Microorganisms are critical indicators of soil quality due to their essential role in maintaining ecosystem services. However, anthropogenic activities can disrupt the vital metabolic functions of these microorganisms. Considering that soil biology is often underestimated and traditional assessment methods do not capture its complexity, molecular methods can be used to assess soil health more effectively. This study aimed to identify the changes in soil microbial diversity and activity under different cocoa agroforestry systems, specially focusing on taxa and functions associated to carbon and nitrogen cycling. Soils from three different cocoa agroforestry systems, including a newly established agroforestry with green fertilization (GF), rubber (Hevea brasiliensis)–cocoa intercropping (RC), and cocoa plantations under Cabruca (cultivated under the shave of native forest) (CAB) were analyzed and compared using metagenomic and metaproteomic approaches. Samples from surrounding native forest and pasture were used in the comparison, representing natural and anthropomorphic ecosystems. Metagenomic analysis revealed a significant increase in Proteobacteria and Basidiomycota and the genes associated with dissimilatory nitrate reduction in the RC and CAB areas. The green fertilization area showed increased nitrogen cycling activity, demonstrating the success of the practice. In addition, metaproteomic analyses detected enzymes such as dehydrogenases in RC and native forest soils, indicating higher metabolic activity in these soils. These findings underscore the importance of soil management strategies to enhance soil productivity, diversity, and overall soil health. Molecular tools are useful to demonstrate how changes in agricultural practices directly influence the microbial community, affecting soil health.

Opencast mining drastically alters the landscape due to complete vegetation suppression and removal of topsoil layers. Precise indicators able to address incremental changes in soil quality are necessary to monitor and evaluate mineland rehabilitation projects. For this purpose, metaproteomics may be a useful tool due to its capacity to shed light on both taxonomic and functional overviews of soil biodiversity, allowing the linkage between proteins found in soil and ecosystem functioning. We investigated bacterial proteins and peptide abundance of three different mineland rehabilitation stages and compared it with a non-rehabilitated site and a native area (evergreen dense forest) in the eastern Amazon. The total amount of identified soil proteins was significantly higher in the rehabilitating and native soils than in the non-rehabilitated site. Regarding soil bacterial composition, the intermediate and advanced sites were shown to be most similar to native soil. Cyanobacteria and Firmicutes phyla are abundant in the early stages of environmental rehabilitation, while Proteobacteria population dominates the later stages. Enzyme abundances and function in the three rehabilitation stages were more similar to those found in the native soil, and the higher accumulation of many hydrolases and oxidoreductases reflects the improvement of soil biological activity in the rehabilitating sites when compared to the non-rehabilitated areas. Moreover, critical ecological processes, such as carbon and nitrogen cycling, seem to return to the soil in short periods after the start of rehabilitation activities (i.e., 4 years). Metaproteomics revealed that the biochemical processes that occur belowground can be followed throughout rehabilitation stages, and the enzymes shown here can be used as targets for environmental monitoring of mineland rehabilitation projects.

To gain insight into the active microbiota during spontaneous fermentation of Theobroma cacao L., this study assessed protein diversity during 120 h using a combined metabarconding and metaproteomics approach. During the first days of fermentation, most of the peptides were associated with T. cacao and yeast (0–72 h). Peptides associated with bacteria became more abundant after 72 h of fermentation, coinciding with a decrease in peptides associated with cocoa (96–120 h). In addition to the known microorganisms involved in fermentation, such as Saccharomyces, Lactobacillus and Acetobacter, novel genera were also metabolically active, including Microvirga, Inquilinus, Candolleomyces and Lasiodiplodia.. The results showed a consistency in the main genera detected by both techniques, but the identification of unexplored genera such as Inquilinus, Microvirga, Cyphellophora and Ashbya gossypii, among others, suggests that this omics approach needs to be used together for more comprehensive results on spontaneous fermentation. In conclusion, studies combining techniques such as metabarcoding and metaproteomics should be considered in fermentation studies, as a single technique would result in omissions regarding the activity of certain microorganisms that may be important for the course of spontaneous fermentation.

Mimosa acutistipula is endemic to Brazil and grows in ferruginous outcrops (canga) in Serra dos Carajás, eastern Amazon, where one of the largest iron ore deposits in the world is located. Plants that develop in these ecosystems are subject to severe environmental conditions and must have adaptive mechanisms to grow and thrive in cangas. Mimosa acutistipula is a native species used to restore biodiversity in post-mining areas in canga. Understanding the molecular mechanisms involved in the adaptation of M. acutistipula in canga is essential to deduce the ability of native species to adapt to possible stressors in rehabilitating minelands over time. In this study, the root proteomic profiles of M. acutistipula grown in a native canga ecosystem and rehabilitating minelands were compared to identify essential proteins involved in the adaptation of this species in its native environment and that should enable its establishment in rehabilitating minelands. The results showed differentially abundant proteins, where 436 proteins with significant values (p < 0.05) and fold change ≥ 2 were more abundant in canga and 145 in roots from the rehabilitating minelands. Among them, a representative amount and diversity of proteins were related to responses to water deficit, heat, and responses to metal ions. Other identified proteins are involved in biocontrol activity against phytopathogens and symbiosis. This research provides insights into proteins involved in M. acutistipula responses to environmental stimuli, suggesting critical mechanisms to support the establishment of native canga plants in rehabilitating minelands over time.

Mimosa acutistipula is endemic to Brazil and grows in ferruginous outcrops (canga) in Serra dos Carajás, eastern Amazon, where one of the largest iron ore deposits in the world is located. Plants that develop in these ecosystems are subject to severe environmental conditions and must have adaptive mechanisms to grow and thrive in cangas. Mimosa acutistipula is a native species used to restore biodiversity in post-mining areas in canga. Understanding the molecular mechanisms involved in the adaptation of M. acutistipula in canga is essential to deduce the ability of native species to adapt to possible stressors in rehabilitating minelands over time. In this study, the root proteomic profiles of M. acutistipula grown in a native canga ecosystem and rehabilitating minelands were compared to identify essential proteins involved in the adaptation of this species in its native environment and that should enable its establishment in rehabilitating minelands. The results showed differentially abundant proteins, where 436 proteins with significant values (p < 0.05) and fold change ≥ 2 were more abundant in canga and 145 in roots from the rehabilitating minelands. Among them, a representative amount and diversity of proteins were related to responses to water deficit, heat, and responses to metal ions. Other identified proteins are involved in biocontrol activity against phytopathogens and symbiosis. This research provides insights into proteins involved in M. acutistipula responses to environmental stimuli, suggesting critical mechanisms to support the establishment of native canga plants in rehabilitating minelands over time.