An increasing amount of sewage sludge requires reasonable management, whereas its storage might be environmentally hazardous. Due to the organic matter and nutrient presence in sediments, it may be used as organic fertilizer. However, beyond the valuable contests, sewage sludge can also contain toxic or dangerous ingredients like heavy metals. Therefore, there is a need to develop methods for rapid assessment of sediment ecotoxicity that will determine its possible applicability in agriculture. The Biolog® EcoPlate enables the metabolic profile diversity evaluation of microbial populations in environmental samples, which reflects the state of their activity. It is regarded as a modern technology that by means of biological properties allows quick characterization of the ecological status of environmental samples, such as sewage sludge.

The aim of the present work was to assess the influence of organic amendment applications compared to mineral fertilization on soil microbial activity and functional diversity. The field experiment was set up on a soil classified as an Eutric Cambisol developed from loess (South-East Poland). Two doses of both dairy sewage sludge (20 Mg·ha⁻¹ and 26 Mg·ha⁻¹) and of mineral fertilizers containing the same amount of nutrients were applied. The same soil without any amendment was used as a control. The soil under undisturbed native vegetation was also included in the study as a representative background sample. The functional diversity (catabolic potential) was assessed using such indices as Average Well Color Development (AWCD), Richness (R) and Shannon–Weaver index (H). These indices were calculated, following the community level physiological profiling (CLPP) using Biolog Eco Plates. Soil dehydrogenase and respiratory activity were also evaluated. The indices were sensitive enough to reveal changes in community level physiological profiles due to treatment effects. It was shown that dairy sewage amended soil was characterized by greater AWCD, R, H and dehydrogenase and respiratory activity as compared to control or mineral fertilized soil. Analysis of variance (ANOVA) and principal component analysis (PCA) were used to depict the differences of the soil bacterial functional diversity between the treatments.

The demand for ecologically cultivated fruits is growing each year, but the yields in organic farming are still lower than the yields in conventional farming. Moreover plant pathogens are a serious threat in organic fruit production and the assortment of conventional pesticides is limited in organic farming. The European Commission has established regulations that state which types of bioproducts can be used in organic farming. Appropriately chosen biopreparations might be a solution to this problem. Biopreparations are products used to inhibit the growth of pathogenic fungi or bacteria, stimulate plants growth and enhance plant nutrient uptake. They can be composed of plant growth promoting bacteria and fungi, plant extracts or animals-derived compounds. The second category of bioproducts useful for enhancing yield and nutrient uptake are biostimulants. They can be composed of microorganisms, protein hydrolysates, seaweed extracts and other substances. Bacteria, fungi and yeasts are used in biocontrol of plant pathogens and in enhancing plants growth by producing hormone-like substances and reducing symptoms of environmental stress caused by weather or soil factors such as drought or low nutrient availability.

We present a case study report into nutritional competition between Trichoderma spp. isolated from wild raspberries and fungal phytopathogenic isolates (Colletotrichum sp., Botrytis sp., Verticillium sp. and Phytophthora sp.), which infect soft fruit ecological plantations. The competition was evaluated on the basis of nutritional potentiates. Namely, these were consumption and growth, calculated on the basis of substrate utilization located on Biolog^® Filamentous Fungi (FF) plates. The niche size, total niche overlap and Trichoderma spp. competitiveness indices along with the occurrence of a stressful metabolic situation towards substrates highlighted the unfolding step-by-step approach. Therefore, the Trichoderma spp. and pathogen niche characteristics were provided. As a result, the substrates in the presence of which Trichoderma spp. nutritionally outcompete pathogens were denoted. These were adonitol, D-arabitol, i-erythritol, glycerol, D-mannitol and D-sorbitol. These substrates may serve as additives in biopreparations of Trichoderma spp. dedicated to plantations contaminated by phytopathogens of the genera Colletotrichum sp., Botrytis sp., Verticillium sp. and Phytophthora sp.

The widespread use and consumption of crude oil draws the public’s attention to the fate of petroleum hydrocarbons in the environment, as they can permeate the soil environment in an uncontrollable manner. Contamination of soils with petroleum products, including diesel oil (DO), can cause changes in the microbiological soil properties. The effect of diesel oil on the functional diversity of fungi was tested in a model experiment during 270 days. Fungi were isolated from soil and identified. The functional diversity of fungal communities was also determined. Fungi were identified with the MALDI-TOF method, while the functional diversity was determined using FF-plates made by Biolog®, with 95 carbon sources. Moreover, the diesel oil degradation dynamics was assessed. The research showed that soil contaminated with diesel oil is characterised by a higher activity of oxireductases and a higher number of fungi than soil not exposed to the pressure of this product. The DO pollution has an adverse effect on the diversity of fungal community. This is proved by significantly lower values of the Average Well-Color Development (AWCD), substrates Richness (R) and Shannon-Weaver (H) indices at day 270 after contamination. The consequences of DO affecting soil not submitted to remediation are persistent. After 270 days, only 64% of four-ringed, 28% of five-ringed, 21% of 2-3-ringed and 16% of six-ringed PAHs underwent degradation. The lasting effect of DO on communities of fungi led to a decrease in their functional diversity. The assessment of the response of fungi to DO pollution made on the basis of the development of colonies on Petri dishes (Colony Development (CD) and Eco-physiological Diversity (EP) indices) is consistent with the analysis based on the FF MicroPlate system by Biolog®. Thus, a combination of the FF MicroPlate system by Biolog® with the simultaneous calculation of CD and EP indices alongside the concurrent determination of the content of PAHs and activity of oxireductases provides an opportunity to achieve relatively complete characterisation of the consequences of a long-term impact of diesel oil on soil fungi.