Margarita Ros

Soil microbial activity after restoration of a semiarid soil by organic amendments

Unsuitable agricultural practices together with adverse environmental conditions have led to degradation of soil in many Mediterranean areas. One method for recovering degraded soils in semiarid regions, is to add organic matter in order to improve soil characteristics, thereby enhancing biogeochemical nutrient cycles. In this study, the effect of adding the organic fraction of urban wastes (both fresh and composted) on different carbon fractions and on microbiological and biochemical parameters (microbial biomass C, basal respiration and different enzymatic activities) of a degraded soil of SE Spain has been assessed in a 2 year experiment. Three months after the addition of the organic material, spontaneous plant growth occurred and the plant cover lasted until the end of the experiment. Organic soil amendment initially increased the levels of soil organic matter, microbial biomass, basal respiration and some enzyme activities related to the C and N cycles These values decreased but always remained higher than those of the unamended soil. The results indicate that the addition of urban organic waste is beneficial for recovering degraded soils, the microbial activity of which clearly increases with amendment. The incorporation of compost seemed to have a greater positive effect on the soil characteristics studied than the incorporation of fresh organic matter.

16S rDNA analysis reveals low microbial diversity in community level physiological profile assays

The metabolic diversity of microbial communities is fundamental for the multiple soil functions mediated by microorganisms. Community level physiological profiles (CLPPs) based on sole C source oxidation have been used as a fast and reproducible tool to study soil microbial functional diversity because the utilisation of available carbon is the key factor governing microbial growth in soil. Our aim was to assess the phylogenetic affiliation of the microorganisms responsible for C consumption after inoculating Biolog plates. For this purpose, two semi-arid Mediterranean forest soils with significantly different patterns of C consumption and microbial community structure were used. Following the inoculation of the Biolog plates, suspensions from seven wells were sampled after 1, 2 and 7 d of incubation. DNA was extracted and the microbial communities analysed by polymerase chain reaction followed by denaturing gradient gel electrophoresis (PCR-DGGE) and sequencing of excised bands. Despite major differences in the microbial communities of the soils studied, their DGGE banding patterns after incubation were similar for all the analysed C source suspensions. Microorganisms belonging to beta-Proteobacteria (Ralstonia sp. and Burkholderia sp.) and alpha-Proteobacteria (Rhizobium sp.) were dominant. These opportunists had a competitive advantage under the conditions at which the CLPPs were analysed. This study reveals that significantly different CLPP patterns can be generated on the basis of only 3-4 genera, as reflected by PCR-DGGE analysis. Also for this reason, CLPPs based on incubations of soil suspensions should just be used as a screening method and always be accompanied by other techniques for community analysis.

Citrus compost and its water extract for cultivation of melon plants in greenhouse nurseries. Evaluation of nutriactive and biocontrol effects.

Two different types of citrus composts, and their water extracts, were tested with regard to their utilisations as partial substitutes for peat in growing media for melon seedlings in greenhouse nurseries. Both compost showed higher plant growth than peat. Compost composed by citrus waste and green residue (C2) showed greater plant growth than compost obtained from the same organic matrices mentioned above further the addition of sludge obtained from citrus industry (C1). Compost C2 showed a greater auxinic effect than C1 and it was the only one that showed cytokinic effect. Both composts also demonstrated a biocontrol effect against Fusarium oxysporum for melon plants: the effects were also higher in C2 than in C1. Higher number of isolated fungi was active against F. oxysporum in compost C2, than compost C1. No different bacterial biocontrol efficacy was observed between both composts. The water extracts of both composts gave lower plant yields than their solid matrices, their relative effects being similar to those of the solid composts (C2 extract gave higher plant yields than the extract from C1). The biocontrol effects of compost water extracts followed the same trend.

Biopesticide effect of green compost against fusarium wilt on melon plants

Aims:  The biopesticide effect of four green composts against fusarium wilt in melon plants and the effect of soil quality in soils amended with composts were assayed.

Quantification of the biocontrol agent Trichoderma harzianum with real-time TaqMan PCR and its potential extrapolation to the hyphal biomass.

The species of the genus Trichoderma are used successfully as biocontrol agents against a wide range of phytopathogenic fungi. Among them, Trichoderma harzianum is especially effective. However, to develop more effective fungal biocontrol strategies in organic substrates and soil, tools for monitoring the control agents are required. Real-time PCR is potentially an effective tool for the quantification of fungi in environmental samples. The aim of this study consisted of the development and application of a real-time PCR-based method to the quantification of T. harzianum, and the extrapolation of these data to fungal biomass values. A set of primers and a TaqMan probe for the ITS region of the fungal genome were designed and tested, and amplification was correlated to biomass measurements obtained with optical microscopy and image analysis, of the hyphal length of the mycelium of the colony. A correlation of 0.76 between ITS copies and biomass was obtained. The extrapolation of the quantity of ITS copies, calculated based on real-time PCR data, into quantities of fungal biomass provides potentially a more accurate value of the quantity of soil fungi.

Bacterial community patterns and thermal analyses of composts of various origins.

During composting, the degradation of organic waste is accompanied and driven by a succession of microbial populations exhibiting a broad range of functional capabilities. Detailed inventories of the microbial communities in mature compost, however, are not available. Mature composts, originating from biowaste as well as sewage sludge and anaerobic sludge, were studied by denaturing gradient gel electrophoresis-fingerprints after polymerase chain reaction (PCR) amplification of the 16S rRNA genes using three different universal primer pairs, as well as by differential scanning calorimetry and thermogravimetry. The composts of different origin had different bacterial communities. The influence of different 16S rDNA primer sets on the same batches of compost DNA was evaluated. The clearest separation of different compost types was obtained by using the PCR primer pair 338f + 518r which is suggested for future applications. Communities from the different biowaste compost samples clustered together and could be separated from sewage sludge communities indicating the establishment of different microbial consortia. A similar differentiation of composts was found with the thermogavimetric analyses. It may thus be concluded that the resulting humus quality is closely linked to the microbial communities involved.

Effects of biosolarization as methyl bromide alternative for Meloidogyne incognita control on quality of soil under pepper

The Adenosine triphosphate (ATP) content, dehydrogenase, phosphatase, urease, and β-glucosidase activity decreased after manure amendment plus solarization (biosolarization), but they recovered after cropping, reaching levels higher than or similar to those before the biosolarization. However, these biochemical parameters decreased and did not recover with time in the methyl bromide (MeBr) treatment. Potential negative soil effects were assayed by measuring, ecotoxicity (Vibrio fisheri luminescence), germination index, electrical conductivity, and heavy metals content. Biosolarization did not negatively affect these parameters, while MeBr application irreversibly decreased the germination index and ecotoxicity. Higher-quality pepper production (extra and first class) were observed with biosolarization but not with MeBr, but no differences were found for pepper yield. Biosolarization gave a Meloidogyne incognita (M. incognita) incidence similar to that of MeBr application.

Impact of organic soil amendments on phytochemicals and microbial quality of rocket leaves (Eruca sativa).

The effect of soil amendments prepared from organic wastes (sewage sludge and urban solid waste) at two concentrations (45 t ha(-1) as D1 and 135 t ha(-1) as D2) was evaluated on phytochemicals and microbial quality of rocket, a highly valuable vegetable. The addition of sewage sludge to the soil increased rocket yield 5.5 times compared to control and urban solid waste. Organic amendments increased the water content and the maturity stage of the leaves, which contributed to a reduction in the content of total and individual glucosinolates as well as flavonols and anthocyanins. However, higher content of vitamin C was observed after cultivation with sewage sludge at D2 compared to control leaves (204.6 and 177.4 mg 100 g(-1) of fw, respectively). This study shows that sewage sludge at optimum doses can be considered a suitable amendment because of increased crop yield without detrimental effects on phytochemicals, including vitamin C content, when the leaves reached the commercial maturity stage.

Archaeal community dynamics and abiotic characteristics in a mesophilic anaerobic co-digestion process treating fruit and vegetable processing waste sludge with chopped fresh artichoke waste

This study evaluated the feasibility of obtaining methane in anaerobic digestion (AD) from the waste products generated by the processing of fruit and vegetables. During the first phase (0-55 d) of the AD using sludge from fruit and vegetable processing, an average value of 244±88 L kg(-1) dry matter d(-1)of biogas production was obtained, and methane content reached 65% of the biogas. Co-digestion with chopped fresh artichoke wastes in a second phase (55-71 d) enhanced biogas production, and resulted in an average value of 354±68 L kg(-1) dry matter d(-1), with higher methane content (more than 70%). The archaeal community involved in methane production was studied using the ANAEROCHIP microarray and real-time PCR. Results indicated that species of Methanosaeta and Methanosarcina were important during the AD process. Methanosarcina numbers increased after the addition of chopped fresh artichoke, while Methanosaeta numbers decreased.

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.