sandy loam) from sites historically contaminated with total petroleum hydrocarbon (TPH) were amended with NH(4)NO(3) at concentrations ranging from 16 to 2133 mg/kg soil(dry weight). Microbial activity was measured as O(2) consumption and CO(2) production in order to assess nitrogen limitation. Although activity was stimulated in all three soils under NH(4)NO(3) amendment (after 72 h), the level of nitrogen required was soil specific. For the sandy gravel and silty clay soils, O(2) consumption and CO(2) production both showed enhanced microbial activity when amended with 16 mg/kg soil(dry weight) NH(4)NO(3), whereas, these two parameters gave differing results for the sandy loam soil. Specifically, CO(2) production and O(2) consumption were stimulated with 66 mg/kg and 133 mg/kg soil(dry weight) of NH(4)NO(3) respectively. In addition, respiratory quotient kinetic analysis suggested different decomposition processes occurring in this soil under different NH(4)NO(3) amendment concentrations.

[Mathematical simulation of accumulation of opportunistic micromycetes in petroleum-polluted soils].

The impact of pollution of different types of soils (leached chernozem, grey wood and dark-grey wood soils) with petroleum and its products on the size, species-specific composition, and accumulation of opportunistic micromycetes was studied in long-term field microallotment and laboratory conditions. Petroleum and its refining products were shown to increase the size of micromycetes and to change their structure and species diversity. A mathematical model has been developed, which describes the time course of changes in the size of mushroom propagules under different environmental conditions.

Pilot-scale electrokinetic treatment of a Cu contaminated red soil.

A pilot-scale experiment for electrokinetic treatment of 700 kg of copper contaminated red soil was conducted using a constant voltage of 80 V. Dynamic removal percentages of Cu from the soil and energy consumption during the treatment were evaluated together with changes of soil pH, electrical conductivity and soil microbial functional diversity before and after the electrokinetic treatment. The results indicate that 76% of Cu was successfully removed from the soil after 140 d of treatment when lactic acid was used as enhancing reagent for adjusting the catholyte pH and dissolving soil Cu by complexation, and the pilot-scale electrokinetic experiment consumed electric energy of 224 kW h t-1 soil. The post-treatment soil pH values decreased about 0.1-1.6 units compared with the initial value (pH 4.8), and soil electrical conductivities in most of soil sections also significantly decreased. Soil microbial functional diversity varied after the electrokinetic treatment, particularly the increase of substrate richness index, which is possibly due to the stimulation of lactic acid that was introduced into the soil column during the experiment.

Bioremediation of chlorate or perchlorate contaminated water using permeable barriers containing vegetable oil.

A scale model of an in situ permeable barrier, formed by injecting vegetable oil onto laboratory soil columns, was used to remove chlorate and perchlorate from flowing groundwater. The hypothesis that trapped oil would serve as a substrate enabling native microorganisms to reduce chlorate or perchlorate to chloride as water flowed through the oil-rich zone had merit. Approximately 96% of the 0.2 mM chlorate and 99% of the 0.2 mM perchlorate present in the water was removed as water was pumped through columns containing vegetable oil barriers. The product formed was chloride. When nitrate at 1.4 mM was added to the water, both nitrate and chlorate were removed. High concentrations of chlorate or perchlorate can be treated; 24 m M chlorate and 6 mM perchlorate were completely reduced to chloride during microcosm incubations. Microorganisms capable of reducing perchlorate are plentiful in the environment.

Soil and solid poultry waste nutrient management and water quality.

Concerns about the impacts of nitrogen, phosphorus, and pathogens on surface and ground water quality has forced the poultry industry to implement voluntary waste management guidelines for use by growers. In some states, animal waste guidelines are being enforced by regulatory agencies. Strategies that growers may use to properly dispose of poultry waste include: 1) local land application as a fertilizer; 2) offsite marketing for use as a fertilizer or soil amendment, feed additive, or energy source; and 3) chemical additives that will immobilize nitrogen and phosphorus in the manure or litter. If properly followed, these and other innovative strategies should be adequate to protect surface and ground water quality without adversely affecting the economics of poultry production.