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There is still no consensus on the true origin of fatal yellowing, one of the most important diseases affecting oil palm (Elaeis guineensis Jacq.) plantations. This study involved two-dimensional liquid chromatography coupled with tandem mass spectrometry (2D-UPLC-MSE) analyses to identify changes in protein profiles of oil palms affected by FY disease. Oil palm roots were sampled from two growing areas. Differential accumulation of proteins was assessed by comparing plants with and without symptoms and between plants at different stages of FY development. Most of the proteins identified with differential accumulation were those related to stress response and energy metabolism. The latter proteins include the enzymes alcohol dehydrogenase and aldehyde dehydrogenase, related to alcohol fermentation, which were identified in plants with and without symptoms. The presence of these enzymes suggests an anaerobic condition before or during FY. Transketolase, isoflavone reductase, cinnamyl alcohol dehydrogenase, caffeic acid 3-O-methyltransferase, S-adenosylmethionine synthase, aldehyde dehydrogenase and ferritin, among others, were identified as potential marker proteins and could be used to guide selection of FY-tolerant oil palm genotypes or to understand the source of this anomaly. When comparing different stages of FY, we observed high accumulation of alcohol dehydrogenase and other abiotic stress related-proteins at all disease stages. On the other hand, biological stress-related proteins were more accumulated at later stages of the disease. These results suggest that changes in abiotic factors can trigger FY development, creating conditions for the establishment of opportunistic pathogens.

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.

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.

Fruit ripening involves coordinated metabolic and molecular changes that shape quality traits, yet tissue-specific regulation in Selenicereus megalanthus remains unclear. Fruit development in S. megalanthus was investigated through an integrated analysis of pulp and peel across five developmental stages to elucidate tissue-specific metabolic and molecular regulatory dynamics. Proteomic profiling combined with targeted metabolomic analyses of sugars and phenolic compounds, multivariate statistics, and protein–protein interaction analysis was applied. A total of 411 proteins were identified in the pulp and 812 in the peel, of which 255 and 362 proteins, respectively, showed significant differential accumulation across development (p < 0.05), indicating higher regulatory plasticity in the peel. Multivariate analyses revealed clear stage-dependent reorganization of the proteome in both tissues. Functional annotation highlighted coordinated modulation of pathways related to cell wall remodeling, carbohydrate metabolism, antioxidant and detoxification systems, protein folding, and myo-inositol biosynthesis, directly associated with fruit texture and quality attributes. Metabolomic analyses revealed progressive sugar accumulation during ripening, with sucrose predominating at advanced stages, and pronounced tissue- and stage-dependent modulation of phenolic compounds, characterized by early enrichment in the pulp and sustained accumulation in the peel. Overall, these results demonstrate that yellow pitaya development involves tightly coordinated biochemical and regulatory mechanisms and identify the peel as a metabolically active tissue with relevance for postharvest management, fruit quality, and sustainable horticultural valorization.

Mimosa acutistipula var. ferrea (Fabaceae) is endemic to ferruginous tropical rocky outcrops in the eastern Amazon, also known as canga. Canga are often associated with mining activities and are the target of protection and rehabilitation projects. M. acutistipula stands out in this biodiversity hotspot with high growth rates, even in rehabilitating minelands (RMs). However, little is known about the diversity of soil microorganisms interacting with M. acutistipula in canga and RMs. This study analyzed the rhizosphere-associated bacterial and fungal microbial communities associated with M. acutistipula growing in an RM and a native shrub canga. The fungal phylum Ascomycota was the dominant taxa identified in the rhizosphere of the canga (RA: 98.1) and RM (RA: 93.1). The bacterial phyla Proteobacteria (RA: 54.3) and Acidobacteria (RA: 56.2) were the dominant taxa identified in the rhizosphere in the canga and RM, respectively. Beneficial genera such as Bradyrhizobium, Rhodoplanes, and Paraconiothyrium were identified in the rhizosphere of M. acutistipula in both areas. However, the analyses showed that the fungal and bacterial diversity differed between the rhizosphere of the canga and RM, and that the microbial taxa adapted to the canga (i.e., Rasamsonia, Scytalidium, Roseiarcus, and Rhodomicrobium) were lacking in the RM. This influences the microbe-mediated soil processes, affecting long-term rehabilitation success. The results showed that M. acutistipula established non-specific interactions with soil microorganisms, including beneficial taxa such as nitrogen-fixing bacteria, mycorrhizal fungi, and other beneficial endophytes, well known for their importance in plant adaptation and survival. High levels of microbe association and a plant’s ability to recruit a wide range of soil microorganisms help to explain M. acutistipula’s success in rehabilitating minelands.

We promoted microbial iron reduction and subsequent iron oxidation, in crushed iron‐rich mine waste at pilot scale (~1 m3). Repeated iron cycling led to the formation of new iron oxide cements cementing grains and aggregating the waste material. The technology has promise for accelerating remediation of iron ore mine sites. Summary Accelerating microbial iron cycling is an innovative environmentally responsible strategy for mine remediation. In the present study, we extend the application of microbial iron cycling in environmental remediation, to include biocementation for the aggregation and stabilization of mine wastes. Microbial iron reduction was promoted monthly for 10 months in crushed canga (a by‐product from iron ore mining, dominated by crystalline iron oxides) in 1 m3 containers. Ferrous iron concentrations reached 445 ppm in treatments and diverse lineages of the candidate phyla radiation dominated pore waters, implicating them in fermentation and/or metal cycling in this system. After a 6‐month evaporation period, iron‐rich cements had formed between grains and 20‐cm aggregates were recoverable from treatments throughout the 1‐m depth profile, while material from untreated and water‐only controls remained unconsolidated. Canga‐adapted plants seeded into one of the treatments germinated and grew well. Therefore, application of this geobiotechnology offers promise for stabilization of mine wastes, as well as re‐formation of surface crusts that underpin unique and threatened plant ecosystems in iron ore regions.

Background and aims Wildfires can dramatically alter forests, their biodiversity and goods they provide to society. In the Andes Cordillera, Nothofagus pumilio is a native, fire-sensitive tree species that is completely excluded from severely burned areas. Therefore, it is of interest to evaluate whether there are differences in the microbial soil communities that could contribute to improve the recruitment of N. pumilio after a fire. We aimed at determining the diversity of soil bacteria and fungi associated with Nothofagus pumilio in old-growth forests affected by a moderate severity wildfire in the Andes Cordillera of south-central Chile in 2015. Methods Eight years after fire, soil samples were collected from selected N. pumilio rhizosphere and bulk soil in fire-affected areas, and were compared with those from unburned areas using a metabarcoding approach. Results We found that symbiotic microorganisms such as saprophytic, ectomycorrhizal fungi, ericoid mycorrhizal taxa and N-fixing bacteria were present with high abundances in the burned area. The most abundant bacterial genera were Mycobacterium , Rhodoplanes and Bryobacter . Meanwhile, Cortinarius and Penicillium were the most common fungal genera identified in burned and unburned sites. Conclusions Moderate severity wildfires in Nothofagus pumilio forests do not result in significantly different soil microbiomes eight years post-burn in either the rhizosphere or bulk soil, which could be key for N. pumilio establishment and survival after fire. Identifying the microbial diversity associated with native trees after fire is essential to know symbiotic microorganisms supporting the recovery of plant species.

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.

Symbiotic microorganisms are essential for promoting plant growth and establishment from the early stages of plant development. However, the diversity of seed-associated endophytes in native Andean trees and their role in growth promotion and seedling establishment have scarcely been studied. This study aimed to characterize the microbial diversity associated with seeds of Nothofagus obliqua (Mirb.) Oerst. Viable seeds were collected from healthy young trees in a section of the Nahuelbuta Mountains, south-central Chile. Then, they were processed to characterize total microbial diversity using a 16S rRNA gene and an internal transcribed spacer (ITS) region metabarcoding approach. The diversity of culturable bacteria was determined and tested for plant growth-promoting effects. Effects on seed germination, seedling development, and plantlet establishment were evaluated by in vivo inoculations. Seed-associated microbial diversity was dominated by Ascomycota and Proteobacteria, with Diaphorte and Pantoea being the most abundant genera. Five different strains of culturable bacteria were identified, with Rahnella aquatilis being the strain with the most traits that promote plant growth. Bioaugmentation with R. aquatilis improved seed germination, plantlet growth, and establishment of N. obliqua plantlets in the field. Specifically, bioaugmentation with R. aquatilis stimulated height (+ 52%), stem cross-sectional area (+ 89%), stomatal conductance to water vapor (+ 25%), and leaf mass area (+ 29%). These results provide evidence for the beneficial properties of seed-associated bacteria that can support the establishment of native forest tree species in the southern Andes.