Trichoderma spp. are a rich source of secondary metabolites and volatile organic compounds (VOCs), which may induce plant defenses and modulate plant growth. In filamentous fungi, chromatin modifications regulate secondary metabolism. In this study we investigated how the absence of histone deacetylase HDA-2 in the Trichoderma atroviride strain Δhda-2 impacts its effect on a host, Arabidopsis (Arabidopsis thaliana). The production of VOCs and their impact on plant growth and development were assessed as well. The Δhda-2 strain was impaired in its ability to colonize Arabidopsis roots, thus affecting the promotion of plant growth and modulation of plant defenses against foliar pathogens Botrytis cinerea and Pseudomonas syringae, which normally result from interaction with T. atroviride. Furthermore, Δhda-2 VOCs were incapable of triggering plant defenses to counterattack foliar pathogens. The Δhda-2 overproduced the VOC 6-pentyl-2H-pyran-2-one (6-PP), which resulted in enhanced root branching and differentially regulated phytohormone-related genes. Analysis of ten VOCs (including 6-PP) revealed that three of them positively regulated plant growth, whereas six had the opposite effect. Assessment of secondary metabolites, detoxification, and communication with plant-related genes showed a dual role for HDA-2 in T. atroviride gene expression regulation during its interaction with plants. Chromatin immunoprecipitation of acetylated histone H3 on the promoters of plant-responsive genes in Δhda-2 showed, in the presence of Arabidopsis, low levels of epl-1 and abc-2 compared with that in the wild type; whereas ctf-1 presented high constitutive levels, supporting a dual role of HDA-2 in gene regulation. This work highlights the importance of HDA-2 as a global regulator in Trichoderma to modulate multiple responses in Arabidopsis.

Surface-Enhanced Raman Spectroscopy (SERS) substrates offer a promising solution for the sensitive and specific detection of agrochemicals, enabling timely interventions to mitigate their harmful effects on humans and ecosystems. However, the analysis of SERS spectra can be challenging due to the complexity of interpreting the data, often requiring advanced computational tools and expertise. This limitation highlights the need for continued innovation in both SERS technology and data analysis methods to fully realize its potential in real-world applications. In this context, we present a machine-learning model based on a feedforward neural network for the rapid and accurate classification of SERS spectra. Our approach consists of a highly compact neural network combined with feature engineering that was trained using SERS patterns from experimental measurements. The spectra used to train this model were acquired using substrates made of gold nanostars, which were deposited onto aluminum foil via drop-casting. The model utilizes a compact two-layer architecture, with five Leaky ReLU neurons in the hidden layer and four softmax neurons in the output layer. This design ensures computational efficiency by using only dense layers for matrix-vector multiplications. Notably, we performed feature engineering to optimize the input data; specifically, we derived 20 key features from transformation functions applied to the SERS spectra. The model demonstrates strong predictive performance, achieving high precision and recall values across all classes, with an overall classification accuracy of 98.5% for organophosphate pesticides and their mixtures. Compared to other machine-learning algorithms, our approach offers reduced computational complexity while maintaining or exceeding the accuracy of more complex models. This makes the proposed model particularly suitable for deployment in resource-limited environments, providing an efficient and effective tool for agrochemical compound classification in diverse environmental and food matrices.

While mining provides critical raw materials for modern infrastructure and the energy transition, it leaves behind severe environmental damages, such as soil mercury (Hg) contamination. In the present study, we present the first study evaluating the relationship of the ectomycorrhizal fungus Pisolithus arhizus with Trifolium repens (white clover) as a novel nature-based mycoremediation strategy for mercury-stressed soils. Through a controlled 2 × 2 factorial experiment over six months, we demonstrate that P. arhizus significantly enhances both plant biomass and heavy-metal tolerance. Inoculation achieved a 9.53% reduction in soil Hg and drove a dramatic 53% increase in stem growth under Hg stress (compared to 36% in non-contaminated conditions) once the extraradicular mycelial network was established. Furthermore, we report novel soil-chemistry dynamics under Hg stress, including a 16% shift in electrical conductivity alongside unexpected increases in the available potassium (+9%) and phosphorus (+3%). These findings present first results for a novel approach of mycoremediation by incorporating P. arhizus into T. repens co-cultivation as a viable remediation strategy, prior to field-scale remediation.

The need to research cost-effective alternatives for soil remediation has become an important topic in the recent years. Pollutants like heavy metals or pharmaceuticals are constantly being accumulated in soils, becoming hazardous for the environment, espe-cially if they reach human or animal food-chain. On the other side, the accumulation of anaerobic digestate resulting from the biogas production process, could also represent a latent risk, due to its discharge as biofertilizers, whereas high quantities of nitrogen (N) and phosphorous (P) contained are accumulated. Digestate inoculation by means of fungi represents a cost-effective alternative to treat both, contaminated soils and anaerobic digestate. Through the present systematic review, scientific researches per-formed during the past ten years were summarized. Focus of this research was to un-derstand the impacts of fungi and anaerobic digestate as soil amendment, for contam-inant removal and plant growth. Soil stabilization and remediation showed to have a higher impact than plant growth itself. The origin of the biomass used for anaerobic digestion is very important to determine digestate quality and effect in the soil, being cattle manure more suitable for remediation purposes. Fungal strain, pH, temperature, and existing contaminants must be considered before a successfully practical applica-tion takes place.

This systematic review aims to describe the current state of research on soil remediation utilizing digestates inoculated with fungi, as a cost-effective alternative. This study was performed according to the PRISMA 2020 guidelines, and nine papers were finally selected for review. The application of digestates augments the soil microbial community in terms of bacterial strains, mycorrhizal colonization, and enzymes. Digestates inoculated with fungi have notable impacts on soil stabilization. Some authors reported an improvement of up to 100% in plant growth when using digestates. HM removal rates of 17% for Si, 40% for Cd, and up to 80% for Pb have been achieved. Antibiotics and PFCAs showed low or no accumulation. The biomass source used for anaerobic digestion has a very important impact on the resulting digestate’s quality and effect in soils: the use of cattle manure resulted in an increase in biomass yield from 9% up to 100% when compared to manure co-digested with organic wastes. The fungal strain, environmental conditions, and existing contaminants must be considered with respect to the specific practical application. These insights can contribute to the management of environmental risks and the prevention of negative impacts on human health, ecosystems, and the economy.