Selecting plant species for practical restoration of degraded lands using a multiple-trait approach

Restoration success in former Amazonian mines is driven by soil amendment and forest proximity

Mining contributes importantly to tropical deforestation and land degradation. To mitigate these effects, mining companies are increasingly obliged to restore abandoned mine lands, but factors driving restoration success are hardly evaluated. Here, we investigate the influence of ecological factors (restoration age, soil properties and surrounding forest area) and management factors (diversity and density of planted species, mine zone) on the recovery rate of forest structure and tree diversity on 40 post-mining restoration areas in Southern Amazonia, Brazil, using a 9-year annual monitoring dataset consisting of over 25 000 trees. We found that recovery of forest structure was closely associated with interactions between soil quality and the planted tree communities, and that tree diversity recovery was positively associated with the amount of surrounding forests. We also observed that forest structure and diversity recover more slowly in mine tailings compared to pit surroundings. Our study confirms the complexity of mine land restoration but also reveals that planting design and soil improvement can increase restoration success. For resource-efficient mine restoration, we recommend the focusing of efforts on tailings, which are hardest to restore, and reducing efforts in pit surroundings and areas close to surrounding forest because of their potential for restoration by natural regeneration. This article is part of the theme issue 'Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration'.

The road to recovery: a synthesis of outcomes from ecosystem restoration in tropical and sub-tropical Asian forests

Current policy is driving renewed impetus to restore forests to return ecological function, protect species, sequester carbon and secure livelihoods. Here we assess the contribution of tree planting to ecosystem restoration in tropical and sub-tropical Asia; we synthesize evidence on mortality and growth of planted trees at 176 sites and assess structural and biodiversity recovery of co-located actively restored and naturally regenerating forest plots. Mean mortality of planted trees was 18% 1 year after planting, increasing to 44% after 5 years. Mortality varied strongly by site and was typically ca 20% higher in open areas than degraded forest, with height at planting positively affecting survival. Size-standardized growth rates were negatively related to species-level wood density in degraded forest and plantations enrichment settings. Based on community-level data from 11 landscapes, active restoration resulted in faster accumulation of tree basal area and structural properties were closer to old-growth reference sites, relative to natural regeneration, but tree species richness did not differ. High variability in outcomes across sites indicates that planting for restoration is potentially rewarding but risky and context-dependent. Restoration projects must prepare for and manage commonly occurring challenges and align with efforts to protect and reconnect remaining forest areas. The abstract of this article is available in Bahasa Indonesia in the electronic supplementary material. This article is part of the theme issue 'Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration'.

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.

Initial assemblage characteristics determine the functional dynamics of flower-strip plant communities

In agroecosystems, species‐rich habitats, such as linear field margins and flower strips, are beneficial to the overall biodiversity and contribute to pest control. Their effects are thought to be mediated by plant species composition and diversity. However, the management of plant communities with targeted levels of functional diversity has been little investigated. In an open field landscape, we compared the effects of the sown species richness (9, 14, and 29 species) and functional diversity (high vs. low) of eight different seed mixtures, sown in flower strips, on the 4‐year temporal dynamics of their functional diversity. There was a good agreement between the expected and realized species richness and functional diversity at the start of the experiment. All plant assemblages progressively lost species over time, but this decline was lower for assemblages sown with a high initial functional diversity, in which species evenness was maintained at higher levels. Species‐rich assemblages had a higher degree of functional redundancy, and their functional diversity remained higher over time than less rich assemblages. A possible explanation for this is that functional redundancy would have enabled the compensation for the loss of species by functionally equivalent species. The realized functional diversity of the sown species also limited the establishment of spontaneous species, perhaps due to a higher degree of niche occupancy. This study provides useful insight into the creation of functionally diversified plant communities. A high level of initial species and functional diversity is required to guarantee a greater temporal persistence of the communities.

Effects of Climate Change on Hydrology in the Most Relevant Mining Basin in the Eastern Legal Amazon

The Itacaiúnas River basin, an important watershed for the mining sector in Brazil, has had 51% of its native forest area deforested in the last forty years. It is in the arc of deforestation of the Amazon. It has protected areas essential to local biodiversity maintenance, in addition to owning ore reserves. Here, we present the first study to assess the mean annual, seasonal, and spatialized hydrological processes, providing results on a detailed scale in the basin, including mining sites. We used five future projections of mean monthly temperature and daily precipitation as input to the MGB hydrological model to simulate how hydrological processes, such as evapotranspiration, water availability, and high flows, may change in the next 30 years. The future decrease in precipitation (−8%) and increase in temperature (10%) may strengthen the monsoon seasonal cycle and lengthen the dry month for evapotranspiration. Furthermore, some parts of the basin expect an increase in the high flows (8.1%) and a decrease in water availability (−93.6%). These results provide subsidies to develop adaptation strategies to ensure the viability of mining operations and safeguard the surrounding environment and communities.

Cross-species transcriptomes reveal species-specific and shared molecular adaptations for plants development on iron-rich rocky outcrops soils

Background

Canga is the Brazilian term for the savanna-like vegetation harboring several endemic species on iron-rich rocky outcrops, usually considered for mining activities. Parkia platycephala Benth. and Stryphnodendron pulcherrimum (Willd.) Hochr. naturally occur in the cangas of Serra dos Carajás (eastern Amazonia, Brazil) and the surrounding forest, indicating high phenotypic plasticity. The morphological and physiological mechanisms of the plants’ establishment in the canga environment are well studied, but the molecular adaptative responses are still unknown. To understand these adaptative responses, we aimed to identify molecular mechanisms that allow the establishment of these plants in the canga environment.

Results

Plants were grown in canga and forest substrates collected in the Carajás Mineral Province. RNA was extracted from pooled leaf tissue, and RNA-seq paired-end reads were assembled into representative transcriptomes for P. platycephala and S. pulcherrimum containing 31,728 and 31,311 primary transcripts, respectively. We identified both species-specific and core molecular responses in plants grown in the canga substrate using differential expression analyses. In the species-specific analysis, we identified 1,112 and 838 differentially expressed genes for P. platycephala and S. pulcherrimum, respectively. Enrichment analyses showed that unique biological processes and metabolic pathways were affected for each species. Comparative differential expression analysis was based on shared single-copy orthologs. The overall pattern of ortholog expression was species-specific. Even so, we identified almost 300 altered genes between plants in canga and forest substrates with conserved responses in the two species. The genes were functionally associated with the response to light stimulus and the circadian rhythm pathway.

Conclusions

Plants possess species-specific adaptative responses to cope with the substrates. Our results also suggest that plants adapted to both canga and forest environments can adjust the circadian rhythm in a substrate-dependent manner. The circadian clock gene modulation might be a central mechanism regulating the plants’ development in the canga substrate in the studied legume species. The mechanism may be shared as a common mechanism to abiotic stress compensation in other native species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08449-0.

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.

Flora of Ferruginous Outcrops Under Climate Change: A Study in the Cangas of Carajás (Eastern Amazon)

Climate change has impacted biodiversity, affecting species and altering their geographical distribution. Besides understanding the impact in the species, it has been advocated that answering if different traits will be differently impacted could allow refined predictions of how climate change will jeopardize biodiversity. Our aim was to evaluate if climate change will potentially impact plant species differently, considering their traits. We evaluated 608 plant species that occur in the naturally open areas of ferruginous outcrops (namely, cangas) in the National Forest of Carajás (Eastern Amazon). Firstly, we estimated the effects of climate change on each species using species distribution modeling, and analyzed this impact in the set containing all species. Secondly, we classified plant species considering the following traits: (i) pollination syndromes (melittophily, phalaenophily, psychophily, cantharophily, entomophily, ornithophily, chiropterophily, anemophily); (ii) habit (tree, shrub, herb, liana, parasite); and (iii) the main habitat of occurrence (open areas and forests). Thirdly, we investigated if the effects of climate change could be significantly more intense considering all the different traits quoted. Our results showed that most plant species will potentially face reduction of suitable habitats under future climate and the scenarios showed that 42% of them may not find suitable areas in the cangas of Carajás. We found no significant difference within each analyzed trait, considering the potential impact of climate change. The most climatically suitable areas (i.e., areas with high probability of species occurrence in the future) are those in the southwest of the study area. These areas can be considered as priority areas for species protection against climate change.

Native Amazonian Canga Grasses Show Distinct Nitrogen Growth Responses in Iron Mining Substrates

Native species may have adaptive traits that are advantageous for overcoming the adverse environmental conditions faced during the early stages of mine land rehabilitation. Here, we examined the nitrogen (N) growth responses of two native perennial grasses (Axonopus longispicus and Paspalum cinerascens) from canga in nutrient-poor iron mining substrates. We carried out vegetative propagation and recovered substantial healthy tillers from field-collected tussocks of both species. These tillers were cultivated in mining substrates at increasing N levels. The tillering rates of both species increased with the N application. Nonetheless, only in P. cinerascens did the N application result in significant biomass increase. Such growth gain was a result of changes in leaf pigment, stomatal morphology, gas exchanges, and nutrients absorption that occurred mainly under the low N additions. Reaching optimum growth at 80 mg N dm−3, these plants showed no differences from those in the field. Our study demonstrates that an input of N as fertilizer can differentially improve the growth of native grasses and that P. cinerascens plants are able to deposit high quantities of carbon and protect soil over the seasons, thus, making them promising candidates for restoring nutrient cycling, accelerating the return of other species and ecosystem services.

Forest Matrix Fosters High Similarity in Bee Composition Occurring on Isolated Outcrops Within Amazon Biome

Most studies analyze fragmentation due to habitat loss caused by anthropogenic activities and few of them analyzed fragmentation on naturally fragmented areas. In the Eastern Amazon, it is possible to find areas naturally open and surrounded by pristine forest. Understanding how species respond to isolation in these areas is an important challenge for decision-making processes aiming conservation and restoration. Using standardized methods of bee collection (entomological nets, bait trap, pan trap, and nest trap), the objective of this study was to analyze the composition and diversity of bees occurring on six isolated outcrops located in two protected areas within Amazon biome. More specifically, we tested 1) if the dissimilarity in bee species composition is explained by the isolation of outcrops and 2) if bee richness, abundance, and Shannon diversity can be explained by the outcrop size. We found 118 species, with the Meliponini and Euglossini (Hymenoptera: Apidae) tribes representing the highest number of species. The similarity in species composition across all outcrops is high and is not explained by the isolation. In addition, the richness, abundance, and Shannon diversity are not explained by outcrop size. Forest does not seem to be a barrier to bee movement, and although most species probably nest in the forests, they use the highly diverse plants of the outcrops as a complementary food source.

Seed Functional Traits Provide Support for Ecological Restoration and ex situ Conservation in the Threatened Amazon Ironstone Outcrop Flora

Cangas (ironstone outcrops) host a specialized flora, characterized by high degree of edaphic endemism and an apparent lack of natural history knowledge of its flora. Due to intense pressure from iron ore mining this ecosystem is under threat and in need of restoration. We studied seed functional traits that are relevant for restoration, translocation and ex situ conservation in 48 species from cangas in eastern Amazon. Were determined the thermal niche breadth, classified seed dormancy and determined methods to overcome it, determined the effect of seed storage on germination, tested the association between germination traits and functional groups, and tested whether seed traits are phylogenetically conserved. We found a broad interspecific variation in most seed traits, except for seed water content. Large interspecific variation in the temperature niche breadth was found among the studied species, but only four species, showed optimum germination at high temperatures of 35-40°C, despite high temperatures under natural conditions. Only 35% of the studied species produced dormant seeds. Mechanical scarification was effective in overcoming physical dormancy and application of gibberellic acid was effective in overcoming physiological dormancy in five species. For the 29 species that seeds were stored for 24 months, 76% showed decreases in the germination percentage. The weak association between germination traits and life-history traits indicate that no particular plant functional type requires specific methods for seed-based translocations. Exceptions were the lianas which showed relatively larger seeds compared to the other growth-forms. Dormancy was the only trait strongly related to phylogeny, suggesting that phylogenetic relatedness may not be a good predictor of regeneration from seeds in cangas. Our study provides support to better manage seed sourcing, use, storage and enhancement techniques with expected reduced costs and increased seedling establishment success.

Using large-scale tropical dry forest restoration to test successional theory

Microclimatic conditions change dramatically as forests age and impose strong filters on community assembly during succession. Light availability is the most limiting environmental factor in tropical wet forest succession; by contrast, water availability is predicted to strongly influence tropical dry forest (TDF) successional dynamics. While mechanisms underlying TDF successional trajectories are not well understood, observational studies have demonstrated that TDF communities transition from being dominated by species with conservative traits to species with acquisitive traits, the opposite of tropical wet forest. Determining how functional traits predict TDF tree species' responses to changing environmental conditions could elucidate mechanisms underlying tree performance during TDF succession. We implemented a 6-ha restoration experiment on a degraded Vertisol in Costa Rica to determine (1) how TDF tree species with different resource-use strategies performed along a successional gradient and (2) how ecophysiological functional traits correlated with tree performance in simulated successional stages. We used two management treatments to simulate distinct successional stages including: clearing all remnant vegetation (early-succession), or interplanting seedlings with no clearing (mid-succession). We crossed these two management treatments (cleared/interplanted) with two species mixes with different resource-use strategies (acquisitive/conservative) to examine their interaction. Overall seedling survival after 2 yr was low, 15.1-26.4% in the four resource-use-strategy × management-treatment combinations, and did not differ between the management treatments or resource-use-strategy groups. However, seedling growth rates were dramatically higher for all species in the cleared treatment (year 1, 69.1% higher; year 2, 143.3% higher) and defined resource-use strategies had some capacity to explain seedling performance. Overall, ecophysiological traits were better predictors of species' growth and survival than resource-use strategies defined by leaf and stem traits such as specific leaf area. Moreover, ecophysiological traits related to water use had a stronger influence on seedling performance in the cleared, early-successional treatment, indicating that the influence of microclimatic conditions on tree survival and growth shifts predictably during TDF succession. Our findings suggest that ecophysiological traits should be explicitly considered to understand shifts in TDF functional composition during succession and that using these traits to design species mixes could greatly improve TDF restoration outcomes.

Combining genotype, phenotype, and environmental data to delineate site-adjusted provenance strategies for ecological restoration

Despite the importance of climate-adjusted provenancing to mitigate the effects of environmental change, climatic considerations alone are insufficient when restoring highly degraded sites. Here we propose a comprehensive landscape genomic approach to assist the restoration of moderately disturbed and highly degraded sites. To illustrate it we employ genomic data sets comprising thousands of single nucleotide polymorphisms from two plant species suitable for the restoration of iron-rich Amazonian Savannas. We first use a subset of neutral loci to assess genetic structure and determine the genetic neighbourhood size. We then identify genotype-phenotype-environment associations, map adaptive genetic variation, and predict adaptive genotypes for restoration sites. Whereas local provenances were found optimal to restore a moderately disturbed site, a mixture of genotypes seemed the most promising strategy to recover a highly degraded mining site. We discuss how our results can help define site-adjusted provenancing strategies, and argue that our methods can be more broadly applied to assist other restoration initiatives.

Tree Communities in Three-Year-Old Post-Mining Sites Under Different Forest Restoration Techniques in the Brazilian Amazon

Forest loss and degradation in the Brazilian Amazon due to mining activities has been intense for many years. To reverse this situation, a range of restoration programs for deforested and degraded areas have been created and implemented. The aim of this study was to analyze the tree composition, successional stage, dispersal and pollination syndromes, conservation status of tree species, and proximity to seed sources under different forest restoration techniques (seedling planting, natural regeneration, and assisted natural regeneration or nucleation) implemented in post-mining sites in the Paragominas municipality (Pará, Brazil). Sixty permanent plots with a restoration age of three years were selected for tree sampling. A total of 119 species, 83 genera and 27 botanical families were identified. Sites restored with different techniques significantly differed in tree composition. Seedling planting sites exhibited the highest abundance, species richness, and diversity values. These were dominated less by pioneer species when compared to the natural regeneration and nucleation sites. Entomophilic pollination and zoochory dispersal were highly represented in the three types of restored sites. Abundance and species richness were negatively correlated with distance from plots to seed sources, and they sharply declined in natural regeneration and nucleation plots at >250 m from seed sources. Four threatened species were identified in the restored sites. We conclude that a combination of different restoration strategies at three-year-old post-mining restoration sites in the Brazilian Amazon results in the recovery of considerable levels of local tree diversity.

The role of protected and deforested areas in the hydrological processes of Itacaiúnas River Basin, eastern Amazonia

To protect indigenous land and avoid the spread of deforestation in the Amazon, state and federal Brazilian agencies recognized several protected areas since the 1990s. However, the importance of these protected areas in the water cycle and the hydrologic connection with surrounding landscapes is little analyzed. In this study, we evaluated the role of preserved and deforested areas in the water balance in the Itacaiúnas River Basin using the MGB hydrological model. We estimated the impacts of land cover changes on evapotranspiration and discharge for four scenarios: Preserved (1984 land cover), Recent (2013 land cover, with 50% deforestation), Hypothetical deforestation of protected areas (70% deforestation) and complete deforestation of protected areas (79% deforestation). We showed that deforestation of the remaining preserved area could be responsible for a decrease of 23% (3.5 km³/year) in water transfer to the atmosphere by evapotranspiration. Furthermore, we showed that each 15% of deforestation occurring between the Preserved and Recent scenarios increased the average discharges by 5.4% (40 m³/s). Additionally, past land cover changes in the headwaters of the Itacaiúnas River Basin caused statistically significant changes in discharges inside the protected areas. This insight is considered important due to the association between increases in discharges and water quality issues. The results suggest that headwater areas of secondary drainages that run into the forested domains should be prioritized for reforestation programs. Likewise, the reforestation of nonprotected areas could be responsible for restoring ecosystem services, including hydrological functions, biodiversity and water quality.

Topsoil application during the rehabilitation of a manganese tailing dam increases plant taxonomic, phylogenetic and functional diversity

Rehabilitation of tailing dams poses important challenges because sterile materials and poor or even toxic soils hinder plant development and the regeneration of the pre-mining-activity biota. In this study, we analyzed the effectiveness of rehabilitating a 14-year-old manganese tailing dam by comparing three different regeneration treatments (topsoil application, seedling plantation and spontaneous regeneration) with undisturbed reference sites. We used soil chemical composition, taxonomic, functional and phylogenetic diversity and the above-ground tree biomass as indicators of rehabilitation success. In terms of soil chemical composition, we showed that the seedling and natural regeneration treatments were similar to one another but different from the reference sites. Topsoil application presented an intermediate chemical composition between the reference site and the other two treatments. Moreover, the species richness, Shannon diversity index and phylogenetic diversity indicated faster rehabilitation of ecosystem biodiversity with the topsoil treatment, although levels from reference are not yet achieved. We also observed higher basal area and biomass production in the topsoil treatment. However, these patterns were not observed for functional diversity, for which no differences among treatments were observed. We concluded that topsoil application provided the best results; however, we must emphasize that even this approach was not sufficient to rehabilitate the system to the similar level of biodiversity found in the surrounding ecosystem up to the present.