Pervasive gaps in Amazonian ecological research.

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%-18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost.

The drivers and impacts of Amazon forest degradation.

Approximately 2.5 × 106 square kilometers of the Amazon forest are currently degraded by fire, edge effects, timber extraction, and/or extreme drought, representing 38% of all remaining forests in the region. Carbon emissions from this degradation total up to 0.2 petagrams of carbon per year (Pg C year-1), which is equivalent to, if not greater than, the emissions from Amazon deforestation (0.06 to 0.21 Pg C year-1). Amazon forest degradation can reduce dry-season evapotranspiration by up to 34% and cause as much biodiversity loss as deforestation in human-modified landscapes, generating uneven socioeconomic burdens, mainly to forest dwellers. Projections indicate that degradation will remain a dominant source of carbon emissions independent of deforestation rates. Policies to tackle degradation should be integrated with efforts to curb deforestation and complemented with innovative measures addressing the disturbances that degrade the Amazon forest.

Linking land-use and land-cover transitions to their ecological impact in the Amazon.

Human activities pose a major threat to tropical forest biodiversity and ecosystem services. Although the impacts of deforestation are well studied, multiple land-use and land-cover transitions (LULCTs) occur in tropical landscapes, and we do not know how LULCTs differ in their rates or impacts on key ecosystem components. Here, we quantified the impacts of 18 LULCTs on three ecosystem components (biodiversity, carbon, and soil), based on 18 variables collected from 310 sites in the Brazilian Amazon. Across all LULCTs, biodiversity was the most affected ecosystem component, followed by carbon stocks, but the magnitude of change differed widely among LULCTs and individual variables. Forest clearance for pasture was the most prevalent and high-impact transition, but we also identified other LULCTs with high impact but lower prevalence (e.g., forest to agriculture). Our study demonstrates the importance of considering multiple ecosystem components and LULCTs to understand the consequences of human activities in tropical landscapes.

Functional susceptibility of tropical forests to climate change.

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 forests' 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.

Tracking the impacts of El Niño drought and fire in human-modified Amazonian forests.

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.

Assessing invertebrate herbivory in human-modified tropical forest canopies.

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 span different trophic levels. Herbivory is a fundamental ecological process for ecosystem functioning, but it remains poorly quantified in human-modified tropical rainforests.Here, we present the results of the largest study to date on the impacts of human disturbances on herbivory. We quantified the incidence (percentage of leaves affected) and severity (the percentage of leaf area lost) of canopy insect herbivory caused by chewers, miners, and gall makers in leaves from 1,076 trees distributed across 20 undisturbed and human-modified forest plots in the Amazon.We found that chewers dominated herbivory incidence, yet were not a good predictor of the other forms of herbivory at either the stem or plot level. Chewing severity was higher in both logged and logged-and-burned primary forests when compared to undisturbed forests. We found no difference in herbivory severity between undisturbed primary forests and secondary forests. Despite evidence at the stem level, neither plot-level incidence nor severity of the three forms of herbivory responded to disturbance. Synthesis. Our large-scale study of canopy herbivory confirms that chewers dominate the herbivory signal in tropical forests, but that their influence on leaf area lost cannot predict the incidence or severity of other forms. We found only limited evidence suggesting that human disturbance affects the severity of leaf herbivory, with higher values in logged and logged-and-burned forests than undisturbed and secondary forests. Additionally, we found no effect of human disturbance on the incidence of leaf herbivory.

Integrated terrestrial-freshwater planning doubles conservation of tropical aquatic species.

Conservation initiatives overwhelmingly focus on terrestrial biodiversity, and little is known about the freshwater cobenefits of terrestrial conservation actions. We sampled more than 1500 terrestrial and freshwater species in the Amazon and simulated conservation for species from both realms. Prioritizations based on terrestrial species yielded on average just 22% of the freshwater benefits achieved through freshwater-focused conservation. However, by using integrated cross-realm planning, freshwater benefits could be increased by up to 600% for a 1% reduction in terrestrial benefits. Where freshwater biodiversity data are unavailable but aquatic connectivity is accounted for, freshwater benefits could still be doubled for negligible losses of terrestrial coverage. Conservation actions are urgently needed to improve the status of freshwater species globally. Our results suggest that such gains can be achieved without compromising terrestrial conservation goals.

Secondary forests offset less than 10% of deforestation-mediated carbon emissions in the Brazilian Amazon.

Secondary forests are increasing in the Brazilian Amazon and have been cited as an important mechanism for reducing net carbon emissions. However, our understanding of the contribution of secondary forests to the Amazonian carbon balance is incomplete, and it is unclear to what extent emissions from old-growth deforestation have been offset by secondary forest growth. Using MapBiomas 3.1 and recently refined IPCC carbon sequestration estimates, we mapped the age and extent of secondary forests in the Brazilian Amazon and estimated their role in offsetting old-growth deforestation emissions since 1985. We also assessed whether secondary forests in the Brazilian Amazon are growing in conditions favourable for carbon accumulation in relation to a suite of climatic, landscape and local factors. In 2017, the 129,361 km2 of secondary forest in the Brazilian Amazon stored 0.33 ± 0.05 billion Mg of above-ground carbon but had offset just 9.37% of old-growth emissions since 1985. However, we find that the majority of Brazilian secondary forests are situated in contexts that are less favourable for carbon accumulation than the biome average. Our results demonstrate that old-growth forest loss remains the most important factor determining the carbon balance in the Brazilian Amazon. Understanding the implications of these findings will be essential for improving estimates of secondary forest carbon sequestration potential. More accurate quantification of secondary forest carbon stocks will support the production of appropriate management proposals that can efficiently harness the potential of secondary forests as a low-cost, nature-based tool for mitigating climate change.

Climatic and local stressor interactions threaten tropical forests and coral reefs.

Tropical forests and coral reefs host a disproportionately large share of global biodiversity and provide ecosystem functions and services used by millions of people. Yet, ongoing climate change is leading to an increase in frequency and magnitude of extreme climatic events in the tropics, which, in combination with other local human disturbances, is leading to unprecedented negative ecological consequences for tropical forests and coral reefs. Here, we provide an overview of how and where climate extremes are affecting the most biodiverse ecosystems on Earth and summarize how interactions between global, regional and local stressors are affecting tropical forest and coral reef systems through impacts on biodiversity and ecosystem resilience. We also discuss some key challenges and opportunities to promote mitigation and adaptation to a changing climate at local and global scales. This article is part of the theme issue 'Climate change and ecosystems: threats, opportunities and solutions'.

Assessing the growth and climate sensitivity of secondary forests in highly deforested Amazonian landscapes.

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.

Tree growth and stem carbon accumulation in human-modified Amazonian forests following drought and fire.

Human-modified forests are an ever-increasing feature across the Amazon Basin, but little is known about how stem growth is influenced by extreme climatic events and the resulting wildfires. Here we assess for the first time the impacts of human-driven disturbance in combination with El Niño-mediated droughts and fires on tree growth and carbon accumulation. We found that after 2.5 years of continuous measurements, there was no difference in stem carbon accumulation between undisturbed and human-modified forests. Furthermore, the extreme drought caused by the El Niño did not affect carbon accumulation rates in surviving trees. In recently burned forests, trees grew significantly more than in unburned ones, regardless of their history of previous human disturbance. Wood density was the only significant factor that helped explain the difference in growth between trees in burned and unburned forests, with low wood-density trees growing significantly more in burned sites. Our results suggest stem carbon accumulation is resistant to human disturbance and one-off extreme drought events, and it is stimulated immediately after wildfires. However, these results should be seen with caution-without accounting for carbon losses, recruitment and longer-term changes in species composition, we cannot fully understand the impacts of drought and fire in the carbon balance of human-modified forests.This article is part of a discussion meeting issue 'The impact of the 2015/2016 El Nino on the terrestrial tropical carbon cycle: patterns, mechanisms and implications'.

Quantifying immediate carbon emissions from El Niño-mediated wildfires in humid tropical forests.

Wildfires produce substantial CO2 emissions in the humid tropics during El Niño-mediated extreme droughts, and these emissions are expected to increase in coming decades. Immediate carbon emissions from uncontrolled wildfires in human-modified tropical forests can be considerable owing to high necromass fuel loads. Yet, data on necromass combustion during wildfires are severely lacking. Here, we evaluated necromass carbon stocks before and after the 2015-2016 El Niño in Amazonian forests distributed along a gradient of prior human disturbance. We then used Landsat-derived burn scars to extrapolate regional immediate wildfire CO2 emissions during the 2015-2016 El Niño. Before the El Niño, necromass stocks varied significantly with respect to prior disturbance and were largest in undisturbed primary forests (30.2 ± 2.1 Mg ha-1, mean ± s.e.) and smallest in secondary forests (15.6 ± 3.0 Mg ha-1). However, neither prior disturbance nor our proxy of fire intensity (median char height) explained necromass losses due to wildfires. In our 6.5 million hectare (6.5 Mha) study region, almost 1 Mha of primary (disturbed and undisturbed) and 20 000 ha of secondary forest burned during the 2015-2016 El Niño. Covering less than 0.2% of Brazilian Amazonia, these wildfires resulted in expected immediate CO2 emissions of approximately 30 Tg, three to four times greater than comparable estimates from global fire emissions databases. Uncontrolled understorey wildfires in humid tropical forests during extreme droughts are a large and poorly quantified source of CO2 emissions.This article is part of a discussion meeting issue 'The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications'.

Drought-induced Amazonian wildfires instigate a decadal-scale disruption of forest carbon dynamics.

Drought-induced wildfires have increased in frequency and extent over the tropics. Yet, the long-term (greater than 10 years) responses of Amazonian lowland forests to fire disturbance are poorly known. To understand post-fire forest biomass dynamics, and to assess the time required for fire-affected forests to recover to pre-disturbance levels, we combined 16 single with 182 multiple forest census into a unique large-scale and long-term dataset across the Brazilian Amazonia. We quantified biomass, mortality and wood productivity of burned plots along a chronosequence of up to 31 years post-fire and compared to surrounding unburned plots measured simultaneously. Stem mortality and growth were assessed among functional groups. At the plot level, we found that fire-affected forests have biomass levels 24.8 ± 6.9% below the biomass value of unburned control plots after 31 years. This lower biomass state results from the elevated levels of biomass loss through mortality, which is not sufficiently compensated for by wood productivity (incremental growth + recruitment). At the stem level, we found major changes in mortality and growth rates up to 11 years post-fire. The post-fire stem mortality rates exceeded unburned control plots by 680% (i.e. greater than 40 cm diameter at breast height (DBH); 5-8 years since last fire) and 315% (i.e. greater than 0.7 g cm-3 wood density; 0.75-4 years since last fire). Our findings indicate that wildfires in humid tropical forests can significantly reduce forest biomass for decades by enhancing mortality rates of all trees, including large and high wood density trees, which store the largest amount of biomass in old-growth forests. This assessment of stem dynamics, therefore, demonstrates that wildfires slow down or stall the post-fire recovery of Amazonian forests.This article is part of a discussion meeting issue 'The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications'.

Second rate or a second chance? Assessing biomass and biodiversity recovery in regenerating Amazonian forests.

Secondary forests (SFs) regenerating on previously deforested land account for large, expanding areas of tropical forest cover. Given that tropical forests rank among Earth's most important reservoirs of carbon and biodiversity, SFs play an increasingly pivotal role in the carbon cycle and as potential habitat for forest biota. Nevertheless, their capacity to regain the biotic attributes of undisturbed primary forests (UPFs) remains poorly understood. Here, we provide a comprehensive assessment of SF recovery, using extensive tropical biodiversity, biomass, and environmental datasets. These data, collected in 59 naturally regenerating SFs and 30 co-located UPFs in the eastern Amazon, cover >1,600 large- and small-stemmed plant, bird, and dung beetles species and a suite of forest structure, landscape context, and topoedaphic predictors. After up to 40 years of regeneration, the SFs we surveyed showed a high degree of biodiversity resilience, recovering, on average among taxa, 88% and 85% mean UPF species richness and composition, respectively. Across the first 20 years of succession, the period for which we have accurate SF age data, biomass recovered at 1.2% per year, equivalent to a carbon uptake rate of 2.25 Mg/ha per year, while, on average, species richness and composition recovered at 2.6% and 2.3% per year, respectively. For all taxonomic groups, biomass was strongly associated with SF species distributions. However, other variables describing habitat complexity-canopy cover and understory stem density-were equally important occurrence predictors for most taxa. Species responses to biomass revealed a successional transition at approximately 75 Mg/ha, marking the influx of high-conservation-value forest species. Overall, our results show that naturally regenerating SFs can accumulate substantial amounts of carbon and support many forest species. However, given that the surveyed SFs failed to return to a typical UPF state, SFs are not substitutes for UPFs.

The future of hyperdiverse tropical ecosystems.

The tropics contain the overwhelming majority of Earth's biodiversity: their terrestrial, freshwater and marine ecosystems hold more than three-quarters of all species, including almost all shallow-water corals and over 90% of terrestrial birds. However, tropical ecosystems are also subject to pervasive and interacting stressors, such as deforestation, overfishing and climate change, and they are set within a socio-economic context that includes growing pressure from an increasingly globalized world, larger and more affluent tropical populations, and weak governance and response capacities. Concerted local, national and international actions are urgently required to prevent a collapse of tropical biodiversity.

Is environmental legislation conserving tropical stream faunas? A large-scale assessment of local, riparian and catchment-scale influences on Amazonian fish.

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.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.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.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 <5%).Policy implications. Current rates of agricultural intensification and mechanization in tropical landscapes are unprecedented, yet the existing legislative frameworks focusing on protecting riparian vegetation seem insufficient to conserve stream environments and their fish assemblages. To safeguard the species-rich freshwater biota of small Amazonian streams, conservation actions must shift towards managing whole basins and drainage networks, as well as agricultural practices in already-cleared land.

Anthropogenic disturbance in tropical forests can double biodiversity loss from deforestation.

Concerted political attention has focused on reducing deforestation, and this remains the cornerstone of most biodiversity conservation strategies. However, maintaining forest cover may not reduce anthropogenic forest disturbances, which are rarely considered in conservation programmes. These disturbances occur both within forests, including selective logging and wildfires, and at the landscape level, through edge, area and isolation effects. Until now, the combined effect of anthropogenic disturbance on the conservation value of remnant primary forests has remained unknown, making it impossible to assess the relative importance of forest disturbance and forest loss. Here we address these knowledge gaps using a large data set of plants, birds and dung beetles (1,538, 460 and 156 species, respectively) sampled in 36 catchments in the Brazilian state of Pará. Catchments retaining more than 69­80% forest cover lost more conservation value from disturbance than from forest loss. For example, a 20% loss of primary forest, the maximum level of deforestation allowed on Amazonian properties under Brazil's Forest Code, resulted in a 39­54% loss of conservation value: 96­171% more than expected without considering disturbance effects. We extrapolated the disturbance-mediated loss of conservation value throughout Pará, which covers 25% of the Brazilian Amazon. Although disturbed forests retained considerable conservation value compared with deforested areas, the toll of disturbance outside Pará's strictly protected areas is equivalent to the loss of 92,000­139,000 km2 of primary forest. Even this lowest estimate is greater than the area deforested across the entire Brazilian Amazon between 2006 and 2015 (ref. 10). Species distribution models showed that both landscape and within-forest disturbances contributed to biodiversity loss, with the greatest negative effects on species of high conservation and functional value. These results demonstrate an urgent need for policy interventions that go beyond the maintenance of forest cover to safeguard the hyper-diversity of tropical forest ecosystems.

Toward an integrated monitoring framework to assess the effects of tropical forest degradation and recovery on carbon stocks and biodiversity.

Tropical forests harbor a significant portion of global biodiversity and are a critical component of the climate system. Reducing deforestation and forest degradation contributes to global climate-change mitigation efforts, yet emissions and removals from forest dynamics are still poorly quantified. We reviewed the main challenges to estimate changes in carbon stocks and biodiversity due to degradation and recovery of tropical forests, focusing on three main areas: (1) the combination of field surveys and remote sensing; (2) evaluation of biodiversity and carbon values under a unified strategy; and (3) research efforts needed to understand and quantify forest degradation and recovery. The improvement of models and estimates of changes of forest carbon can foster process-oriented monitoring of forest dynamics, including different variables and using spatially explicit algorithms that account for regional and local differences, such as variation in climate, soil, nutrient content, topography, biodiversity, disturbance history, recovery pathways, and socioeconomic factors. Generating the data for these models requires affordable large-scale remote-sensing tools associated with a robust network of field plots that can generate spatially explicit information on a range of variables through time. By combining ecosystem models, multiscale remote sensing, and networks of field plots, we will be able to evaluate forest degradation and recovery and their interactions with biodiversity and carbon cycling. Improving monitoring strategies will allow a better understanding of the role of forest dynamics in climate-change mitigation, adaptation, and carbon cycle feedbacks, thereby reducing uncertainties in models of the key processes in the carbon cycle, including their impacts on biodiversity, which are fundamental to support forest governance policies, such as Reducing Emissions from Deforestation and Forest Degradation.