Long-Term Compost Amendment Changes Interactions and Specialization in the Soil Bacterial Community, Increasing the Presence of Beneficial N-Cycling Genes in the Soil

Abstract

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.

Effects of inorganic and compost tea fertilizers application on the taxonomic and functional microbial diversity of the purslane rhizosphere

“…On the other hand, the nitrogen is a key driver of soil microbial community composition ( Fierer et al., 2013 ). The knowledge on microbial N cycling genes in an agroecosystem is crucial to decipher the N cycling in them ( Cuartero et al., 2022 ). In this respect, we found that particular chemical fertilization treatments (IT3 and IT4) significantly increased the abundance of genes contributing to ammonia oxidation ( amoA , amoB , amoC ), that are part of the nitrification process and important for reducing nitrate leaching and emissions of NO and N 2 O ( Liu et al., 2017 ).…”

Organic management increases beneficial microorganisms and promotes the stability of microecological networks in tea plantation soil

“…In addition, there was also a partial negative correlation between fungal species in the OM, which was not found in the CM ( Table 4 ). This negative correlation means that there is competition, exclusion, or adaptation to ecological niches among species (Cuartero et al, 2022 ). However, these negative correlations promote the stability of the microbial network of the soil ecosystem because they compensate for the overexpression of some members.…”

Impacts of Snow-Farming on Alpine Soil and Vegetation: A Case Study from the Swiss Alps

“…We estimated microbial alpha-diversity (richness and Shannon index) on rarefied microbial data using the 'trans_alpha' function in microeco. To test the difference between the different locations, we assessed normality and homogeneity of variance using Shapiro-Wilk and Levene's tests using the 'car' package, following the assumptions and using the functions described by Cuartero et al (2022). We performed principal coordinates analysis (PCoA) using the Bray-Curtis distance to visualize the variation in microbial community composition using the 'trans beta' function in 'microeco'.…”