Land-Use System and Forest Floor Explain Prokaryotic Metacommunity Structuring and Spatial Turnover in Amazonian Forest-to-Pasture Conversion Areas

Chemical attributes, bacterial community, and antibiotic resistance genes are affected by intensive use of soil in agro-ecosystems of the Atlantic Forest, Southeastern Brazil

Soil is one of the largest reservoirs of microbial diversity in nature. Although soil management is vital for agricultural purposes, intensive practices can have a significant impact on fertility, microbial community, and resistome. Thus, the aim of this study was to evaluate the effects of an intensive soil management system on the chemical attributes, composition and structure of prevalent bacterial communities, and presence and abundance of antimicrobial resistance genes (ARGs). The chemical characterization, bacterial diversity and relative abundance of ARGs were evaluated in soils from areas of intensive vegetable cultivation and forests. Results indicate that levels of nutrients and heavy metals were higher in soil samples from cultivated areas. Similarly, greater enrichment and diversity of bacterial genera was detected in agricultural areas. Of the 18 target ARGs evaluated, seven were detected in studied soils. The oprD gene exhibited the highest abundance among the studied genes and was the only one that showed a significantly different prevalence between areas. The oprD gene was identified only from soil of the cultivated areas. The blaSFO, erm(36), oprD and van genes, in addition to the pH, showed greater correlation with in soil of cultivated areas, which in turn exhibited higher contents of nutrients. Thus, in addition to changes in chemical attributes and in the microbial community of the soil, intensive agricultural cultivation systems cause a modification of its resistome, reinforcing the importance of the study of antimicrobial resistance in a One Health approach.

Soil type determines the magnitude of soil fertility changes by forest-to-pasture conversion in Western Amazonia

The deforestation of tropical forests raises environmental concerns worldwide. Removing the pristine forest impacts the soil, consequently affecting the environmental services it provides. Within this context, the main goal of this study was to determine how the conversion of the tropical rainforest to pasture affects soil fertility across an extended range of soil heterogeneity, including different soil types. We sampled 13 sites, among forests, recent pastures (≤7-year-old), and old pastures (≥10-year-old), on Acrisols, Ferralsols, Plinthosols, and Luvisols, across a ± 800 km geographical range in the Western Brazilian Amazon. Soils were classified taxonomically, and their superficial layer's chemical and physical properties (0-10 cm) were analyzed. Furthermore, we tested the sensibility of Actinobacteria and Proteobacteria to detect changes in these soil properties based on their ecological habitat. An inter-regional gradient of soil fertility was observed, and the sampling sites were clustered mostly by soil type and associated land use than by spatial distance. The Sum of bases, Ca + Mg, base saturation, Al saturation, and pH were consistently affected by land use, increasing after conversion to pasture, at different degrees and with a more pronounced effect on oxidic soils. The Sum of bases was the only property that increased significantly among the study sites (R_adj = 0.860, p < 0.001), being able to detect the effect of anthropic land use on a larger coverage of soil types. Finally, the Actinobacteria:Proteobacteria ratio was also sensitive to the impact of forest-to-pasture conversion, with a higher ratio observed in pasture systems, and it was positively correlated with soil pH (rho = 0.469, p < 0.001). Our results consistently show that the forest-to-pasture conversion leads to strong alterations in the soil environment, with varying intensities depending on soil type.

Dysbiosis and predicted function of dental and ruminal microbiome associated with bovine periodontitis

Extensive cattle livestock is advancing in Amazonia and its low productivity, with consequent pressure to open new areas, is partly due to sanitary problems and, among them, the periodontal diseases, whose environmental triggers or modifying factors are unknown. In this study, we used high-throughput sequencing, network analysis and predicted functions to investigate the dental and ruminal microbiota of cattle raised in new livestock areas in the Amazon and identify possible keystone pathogens and proteins associated with the disease. Ninety-three genera were common in dental and ruminal fluid microbiomes and among them periodontal pathogens such as Fusobacterium, Prevotella, Porphyromonas and Actinomyces were recognized. Network analysis showed that dental microbiomes of clinically healthy animals tend to comprise a group of OTUs in homeostasis and when analyzed together, dental and ruminal fluid microbiomes of animals with periodontitis had almost twice the number of negative edges, indicating possible competition between bacteria and dysbiosis. The incisor dental and ruminal fluid microbiomes were dominated by a core community composed of members of the phyla Firmicutes and Bacteroidetes. Network results showed that members of the Prevotella genus stood out among the top five OTUs, with the largest number of hubs in the dental and ruminal microbiota of animals with periodontitis. Protein families linked to an inflammatory environment were predicted in the dental and ruminal microbiota of cattle with periodontitis. The dissimilarity between dental microbiomes, discriminating between healthy cattle and those with periodontitis and the identification of possible key pathogens, represent an important reference to elucidate the triggers involved in the etiopathogenesis of bovine periodontitis, and possibly in the development of measures to control the disease and reduce the pressures for deforestation.