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Agriculture is a significant source of methane, contributing about 12% of the global anthropogenic methane emissions. Major sources of methane from agricultural activities are fermentation in the reticulo-rumen of ruminant animals (i.e., enteric methane), fermentation in animal manure, and rice cultivation. Enteric methane is the largest agricultural source of methane and is mainly controlled by feed dry matter intake and composition of the animal diet (i.e., fiber, starch, lipids). Processes that lead to generation of methane from animal manure are similar to those taking place in the reticulo-rumen. Methane emissions from manure, however, are greatly influenced by factors such as manure management system and ambient temperature. Systems that handle manure as a liquid generate much more methane than systems in which manure is handled as a solid. Low ambient temperatures drastically decrease methane emissions from manure. Once applied to soil, animal manure does not generate significant amounts of methane. Globally, methane emissions from rice cultivation represent about 10% of the total agricultural greenhouse gas emissions. In the rice plant, methane dissolves in the soil water surrounding the roots, diffuses into the cell-wall water of the root cells, and is eventually released through the micropores in the leaves. Various strategies have been explored to mitigate agricultural methane emissions. Animal nutrition, including balancing dietary nutrients and replacement of fiber with starch or lipids; alternative sinks for hydrogen; manipulation of ruminal fermentation; and direct inhibition of methanogenesis have been shown to effectively decrease enteric methane emissions. Manure management solutions include solid-liquid separation, manure covers, flaring of generated methane, acidification and cooling of manure, and decreasing manure storage time before soil application. There are also effective mitigation strategies for rice that can be categorized broadly into selection of rice cultivars, water regime, and fertilization. Alternate wetting and drying and mid-season drainage of rice paddies have been shown to be very effective practices for mitigating methane emissions from rice production.

Industrialized livestock production can be characterized by five key attributes: confinement feeding of animals, separation of feed and livestock production, specialization, large size, and close vertical linkages with buyers. Industrialized livestock operations—popularly known as CAFOs, for Concentrated Animal Feeding Operations—have spread rapidly in developed and developing countries; by the early 21st century, they accounted for three quarters of poultry production and over half of global pork production, and held a growing foothold in dairy production. Industrialized systems have created significant improvements in agricultural productivity, leading to greater output of meat and dairy products for given commitments of land, feed, labor, housing, and equipment. They have also been effective at developing, applying, and disseminating research leading to persistent improvements in animal genetics, breeding, feed formulations, and biosecurity. The reduced prices associated with productivity improvements support increased meat and dairy product consumption in low and middle income countries, while reducing the resources used for such consumption in higher income countries. The high-stocking densities associated with confined feeding also exacerbate several social costs associated with livestock production. Animals in high-density environments may be exposed to diseases, subject to attacks from other animals, and unable to engage in natural behaviors, raising concerns about higher levels of fear, pain, stress, and boredom. Such animal welfare concerns have realized greater salience in recent years. By consolidating large numbers of animals in a location, industrial systems also concentrate animal wastes, often in levels that exceed the capacity of local cropland to absorb the nutrients in manure. While the productivity improvements associated with industrial systems reduce the resource demands of agriculture, excessive localized concentrations of manure can lean to environmental damage through contamination of ground and surface water and through volatilization of nitrogen nutrients into airborne pollutants. Finally, animals in industrialized systems are often provided with antibiotics in their feed or water, in order to treat and prevent disease, but also to realize improved feed absorption (“a production purpose”). Bacteria are developing resistance to many important antibiotic drugs; the extensive use of such drugs in human and animal medicine has contributed to the spread of antibiotic resistance, with consequent health risks to humans. The social costs associated with industrialized production have led to a range of regulatory interventions, primarily in North America and Europe, as well as private sector attempts to alter the incentives that producers face through the development of labels and through associated adjustments within supply chains.

Growing a cover crop between main crops imitates natural ecosystems where the soil is continuously covered with vegetation. This is an important management practice in preserving soil nutrient resources and reducing nitrogen (N) losses to waters. Cover crops also provide other functions that are important for the resilience and long-term stability of cropping systems, such as reduced erosion, increased soil fertility, carbon sequestration, increased soil phosphorus (P) availability, and suppression of weeds and pathogens. Much is known about how to use cover crops to reduce N leaching, for climates where there is a water surplus outside the growing season. Non-legume cover crops reduce N leaching by 20%–80% and legumes reduce it by, on average, 23%. There are both synergies and possible conflicts between different environmental and production aspects that should be considered when developing efficient and multifunctional cover crop systems, but contradictions about different functions provided by cover crops can sometimes be overcome with site-specific adaptation of measures. One example is cover crop effects on P losses. Cover crops reduce losses of total P, but extract soil P to available forms and may increase losses of dissolved P. How to use this effect to increase soil P availability on subtropical soils needs further studies. Knowledge and examples of how to maximize the positive effects of cover crops on cropping systems are improving, thereby increasing the sustainability of agriculture. One example is combined weed suppression in order to reduce dependence on herbicides or intensive mechanical treatment.

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.