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.

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.

Crop diversification is becoming increasingly important for preserving soil and ecosystems’ health and, subsequently, crop productivity and sustainability. Intercropping practices adopted in monocultural woody crops, with herbaceous crops covering the otherwise bare alleyways, foster ecological interactions and can provide both environmental and economic advantages. In this study, intercropping practices were implemented in a traditional mandarin orchard in south-eastern Spain, which was monitored for three years to assess their impact on the environmental footprint and profitability. The footprint was quantified with a cradle-to-gate life cycle assessment (LCA), while the costs and revenues assessment was based on materials, labor, and machinery used in the trial. The calculated LCA indicators evidenced that, although the cultivated surface area increases with the integration of the intercrops (fava bean, purslane, cowpea, and barley/vetch mix), this does not imply any additional detrimental effects (resource depletion, acidification, eutrophication, global warming). The economic analysis showed that while intercrops may involve additional production costs, the correct choice of intercrops, purslane, and fava bean, in this case, can reduce the market risks for farmers. Overall, this study shows that positive environmental and economic impacts are to be expected of co-integrated herbaceous crops within the same field as mandarin trees.

High rates of fertilizer applications potentially have significant environmental consequences, such as soil and water contamination and biodiversity loss. This study aimed to compare the use of biofertilizers and inorganic fertilizers in a broccoli crop to determine their impact on soil microorganism abundance, microbial community structure, functional gene diversity, yield, and greenhouse gas emissions. Four different fertilization treatments were designed: (i) inorganic fertilizers applied at a rate to cover the nutritional demands of the crop (F100); (ii) 50% of the rate of inorganic fertilizers added in F100 (F50); (iii) F50 + the application of a formulation of various bacteria (BA); and (iv) F50 + the application of a formulation of bacteria and non-mycorrhizal fungi (BA + FU). The results showed that reduced fertilization and the addition of both biofertilizer products had no significant effect on soil nutrients, microbial population, microbial activity, or yield when compared to conventional inorganic fertilization. Thus, microbial inoculants were ineffective in enhancing soil microbial abundance and activity, and there were no changes in GHG emissions or crop yields. Nonetheless, crop yield was positively related to total soil N, microbial activity, and CO₂ emissions, confirming the positive effect of soil biodiversity on production. The application of biofertilizers can help reduce mineral fertilization in a broccoli crop with no negative effect on yield.

The introduction of nitrogen fixing bacteria (NFB) and arbuscular mycorrhizal fungi (AMF) into the soil is an advisable agricultural practice for the crop, since it enhances nutrient and water uptake and tolerance to biotic and abiotic stresses. The aim of this work was to study plant nutrition, biological nitrogen fixation (BNF) and crop yield and quality, after inoculating seeds with NFBs ((Rhizobium leguminosarum, Burkholderia cenocepacia, Burkholderia vietnamiensis)) and/or AMFs (Rhizophagus irregularis, Claroideoglomus etunicatum, Claroideoglomus claroideum and Funneliformis mosseae) in a fava bean crop in two seasons. The composition of the nodule bacterial community was evaluated by the high-throughput sequencing analysis of bacterial 16 S rRNA genes. It was found that microbial inoculation accompanied by a 20% decrease in mineral fertilization had no significant effect on crop yield or the nutritional characteristics compared with a non-inoculated crop, except for an increase in the grain protein content in inoculated plants. None of the inoculation treatments increased biological nitrogen fixation over a non-inoculated level. The bacterial rRNA analysis demonstrated that the genus Rhizobium predominated in all nodules, both in inoculated and non-inoculated treatments, suggesting the previous presence of these bacteria in the soil. In our study, inoculation with Rhizobium leguminosarum was the most effective treatment for increasing protein content in seeds, while Burkholderia sp. was not able to colonise the plant nodules. Inoculation techniques used in fava beans can be considered an environmentally friendly alternative, reducing the input of fertilizers, while maintaining crop yield and quality, with the additional benefit of increasing the grain protein content. However, further research is required on the selection and detection of efficient rhizobial strains under local field conditions, above all those related to pH and soil type, in order to achieve superior nitrogen-fixing bacteria.

Mineral fertilization is considered to be useful for improving soil fertility and yields. However, its use is linked to global warming and soil and water pollution by its rapid mobilization. On the other hand, organic fertilization is recommended to maintain or improve soil organic carbon and total nitrogen stocks while contributing to climate change mitigation. The main goal of this study was to assess the effect of two different fertilizer types, mineral and organic, during three cowpea crop cycles on the soil’s physicochemical properties, enzyme activities, crop yield, crop quality and nutritional composition when considering two cowpea cultivars (Feijão frade de fio preto (FP) and Feijão frade de fio claro (FC)). The use of mineral fertilizers was seen to contribute to improved soil fertility due to the increase in soil properties, such as recalcitrant carbon, total nitrogen, ammonium content, available K and available Mg. On the other hand, organic fertilizers only increased the nitrate content in the soil. There were no differences in terms of cowpea crop yield, quality and nutritional composition by fertilizer type. Thus, both fertilizer types contributed to the same crop yield and quality, and thus the use of organic fertilizers can result in a sustainable alternative for maintaining cowpea crop yield and quality.