Anthropogenic activities have resulted in land desertification in various regions of the world, leading to the degradation of critical soil characteristics such as organic matter (OM) content, nutrient stock, and prevailing biodiversity. Restoring such degraded soils through organic matter amendments and diversified crop rotations is thus an intrinsic part of organic farming. This review discusses a wide range of organic farming impacts on soil health and crop productivity by focusing on organic fertilizers and crop diversification. Conventional fertilizers were considered vital for agricultural production to harvest high crop yields. Nevertheless, they are now deemed as environmentally hazardous and an obstacle to sustainable agroecosystems due to intensive chemical inputs that damage the soil over time and have long-lasting impacts. Conventional fertilization results in nutrient depletion, loss of microbial diversity, organic matter reduction, and deterioration of physical characteristics of the soil. Conversely, organic fertilization makes use of naturally existing resources to improve soil health. Organic amendments such as biochar, manure, and fermented grass improve soil’s physical, chemical, and biological properties and promote the growth and diversity of beneficial soil microorganisms—important in nutrient cycling and soil stability. They facilitate the uptake of nutrients, hinder crop pathogen growth, mitigate heavy metals, and decompose xenobiotic organic substances. Moreover, growing cover crops is also a major strategy to improve soil health. Diversified crop rotation with combinatorial use of organic fertilizers may improve soil health and agricultural yields without any detrimental impacts on the environment and soil, ensuring sustainable food production, safety, and security. This integrated approach contributes to minimizing the use of chemical fertilizers and their effects on environmental health. It also contributes to reducing agricultural inputs along with enhancing OM, soil microbial diversity and biomass, nitrogen fixation, and carbon sequestration. Therefore, cover crops and organic fertilization may offer sustainable agroecosystems and climate change mitigation.

Soil organic matter (SOM) decomposition is a critical biogeochemical process that regulates the carbon cycle, nutrient availability, and agricultural sustainability of cropland systems. Recent progress in multi-omics and microbial network analyses has provided us with a better understanding of the decomposition process at different spatial and temporal scales. Climate factors, such as temperature and seasonal variations in moisture, play a critical role in microbial activity and enzyme kinetics, and their impacts are mediated by soil physical and chemical properties. Soil mineralogy, texture, and structure create different soil microenvironments, affecting the connectivity of microbial habitats, substrate availability, and protective mechanisms of organic matter. Moreover, different microbial groups (bacteria, fungi, and archaea) contribute differently to the decomposition of plant residues and SOM. Recent findings suggest the paramount importance of living microbial communities as well as necromass in forming soil organic carbon pools. Microbial functional traits such as carbon use efficiency, dormancy, and stress tolerance are essential drivers of decomposition in the soil. Furthermore, the role of microbial necromass, alongside live microbial communities, in the formation and stabilization of persistent SOM fractions is increasingly recognized. Based on this microbial perspective, feedback between local microbial processes and landscape-scale carbon dynamics illustrates the cross-scale interactions that drive agricultural productivity and regulate soil climate. Understanding these dynamics also highlights the potential for incorporating microbial functioning into sustainable agricultural management, which offers promising avenues for increasing carbon sequestration without jeopardizing soil nutrient cycling. This review explores current developments in intricate relationships between climate, soil characteristics, and microbial communities determining SOM decomposition, serving as a promising resource in organic fertilization and regenerative agriculture. Specifically, we examine how nutrient availability, pH, and oxygen levels critically influence these microbial contributions to SOM stability and turnover.