Pharmaceuticals and their metabolites can reach water bodies through sewage systems, industrial discharges, effluents from sewage treatment plants (STPs), aquaculture, and livestock farming. Pharmaceuticals include a hundred substances which are very different as regards chemical–physical properties and environmental behavior, although they may have strong biochemical activities. At present, pharmaceuticals can reach water concentrations of ng L⁻¹ to µg L⁻¹ and some are considered ubiquitous. Nevertheless, their presence in the aquatic environment and impact on aquatic biota and on human health have not yet been studied adequately. Experimental evidence indicates that pharmaceuticals may cause harmful effects, such as morphological, metabolic and sex alterations on aquatic species, induction of antibiotic resistance in aquatic pathogenic microorganisms, and disruption of biodegradation activities in STPs. Risk assessment studies and evaluations are in progress. Yet, the available scientific data are consistent with the introduction of some pharmaceutical indicators in extensive water monitoring to better define their actual impact on aquatic organisms and humans. Under these perspectives, the inclusion of emerging pharmaceuticals in the revision of EU List of Priority Substances under the Water Framework Directive 2000/60/EC should be implemented as well as the definition of respective environmental quality standards.

The rhizosphere is a microhabitat where there is an intense chemical dialogue between plants and microorganisms. The two coexist and develop synergistic actions, which can promote plants’ functions and productivity, but also their capacity to respond to stress conditions, including heavy metal (HM) contamination. If HMs are present in soils used for agriculture, there is a risk of metal uptake by edible plants with subsequent bioaccumulation in humans and animals and detrimental consequences for their health. Plant productivity can also be negatively affected. Many bacteria have defensive mechanisms for resisting heavy metals and, through various complex processes, can improve plant response to HM stress. Bacteria-plant synergic interactions in the rhizosphere, as a homeostatic ecosystem response to HM disturbance, are common in soil. However, this is hard to achieve in agroecosystems managed with traditional practices, because concentrating on maximizing crop yield does not make it possible to establish rhizosphere interactions. Improving knowledge of the complex interactions mediated by plant exudates and secondary metabolites can lead to nature-based solutions for plant health in HM contaminated soils. This paper reports the main ecotoxicological effects of HMs and the various compounds (including several secondary metabolites) produced by plant-microorganism holobionts for removing, immobilizing and containing toxic elements.

Trees are crucial for sustaining life on our planet. Forests and land devoted to tree crops do not only supply essential edible products to humans and animals, but also additional goods such as paper or wood. They also prevent soil erosion, support microbial, animal, and plant biodiversity, play key roles in nutrient and water cycling processes, and mitigate the effects of climate change acting as carbon dioxide sinks. Hence, the health of forests and tree cropping systems is of particular significance. In particular, soil/rhizosphere/root-associated microbial communities (known as microbiota) are decisive to sustain the fitness, development, and productivity of trees. These benefits rely on processes aiming to enhance nutrient assimilation efficiency (plant growth promotion) and/or to protect against a number of (a)biotic constraints. Moreover, specific members of the microbial communities associated with perennial tree crops interact with soil invertebrate food webs, underpinning many density regulation mechanisms. This review discusses belowground microbiota interactions influencing the growth of tree crops. The study of tree-(micro)organism interactions taking place at the belowground level is crucial to understand how they contribute to processes like carbon sequestration, regulation of ecosystem functioning, and nutrient cycling. A comprehensive understanding of the relationship between roots and their associate microbiota can also facilitate the design of novel sustainable approaches for the benefit of these relevant agro-ecosystems. Here, we summarize the methodological approaches to unravel the composition and function of belowground microbiota, the factors influencing their interaction with tree crops, their benefits and harms, with a focus on representative examples of Biological Control Agents (BCA) used against relevant biotic constraints of tree crops. Finally, we add some concluding remarks and suggest future perspectives concerning the microbiota-assisted management strategies to sustain tree crops.

Hydrocarbons occur in fossil fuels such as crude oil and consist mainly of hydrogen and carbon. Although they are natural chemicals, crude oil refining results in commercial products with new physico-chemical properties, which can increase their complexity and toxicity, and hamper their degradation. The presence of biodiverse natural microbial communities is a prerequisite for an effective homeostatic response to the various hydrocarbons, that contaminate ecosystems. However, their removal depends on the compartment contaminated (water, sediment, soil), their molecular weight, and their toxicity not hampering microbial activity. This paper reports different bacterial species involved in the biodegradation of aliphatic and aromatic hydrocarbons. Hydrocarbon contamination is generally due to the co-presence of a mixture of these chemicals, and their removal from the environment cannot rely on only a single species but generally requires bacterial consortia. Versatile bacterial metabolism relies on specific genes encoding the key enzymes involved in the peripheral metabolic and central metabolic pathways for degrading aliphatic and polycyclic aromatic hydrocarbons. Although microbial metabolism can have the potential for natural attenuation of these contaminants, hydrocarbon bioremediation, through biostimulation (e.g., use of surfactants, plants, earthworms, and nanoparticles) and bioaugmentation, can be a valid tool for removing them from actually contaminated soil, freshwater, groundwater, and seawater.