Intensive vegetable production under plastic mulch: A field study on soil plastic and pesticide residues and their effects on the soil microbiome.

Intensive agriculture relies on external inputs to reach high productivity and profitability. Plastic mulch, mainly in the form of Low-Density Polyethylene (LDPE), is widely used in agriculture to decrease evaporation, increase soil temperature and prevent weeds. The incomplete removal of LDPE mulch after use causes plastic contamination in agricultural soils. In conventional agriculture, the use of pesticides also leaves residues accumulating in soils. Thus, the objective of this study was to measure plastic and pesticide residues in agricultural soils and their effects on the soil microbiome. For this, we sampled soil (0-10 cm and 10-30 cm) from 18 parcels from 6 vegetable farms in SE Spain. The farms were under either organic or conventional management, where plastic mulch had been used for >25 years. We measured the macro- and micro-light density plastic debris contents, the pesticide residue levels, and a range of physiochemical properties. We also carried out DNA sequencing on the soil fungal and bacterial communities. Plastic debris (>100 µm) was found in all samples with an average number of 2 × 103 particles kg-1 and area of 60 cm2 kg-1. We found 4-10 different pesticide residues in all conventional soils, for an average of 140 µg kg-1. Overall, pesticide content was ∼100 times lower in organic farms. The soil microbiomes were farm-specific and related to different soil physicochemical parameters and contaminants. Regarding contaminants, bacterial communities responded to the total pesticide residues, the fungicide Azoxystrobin and the insecticide Chlorantraniliprole as well as the plastic area. The fungicide Boscalid was the only contaminant to influence the fungal community. The wide spread of plastic and pesticide residues in agricultural soil and their effects on soil microbial communities may impact crop production and other environmental services. More studies are required to evaluate the total costs of intensive agriculture.

Molecular methods (digital PCR and real-time PCR) for the quantification of low copy DNA of Phytophthora nicotianae in environmental samples.

BACKGROUND: Currently, real-time polymerase chain reaction (qPCR) is the technique most often used to quantify pathogen presence. Digital PCR (dPCR) is a new technique with the potential to have a substantial impact on plant pathology research owing to its reproducibility, sensitivity and low susceptibility to inhibitors. In this study, we evaluated the feasibility of using dPCR and qPCR to quantify Phytophthora nicotianae in several background matrices, including host tissues (stems and roots) and soil samples. RESULTS: In spite of the low dynamic range of dPCR (3 logs compared with 7 logs for qPCR), this technique proved to have very high precision applicable at very low copy numbers. The dPCR was able to detect accurately the pathogen in all type of samples in a broad concentration range. Moreover, dPCR seems to be less susceptible to inhibitors than qPCR in plant samples. Linear regression analysis showed a high correlation between the results obtained with the two techniques in soil, stem and root samples, with R(2) = 0.873, 0.999 and 0.995 respectively. CONCLUSIONS: These results suggest that dPCR is a promising alternative for quantifying soil-borne pathogens in environmental samples, even in early stages of the disease.

Identification of predictor parameters to determine agro-industrial compost suppressiveness against Fusarium oxysporum and Phytophthora capsici diseases in muskmelon and pepper seedlings.

BACKGROUND: The lack of reliable prediction tools for evaluation of the level and specificity of compost suppressiveness limits its application. In our study, different chemical, biological and microbiological parameters were used to evaluate their potential use as a predictor parameter for the suppressive effect of composts against Fusarium oxysporum f. sp. melonis (FOM) and Phytophthora capsici (P. capsici) in muskmelon and pepper seedlings respectively. Composts were obtained from artichoke sludge, chopped vineyard pruning waste and various agro-industrial wastes (C1: blanched artichokes; C2: garlic waste; C3: dry olive cake). RESULTS: Compost C3 proved to offer the highest level of resistance against FOM, and compost C2 the highest level of resistance against P. capsici. Analysis of phospholipid fatty acids isolated from compost revealed that the three composts showed different microbial community structures. Protease, NAGase and chitinase activities were significantly higher in compost C3, as was dehydrogenase activity in compost C2. CONCLUSION: The use of specific parameters such as general (dehydrogenase activity) and specific enzymatic activities (protease, NAGase and chitinase activities) may be useful to predict compost suppressiveness against both pathogens. The selection of raw materials for agro-industrial composts is important in controlling Fusarium wilt and Phytophthora root rot.

Changes induced by Trichoderma harzianum in suppressive compost controlling Fusarium wilt.

The addition of species of Trichoderma to compost is a widespread technique used to control different plant diseases. The biological control activity of these species is mainly attributable to a combination of several mechanisms of action, which may affect the microbiota involved in the suppressiveness of compost. This study was therefore performed to determine the effect of inoculation of Trichoderma harzianum (T. harzianum) on compost, focusing on bacterial community structure (16S rRNA) and chitinase gene diversity. In addition, the ability of vineyard pruning waste compost, amended (GCTh) or not (GC) with T. harzianum, to suppress Fusarium wilt was evaluated. The addition of T. harzianum resulted in a high relative abundance of certain chitinolytic bacteria as well as in remarkable protection against Fusarium oxysporum comparable to that induced by compost GC. Moreover, variations in the abiotic characteristics of the media, such as pH, C, N and iron levels, were observed. Despite the lower diversity of chitinolytic bacteria found in GCTh, the high relative abundance of Streptomyces spp. may be involved in the suppressiveness of this growing media. The higher degree of compost suppressiveness achieved after the addition of T. harzianum may be due not only to its biocontrol ability, but also to changes promoted in both abiotic and biotic characteristics of the growing media.