Organellar-genome analyses from the lycophyte genus Isoetes L. show one of the highest frequencies of RNA editing in land plants.

RNA editing is a post-transcriptional process that challenges the central dogma of molecular biology by modifying RNA sequences, introducing nucleotide changes at specific sites, and generating functional diversity beyond the genomic code, especially when it concerns organellar transcripts. In plants, this phenomenon is widespread, but its extent varies significantly among species and organellar genomes. Among land plants, the heterosporous lycophytes (i.e., Isoetes and Selaginella) stand out for their exceptionally high numbers of RNA-editing sites, despite their morphological stasis and ancient lineage. In this study, we explore the complete set of organellar protein-coding genes in the aquatic plant group Isoetes, providing a detailed analysis of RNA editing in both the mitochondrial and plastid genomes. Our findings reveal a remarkable abundance of RNA editing, particularly in the mitochondrial genome, with thousands of editing sites identified. Interestingly, the majority of these edits result in non-silent substitutions, suggesting a role in fine-tuning protein structure and function. Furthermore, we observe a consistent trend of increased hydrophobicity in membrane-bound proteins, supporting the notion that RNA editing may confer a selective advantage by preserving gene functionality in Isoetes. The conservation of highly edited RNA sequences over millions of years underscores the evolutionary significance of RNA editing. Additionally, the study sheds light on the dynamic nature of RNA editing, with shared editing sites reflecting common ancestry whereas exclusive edits matching more recent radiation events within the genus. This work advances our understanding of the intricate interplay between RNA editing, adaptation, and evolution in land plants and highlights the unique genomic features of Isoetes, providing a foundation for further investigations into the functional consequences of RNA editing in this enigmatic plant lineage.

Desiccation tolerance in the resurrection plant Barbacenia graminifolia involves changes in redox metabolism and carotenoid oxidation.

Desiccation tolerance in vegetative tissues enables resurrection plants to remain quiescent under severe drought and rapidly recover full metabolism once water becomes available. Barbacenia graminifolia is a resurrection plant that occurs at high altitudes, typically growing on rock slits, exposed to high irradiance and limited water availability. We analyzed the levels of reactive oxygen species (ROS) and antioxidants, carotenoids and its cleavage products, and stress-related phytohormones in fully hydrated, dehydrated, and rehydrated leaves of B. graminifolia. This species exhibited a precise adjustment of its antioxidant metabolism to desiccation. Our results indicate that this adjustment is associated with enhanced carotenoid and apocarotenoids, α-tocopherol and compounds of ascorbate-glutathione cycle. While α-carotene and lutein increased in dried-leaves suggesting effective protection of the light-harvesting complexes, the decrease in ß-carotene was accompanied of 10.2-fold increase in the content of ß-cyclocitral, an apocarotenoid implicated in the regulation of abiotic stresses, compared to hydrated plants. The principal component analysis showed that dehydrated plants at 30 days formed a separate cluster from both hydrated and dehydrated plants for up to 15 days. This regulation might be part of the protective metabolic strategies employed by this resurrection plant to survive water scarcity in its inhospitable habitat.

Clean and accurate soil quality monitoring in mining areas under environmental rehabilitation in the Eastern Brazilian Amazon.

Soil quality monitoring in mining rehabilitation areas is a crucial step to validate the effectiveness of the adopted recovery strategy, especially in critical areas for environmental conservation, such as the Brazilian Amazon. The use of portable X-ray fluorescence (pXRF) spectrometry allows a rapid quantification of several soil chemical elements, with low cost and without residue generation, being an alternative for clean and accurate environmental monitoring. Thus, this work aimed to assess soil quality in mining areas with different stages of environmental rehabilitation based on predictions of soil fertility properties through pXRF along with four machine learning algorithms (projection pursuit regression, PPR; support vector machine, SVM; cubist regression, CR; and random forest, RF) in the Eastern Brazilian Amazon. Sandstone and iron mines in different chronological stages of rehabilitation (initial, intermediate, and advanced) were evaluated, in addition to non-rehabilitated and native forest areas. A total of 81 soil samples (26 from sandstone mine and 55 from iron mine) were analyzed by both traditional wet-chemistry methods and pXRF. The available/exchangeable contents of K, Ca, B, Fe, and Al, in addition to H+Al, cation exchange capacity at pH = 7, Al saturation, soil organic matter, pH, sum of bases, base saturation, clay, and sand were accurately predicted (R2 > 0.70) using pXRF data, with emphasis on the prediction of Fe (R2 = 0.93), clay content (R2 = 0.81), H+Al (R2 = 0.81), and K+ (R2 = 0.85). The best predictive models were developed by RF and CR (86%) and when considering pXRF data + mining area + stage of rehabilitation (73%). The results highlight the potential of pXRF to accurately assess soil properties in environmental rehabilitation areas in the Amazon region (yet scarcely evaluated under this approach), promoting a more agile and cheaper preliminary diagnosis compared to traditional methods.

Exogenous Nitric Oxide Alleviates Water Deficit and Increases the Seed Production of an Endemic Amazonian Canga Grass.

Open pit mining can cause loss in different ecosystems, including damage to habitats of rare and endemic species. Understanding the biology of these species is fundamental for their conservation, and to assist in decision-making. Sporobolus multiramosus is an annual grass endemic to the Amazon canga ecosystems, which comprise rocky outcrop vegetation covering one of the world's largest iron ore reserves. Here, we evaluated whether nitric oxide aids S. multiramosus in coping with water shortages and examined the physiological processes behind these adaptations. nitric oxide application improved the water status, photosynthetic efficiency, biomass production, and seed production and germination of S. multiramosus under water deficit conditions. These enhancements were accompanied by adjustments in leaf and root anatomy, including changes in stomata density and size and root endodermis thickness and vascular cylinder diameter. Proteomic analysis revealed that nitric oxide promoted the activation of several proteins involved in the response to environmental stress and flower and fruit development. Overall, the results suggest that exogenous nitric oxide has the potential to enhance the growth and productivity of S. multiramosus. Enhancements in seed productivity have significant implications for conservation initiatives and can be applied to seed production areas, particularly for the restoration of native ecosystems.

Molecular Mechanisms Underlying Mimosa acutistipula Success in Amazonian Rehabilitating Minelands.

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.

Proteomic Profiling and Rhizosphere-Associated Microbial Communities Reveal Adaptive Mechanisms of Dioclea apurensis Kunth in Eastern Amazon's Rehabilitating Minelands.

Dioclea apurensis Kunth is native to ferruginous rocky outcrops (known as canga) in the eastern Amazon. Native cangas are considered hotspots of biological diversity and have one of the largest iron ore deposits in the world. There, D. apurensis can grow in post-mining areas where molecular mechanisms and rhizospheric interactions with soil microorganisms are expected to contribute to their establishment in rehabilitating minelands (RM). In this study, we compare the root proteomic profile and rhizosphere-associated bacterial and fungal communities of D. apurensis growing in canga and RM to characterize the main mechanisms that allow the growth and establishment in post-mining areas. The results showed that proteins involved in response to oxidative stress, drought, excess of iron, and phosphorus deficiency showed higher levels in canga and, therefore, helped explain its high establishment rates in RM. Rhizospheric selectivity of microorganisms was more evident in canga. The microbial community structure was mostly different between the two habitats, denoting that despite having its preferences, D. apurensis can associate with beneficial soil microorganisms without specificity. Therefore, its good performance in RM can also be improved or attributed to its ability to cope with beneficial soil-borne microorganisms. Native plants with such adaptations must be used to enhance the rehabilitation process.

Copper mining in the eastern Amazon: an environmental perspective on potentially toxic elements.

Mining activity is of great economic and social importance; however, volumes of metallic ore tailings rich in potentially toxic elements (PTEs) may be produced. In this context, managing this environmental liability and assessing soil quality in areas close to mining activities are fundamental. This study aimed to compare the concentrations of PTEs-arsenic (As), barium (Ba), cadmium (Cd), cobalt (Co), chromium (Cr), copper (Cu), mercury (Hg), molybdenum (Mo), nickel (Ni), lead (Pb) and zinc (Zn)-as well as the fertility and texture of Cu tailings and soils of native, urban and pasture areas surrounding a Cu mining complex in the eastern Amazon. The levels of PTEs were compared with soil prevention values, soil quality reference values, global average soil concentrations and average upper continental crust concentrations. The contamination factor (CF), degree of contamination (Cdeg), potential ecological risk index (RI), geoaccumulation index (Igeo) and pollution load index (PLI) were calculated. The levels of Co, Cu and Ni in the tailings area exceeded the prevention values, soil quality reference values and average upper continental crust concentrations; however, the tailings area was considered unpolluted according to PLI and RI and presented a low potential ecological risk. The high concentrations of PTEs are associated with the geological properties of the area, and the presence of PTEs-rich minerals supports these results. For the urban and pasture areas, none of the 11 PTEs analyzed exceeded the prevention values established by the Brazilian National Environment Council.

Conservation implications of genetic structure in the narrowest endemic quillwort from the Eastern Amazon.

The quillwort Isoëtes cangae is a critically endangered species occurring in a single lake in Serra dos Carajás, Eastern Amazon. Low genetic diversity and small effective population sizes (N e) are expected for narrow endemic species (NES). Conservation biology studies centered in a single species show some limitations, but they are still useful considering the limited time and resources available for protection of species at risk of extinction. Here, we evaluated the genetic diversity, population structure, N e, and minimum viable population (MVP) of I. cangae to provide information for effective conservation programs. Our analyses were based on 55 individuals collected from the Amendoim Lake and 35,638 neutral SNPs. Our results indicated a single panmictic population, moderate levels of genetic diversity, and N e in the order of thousands, contrasting the expected for NES. Negative FIS values were also found, suggesting that I. cangae is not under risk of inbreeding depression. Our findings imply that I. cangae contains enough genetic diversity to ensure evolutionary potential and that all individuals should be treated as one demographic unit. These results provide essential information to optimize ex situ conservation efforts and genetic diversity monitoring, which are currently applied to guide I. cangae conservation plans.

Elevated Temperatures Impose Transcriptional Constraints and Elicit Intraspecific Differences Between Coffee Genotypes.

The projected impact of global warming on coffee production may require the heat-adapted genotypes in the next decades. To identify cellular strategies in response to warmer temperatures, we compared the effect of elevated temperature on two commercial Coffea arabica L. genotypes exploring leaf physiology, transcriptome, and carbohydrate/protein composition. Growth temperatures were 23/19°C (day/night), as optimal condition (OpT), and 30/26°C (day/night) as a possible warmer scenario (WaT). The cv. Acauã showed lower levels of leaf temperature (Tleaf) under both conditions compared to cv. Catuaí, whereas slightly or no differences for other leaf physiological parameters. Therefore, to explore temperature responsive pathways the leaf transcriptome was examined using RNAseq. Genotypes showed a marked number of differentially-expressed genes (DEGs) under OpT, however DEGs strongly decrease in both at WaT condition indicating a transcriptional constraint. DEGs responsive to WaT revealed shared and genotype-specific genes mostly related to carbohydrate metabolism. Under OpT, leaf starch content was greater in cv. Acauã and, as WaT temperature was imposed, the leaf soluble sugar did not change in contrast to cv. Catuaí, although the levels of leaf starch, sucrose, and leaf protein decreased in both genotypes. These findings revealed intraspecific differences in the underlying transcriptional and metabolic interconnected pathways responsive to warmer temperatures, which is potentially linked to thermotolerance, and thus may be useful as biomarkers in breeding for a changing climate.

Phosphorus lability increases with the rehabilitation advance of iron mine land in the eastern Amazon.

Impacted areas by iron mining may face challenges in the management of phosphate fertilization and reduced efficiency of rehabilitation practices, thus extending the time required for the rehabilitation of these areas. The objective of this study was to evaluate phosphorus (P) lability in soils of native forest and ferriferous canga areas (savanna vegetation above ironstone outcrops covering iron ore deposits) and in iron mine waste piles undergoing rehabilitation. Benches of the analysed waste pile differ in age of rehabilitation: as the initial rehabilitation stage (INI), we consider benches with fewer than 3 years of rehabilitation; the intermediate stage (INT) were benches with up to 5 years of rehabilitation; and the advanced rehabilitation stage (ADV) corresponds to benches with more than 8 years of rehabilitation activities. Organic and inorganic P fractions were analysed in these areas by chemical fractionation and were classified according to the degree of soil lability. The results show that in the canga environment, there was a predominance of inorganic fractions of moderate lability and moderate stability, with a strong dependency of the soil organic matter (SOM) on the P fractions, whereas there was a greater participation of the moderately labile organic fractions in the forest than in the canga. On the other hand, in the rehabilitation areas, there was an increase in the labile organic and inorganic fractions as the rehabilitation process advanced. The distribution of P in areas undergoing rehabilitation indicates that there is a tendency for P levels to resemble those of native environments, such as the forests.

Integrating environmental variables by multivariate ordination enables the reliable estimation of mineland rehabilitation status.

Despite the wide variety of variables commonly employed to measure the success of rehabilitation, the assessment and subsequent definition of indicators of environmental rehabilitation status are not simple tasks. The main challenges are comparing rehabilitated sites with target ecosystems as well as integrating individual environmental and eventually collinear variables into a single tractable measure for the state of a system before effective indicators that track rehabilitation may be modeled. Furthermore, a consensus is lacking regarding which and how many variables need to be surveyed for a reliable estimation of rehabilitation status. Here, we propose a multivariate ordination to integrate variables related to ecological processes, vegetation structure, and community diversity into a single estimation of rehabilitation status. As a case, we employed a curated set of 32 environmental variables retrieved from nonrevegetated, rehabilitating and reference sites associated with iron ore mines from the Urucum Massif, Mato Grosso do Sul, Brazil. By integrating this set of environmental variables into a single estimation of rehabilitation status, the proposed multivariate approach is straightforward and able to adequately address collinearity among variables. The proposed methodology allows for the identification of biases towards single variables, surveys or analyses, which is necessary to rank environmental variables regarding their importance to the assessment. Furthermore, we show that bootstrapping permitted the detection of the minimum number of environmental variables necessary to achieve reliable estimations of the rehabilitation status. Finally, we show that the proposed variable integration enables the definition of case-specific environmental indicators for more rapid assessments of mineland rehabilitation. Thus, the proposed multivariate ordination represents a powerful tool to facilitate the diagnosis of rehabilitating sites worldwide provided that sufficient environmental variables related to ecological processes, diversity and vegetation structure are gathered from nonrehabilitated, rehabilitating and reference study sites. By identifying deviations from predicted rehabilitation trajectories and providing assessments for environmental agencies, this proposed multivariate ordination increases the effectiveness of (mineland) rehabilitation.

A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining.

Microorganisms are useful environmental indicators, able to deliver essential insights to processes regarding mine land rehabilitation. To compare microbial communities from a chronosequence of mine land rehabilitation to pre-disturbance levels from references sites covered by native vegetation, we sampled non-rehabilitated, rehabilitating and reference study sites from the Urucum Massif, Southwestern Brazil. From each study site, three composed soil samples were collected for chemical, physical, and metagenomics analysis. We used a paired-end library sequencing technology (NextSeq 500 Illumina); the reads were assembled using MEGAHIT. Coding DNA sequences (CDS) were identified using Kaiju in combination with non-redundant NCBI BLAST reference sequences containing archaea, bacteria, and viruses. Additionally, a functional classification was performed by EMG v2.3.2. Here, we provide the raw data and assembly (reads and contigs), followed by initial functional and taxonomic analysis, as a base-line for further studies of this kind. Further investigation is needed to fully understand the mechanisms of environmental rehabilitation in tropical regions, inspiring further researchers to explore this collection for hypothesis testing.

Mine land rehabilitation in Brazil: Goals and techniques in the context of legal requirements.

Environmental legislation in many countries demands the rehabilitation of degraded areas to minimize environmental impacts. Brazilian laws require the restitution of self-sustaining ecosystems to historical conditions but ignore the emergence of novel ecosystems due to large-scale changes, such as species invasions, extinctions, and land-use or climate changes, although these novel ecosystems might fulfill ecosystem services in similar ways as historic ecosystems. Thorough discussions of rehabilitation goals, target ecosystems, applied methods, and approaches to achieving mine land rehabilitation, as well as dialogues about the advantages and risks of chemical inputs or non-native, non-invasive species that include all political, economic, social, and academic stakeholders are necessary to achieve biological feasibility, sociocultural acceptance, economic viability, and institutional tractability during environmental rehabilitation. Scientific knowledge of natural and rehabilitating ecosystems is indispensable for advancing these discussions and achieving more sustainable mining. Both mining companies and public institutions are responsible for obtaining this knowledge.