The use of organic amendments in agriculture is a common practice due to their potential to increase crop productivity and enhance soil health. Indeed, organic amendments of different origin and composition (e.g., animal slurry, manure, compost, sewage sludge, etc.) can supply valuable nutrients to the soil, as well as increase its organic matter content, with concomitant benefits for soil health. However, the application of organic amendments to agricultural soil entails a variety of risks for environmental and human health. Organic amendments often contain a range of pollutants, including heavy metals, persistent organic pollutants, potential human pathogens, and emerging pollutants. Regarding emerging pollutants, the presence of antibiotic residues, antibiotic-resistant bacteria, and antibiotic-resistance genes in agricultural amendments is currently a matter of much concern, due to the concomitant risks for human health. Similarly, currently, the introduction of microplastics to agricultural soil, via the application of organic amendments (mainly, sewage sludge), is a topic of much relevance, owing to its magnitude and potential adverse effects for environmental health. There is, currently, much interest in the development of efficient strategies to mitigate the risks associated to the application of organic amendments to agricultural soil, while benefiting from their numerous advantages.

Bioremediation, based on the use of microorganisms to break down pollutants, can be very effective at reducing soil pollution. But the climate change we are now experiencing is bound to have an impact on bioremediation performance, since the activity and degrading abilities of soil microorganisms are dependent on a series of environmental parameters that are themselves being altered by climate change, such as soil temperature, moisture, amount of root exudates, etc. Many climate-induced effects on soil microorganisms occur indirectly through changes in plant growth and physiology derived from increased atmospheric CO₂ concentrations and temperatures, the alteration of precipitation patterns, etc., with a concomitant effect on rhizoremediation performance (i.e. the plant-assisted microbial degradation of pollutants in the rhizosphere). But these effects are extremely complex and mediated by processes such as acclimation and adaptation. Besides, soil microorganisms form complex networks of interactions with a myriad of organisms from many taxonomic groups that will also be affected by climate change, further complicating data interpretation.

The concept of bioeconomy is a topic of debate, confusion, skepticism, and criticism. Paradoxically, this is not necessarily a negative thing as it is encouraging a fruitful exchange of information, ideas, knowledge, and values, with concomitant beneficial effects on the definition and evolution of the bioeconomy paradigm. At the core of the debate, three points of view coexist: (i) those who support a broad interpretation of the term bioeconomy, through the incorporation of all economic activities based on the production and conversion of renewable biological resources (and organic wastes) into products, including agriculture, livestock, fishing, forestry and similar economic activities that have accompanied humankind for millennia; (ii) those who embrace a much narrower interpretation, reserving the use of the term bioeconomy for new, innovative, and technologically-advanced economic initiatives that result in the generation of high-added-value products and services from the conversion of biological resources; and (iii) those who stand between these two viewpoints. Here, to shed light on this debate, a contextualization of the bioeconomy concept through its links with related concepts (biotechnology, bio-based economy, circular economy, green economy, ecological economics, environmental economics, etc.) and challenges facing humanity today is presented.