Soils, the earth’s skin, are at the intersection of the lithosphere, hydrosphere, atmosphere, and biosphere. The persistence of life on our planet depends on the maintenance of soils as they constitute the biological engines of earth. Human population has increased exponentially in recent decades, along with the demand for food, materials, and energy, which have caused a shift from low-yield and subsistence agriculture to a more productive, high-cost, and intensive agriculture. However, soils are very fragile ecosystems and require centuries for their development, thus within the human timescale they are not renewable resources. Modern and intensive agriculture implies serious concern about the conservation of soil as living organism, i.e., of its capacity to perform the vast number of biochemical processes needed to complete the biogeochemical cycles of plant nutrients, such as nitrogen and phosphorus, crucial for crop primary production. Most practices related to intensive agriculture determine a deterioration even in the short-middle term of their physical, chemical, and biological properties, which all together contribute to soil quality, along with an overexploitation of soils as living organisms. Recent trends are turning toward styles of agriculture management that are more sustainable or conservative for soil quality.
Usually, use of soils for agricultural purposes deflect them at various degrees from the “natural” soil development processes (pedogenesis), and this shift may be assumed as a divergence from soil sustainability principles. For decades, the misuse of land due to intensive crop management has deteriorated soil health and quality. A huge plethora of microorganisms inhabits soils, thus acting as “the biological engine of the earth”; indeed, this microbiota serves the soil ecosystem, performing several fundamental functions. Therefore, management practices might be planned looking at the safeguard of soil microbial diversity and resilience. In addition, each unexpected alteration in numberless soil biochemical processes, being regulated by microbial communities, may represent an early and sensible signal of soil homeostasis weakening and, consequently, warn about soil conservation. Within the vast number of soil biochemical processes and connected features (bioindicators) virtually effective to measure the sustainable soil exploitation, those related to the mineralization or immobilization of the main nutrients (C and N), including enzyme activity (functioning) and composition (diversity) of microbial communities, exert a fundamental role because of their involvement in soil metabolism. Comparing the influence of many cropping factors (tillage, mulching and cover crops, rotations, mineral and organic fertilization) under both intensive and sustainable managements on soil microbial diversity and functioning, through both chemical and biological soil quality indicators, makes it possible to identify the most hazardous diversions from soil sustainability principles.