The aim of this study was to investigate the influence of agricultural intensification on soil microbial diversity, chemical and physical parameters, and the decrease of the incidence of sudden death syndrome (Fusarium crassistipitatum) and charcoal rot (Macrophomina phaseolina) in soybean. Soils under different management systems were evaluated during 2 crop cycles: soybean monoculture for 24 and 11 years, soybean-maize rotation for 15 and 4 years, 1 year of soybean, and native vegetation. The incidence of both soil-borne diseases was higher under monoculture than under rotation. Increased populations of potential biocontrol agents (Trichoderma spp., Gliocladium spp., fluorescent pseudomonads) were associated with rotation treatments, especially in 2010-2011. The comparison of agricultural vs. native vegetation soil and the average of agricultural cycles showed that microbial biomass carbon and glomalin-related soil protein were higher in the rotation system than in monoculture (50% and 77%, respectively). Furthermore, from the community-level functional diversity (Biolog Eco plates), McIntosh index showed lower functional diversity in monoculture than in rotation and native vegetation plots. Agricultural intensification reduced microbial biomass carbon, glomalin-related soil protein, organic matter, total nitrogen, aggregate stability, and yield, and increased bulk density. Soil quality degradation was associated with the establishment of soil-borne pathogens and increased soybean plant susceptibility to disease.

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The effect of crop sequences on soil quality indicators and its relationship with sudden death syndrome (SDS, a complex of Fusarium species) was evaluated by physical, chemical, biochemical and molecular techniques. Regarding physical aspects, soybean/maize and maize monoculture exhibited the highest stable aggregate level, with values 41% and 43% higher than in soybean monoculture, respectively, and 133% higher than in bean monoculture. Bulk density (BD) was higher in soybean monoculture, being 4% higher than in bean monoculture. The chemical parameters organic matter, total N, P, K, Mg, Ca, and water holding capacity also indicated that soybean/maize and maize monoculture improved soil quality. Fungal and bacterial community fingerprints generated using Terminal Restriction Fragment Length Polymorphism analysis of intergenic transcribed spacer regions of rRNA genes and 16S rRNA genes, respectively, indicated a clear separation between the rotations. Fatty acid profiles evaluated by FAME showed that bean monoculture had higher biomass of Gram (+) bacteria and stress indicators than maize monoculture, while the soybean/maize system showed a significant increase in total microbial biomass (total FAMEs content) in comparison with soybean and bean monoculture. The incidence of SDS (Fusarium crassistipitatum) was markedly higher (15%) under soybean monoculture than when soybean was grown in rotation with maize. In the present work, soil microbial properties were improved under soybean/maize relative to continuous soybean. The improvement of soil health was one of the main causes for the reduction of disease pressure and crop yield improvement due to the benefits that crop rotation produces for soil quality.

The aim of this study was to evaluate the response pattern of diazotrophic microbes, denitrifiers and nitrifiers to different types of land use management, such as soybean monoculture (M) during 5 and 24 years (M5 and M24) and soybean-maize rotation (R) during 4 and 15 years (R4 and R15) in two subsequent years at the time point of flowering. Soil samples from a site recently introduced into agriculture (RUA) and a pristine soil under native vegetation (NV) were used as controls. Abundances of different functional groups of microbes were assessed using the direct quantification of marker genes by quantitative real-time PCR using extracted DNA from rhizosphere samples. In addition, soil chemical and physical properties were analysed and correlated with the abundance data from the functional microbial groups under investigation. Overall, the results indicate that the abundance of nifH genes was higher under R treatments compared to M treatments. The abundance of ammonium monooxygenase genes amoA (AOA) was generally higher under rotation systems and decreased under M24. RUA evidenced a negative effect on the establishment and development of AOA communities. The influence of land use on nirS abundance was inconsistent. However, R treatments showed a high abundance of nirK genes compared to M treatments. In both growing seasons, the abundance of nosZ genes was higher under NV compared with the other treatments. Furthermore, M24 treatment was related to strongly changed chemical and physical soil properties compared with the other sites. As expected, soil samples from RUA showed the strong dynamics of measured parameters indicating the high sensitivity of soils under transition to environmental parameters. Our results also indicated that the long-term crop rotation modified the abundance of the investigated microbial groups compared to the monoculture and increased soil chemical and physical quality. Therefore, our results provide evidence for a stimulatory effect of the long-term crop rotation on the abundance of microbes involved in N transformation.