Amazon dark earth (ADE) is known for its high organic matter content, biochar concentration and microbial diversity. The biochar amount suggests the existence of microorganisms capable of degrading aromatic hydrocarbons (AHs). In an effort to investigate the influence of bacteria on the resilience and fertility of these soils, we enriched five ADE soils with naphthalene and phenanthrene, and biodegradation assays with phenanthrene and diesel oil were carried out, as well. After DNA extraction, amplification and sequencing of the 16S rRNA bacterial gene, we identified 148 isolates as the Proteobacteria, Firmicutes and Actinobacteria phyla comprising genera closely related to AHs biodegradation. We obtained 128 isolates that degrade diesel oil and 115 isolates that degrade phenanthrene. Some isolates were successful in degrading both substrates within 2 h. In conclusion, the obtained isolates from ADE have degrading aromatic compound activity, and perhaps, the biochar content has a high influence on this.

Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with increases in soil methane (CH₄) emission. To better understand the drivers of this change, we measured soil CH₄ flux, environmental conditions, and belowground microbial community structure across primary forests, cattle pastures, and secondary forests in two Amazonian regions. We show that pasture soils emit high levels of CH₄ (mean: 3454.6 ± 9482.3 μg CH₄ m^-2 d^-1), consistent with previous reports, while forest soils on average emit CH₄ at modest rates (mean: 9.8 ± 120.5 μg CH₄ m^-2 d^-1), but often act as CH₄ sinks. We report that secondary forest soils tend to consume CH₄ (mean: -10.2 ± 35.7 μg CH₄ m^-2 d^-1), demonstrating that pasture CH₄ emissions can be reversed. We apply a novel computational approach to identify microbial community attributes associated with flux independent of soil chemistry. While this revealed taxa known to produce or consume CH₄ directly (i.e. methanogens and methanotrophs, respectively), the vast majority of identified taxa are not known to cycle CH₄. Each land use type had a unique subset of taxa associated with CH₄ flux, suggesting that land use change alters CH₄ cycling through shifts in microbial community composition. Taken together, we show that microbial composition is crucial for understanding the observed CH₄ dynamics and that microorganisms provide explanatory power that cannot be captured by environmental variables.

Studies in the Amazon are being intensified to evaluate the alterations in the microbial communities of soils and sediments in the face of increasing deforestation and land-use changes in the region. However, since these environments present highly heterogeneous physicochemical properties, including contaminants that hinder nucleic acids isolation and downstream techniques, the development of best molecular practices is crucial. This work aimed to optimize standard protocols for DNA extraction and gene quantification by quantitative real-time PCR (qPCR) based on natural and anthropogenic soils and sediments (primary forest, pasture, Amazonian Dark Earth, and várzea, a seasonally flooded area) of the Eastern Amazon. Our modified extraction protocol increased the fluorometric DNA concentration by 48%, reaching twice the original amount for most of the pasture and várzea samples, and the 260/280 purity ratio by 15% to values between 1.8 to 2.0, considered ideal for DNA. The addition of bovine serum albumin in the qPCR reaction improved the quantification of the 16S rRNA genes of Archaea and Bacteria and its precision among technical replicates, as well as allowed their detection in previously non-amplifiable samples. It is concluded that the changes made in the protocols improved the parameters of the DNA samples and their amplification, thus increasing the reliability of microbial communities' analysis and its ecological interpretations.

Here, we report 17 metagenome-assembled genomes (MAGs) recovered from microbial consortia of forest and pasture soils in the Brazilian Eastern Amazon. The bacterial MAGs have the potential to act in important ecological processes, including carbohydrate degradation and sulfur and nitrogen cycling.