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Long-term organic farming aims to reduce synthetic fertilizer and pesticide use in order to sustainably produce and improve soil quality. To do this, there is a need for more information about the soil microbial community, which plays a key role in a sustainable agriculture. In this paper, we assessed the long-term effects of two organic and one conventional cropping systems on the soil microbial community structure using high-throughput sequencing analysis, as well as the link between these communities and the changes in the soil properties and crop yield. The results showed that the crop yield was similar among the three cropping systems. The microbial community changed according to cropping system. Organic cultivation with manure compost and compost tea (Org_C) showed a change in the bacterial community associated with an improved soil carbon and nutrient content. A linear discriminant analysis effect size showed different bacteria and fungi as key microorganisms for each of the three different cropping systems, for conventional systems (Conv), different microorganisms such as Nesterenkonia, Galbibacter, Gramella, Limnobacter, Pseudoalteromonas, Pantoe, and Sporobolomyces were associated with pesticides, while for Org_C and organic cultivation with manure (Org_M), other types of microorganisms were associated with organic amendments with different functions, which, in some cases, reduce soil borne pathogens. However, further investigations such as functional approaches or network analyses are need to better understand the mechanisms behind this behavior.

Significant differences in the microbial community and diversity in soil have been observed due to organic farming, but little research has been performed for exploring microbial functionality and the co-occurrence of patterns among microbial taxa. In this work, we study soil 16S rDNA amplicons from two long-term organic farming systems (Org_C and Org_M) and a conventional system (Conv) to decipher the differences in microbial interaction and network organization and to predict functional genes (principally related to the N cycle). In general, the network organizations were different in all cropping systems due to agricultural management. Org_C showed the highest negative interactions and modularity and the most altered bacterial niches and interactions, which led to an increase in generalist species that stabilize the bacterial community and improve the response of the soil to adverse conditions. These changes altered the predicted functionality of the bacterial community; Org_C showed higher referred numbers of nitrogen fixation genes, a decrease in the N2O emission genes and could favor the uptake of environmental CO2. Thus, long-term compost amendment application has significant benefits for the farmer and the environment, since prolonged application can reduce the use of fertilizers and pesticides and could create a more stable soil, which could resist the effects of climate change.

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