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Passive acoustic monitoring can be an effective method for monitoring species, allowing the assembly of large audio datasets, removing logistical constraints in data collection and reducing anthropogenic monitoring disturbances. However, the analysis of large acoustic datasets is challenging and fully automated machine learning processes are rarely developed or implemented in ecological field studies. One of the greatest uncertainties hindering the development of these methods is spatial generalisability—can an algorithm trained on data from one place be used elsewhere?We demonstrate that heterogeneity of error across space is a problem that could go undetected using common classification accuracy metrics. Second, we develop a method to assess the extent of heterogeneity of error in a random forest classification model for six Amazonian bird species. Finally, we propose two complementary ways to reduce heterogeneity of error, by (i) accounting for it in the thresholding process and (ii) using a secondary classifier that uses contextual data.We found that using a thresholding approach that accounted for heterogeneity of precision error reduced the coefficient of variation of the precision score from a mean of 0.61 ± 0.17 (SD) to 0.41 ± 0.25 in comparison to the initial classification with threshold selection based on F-score. The use of a secondary, contextual classification with thresholding selection accounting for heterogeneity of precision reduced it further still, to 0.16 ± 0.13, and was significantly lower than the initial classification in all but one species. Mean average precision scores increased, from 0.66 ± 0.4 for the initial classification, to 0.95 ± 0.19, a significant improvement for all species.We recommend assessing—and if necessary correcting for—heterogeneity of precision error when using automated classification on acoustic data to quantify species presence as a function of an environmental, spatial or temporal predictor variable.

Species sensitivity to forest fragmentation varies latitudinally, peaking in the tropics. A prominent explanation for this pattern is that historical landscape disturbance at higher latitudes has removed fragmentation-sensitive species or promoted the evolution of more resilient survivors. However, it is unclear whether this so-called extinction filter is the dominant driver of geographic variation in fragmentation sensitivity, particularly because climatic factors may also cause latitudinal gradients in dispersal ability, a key trait mediating sensitivity to habitat fragmentation. Here we combine field survey data with a morphological proxy for avian dispersal ability (hand-wing index) to assess responses to forest fragmentation in 1,034 bird species worldwide. We find that fragmentation sensitivity is strongly predicted by dispersal limitation and that other factors—latitude, body mass and historical disturbance events—have relatively limited explanatory power after accounting for species differences in dispersal. We also show that variation in dispersal ability is only weakly predicted by historical disturbance and more strongly associated with intra-annual temperature fluctuations (seasonality). Our results suggest that climatic factors play a dominant role in driving global variation in the impacts of forest fragmentation, emphasizing the need for more nuanced environmental policies that take into account local context and associated species traits.

PAM has proven to be an effective tool for monitoring biotic soundscapes in the marine, terrestrial, and aquatic realms. Recently it has been suggested that it could also be an effective method for monitoring soil fauna, but has so far been used in only four studies in temperate and polar regions. We present the first study of soil soundscapes in tropical forests, using a novel analytical pipeline allowing for the use of in-situ recording of soundscapes with minimal soil disturbance. We found significant differences in soil soundscapes between burnt and unburnt forests and the first indications of a diel cycle in soil soundscapes. These promising results and methodological advances highlight the potential of PAM for large-scale and long-term monitoring of soil biodiversity. We use the results to discuss research priorities, including relating soil biophony to biodiversity, community structure and ecosystem functioning, and the use of appropriate hardware and analytical techniques.

Inner phenomena, such as personal motivations for pursuing sustainability, may be critical levers for improving conservation outcomes. Most conservation research and policies, however, focus on external phenomena (e.g., ecological change or economic processes). We explored the factors shaping 9 conservation attitudes toward forest and wildlife protection among colonist farmers around an Amazonian deforestation frontier. Our data comprised 241 face-to-face quantitative surveys, complemented with qualitative insights from open-ended questionnaire responses and opportunistic semistructured interviews. To account for the full spectrum of possible inner motivations, we employed measures of nature connection (indicating biospheric motivation) and personal values organized around the traditionalism (traditionalist through to high openness to change) and universalism dimensions (egoistic through to altruistic motivations). We used averaged beta-binomial generalized linear models to assess the role of external factors (socioeconomic, sociodemographic, and environmental) and personal (inner) motivations on the variation in attitudes. Each attitude was modeled separately. The relative importance of each predictor was judged by the proportion of models where it appeared as significant. Proconservation views were expressed by the majority (at least 65%) of the respondents in 7 out of the 9 attitude models. The most consistent predictors were emotional nature connection and personal values (significant in 4–6 out of 9 models), rather than external phenomena (significant in 0–5 models). However, the poorest farmers had lower scores on the agreement with prioritizing nature over development (β = –0.52, 95% CI: –0.96 to –0.07). Qualitative data also indicated that economic barriers hinder forest conservation on farms. These results suggest that biospheric, traditionalistic, and altruistic motivations promote people's proconservation attitudes, but nurturing these latent motivations is unlikely to improve conservation outcomes if material poverty remains unaddressed. Integrating the inner–outer perspective into conservation thinking and practical interventions could foster environmental stewardship and increase human well-being.

Human activities pose a major threat to tropical forest biodiversity and ecosystem serv-ices. Although the impacts of deforestation are well studied, multiple land-use andland-cover transitions (LULCTs) occur in tropical landscapes, and we do not knowhow LULCTs differ in their rates or impacts on key ecosystem components. Here, wequantified the impacts of 18 LULCTs on three ecosystem components (biodiversity,carbon, and soil), based on 18 variables collected from 310 sites in the BrazilianAmazon. Across all LULCTs, biodiversity was the most affected ecosystem component,followed by carbon stocks, but the magnitude of change differed widely amongLULCTs and individual variables. Forest clearance for pasture was the most prevalentand high-impact transition, but we also identified other LULCTs with high impact butlower prevalence (e.g., forest to agriculture). Our study demonstrates the importanceof considering multiple ecosystem components and LULCTs to understand the conse-quences of human activities in tropical landscapes Made available in DSpace on 2022-10-06T16:05:22Z (GMT). No. of bitstreams: 1 pnas.2202310119.pdf: 1994033 bytes, checksum: 7b87b3ce0f689008a66ab5755a038d75 (MD5) Previous issue date: 2022

Funding: Floristic identification in plots in the RAINFOR forest monitoring network have been supported by the Natural Environment Research Council (grants NE/B503384/1, NE/ D01025X/1, NE/I02982X/1, NE/F005806/1, NE/D005590/1 and NE/I028122/1) and the Gordon and Betty Moore Foundation. In a time of rapid global change, the question of what determines patterns in species abundance distribution remains a priority for understanding the complex dynamics of ecosystems. The constrained maximization of information entropy provides a framework for the understanding of such complex systems dynamics by a quantitative analysis of important constraints via predictions using least biased probability distributions. We apply it to over two thousand hectares of Amazonian tree inventories across seven forest types and thirteen functional traits, representing major global axes of plant strategies. Results show that constraints formed by regional relative abundances of genera explain eight times more of local relative abundances than constraints based on directional selection for specific functional traits, although the latter does show clear signals of environmental dependency. These results provide a quantitative insight by inference from large-scale data using cross-disciplinary methods, furthering our understanding of ecological dynamics. Publisher PDF

Habitat conversion is a major driver of tropical biodiversity loss, but its effects are poorly understood in montane environments. While community-level responses to habitat loss display strong elevational dependencies, it is unclear whether these arise via elevational turnover in community composition and interspecific differences in sensitivity or elevational variation in environmental conditions and proximity to thermal thresholds. Here we assess the relative importance of inter- and intraspecific variation across the elevational gradient by quantifying how 243 forest-dependent bird species vary in sensitivity to landscape-scale forest loss across a 3000-m elevational gradient in the Colombian Andes. We find that species that live at lower elevations are strongly affected by loss of forest in the nearby landscape, while those at higher elevations appear relatively unperturbed, an effect that is independent of phylogeny. Conversely, we find limited evidence of intraspecific elevational gradients in sensitivity, with populations displaying similar sensitivities to forest loss, regardless of where they exist in a species' elevational range. Gradients in biodiversity response to habitat loss thus appear to arise via interspecific gradients in sensitivity rather than proximity to climatically limiting conditions.

Es necesaria con urgencia una restauración a gran escala y de forma generalizada en la Amazonia, que por décadas ha sufrido un deterioro en las condiciones ecológicas y es frágil ante el cambio climático. La restauración a escala puede ser alcanzada a través de siete metas complementarias: (a) Lograr cero deforestación para 2030; (b) Evitar la degradación forestal; (c) Restaurar bosques en áreas protegidas; (d) Restaurar bosques en tierras no-asignadas; (e) Restaurar áreas que han sido deforestadaspor encima de la asignación legal en tierras privadas; (f) Restaurar la cubierta arbórea más allá del cumplimiento legal; y (g) la restauración sostenible de tierras de cultivo degradadas.

There is an urgent need for large-scale restoration across the Amazon, which has suffered decades of deteriorating ecological conditions and is fragile in the face of climate change. Restoration at scale can be achieved through seven complementary targets: (a) Achieve zero deforestation by 2030; (b) Avoiding forest degradation; (c) Restoring forests in protected areas; (d) Restoring forests in undesignated lands; (e) Restoring areas that have been cleared above the legal allowance on private lands; (f) Restoring forest cover beyond legal compliance; and (g) Sustainable restoration of degraded farmland.

Existe uma necessidade urgente de restauração em larga escala na Amazônia, região que tem sofrido por décadas com a deterioração de suas condições ecológicas e encontra-se em situação de fragilidade diante das mudanças climáticas. A restauração em escala pode ser alcançada através de sete objetivos complementares: (a) Alcançar o desmatamento zero até 2030; (b) Evitar a degradação florestal; (c) Restaurar florestas em áreas protegidas; (d) Restaurar florestas em terras devolutas; (e) Restaurar áreas em propriedades privadas que tenham sido desmatadas acima do limite permitido por lei; (f) Restaurar a cobertura florestal além da conformidade legal; e (g) Restauração sustentável de terras agrícolas degradadas.

Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH4) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH4 cycle. To better predict the responses of soil CH4-cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.

Unprecedented forest fires are affecting large swathes of what were once fire‐free Amazonian forests, including extensive areas of community‐managed reserves. This shared overview of experiences of practitioners and researchers examines ways in which these reserves can be supported to reduce the risk of forest fires. We highlight six considerations that are key to fire reduction: inclusive management and community leadership, adapting to demographic and cultural changes, identifying examples of good practice, socially just alternative livelihoods, forecasting and planning and bridging scientific research and innovation. Policy implications. The escalating fire problem in Amazonia and elsewhere means we urgently need to learn from past experiences. Co‐developed ecological and social research can support novel approaches to reserve management, but achieving this will require sustained investment and ongoing dialogue between communities, managers, researchers and the government. Made available in DSpace on 2020-09-19T04:38:52Z (GMT). No. of bitstreams: 1 1365-2664.13690.pdf: 903603 bytes, checksum: b54cf92b4eb68e7ef7776408adfe8887 (MD5) Previous issue date: 2020

Estimation of avian biodiversity is a cornerstone measure of ecosystem condition. Surveys conducted using autonomous recorders are often more efficient at estimating diversity than traditional point‐count surveys. However, there is limited research into the optimal temporal resolution for sampling—the trade‐off between the number of samples and sample duration when sampling a survey window with a fixed survey effort—despite autonomous recorders allowing easy repeat sampling compared to traditional survey methods. We assess whether the additional temporal coverage from high temporal resolution (HTR) sampling, consisting of 240 15‐s samples spread randomly across a survey window detects higher alpha and gamma diversity than low temporal resolution (LTR) sampling of four 15‐min samples at the same locations. We do so using an acoustic dataset collected from 29 locations in a region of very high avian biodiversity—the eastern Brazilian Amazon. We find HTR sampling outperforms LTR sampling in every metric considered, with HTR sampling predicted to detect approximately 50% higher alpha diversity, and 10% higher gamma diversity. This effect is primarily driven by increased coverage of variation in detectability across the morning, with the earliest period containing a distinct community that is often under sampled using LTR sampling. LTR sampling produced almost four times as many false absences for species presence. Additionally, LTR sampling incorrectly found 70 species (34%) at only a single forest type when they were in fact present in multiple forest types, while the use of HTR sampling reduced this to just two species (0.9%). When considering multiple independent detections of species, HTR sampling detected three times more uncommon species than LTR sampling. We conclude that high temporal resolution sampling of passive‐acoustic monitoring‐based surveys should be considered the primary method for estimating the species richness of bird communities in tropical forests.

Tropical forest biodiversity is being threatened by human activities, and species losses during forest disturbance can compromise important ecosystem functions and services. We assessed how species losses due to tropical forest disturbance affect community functional structure, using Amazonian dung beetles as a model group. We collected empirical data from 106 forest transects and used simulated extinction scenarios to determine how species loss influences community structure at regional and local scales. Although functional and taxonomic community metrics were largely unaffected by primary forest disturbance, they differed markedly between primary and secondary forests. However, our extinction scenarios demonstrated scale-dependence of species losses, whereby functional structure only eroded with species extinction at the local scale. Hence, we extend the spatial insurance hypothesis by demonstrating that landscape-scale functional redundancy offsets the impact of local species losses and confers community-level resistance to primary forest disturbance.

La deforestación y la degradación forestal son el resultado de la interacción entre varios impulsores directos que a menudo operan en tándem. El bioma amazónico había perdido aproximadamente 870.000 km2 de su cobertura forestal original, principalmente debido a la expansión agrícola (pastizales y tierras de cultivo). Otros impulsores directos incluyen la apertura de nuevas carreteras, la construcción de represas hidroeléctricas, la explotación de minerales y petróleo y la urbanización.

Este capítulo examina las oportunidades y los enfoques sitio específicos para restaurar los sistemas terrestres y acuáticos, centrándose en las acciones locales y sus beneficios inmediatos. Las considera-ciones sobre el paisaje, la cuenca y el bioma se abordan en el Capítulo 29. Los enfoques de conserva-ción se abordan en el Capítulo 27.

Este capítulo describe algunos de los enfoques necesarios para abordar las principales amenazas a la biodiversidad y los ecosistemas de la Amazonía, es decir, la deforestación, la construcción de represas en los ríos, la minería, la caza, el comercio ilegal, la producción y el tráfico de drogas, la tala ilegal, la sobrepesca y la expansión de la infraestructura.

Extensive and dense macroalgal fields can compromise the ecosystem function of habitat mosaics on reefs owing to their limiting effect on patch connectivity. Macroalgae can maintain and increase their dominance with effective self-reinforcing feedback mechanisms. For example, macroalgae can form dense beds, supressing coral settlement and grazing by herbivores. This compromised ecosystem function can lead to major socioeconomic and ecological changes. Dense macroalgal beds were shaded with submerged shade sails of two sizes and changes to the underlying benthos and feeding rates of herbivorous fishes were recorded. The shade sails reduced the algae's ability to photosynthesize by 29%. After 6 weeks, macroalgal cover was reduced by 24% under small sails and by 51% under large sails. Small shade sails reduced turf algal growth by 23%, while large sails reduced growth by 82%. Three months after removal of the shade sails, algal beds had almost completely regrown. During this regrowth period, herbivore bites taken from the experiment's substrates were recorded, with grazing impact reducing significantly with time. This study is the first to achieve macroalgal reduction via the alteration of the light regime. While macroalgae regrew in this relatively short-term experiment, shading may be a viable reef management approach that aims to maximize habitat mosaics on coral reefs, particularly if used in combination with other intervention methods.

Efforts by conservation scientists to draw public attention to the biodiversity crisis are increasingly met with denialist rhetoric. We summarize some of the methods used by denialists to undermine scientific evidence on biodiversity loss, and outline pathways forward for the scientific community to counter misinformation.

Billions of people rely on harvesting wildlife for food, and must contend with catch rates that vary in space (e.g. overharvesting near communities) and time (e.g. seasonal migrations). Yet, research has overlooked potential linkages between reduced wildlife catch rates (catch‐per‐unit‐effort) and food security. Moreover, assumptions that people living in biologically rich environments are food secure lack empirical testing. This is problematic given that food security rests on having stable access to sufficient food, rather than there being sufficient food. We examine spatiotemporal variation in fish catch rates and perceived food security among rural communities in Amazonian flooded forests. We also assess social inequities in food insecurity. We used structured interviews to collect data on fishing, hunting, chicken and beef consumption, and perceptions of food security. We did so during 556 household visits along a spatial gradient (1,267 km) of commercial fishing pressure, during high‐ and low‐water seasons. We provide the first empirical evidence of simultaneous seasonal crashes in wildlife catch rates and food insecurity. During the high‐water season, fish catch rates were 73% lower, and the probability of not eating for a whole day was four times higher. With a third of households skipping meals and a sixth not eating for a whole day during this season, food security can be classed as severe. However, less‐deprived households tended to avoid severe food insecurity. Fish catch rates and perceived food security did not vary along a spatial gradient of commercial overfishing. River‐dwelling Amazonians increased fishing and hunting efforts during the high‐water season, without eating more chicken and beef, emphasizing the importance of stable access to wild fish and bushmeat. This study shows how wildlife catch rates and food security can crash seasonally and simultaneously, demonstrating the fallacies of environmental and social policies which assume stability of food availability in resource‐rich areas. Our results have implications for degraded habitats where falls in catch rates also occur. This suggests that overharvesting, as with other causes of reduced catch rates, could cause food insecurity in wildlife‐reliant populations. A free Plain Language Summary can be found within the Supporting Information of this article.

1. Quantifying the impact of habitat disturbance on ecosystem function is critical to understanding and predicting the future of tropical forests. Many studies have examined post-disturbance changes in animal traits related to mutualistic interactions with plants, but the effect of disturbance on plant traits in diverse forests has received much less attention. 2. Focusing on two study regions in the eastern Brazilian Amazon, we used a trait-based approach to examine how seed dispersal functionality within tropical plant communities changes across a landscape-scale gradient of human modification, including both regenerating secondary forests and primary forests disturbed by burning and selective logging. 3. Surveys of 230 forest plots recorded 26,533 live stems from 846 tree species. Using herbarium material and literature, we compiled trait information for each tree species, focusing on dispersal mode and seed size. 4. Disturbance reduced tree diversity and increased the proportion of lower wood density and small-seeded tree species in study plots. Disturbance also increased the proportion of stems with seeds that are ingested by animals and reduced those dispersed by other mechanisms (e.g. wind). Older secondary forests had function-ally similar plant communities to the most heavily disturbed primary forests. Mean seed size and wood density per plot were positively correlated for plant species with seeds ingested by animals. 5. Synthesis. Anthropogenic disturbance has major effects on the seed traits of tree communities, with implications for mutualistic interactions with animals. The important role of animal-mediated seed dispersal in disturbed and recovering forests highlights the need to avoid defaunation or promote faunal recovery. The changes in mean seed width suggest larger vertebrates hold especially important functional roles in these human-modified forests. Monitoring fruit and seed traits can provide a valuable indicator of ecosystem condition, emphasizing the importance of developing a comprehensive plant traits database for the Amazon and other biomes.

There is growing recognition of the potential of large-scale restoration in the Amazon as a “nature-based solution” to climate change. However, our knowledge of forest loss and recovery beyond Brazil is limited, and carbon emissions and accumulation have not been estimated for the whole biome. Combining a 33-year land cover dataset with estimates of above-ground biomass and carbon sequestration rates, we evaluate forest loss and recovery across nine Amazonian countries and at a local scale. We also estimate the role of secondary forests in offsetting old-growth deforestation emissions and explore the temporal trends in forest loss and recovery. We find secondary forests across the biome to have offset just 9.7% of carbon emissions from old-growth deforestation, despite occupying 27.6% of deforested land. However, these numbers varied between countries ranging from 9.0% in Brazil to 23.8% in Guyana for carbon offsetting, and 24.8% in Brazil to 56.9% in Ecuador for forest area recovery. We reveal a strong, negative spatial relationship between old-growth forest loss and recovery by secondary forests, showing that regions with the greatest potential for large-scale restoration are also those that currently have the lowest recovery (e.g. Brazil dominates deforestation and emissions but has the lowest recovery). Our findings identify three important challenges for policy makers: (1) incentivising large-scale restoration in highly deforested regions, (2) protecting secondary forests without disadvantaging landowners who depend on farm-fallow systems, and (3) preventing further deforestation. Combatting all of these successfully is essential to ensuring that the Amazon biome achieves its potential in mitigating anthropogenic climate change.

Made available in DSpace on 2022-04-28T19:50:14Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-03-15 Secondary forests (SFs) growing on previously cleared land could be a low-cost climate change mitigation strategy due to their potential to sequester CO2. However, given widespread changes in climate and land-use in the Amazon in the past 20 years, it is not clear whether current rates of carbon uptake by SFs reflect estimates based on dividing the carbon stock by the estimated age of the forest. This is important, as differences between methodological approaches could lead to important discrepancies in estimates of carbon accumulation. Furthermore, we know little about how carbon uptake rates of secondary forests vary across some of the most deforested regions of the Amazon, where reforestation actions are most needed. Here, we compare the rates of carbon accumulation estimated over the lifetime of a stand (by stand age) with the contemporary rates estimated by recensus data, based on 28 permanent SFs plots distributed across four regions. Then, we compare how carbon uptakes rates vary across regions and how they compare to previous studies. The average rates of contemporary (1.23 ± 0.57 Mg C ha−1 yr−1) and lifetime (1.14 ± 0.63 Mg C ha−1 yr−1) carbon accumulation were strongly correlated (r = 0.78) and similar between regions. Overall, our carbon accumulation rates were much lower than other estimates of Amazonian SFs, which suggests that regions with the greatest opportunities for large-scale implementation of SFs have some of the slowest rates of carbon accumulation. Contrary to predictions from chronosequence analysis, the lack of difference between lifetime and contemporary rates of carbon accumulation suggests forests are maintaining a consistent rate of growth in the first decades after abandonment. These results—combined with the high rates of ongoing environmental change - highlight the importance of continuing to monitor the rate of carbon accumulation in secondary forests. This is necessary to support the implementation and monitoring of large-scale passive restoration in the highly-deforested Amazon. Universidade Federal do Pará Instituto de Ciências Biológicas Programa de Pós-Graduação em Ecologia, Campus Guamá Embrapa Amazônia Oriental Rede Amazônia Sustentável Environmental Change Institute University of Oxford Lancaster Environment Centre Lancaster University School of Biological Sciences University of Bristol Universidade Estadual Paulista Departamento de Ecologia Universidade Federal Rural da Amazônia, Campus Capitão Poço Universidade Estadual Paulista Departamento de Ecologia

The Brazilian Amazonian Forest is undergoing significant changes in land use and land cover in the last few decades. This land-use transition, besides climate change, may be responsible for the fire regime transition in this territory. Therefore, we aimed at investigating how the fire-transition occurs over time in the Brazilian Amazonia Forest and identifying the key parameters that can help to predict this change. For this, we collected yearly data on fire occurrence, forest cover, deforestation rates, and cropland areas. We used a 0.45° spatial surface grid, and with these annual values, we produced: (i) generalised linear mixed models of fire occurrence against forest cover, using years and grids as random factors; (ii) annual linear models of fire occurrence against forest cover; (iii) linear models of the apex values against the years; and (iv) generalised linear models of these apex values against deforestation and cropland areas. We found that there is a fire-transition process in the Brazilian Amazon Forest since a quadratic model better predicted the fire occurrence behaviour. Moreover, the fire occurrence apex is transitioning to more forested landscapes, from 50.7% in 2003 to 55% in 2019 (R² = 0.3). The deforestation rates and the cropland expansion had important relationships with the fire-transition, the first is related to the fire occurrence in the landscape (R² = 0.62), while the second better predicts the transition to more forested areas (R² = 0.38). Thus, we found that the fire-transition in the Brazilian Amazon Forest is strongly related to the land-use transition stages in this region.

Restoration can be applied in many different Amazonian contexts, but will be most effective at leveraging environmental and social benefits when it is prioritized across the Amazon basin, landscapes, and catchments. Here we outline the considerations that are most relevant for planning and scaling restoration across the Amazon.

This chapter discusses the main drivers of deforestation and forest degradation in the Amazon, particularly agricultural expansion, road construction, mining, oil and gas development, forest fires, edge effects, logging, and hunting. It also examines these activities’ impacts and synergies between them.

This chapter examines site-specific opportunities and approaches to restore terrestrial and aquatic systems, focusing on the local actions and benefits. Landscape and biome-wide considerations are addressed in Chapter 29.

Human activities destroy biodiversity and disrupt the functioning of aquatic and terrestrial ecosystems at different levels. This chapter provides sustainable approaches to address some of the biggest threats to the Amazon’s biodiversity and ecosystems, i.e., deforestation, damming of rivers, mining, hunting, illegal trade, drug, production and trafficking, illegal logging, overfishing, and infrastructure expansion. The role of restoration is addressed in chapters 28 and 29.

Tropical forests are some of the most biodiverse ecosystems in the world, yet their functioning is threatened by anthropogenic disturbances and climate change. Global actions to conserve tropical forests could be enhanced by having local knowledge on the forestsʼ functional diversity and functional redundancy as proxies for their capacity to respond to global environmental change. Here we create estimates of plant functional diversity and redundancy across the tropics by combining a dataset of 16 morphological, chemical and photosynthetic plant traits sampled from 2,461 individual trees from 74 sites distributed across four continents together with local climate data for the past half century. Our findings suggest a strong link between climate and functional diversity and redundancy with the three trait groups responding similarly across the tropics and climate gradient. We show that drier tropical forests are overall less functionally diverse than wetter forests and that functional redundancy declines with increasing soil water and vapour pressure deficits. Areas with high functional diversity and high functional redundancy tend to better maintain ecosystem functioning, such as aboveground biomass, after extreme weather events. Our predictions suggest that the lower functional diversity and lower functional redundancy of drier tropical forests, in comparison with wetter forests, may leave them more at risk of shifting towards alternative states in face of further declines in water availability across tropical regions.

1. There is an increasing recognition that, although the climate change and biodiversity crises are fundamentally connected, they have been primarily addressed independently and a more integrated global approach is essential to tackle these two global challenges. 2. Nature-based Solutions (NbS) are hailed as a pathway for promoting synergies between the climate change and biodiversity agendas. There are, however, uncertainties and difficulties associated with the implementation of NbS, while the evidence regarding their benefits for biodiversity remains limited. 3. We identify five key research areas where incomplete or poor information hinders the development of integrated biodiversity and climate solutions. These relate to refining our understanding of how climate change mitigation and adaptation approaches benefit biodiversity conservation; enhancing our ability to track and predict ecosystems on the move and/or facing collapse; improving our capacity to predict the impacts of climate change on the effectiveness of NbS; developing solutions that match the temporal, spatial and functional scale of the challenges; and developing a comprehensive and practical framework for assessing, and mitigating against, the risks posed by the implementation of NbS. 4. Policy implications. The Conference of the Parties (COP) for the United Nations Framework Convention on Climate Change (COP26) and the Convention on Biological Diversity (COP15) present a clear policy window for developing coherent policy frameworks that align targets across the nexus of biodiversity and climate change. This window should (a) address the substantial and chronic underfunding of global biodiversity conservation, (b) remove financial incentives that negatively impact biodiversity and/or climate change, (c) develop higher levels of integration between the biodiversity and climate change agendas, (d) agree on a monitoring framework that enables the standardised quantification and comparison of biodiversity gains associated with NbS across ecosystems and over time and (e) rethink environmental legislation to better support biodiversity conservation in times of rapid climatic change.

Significance Amazonia is experiencing an increase in the frequency of extreme droughts and wildfires. However, the duration of their impacts on plant mortality and carbon stocks are poorly known, and it is unclear whether impacts are amplified in forests with a history of previous human disturbance. We show that plant mortality rates remain above baseline levels for over 3 y in forests affected by drought and 2.5 y in forests affected by both drought and fire. A history of human disturbance led to greater plant mortality in forests simultaneously affected by drought and fire. Our assessment of an area covering 1.2% of the Brazilian Amazon shows that regional drought and fires can have globally relevant impacts on the world’s carbon balance., With humanity facing an unprecedented climate crisis, the conservation of tropical forests has never been so important – their vast terrestrial carbon stocks can be turned into emissions by climatic and human disturbances. However, the duration of these effects is poorly understood, and it is unclear whether impacts are amplified in forests with a history of previous human disturbance. Here, we focus on the Amazonian epicenter of the 2015–16 El Niño, a region that encompasses 1.2% of the Brazilian Amazon. We quantify, at high temporal resolution, the impacts of an extreme El Niño (EN) drought and extensive forest fires on plant mortality and carbon loss in undisturbed and human-modified forests. Mortality remained higher than pre-El Niño levels for 36 mo in EN-drought–affected forests and for 30 mo in EN-fire–affected forests. In EN-fire–affected forests, human disturbance significantly increased plant mortality. Our investigation of the ecological and physiological predictors of tree mortality showed that trees with lower wood density, bark thickness and leaf nitrogen content, as well as those that experienced greater fire intensity, were more vulnerable. Across the region, the 2015–16 El Niño led to the death of an estimated 2.5 ± 0.3 billion stems, resulting in emissions of 495 ± 94 Tg CO2. Three years after the El Niño, plant growth and recruitment had offset only 37% of emissions. Our results show that limiting forest disturbance will not only help maintain carbon stocks, but will also maximize the resistance of Amazonian forests if fires do occur.*

Human-modified forests, including plantations and managed forest, will be a major component of tropical landscapes in the near future. To conserve biodiversity across modified tropical landscapes we must first understand what influences diversity in planted areas. We studied dung beetle communities in Eucalyptus plantations to assess the influence of local (canopy openness and soil texture)and landscape factors (surrounding native forest cover)on taxonomic and functional diversity, and to determine whether biodiversity in plantations is affected by timber production. Dung beetle community composition in Eucalyptus plantations was largely explained by the surrounding native forest cover, as Simpson's diversity and functional diversity (Rao's quadratic entropy)increased with the extent of native forest in buffer areas. However, the abundance of dung beetle species associated with native forest was not explained by any of the explanatory variables. The coarse sand content of the soil explained much of the functional similarity between plantations and native forests, as well as variation in dung beetle community structure. The total abundance of dung beetles in plantations increased with coarse sand content, whereas body mass declined, and dung beetle abundance and functional originality decreased with canopy openness. Timber production intensity did not explain the variation in any of the measured diversity parameters. If enhancing biodiversity in plantations is a management goal, then these results highlight the importance of restoring or retaining native forest areas in modified landscapes. They also suggest that integrated management could improve biodiversity in Eucalyptus plantations without reducing timber production. © 2019 Elsevier B.V.

Riparian forests play a vital role in conserving biodiversity, maintaining ecological connectivity and assisting the delivery of key ecosystem services (i.e. maintenance of water flows). Nevertheless, riparian forests are particularly threatened across the tropics, including in Brazil following widespread forest conversion for pasturelands and agriculture. Despite the significance of the landmark Brazilian Forest Code as the basis of environmental protection on private properties, the effectiveness of the legal protection afforded to riparian vegetation in permanent preservation areas (APP, in Portuguese) has been very poorly assessed. We provide the first fine-scale estimation of the total riparian APP distribution and deficit for the 1.25 Mkm2 Brazilian state of Para, which has the highest deforestation rate in the Brazilian Amazon in recent years, using the available properties boundaries. We demonstrate how coarse-resolution mapping data (for landscape scale mapping, e.g. 1:100,000) consistently underestimates the extent of APP areas, highlighting the scale of the challenge involved in achieving compliance with the Brazilian Forest Code. Moreover, despite nearly half (49%) of the total extent of riparian APPs being forested, following the 2012 revision of the Forest Code, the area that does not need to be restored is six times the area obligated for restoration (940,000 ha). This suggests that some catchments in Para may not recover fully functioning hydrological and ecological services, as around 5.7 Mha of already cleared APP are likely to remain deforested because there was a law amnesty. We also found that deforestation within APPs was greater than outside APPs for most municipalities in Para, indicating that implementation of the Forest Code has not been sufficient to protect riparian forests to date. This shortfall in the legal requirement to restore riparian forest cover suggests that under the current enforcement regime regulatory measures on their own are insufficient and incentive-based mechanisms are needed to encourage restoration – even within the existing legal framework. Our work demonstrates the importance of using finer resolution land cover data and improved hydrological models for ensuring the effective implementation of Brazilian legislation and the safeguarding of the environmental benefits provided by these critically important ecosystems.

Functional diversity is commonly used to assess the conservation value of ecosystems, but we have not yet established whether functional and taxonomic approaches are interchangeable or complementary to evaluate community dynamics over time and in response to disturbances. We used a five-year dataset of dung beetles from undisturbed forest, primary forest corridors, and Eucalyptus plantations to compare the sensitivity of conceptually equivalent metrics to temporal variation in different anthropogenic disturbances. We compared species richness with functional richness, Pielou’s evenness with functional evenness, and Simpson’s diversity with Rao’s quadratic entropy. We assessed the sensitivity of the metrics to anthropogenic changes. The indices showed complex patterns among habitat types, with with similar responses in some cases and not in other, and little incongruence between the pairs within the same year. The influence of disturbance on longer-term temporal variation over the five-year period revealed lower temporal variation in functional than taxonomic metrics. Both approaches showed greater variation in plantations compared to native forests. We evaluated the variation in taxonomic and functional metrics between consecutive years and among habitats. Most metrics showed similar shifts between years in all habitats, except for species and functional richness. We demonstrate that even conceptually similar indices may not provide similar information on dung beetles responses to disturbance. However, the differences between the indices can yield key insights about the drivers of change, especially over the long-term. It is important to use taxonomic and functional diversity in tandem to better understand community responses to environmental and anthropogenic changes.

The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could drive increased soil methane emissions. Furthermore, we found that secondary rainforests had decreased methanogenic activity similar to primary rainforests, and thus a potential to recover as methane sinks, making it conceivable for forest restoration to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.

Natural regeneration of forests has significantly led to increased native forest cover in some regions. Several studies have explored the spatial drivers of forest cover increase, yet little is known about their effects on forest structure and species richness and diversity. We quantified the effects of local (forest age, remnant Eucalyptus basal area, slope, soil fertility, and clay content) and landscape drivers (surrounding land use, distance from streams, and surrounding forest cover and its change over time) on the aboveground biomass, species density, and phylogenetic diversity of native trees in second-growth forests. We sampled 44 naturally regenerating forests established on former pastures and abandoned Eucalyptus plantations for 11–46 years in agricultural landscapes of the southeastern Atlantic Forest, Brazil. We used generalized linear mixed effect models to quantify the effect drivers on forest attributes. While only Eucalyptus basal area and proximity to sugarcane plantations had a consistent negative effect on forest biomass, other drivers were among the best models to explain forest attributes, but their effect was variable. Age increased tree biomass but the effect was not consistent. Similarly, species richness and phylogenetic diversity were mainly affected by landscape drivers such as surrounding forest cover. In tropical agricultural landscapes, effective forest recovery requires more than just time, as forest age can be less important in determining forest attributes than human land uses and surrounding native forest cover. Crucially, forest recovery can be improved through interventions and policies that promote less impactful human activities and enhance existing forest cover. Abstract in Portuguese is available with online material.

Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with increases in soil methane (CH4) emission. To better understand the drivers of this change, we measured soil CH4 flux, environmental conditions, and belowground microbial community structure across primary forests, cattle pastures, and secondary forests in two Amazonian regions. We show that pasture soils emit high levels of CH4 (mean: 3454.6±9482.3μg CH4 m-2 d-1), consistent with previous reports, while forest soils on average emit CH4 at modest rates (mean: 9.8±120.5μg CH4 m-2 d-1), but often act as CH4 sinks. We report that secondary forest soils tend to consume CH4 (mean: -10.2±35.7μg CH4 m-2 d-1), demonstrating that pasture CH4 emissions can be reversed. We apply a novel computational approach to identify microbial community attributes associated with flux independent of soil chemistry. While this revealed taxa known to produce or consume CH4 directly (i.e. methanogens and methanotrophs, respectively), the vast majority of identified taxa are not known to cycle CH4. Each land use type had a unique subset of taxa associated with CH4 flux, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, we show that microbial composition is crucial for understanding the observed CH4 dynamics and that microorganisms provide explanatory power that cannot be captured by environmental variables.

1. Agricultural expansion and intensification are major threats to tropical biodiversity. In addition to the direct removal of native vegetation, agricultural expansion often elicits other human-induced disturbances, many of which are poorly addressed by existing environmental legislation and conservation programmes. This is particularly true for tropical freshwater systems, where there is considerable uncertainty about whether a legislative focus on protecting riparian vegetation is sufficient to conserve stream fauna. 2. To assess the extent to which stream fish are being effectively conserved in agricultural landscapes, we examined the spatial distribution of assemblages in river basins to identify the relative importance of human impacts at instream, riparian and catchment scales, in shaping observed patterns. We used an extensive dataset on the ecological condition of 83 low-order streams distributed in three river basins in the eastern Brazilian Amazon. 3. We collected and identified 24,420 individual fish from 134 species. Multiplicative diversity partitioning revealed high levels of compositional dissimilarity (DS) among stream sites (DS = 0.74 to 0.83) and river basins (DS = 0.82), due mainly to turnover (77.8% to 81.8%) rather than nestedness. The highly heterogeneous fish faunas in small Amazonian streams underscore the vital importance of enacting measures to protect forests on private lands outside of public protected areas. 4. Instream habitat features explained more variability in fish assemblages (15%–19%) than riparian (2%–12%), catchment (4%–13%) or natural covariates (4%–11%). Although grouping species into functional guilds allowed us to explain up to 31% of their abundance (i.e. for nektonic herbivores), individual riparian - and catchment - scale predictor variables that are commonly a focus of environmental legislation explained very little of the observed variation (partial R2 values mostly

Estimation of avian biodiversity is a cornerstone measure of ecosystem condition, with turnover in avian community composition underpinning many studies of land-use change in tropical forests. Surveys conducted using autonomous recorders have been frequently found to be more efficient than traditional point-count surveys. However, there has been limited research into optimal survey duration, despite autonomous recordings allowing for many more repeats of short-duration surveys with relative ease in comparison to traditional survey methods.We use an acoustic dataset collected from a region of very high avian biodiversity - the eastern Brazilian Amazon - to test the effect of using short-duration surveys to increase temporal coverage without increasing total survey duration. We use this dataset to assess whether a survey protocol consisting of 240 15-second surveys at 29 locations, ‘short-duration surveys’, has an influence on resulting alpha and gamma diversity, and detection frequency, than ‘standard-duration surveys’ of four 15-minute surveys per location.We find that repeated short-duration surveys outperform longer duration surveys in every metric considered herein, with short-duration surveys predicted to detect approximately 50% higher alpha diversity, and 10% higher gamma diversity. Short-duration surveys also detect species more often, at more survey locations. Conversely, standard-duration surveys are almost four times more likely to produce false negatives (i.e. to fail to detect species presence). Whilst there is no difference between the proportion of uncommon species detected by the two methods, when considering species detected multiple times at multiple locations, short-duration surveys detected three times more uncommon species than standard-duration surveys.We conclude that short-duration recorded surveys should be considered the primary method for sampling the species richness of bird communities in tropical forests and is likely to be preferable to longer duration or traditional surveys in most environments.

1. Studies on the effects of human-driven forest disturbance usually focus on either biodiversity or carbon dynamics but much less is known about ecosystem processes that integrate trophic levels. Herbivory is one fundamental ecological process for ecosystem functioning that remains underexplored and is poorly quantified in human-modified tropical rainforests. 2. Here, we present the results of the largest study to date on the impacts of human disturbances on herbivory. We quantified the incidence and severity of herbivory caused by chewers, miners and gall-formers in 199,869 canopy leaf blades from 1,102 trees distributed across 20 forest plots located along a gradient of human disturbance in the Amazon. 3. We found that chewers dominated herbivory incidence, yet were not a good predictor of the other forms of herbivory either at the stem or plot level. Herbivory severity was correlated with disturbance intensity, being greater at more disturbed sites. 4. Synthesis. Although our large-scale study of canopy herbivory in Amazonian forests suggests that human disturbance increases the severity of leaf herbivory, effects were weak. Additionally, we found no effect of human disturbance in incidence of leaf herbivory. These results combined indicate that herbivory is a relatively resilient process to human impacts.

Tropical forests hold 30% of Earth's terrestrial carbon and at least 60% of its terrestrial biodiversity, but forest loss and degradation are jeopardizing these ecosystems. Although the regrowth of secondary forests has the potential to offset some of the losses of carbon and biodiversity, it remains unclear if secondary regeneration will be affected by climate changes such as higher temperatures and more frequent extreme droughts. We used a data set of 10 repeated forest inventories spanning two decades (1999-2017) to investigate carbon and tree species recovery and how climate and landscape context influence carbon dynamics in an older secondary forest located in one of the oldest post-Columbian agricultural frontiers in the Brazilian Amazon. Carbon accumulation averaged 1.08 Mg·ha-1 ·yr-1 , and species richness was effectively constant over the studied period. Moreover, we provide evidence that secondary forests are vulnerable to drought stress: Carbon balance and growth rates were lower in drier periods. This contrasts with drought responses in primary forests, where changes in carbon dynamics are driven by increased stem mortality. These results highlight an important climate change-vegetation feedback, whereby the increasing dry-season lengths being observed across parts of Amazonia may reduce the effectiveness of secondary forests in sequestering carbon and mitigating climate change. In addition, the current rate of forest regrowth in this region was low compared with previous pan-tropical and Amazonian assessments-our secondary forests reached just 41.1% of the average carbon and 56% of the tree diversity in the nearest primary forests-suggesting that these areas are unlikely to return to their original levels on politically meaningful time scales.

Habitat loss is a primary threat to biodiversity across the planet, yet contentious debate has ensued on the importance of habitat fragmentation ‘per se’ (i.e., altered spatial configuration of habitat for a given amount of habitat loss). Based on a review of landscape-scale investigations, Fahrig (2017; Ecological responses to habitat fragmentation per se. Annual Review of Ecology, Evolution, and Systematics 48:1-23) reports that biodiversity responses to habitat fragmentation ‘per se’ are more often positive rather than negative and concludes that the widespread belief in negative fragmentation effects is a ‘zombie idea’. We show that Fahrig's conclusions are drawn from a narrow and potentially biased subset of available evidence, which ignore much of the observational, experimental and theoretical evidence for negative effects of altered habitat configuration. We therefore argue that Fahrig's conclusions should be interpreted cautiously as they could be misconstrued by policy makers and managers, and we provide six arguments why they should not be applied in conservation decision-making. Reconciling the scientific disagreement, and informing conservation more effectively, will require research that goes beyond statistical and correlative approaches. This includes a more prudent use of data and conceptual models that appropriately partition direct vs indirect influences of habitat loss and altered spatial configuration, and more clearly discriminate the mechanisms underpinning any changes. Incorporating these issues will deliver greater mechanistic understanding and more predictive power to address the conservation issues arising from habitat loss and fragmentation.

Most of the world's remaining tropical forests have been affected by either selective logging, understorey fires, fragmentation or are regrowing in areas that were previously deforested. Despite the ubiquity of these human‐modified forests, we have a limited knowledge of their potential to recover key traits linked to ecosystem processes and consequent services. Here we present data from 31,095 trees and saplings distributed across 121 plots of undisturbed and disturbed primary forests as well as secondary forests in the eastern Amazon. We examined the post‐disturbance recovery trajectory of an important plant functional trait, wood density. We tested whether human‐modified Amazonian forests are experiencing a rapid or a slow, or even impeded, recovery of this trait, which is associated with the provision of a fundamental ecosystem service—carbon storage. As expected, we found that the plot‐level wood density of trees and saplings in disturbed primary and secondary forests was significantly lower than in undisturbed forests. However, there was no significant difference in the average wood density of saplings between disturbed primary and secondary forests, possibly indicating a process of secondarization. We also found evidence that the recovery of wood density in human‐modified forests is being severely disrupted due to edge effects (in the case of disturbed primary forests) and high liana densities (in the case of both disturbed primary and secondary forests). Surprisingly, these two factors were more important predictors of wood density recovery than the time elapsed since the disturbance event. Synthesis. Plant communities in human‐modified Amazonian forests appear to not be recovering a key functional property—wood density, which in turn may affect their ability to store carbon in the future. If the aim of conservation programs in tropical forests is to maintain existing rates of ecosystem functions, processes and services, then they must concentrate efforts on avoiding anthropogenic disturbance in areas of currently undisturbed forests. It is also vital to prevent further disturbance in human‐modified forests to avoid disrupting even more their recovery.

Current debates in the conservation sciences argue for better integration between research and practice, often citing the importance of the diffusion, dissemination and implementation of scientific knowledge for environmental management and policy. This paper focuses on a relatively well-researched protected area (Madidi National Park) in Bolivia in order to present different interpretations and understandings of the implications and availability of research findings. We draw on findings from quantitative and qualitative methods to determine the extent to which research carried out in the region was disseminated and/or implemented for management actions, and to understand subsequent implications for how local actors perceive the value of research and its role in management and conservation. We discuss the critical consequences of these findings for the future of conservation science and practice in biologically and culturally diverse landscapes, with an explicit call to action for academic institutions to support researchers in developing appropriate dissemination strategies. Electronic supplementary material The online version of this article (10.1007/s13280-018-1056-5) contains supplementary material, which is available to authorized users.