Assessment of soil bacterial communities in integrated crop production systems within the Amazon Biome, Brazil: a comparative study

Abstract

Integrated production systems have been proposed as alternative to sustainable land use. However, information regarding bacterial community structure and diversity in soils of integrated Crop-Livestock-Forest systems remains unknown. We hypothesize that these integrated production systems, with their ecological intensification, can modulate the soil bacterial communities. However, Yet, it remains unclear whether the modulation of bacterial biodiversity is solely attributable to the complexity of root exudates or if seasonal climatic events also play a contributory role. The objective of this study is to evaluate the impact of monoculture and integrated production systems on bacterial soil communities in the Amazon Biome, Brazil. Three monoculture systems, each with a single crop over time and space (Eucalyptus (E), Crop Soybean (C), Pasture (P)), and three integrated systems with multiple crops over time and space (ECI, PI, ECPI) were evaluated, along with a Native forest serving as a reference area. Soil samples were collected at a depth of 0-10 cm during both the wet and dry seasons. Bacterial composition was determined using Illumina high-throughput sequencing of the 16 S rRNA gene. The sequencing results revealed the highest abundance classified under the phyla Firmicutes, Actinobacteria, and Proteobacteria. The Firmicutes correlated with the Crop in the rainy period and in the dry only ECPI and Forest. For five classes corresponding to the three phyla, the Crop stood out with the greatest fluctuations in their relative abundance compared to other production systems. In cluster analysis by genus during the rainy season, only Forest and ECPI showed no similarity with the other production systems. However, in the dry season, both were grouped with Forest and EPI. Therefore, the bacterial community in integrated systems proved to be sensitive to management practices, even with only two years of use. ECPI demonstrated the greatest similarity in bacterial structure to the Native forest, despite just two years of experimental deployment. Crop exhibited fluctuations in relative abundance in both seasons, indicating an unsustainable production system with changes in soil microbial composition. These findings support our hypothesis that integrated production systems and their ecological intensification, as exemplified by ECPI, can indeed modulate soil bacterial communities.

Keywords: 16S rRNA sequencing; Illumina; Integrated crop-livestock-forest; Tropical forest biodiversity.

Fig. 1

Mean relative abundance at phylum level above 1%. Seasons: (a) rainy, and (b) dry. Treatments: Eucalyptus - monospecific cultivation of eucalyptus; Crop; Pasture; Eucalyptus-Crop integration (ECI); Eucalyptus-Pasture integration (EPI); Eucalyptus-Crop-Pasture integration (ECPI); and reference area Native Forest (Forest)

Fig. 2

Principal component analysis (correlation-based PCA) among the three most abundant phyla. Treatments were used as supplementary variables. D: dry; R: rainy; ECI: Eucalyptus-Crop integration; EPI: Eucalyptus-Pasture integration; ECPI: Eucalyptus-Crop-Pasture integration; Forest: Cerrado/Amazon biomes

Fig. 3

Distribution of the most abundant classes with their respective phyla (Actinobacteria, Firmicutes, and Proteobacteria) in each treatment during the rainy (A) and dry (B) seasons. Treatments: Eucalyptus - monospecific cultivation of eucalyptus; Crop; Pasture; Eucalyptus-Crop integration (ECI); Eucalyptus-Pasture integration (EPI); Eucalyptus-Crop-Pasture integration (ECPI); and reference Native Forest area (Forest)

Fig. 4

PCA of treatments according to the minimum value of 95% of similarity between genera ≥ 0.05% relative abundance in the rainy (a) and dry (b) seasons. Treatments: Eucalyptus - monospecific cultivation of eucalyptus; Crop; Pasture; Eucalyptus-Crop integration (ECI); Eucalyptus-Pasture integration (EPI); Eucalyptus-Crop-Pasture integration (ECPI); and reference Native Forest area (Forest)