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Forest restoration mitigates climate change by removing CO2 and storing C in terrestrial ecosystems. However, incomplete information on C storage in restored tropical forests often fails to capture the ecosystem's holistic C dynamics. This study provides an integrated assessment of C storage in above to belowground subsystems, its consequences for greenhouse gas (GHG) fluxes, and the quantity, quality, and origin of soil organic matter (SOM) in restored Atlantic forests in Brazil. Relations between SOM properties and soil health indicators were also explored. We examined two restorations using tree planting ('active restoration'): an 8-year-old forest with green manure and native trees planted in two rounds, and a 15-year-old forest with native-planted trees in one round without green manure. Restorations were compared to reformed pasture and primary forest sites. We measured C storage in soil layers (0-10, 10-20, and 20-30 cm), litter, and plants. GHG emissions were assessed using CH4 and CO2 fluxes. SOM quantity was evaluated using C and N, quality using humification index (HLIFS), and origin using δ13C and δ15N. Nine soil health indicators were interrelated with SOM attributes. The primary forest presented the highest C stocks (107.7 Mg C ha-1), followed by 15- and 8-year-old restorations and pasture with 69.8, 55.5, and 41.8 Mg C ha-1, respectively. Soil C stocks from restorations and pasture were 20% lower than primary forest. However, 8- and 15-year-old restorations stored 12.3 and 28.3 Mg ha-1 more aboveground C than pasture. The younger forest had δ13C and δ15N values of 2.1 and 1.7‰, respectively, lower than the 15-year-old forest, indicating more C derived from C3 plants and biological N fixation. Both restorations and pasture had at least 34% higher HLIFS in deeper soil layers (10-30 cm) than primary forest, indicating a lack of labile SOM. Native and 15-year-old forests exhibited higher soil methane influx (141.1 and 61.9 µg m-2 h-1). Forests outperformed pasture in most soil health indicators, with 69% of their variance explained by SOM properties. However, SOM quantity and quality regeneration in both restorations approached the pristine forest state only in the top 10 cm layer, while deeper soil retained agricultural degradation legacies. In conclusion, active restoration of the Atlantic Forest is a superior approach compared to pasture reform for GHG mitigation. Nonetheless, the development of restoration techniques to facilitate labile C input into deeper soil layers (>10 cm) is needed to further improve soil multifunctionality and long-term C storage.

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The UN Decade on Ecosystem Restoration is focussing attention and resources on restoration globally. Nowhere is this more crucial than in tropical forests that harbor immense biodiversity, but have also undergone widespread deforestation over the past few decades. We performed a meta-analysis to investigate how biodiversity features respond to forest restoration across the Brazilian Atlantic Forest (BAF), one of the most threatened biodiversity hotspots in the world. We assembled biodiversity in different metrics of structure and diversity features of three taxonomic groups (vascular plants, soil microorganisms, and invertebrates), generating a dataset with 2370 observations from 76 primary studies. We quantified the incomplete recovery of biodiversity (i.e., the rate of recovery to a pre-disturbance state) occurring during the restoration process, which we called the 'recovery gap'. Our results revealed that forests undergoing restoration in the BAF show a recovery gap of 34% for structure features and 22% for diversity features in comparison to reference reforests, considering all taxonomic groups investigated. For vascular plants, soil microorganisms, and invertebrates the recovery gap ranged between 46 and 47%, 16-26%, and 4-7%, respectively. Overall, the recovery gap was influenced by the interaction of restoration actions (i.e., the past land use, restoration age and restoration approach - active and passive restoration), however, structure features responded more sensitively to the time elapsed since restoration started, while the recovery gap for diversity features depended more on the past land-use. Our study can help guide the prioritization of the aforenamed taxonomic groups in restoration, the regulation of potential biodiversity offsetting policies in the BAF, and understanding how coupled biodiversity features respond to the interaction of environmental conditions and restoration actions in a high fragmented tropical landscape.

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Abstract Natural ecosystems are under severe threat worldwide and environmental policies are essential to minimize present and future impacts on biodiversity, ecosystem services and climate change. The New Forest Act in Brazil is the main policy to protect native vegetation in private lands, which comprise 54% of the remaining Brazilian native vegetation. However, conflicts between environmental and agricultural concerns in its implementation demand for balanced solutions based on scientific evidence. To face the challenge of applying science in environmental policy establishment, we developed a scientific project funded by the São Paulo State Research Foundation (FAPESP) to support the implementation of the New Forest Act in São Paulo State, as part of the Biota/FAPESP Program. The project was conducted differently from a regular research project: the broad objective was to provide scientific support to the State's implementation of the New Forest Act, based on a participatory interaction among stakeholders to build specific objectives, methods, and discussion of results, within an interdisciplinary and intersectoral research team. Here, we present the lessons learned during and after the four years of the research project development to evaluate how scientific knowledge can be produced and adopted in the implementation of a specific environmental policy. We present the main outcomes and the challenges faced in trying to include scientific data in the decision-making process. We also present current and future challenges in the New Forest Act implementation that could be solved with scientific evidence. The lessons learned showed that even designing the project in order to meet the needs to support the implementation of the environmental policy, avoiding difficulties normally pointed out by similar projects, there was a great difficulty for scientific contributions to be adopted in the decision-making process. Most of the scientific information and advice, even after discussion and common understanding among a diverse stakeholder group, were ignored or over-ruled in the final decision-making phases.

Resumo Os ecossistemas naturais estão sob grave ameaça em todo o mundo e as políticas ambientais são essenciais para minimizar os impactos presentes e futuros na biodiversidade, nos serviços ecossistêmicos e nas mudanças climáticas. O Novo Código Florestal no Brasil é a principal política de proteção da vegetação nativa em terras privadas, que compreende 54% da vegetação nativa remanescente brasileira. No entanto, os conflitos entre as preocupações ambientais e agrícolas na sua implementação exigem soluções equilibradas e baseadas em evidências científicas. Para enfrentar o desafio de aplicar a ciência no estabelecimento de políticas ambientais, desenvolvemos um projeto científico financiado pela Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) para apoiar a implementação do Novo Código Florestal no Estado de São Paulo, como parte do Programa Biota/FAPESP. O projeto foi conduzido de forma diferente de um projeto de pesquisa regular: o objetivo amplo foi fornecer suporte científico para a implementação do Novo Código Florestal pelo Estado, a partir de uma interação participativa entre as partes interessadas para construir objetivos específicos, métodos e discussão de resultados, dentro de uma equipe de pesquisa interdisciplinar e intersetorial. Aqui, apresentamos as lições aprendidas durante e após os quatro anos de desenvolvimento do projeto de pesquisa para avaliar como o conhecimento científico pode ser produzido e adotado na implementação de uma política ambiental específica. Apresentamos os principais resultados e os desafios enfrentados na tentativa de incluir dados científicos no processo decisório. Apresentamos também desafios atuais e futuros na implementação do Novo Código Florestal que podem ser resolvidos com evidências científicas. As lições aprendidas mostraram que mesmo concebendo o projeto de forma a atender as necessidades de apoio à implementação da política ambiental, evitando dificuldades normalmente apontadas por projetos semelhantes, houve uma grande dificuldade para que contribuições científicas fossem adotadas no processo decisório. A maioria das informações e conselhos científicos, mesmo após discussão e entendimento comum entre um grupo diversificado de partes interessadas, foi ignorada nas fases finais de tomada de decisão.

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An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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International commitments for ecosystem restoration add up to one-quarter of the world's arable land. Fulfilling them would ease global challenges such as climate change and biodiversity decline but could displace food production and impose financial costs on farmers. Here, we present a restoration prioritization approach capable of revealing these synergies and trade-offs, incorporating ecological and economic efficiencies of scale and modelling specific policy options. Using an actual large-scale restoration target of the Atlantic Forest hotspot, we show that our approach can deliver an eightfold increase in cost-effectiveness for biodiversity conservation compared with a baseline of non-systematic restoration. A compromise solution avoids 26% of the biome's current extinction debt of 2,864 plant and animal species (an increase of 257% compared with the baseline). Moreover, this solution sequesters 1 billion tonnes of CO2-equivalent (a 105% increase) while reducing costs by US$28 billion (a 57% decrease). Seizing similar opportunities elsewhere would offer substantial contributions to some of the greatest challenges for humankind.

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Abstract: The Native Vegetation Protection Law - 2012 - (NVPL) is the main Brazilian regulation for protecting native vegetation (NV) on private land. The NVPL, currently in the implementation phase, reduced Legal Reserves (LR) requirements compared to its previous version, the 1965's Forest Act (FA), through several legal mechanisms. Among them, Article 68 (Art.68) exempts landholders from LR obligations if NV was converted without offending the legislation in place at the time of the conversion. The technical implementation of Art. 68 is controversial and its effects are still unknown. We developed a model to estimate the effects of Art.68 on LR using São Paulo State (Brazil) as case study. We analyzed former environmental laws to identify key periods in which NV preservation requirements had changed. After, we searched for past spatial data on NV cover with sufficient accuracy for each legal benchmark. Combining legal benchmarks with spatial data, we created two scenarios for Art.68 effects, plus a baseline scenario. The first scenario considered a single legal benchmark, the 1965's FA (scenario "1965"), while the other included the 1989 Cerrado's protection Federal Law as a second benchmark (scenario "1965/89"). The baseline scenario did not include Art.68 effects. Scenario "1965" reduced LR deficits in 49% compared to the baseline scenario, waiving landholders from restoration or offsetting needs in 423 thousand hectares (kha) of NV. Scenario "1965/89" waved 507 kha of NV from restoration needs and represented a 59% reduction in LR deficit compared to the baseline scenario. The LR reduction by scenario "1965/89" assumed particular importance considering that the additional cutback was concentrated on Cerrado, an already very fragmented and impacted region. Together with reductions from other NVPL rules, the additional effects of Art. 68 unfolded great concerns about the role of LR as a tool for NV preservation on private land, threating governmental restoration commitments, and pointing that conservation command and control approaches should be complemented with incentive policies to achieve the desired and committed standards.

Resumo: A Lei de Proteção da Vegetação Nativa - 2012 - (LPVN) é a principal lei brasileira para proteção da vegetação nativa (VN) em terras privadas. A LPVN, atualmente em fase de implementação, reduziu os requerimentos de Reserva Legal (RL) presentes no Código Florestal (CF) de 1965 através de uma série de mecanismos legais. Entre eles, o Artigo 68 (Art.68) elimina a obrigação de recomposição ou restauração da VN convertida sem violação da lei vigente à época da conversão. O Art.68 é um dos mais controversos mecanismos da LPVN e cujos efeitos ainda não são conhecidos. Nós desenvolvemos um modelo para estimar os efeitos do Art.68 utilizando o estado de São Paulo, Brasil, como estudo de caso. Para isso, levantamos marcos legais nos quais os requerimentos mínimos de preservação da VN foram alterados. Em seguida, levantamos a existência de dados espaciais da cobertura de VN com a precisão necessária para cada marco legal. Combinando os marcos legais com os dados espaciais encontrados, criamos dois cenários incluindo os efeitos do Art.68 e um cenário linha de base para controlar tais efeitos. O primeiro cenário considerou apenas um marco legal, o CF de 1965 (cenário "1965"), enquanto o segundo incluiu a Lei Federal de proteção ao Cerrado de 1989 (cenário "1965/89"). O cenário "1965" reduz os déficits de RL em 49% quando comparado ao cenário de base, dispensando os proprietários de terra da obrigação de restaurar ou recompor 423 mil hectares (kha) de VN. O cenário "1989/65" dispensa da obrigação de restauração ou recomposição 507 kha de VN, representando uma redução de 59% do déficit de RL em comparação ao cenário base. A redução apresentada pelo cenário "1965/89" assume grande importância uma vez que se concentra em áreas de Cerrado, bioma já extremamente fragmentado e impactado. Em conjunto com as reduções promovidas por outros Artigos da LPVN, estes efeitos revelam grande preocupação sobre o papel das RL como uma ferramenta para a conservação de VN em terras privadas, ameaçando compromissos governamentais de restauração e indicando que estratégias de comando e controle deverão ser complementadas por políticas de incentivo para atingir os objetivos de conservação desejados.

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DNA barcoding helps to identify species, especially when identification is based on parts of organisms or life stages such as seeds, pollen, wood, roots or juveniles. However, the implementation of this approach strongly depends on the existence of complete reference libraries of DNA sequences. If such a library is incomplete, DNA-based identification will be inefficient. Here, we assess if DNA barcoding can already be implemented in species-rich tropical regions. We focus on the tree flora of São Paulo state, Brazil, which contains more than 2000 tree species. Using new DNA sequence data and carefully assembled GenBank accessions, we assembled 12,113 sequences from ten different regions. The ITS, rbcL, psbA-trnH, matK and trnL regions were better represented within the available sequences for São Paulo tree flora. Currently, only 58% of the São Paulo tree flora currently have at least one barcoding sequence available. However, these species represent on average 89% of the trees in São Paulo state forests. Therefore, conservation-oriented and ecological studies can already benefit from DNA barcoding to obtain more accurate species identifications. We present which taxa remain underrepresented for the São Paulo tree flora and discuss the implications of this result for other species-rich tropical regions.

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The primary focus of tropical forest restoration has been the recovery of forest structure and tree taxonomic diversity, with limited attention given to genetic conservation. Populations reintroduced through restoration plantings may have low genetic diversity and be genetically structured due to founder effects and genetic drift, which limit the potential of restoration to recover ecologically resilient plant communities. Here, we studied the genetic diversity, genetic structure and differentiation using single nucleotide polymorphisms (SNP) markers between restored and natural populations of the native tree Casearia sylvestris in the Atlantic Forest of Brazil. We sampled leaves from approximately 24 adult individuals in each of the study sites: two restoration plantations (27 and 62 years old) and two forest remnants. We prepared and sequenced a genotyping-by-sequencing library, SNP markers were identified de novo using Stacks pipeline, and genetic parameters and structure analyses were then estimated for populations. The sequencing step was successful for 80 sampled individuals. Neutral genetic diversity was similar among restored and natural populations (AR = 1.72 ± 0.005; HO = 0.135 ± 0.005; HE = 0.167 ± 0.005; FIS = 0.16 ± 0.022), which were not genetically structured by population subdivision. In spite of this absence of genetic structure by population we found genetic structure within populations but even so there is not spatial genetic structure in any population studied. Less than 1% of the neutral alleles were exclusive to a population. In general, contrary to our expectations, restoration plantations were then effective for conserving tree genetic diversity in human-modified tropical landscapes. Furthermore, we demonstrate that genotyping-by-sequencing can be a useful tool in restoration genetics.

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Several factors decrease plant survival throughout their lifecycles. Among them, seed dispersal limitation may play a major role by resulting in highly aggregated (contagious) seed and seedling distributions entailing increased mortality. The arrival of seeds, furthermore, may not match suitable environments for seed survival and, consequently, for seedling establishment. In this study, we investigated spatio-temporal patterns of seed and seedling distribution in contrasting microhabitats (bamboo and non-bamboo stands) from the Brazilian Atlantic Forest. Spatial distribution patterns, spatial concordance between seed rain and seedling recruitment between subsequent years in two fruiting seasons (2004-2005 and 2007-2009), and the relation between seeds and seedlings with environmental factors were examined within a spatially-explicit framework. Density and species richness of both seeds and seedlings were randomly distributed in non-bamboo stands, but showed significant clustering in bamboo stands. Seed and seedling distributions showed across-year inconsistency, suggesting a marked spatial decoupling of the seed and seedling stages. Generalized linear mixed effects models indicated that only seed density and seed species richness differed between stand types while accounting for variation in soil characteristics. Our analyses provide evidence of marked recruitment limitation as a result of the interplay between biotic and abiotic factors. Because bamboo stands promote heterogeneity in the forest, they are important components of the landscape. However, at high densities, bamboos may limit recruitment for the plant community by imposing marked discordances of seed arrival and early seedling recruitment.

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Investigations of seed size and number differences among plant populations growing in contrasting habitats can provide relevant information about ecological strategies that optimize reproductive effort. This may imply important consequences for biodiversity conservation and restoration. Therefore, we sought to investigate seed size-number trade-off in Euterpe edulis populations growing in plant communities in the Brazilian Atlantic Forest. Seed dry mass and seed number per bunch were evaluated in 2008 and 2009 in large remnants of the Seasonally Dry Forest, Restinga Forest and Atlantic Rainforest in southeastern Brazil, in 20 individuals per site and year. Seed size and seed number varied among forest types, but a seed size-number trade-off was neither observed within nor among populations. Positive association between seed size and number was found in the Atlantic Rainforest, and reduced seed crop was not accompanied by heavier seeds in the Restinga Forest. Seed dry mass declined in 2009 in all three forest types. Compared to seed number in 2008, palms of both the Restinga Forest and the Atlantic Rainforest produced in 2009 higher yields of smaller seeds - evidence of between years seed size-number trade-off -, while the Seasonally Dry Forest population produced a reduced number of smaller seeds. Such a flexible reproductive strategy, involving neutral, positive, and negative associations between seed size and number could enhance the ecological amplitude of this species and their potential to adapt to different environment conditions.

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