The use of organic fertilizers constitutes a sustainable strategy to recycle nutrients, increase soil carbon (C) stocks and mitigate climate change. Yet, this depends largely on balance between soil C sequestration and the emissions of the potent greenhouse gas nitrous oxide (N₂O). Organic fertilizers strongly influence the microbial processes leading to the release of N₂O. The magnitude and pattern of N₂O emissions are different from the emissions observed from inorganic fertilizers and difficult to predict, which hinders developing best management practices specific to organic fertilizers. Currently, we lack a comprehensive evaluation of the effects of OFs on the function and structure of the N cycling microbial communities. Focusing on animal manures, here we provide an overview of the effects of these organic fertilizers on the community structure and function of nitrifying and denitrifying microorganisms in upland soils. Unprocessed manure with high moisture, high available nitrogen (N) and C content can shift the structure of the microbial community, increasing the abundance and activity of nitrifying and denitrifying microorganisms. Processed manure, such as digestate, compost, vermicompost and biochar, can also stimulate nitrifying and denitrifying microorganisms, although the effects on the soil microbial community structure are different, and N₂O emissions are comparatively lower than raw manure. We propose a framework of best management practices to minimize the negative environmental impacts of organic fertilizers and maximize their benefits in improving soil health and sustaining food production systems. Long-term application of composted manure and the buildup of soil C stocks may contribute to N retention as microbial or stabilized organic N in the soil while increasing the abundance of denitrifying microorganisms and thus reduce the emissions of N₂O by favoring the completion of denitrification to produce dinitrogen gas. Future research using multi-omics approaches can be used to establish key biochemical pathways and microbial taxa responsible for N₂O production under organic fertilization.

Smallholder rice farming is characterized by low returns and substantial environmental impact. Conversion to organic management and linking farmers to fair trade markets could offer an alternative. Engaging in certified cash-crop value chains could thereby provide an entry path to simultaneously reduce poverty and improve environmental sustainability. Based on comprehensive data from a representative sample of approximately 80 organic and 80 conventional farms in northern India, we compared yield and profitability of the main rotation crops over a period of five years. Contrary to the widespread belief that yields in organic farming are inevitably lower, our study shows that organic farmers achieved the same yields in cereals and pulses as conventional farmers, with considerably lower external inputs. Due to 45% lower production costs and higher sales prices, organic basmati cultivation was 105% more profitable than cultivating ordinary rice under conventional management. However, since holdings are small and the share of agricultural income of total household income is declining, conversion to organic basmati farming alone will not provide households a sufficiently attractive perspective into the future. We propose that future efforts to enhance the long-term viability of rice-based organic farming systems in this region focus on diversification involving higher value crops.