Effects of a phosphinothricin based herbicide on selected groups of soil microorganisms

Heterologous expression of a deacetylase and its application in L-glufosinate preparation

With potent herbicidal activity, biocatalysis synthesis of L-glufosinate has drawn attention. In present research, NAP-Das2.3, a deacetylase capable of stereoselectively resolving N-acetyl-L-glufosinate to L-glufosinate mined from Arenimonas malthae, was heterologously expressed and characterized. In Escherichia coli, NAP-Das2.3 activity only reached 0.25 U/L due to the formation of inclusive bodies. Efficient soluble expression of NAP-Das2.3 was achieved in Pichia pastoris. In shake flask and 5 L bioreactor fermentation, NAP-Das2.3 activity by recombinant P. pastoris reached 107.39 U/L and 1287.52 U/L, respectively. The optimum temperature and pH for N-acetyl-glufosinate hydrolysis by NAP-Das2.3 were 45 °C and pH 8.0, respectively. The Km and Vmax of NAP-Das2.3 towards N-acetyl-glufosinate were 25.32 mM and 19.23 μmol mg-1 min-1, respectively. Within 90 min, 92.71% of L-enantiomer in 100 mM racemic N-acetyl-glufosinate was converted by NAP-Das2.3. L-glufosinate with high optical purity (e.e.P above 99.9%) was obtained. Therefore, the recombinant NAP-Das2.3 might be an alternative for L-glufosinate biosynthesis.

Insights into the effects of sublethal doses of pesticides glufosinate-ammonium and sulfoxaflor on honey bee health

Insect pollinators are threatened worldwide, being the exposure to multiple pesticides one of the most important stressor. The herbicide Glyphosate and the insecticide Imidacloprid are among the most used pesticides worldwide, although different studies evidenced their detrimental effects on non-target organisms. The emergence of glyphosate-resistant weeds and the recent ban of imidacloprid in Europe due to safety concerns, has prompted their replacement by new molecules, such as glufosinate-ammonium (GA) and sulfoxaflor (S). GA is a broad-spectrum and non-selective herbicide that inhibits a key enzyme in the metabolism of nitrogen, causing accumulation of lethal levels of ammonia; while sulfoxaflor is an agonist at insect nicotinic acetylcholine receptors (nAChRs) and generates excitatory responses including tremors, paralysis and mortality. Although those molecules are being increasingly used for crop protection, little is known about their effects on non-target organisms. In this study we assessed the impact of chronic and acute exposure to sublethal doses of GA and S on honey bee gut microbiota, immunity and survival. We found GA significantly reduced the number of gut bacteria, and decreased the expression of glucose oxidase, a marker of social immunity. On the other hand, S significantly increased the number of gut bacteria altering the microbiota composition, decreased the expression of lysozyme and increased the expression of hymenoptaecin. These alterations in gut microbiota and immunocompetence may lead to an increased susceptibility to pathogens. Finally, both pesticides shortened honey bee survival and increased the risk of death. Those results evidence the negative impact of GA and S on honey bees, even at single exposition to a low dose, and provide useful information to the understanding of pollinators decline.

Impact of Weed Management Practices on Soil Microflora and Dehydrogenase Enzyme Activity Under Varying Levels of Nitrogen in Winter Season Onion (Allium cepa L.)

The study was conducted to evaluate the suitability of different weed management practices under influence of varying levels of N doses to test their effects on the various soil microflora and dehydrogenase enzyme activity in the winter onion field during 2016-2017 and 2017-2018. There were a total of twenty eight treatments replicated three times under the split-plot design (SPD). The treatments associated with weed management practices were applied to the main plots and the different N doses were given in each subplot. Microbial population and dehydrogenase enzyme activity in soil and crop weed competition index were determined. The two-hand weeding (HW) at 20 and 40 days after transplanting (DAT) of onion seedlings as well as preplant application of oxyfluorfen along with one HW at 40 DAT, exhibited a significant increase in dehydrogenase activity and microbial population in the soil when the N was applied at 100 kg ha^-1. The study suggests that suitable weed management practices for the winter onion exerts a transient impact on soil microbial population, maintained good soil health and reduced crop-weed competition (CWC) with relatively less environmental hazards.

Herbicides in vineyards reduce grapevine root mycorrhization and alter soil microorganisms and the nutrient composition in grapevine roots, leaves, xylem sap and grape juice

Herbicides are increasingly applied in vineyards worldwide. However, not much is known on potential side effects on soil organisms or on the nutrition of grapevines (Vitis vinifera). In an experimental vineyard in Austria, we examined the impacts of three within-row herbicide treatments (active ingredients: flazasulfuron, glufosinate, glyphosate) and mechanical weeding on grapevine root mycorrhization; soil microorganisms; earthworms; and nutrient concentration in grapevine roots, leaves, xylem sap and grape juice. The three herbicides reduced grapevine root mycorrhization on average by 53% compared to mechanical weeding. Soil microorganisms (total colony-forming units, CFU) were significantly affected by herbicides with highest CFUs under glufosinate and lowest under glyphosate. Earthworms (surface casting activity, density, biomass, reproduction) or litter decomposition in soil were unaffected by herbicides. Herbicides altered nutrient composition in grapevine roots, leaves, grape juice and xylem sap that was collected 11 months after herbicide application. Xylem sap under herbicide treatments also contained on average 70% more bacteria than under mechanical weeding; however, due to high variability, this was not statistically significant. We conclude that interdisciplinary approaches should receive more attention when assessing ecological effects of herbicides in vineyard ecosystems.

The effects of glyphosate, glufosinate, paraquat and paraquat-diquat on soil microbial activity and bacterial, archaeal and nematode diversity

In this study, we investigated the effects of one-off applications of glyphosate, glufosinate, paraquat, and paraquat-diquat on soil microbial diversity and function. All herbicides were added to soil as pure compounds at recommended dose and were incubated under laboratory conditions for 60 days. High-throughput phylogenetic marker gene sequencing revealed that none of the herbicides significantly influenced the richness, evenness and composition of bacterial and archaeal communities. Likewise, the diversity, composition and size of nematode communities were not significantly influenced by any of the herbicides. From a functional perspective, herbicides did not significantly affect fluorescein diacetate hydrolysis (FDA) and beta-glucosidase activities. Furthermore, the ability of soil organisms to utilise 15 substrates was generally unaffected by herbicide application. The only exception to this was a temporary impairment in the ability of soil organisms to utilise three organic acids and an amino acid. Given the global and frequent use of these herbicides, it is important that future studies evaluate their potential impacts on microbial communities in a wider-range of soils and environmental conditions.

Assessing the impact of copper and zinc oxide nanoparticles on soil: a field study

It is not known if the annual production of tonnes of industrial nanoparticles (NPs) has the potential to impact terrestrial microbial communities, which are so necessary for ecosystem functioning. Here, we have examined the consequences of adding zero valent copper and zinc oxide NPs to soil in pots that were then maintained under field conditions. The fate of these NPs, as well as changes in the microbial communities, was monitored over 162 days. Both NP types traveled through the soil matrix, albeit at differential rates, with Cu NPs retained in the soil matrix at a higher rate compared to ZnO NPs. Leaching of Cu and Zn ions from the parent NPs was also observed as a function of time. Analysis of microbial communities using culture-dependent and independent methods clearly indicated that Cu and ZnO NPs altered the microbial community structure. In particular, two orders of organisms found in rhizosphere, Flavobacteriales and Sphingomonadales, appeared to be particularly susceptible to the presence of NPs. Together, the migration of NPs through soil matrix and the ability of these potential pollutants to influence the composition of microbial community in this field study, cannot help but raise some environmental concerns.

Effect of methyl parathion on nitrous oxide production: a laboratory study

We investigated the diversity of a denitrifying gene (nirK) and the emission of CO(2) and N(2)O, in a "chinampa" soil contaminated with methyl parathion. Soil at 40% of water holding capacity was spiked with methyl parathion at four concentrations (i.e. 0, 0.7, 1.47 and 4.27 g kg(-1) dry soil), while emission of N(2)O and CO(2) and nirK diversity was determined after 0, 1, 14, 30, 60 and 90 days. The emission of N(2)O on a daily base and the cumulative emission of CO(2) was not affected by the different concentrations of methyl parathion applied to soil. The diversity of the nirK gene, determined by using temperature gradient gel electrophoresis (TGGE), decreased with increased methyl parathion application. It was found that methyl parathion had effect on the emissions of N(2)O and CO(2), and reduced the diversity of the nirK gene. Consequently, the reduced diversity of the nirK gene could affect the emission of N(2)O.

Bacterial and archaea community present in the Pine Barrens Forest of Long Island, NY: unusually high percentage of ammonia oxidizing bacteria

Of the few preserved areas in the northeast of United States, the soil in the Pine Barrens Forests presents a harsh environment for the microorganisms to grow and survive. In the current study we report the use of clustering methods to scientifically select the sampling locations that would represent the entire forest and also report the microbial diversity present in various horizons of the soil. Sixty six sampling locations were selected across the forest and soils were collected from three horizons (sampling depths). The three horizons were 0-10 cm (Horizon O); 11-25 cm (Horizon A) and 26-40 cm (Horizon B). Based on the total microbial substrate utilization pattern and K-means clustering analysis, the soil in the Pine Barrens Forest can be classified into four distinct clusters at each of the three horizons. One soil sample from each of the four clusters were selected and archaeal and bacterial populations within the soil studied using pyrosequencing method. The results show the microbial communities present in each of these clusters are different. Within the microbial communities present, microorganisms involved in nitrogen cycle occupy a major fraction of microbial community in the soil. High level of diversity was observed for nitrogen fixing bacteria. In contrast, Nitrosovibrio and Nitrosocaldus spp are the single bacterial and archaeal population respectively carrying out ammonia oxidation in the soil.

Impacts of wastewater sludge amendments in restoring nitrogen cycle in p-nitrophenol contaminated soil

The possible impacts on nitrogen-cycle in a p-nitrophenol (PNP) polluted soil and the effectiveness of wastewater sludge amendments in restoring nitrification potential and urease activity were evaluated by an incubation study. The results indicated that PNP at 250 mg/kg soil inhibited urease activity, nitrification potential, arginine ammonification rate and heterotrophic bacteria counts to some extents. After exposure to PNP, the nitrification potential of the tested soil was dramatically reduced to zero over a period of 30 days. Based on the findings, nitrification potential was postulated as a simple biochemical indicator for PNP pollution in soils. Nitrogen-cycling processes in soils responded positively to the applications of wastewater sludges. A sludge application rate of 200 tons/ha was sufficient for successful biostimulation of these nitrogen processes. The microbial activities in sludge-amended, heavy PNP-polluted soils seemed to recover after 30-45 days, indicating the effectiveness of sludge as a useful soil amendment.

Comparison of neem or oregano with thiram on organic matter decomposition of a sand loam soil amended with compost, and on soil biological activity

BACKGROUND

Oregano essential oil and neem have been reported to be effective against soil-borne pathogens and nematodes. The possibility of having an effect on soil properties was the aim of this investigation. Moreover, thiram, a common widely used chemical pesticide, was used for comparison.

RESULTS

The effects of all three above-mentioned substances were investigated during an incubation experiment, for 15 weeks. Crushed neem pellets were added at 1.0, 2.0 or 3.0 g per 50 g of soil. Oregano dry matter was applied at 0.2, 0.4 or 0.6 g per 50 g of soil. Finally, thiram was applied at 0.1, 0.2 and 0.3 g per 50 g of soil. The addition of neem resulted in a decrease in organic carbon mineralisation, higher than that of oregano, but not as prominently as thiram. The addition of neem resulted in an increase in the content of nitrate, organic P, bioavailable P, bioavailable K and bioavailable Mn. Oregano had a slight negative effect on organic matter biodegradation, but caused an increase of nutritional mineral elements. Microbe colonies in soil were increased by the addition of neem cake granules, whereas oregano and thiram treatments caused a decrease. The addition of thiram reduced nitrate and available Mn contents, but at the lowest dose increased organic P and available K. Thiram reduced prominently available Cu at the upper rates, but it increased these forms at the lowest rate, while available Zn content was increased in two lowest rates.

CONCLUSION

The results of this study indicated that neem or oregano could be applied to the soil without any extremely negative effect on the available forms of nutritional mineral elements, as thiram does.

Recovery of useful traits from isolates inhabiting an agricultural soil cultivated with herbicide-resistant poplars

The aim of this study was to investigate the culturable bacteria living in soil cultivated with Basta-tolerant transgenic white poplars (Populus alba L. 'Villafranca'). Plate Count Agar medium containing phosphinothricin, the active component of Basta, was used to isolate the herbicide-resistant bacteria (HRB). No significant changes in the size of the soil microbial flora following herbicide treatment were observed. The characterization of HRB isolates by 16S rDNA-based taxonomy revealed a predominance of Pseudomonas and Bacillus species. The screening carried out on soil samples allowed for the recovery of isolates with useful properties for biotechnological and agronomical purposes, particularly in relation to root development. Among the tested isolates, only HRB-1b, HRB-1c, and HRB-7 showed remarkable swarming ability, a valuable trait supporting the beneficial plant-microbe interactions. HRB-1c was also characterized by consistent production of indoleacetic acid (17.8 +/- 0.09 microg x mL-1 x (OD600 unit)-1), and it was able to stimulate the in vitro growth of Villafranca explants. Since novel tools are constantly required to enhance productivity of perennial species and to expand their use for practical purposes, the availability of bacteria that support tree growth, such as the HRB-1c isolate, represents a significant advantage.