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The authors discuss development pressures related to the demands for hydropower and mineral resources and shifts in legislation that are compromising the Brazilian government's environmental successes, such as deforestation control, and threatening its protected areas (PAs). Topics include the critical role that Brazil's existing PA network plays in biodiversity conservation, the cumulative effects of large-scale development projects, and poorly conceived environmental mitigation policies.

Amazonia's floodplain system is the largest and most biodiverse on Earth. Although forests are crucial to the ecological integrity of floodplains, our understanding of their species composition and how this may differ from surrounding forest types is still far too limited, particularly as changing inundation regimes begin to reshape floodplain tree communities and the critical ecosystem functions they underpin. Here we address this gap by taking a spatially explicit look at Amazonia-wide patterns of tree-species turnover and ecological specialization of the region's floodplain forests. We show that the majority of Amazonian tree species can inhabit floodplains, and about a sixth of Amazonian tree diversity is ecologically specialized on floodplains. The degree of specialization in floodplain communities is driven by regional flood patterns, with the most compositionally differentiated floodplain forests located centrally within the fluvial network and contingent on the most extraordinary flood magnitudes regionally. Our results provide a spatially explicit view of ecological specialization of floodplain forest communities and expose the need for whole-basin hydrological integrity to protect the Amazon's tree diversity and its function., (© 2024. The Author(s).)

Indigenous societies are known to have occupied the Amazon basin for more than 12,000 years, but the scale of their influence on Amazonian forests remains uncertain. We report the discovery, using LIDAR (light detection and ranging) information from across the basin, of 24 previously undetected pre-Columbian earthworks beneath the forest canopy. Modeled distribution and abundance of large-scale archaeological sites across Amazonia suggest that between 10,272 and 23,648 sites remain to be discovered and that most will be found in the southwest. We also identified 53 domesticated tree species significantly associated with earthwork occurrence probability, likely suggesting past management practices. Closed-canopy forests across Amazonia are likely to contain thousands of undiscovered archaeological sites around which pre-Columbian societies actively modified forests, a discovery that opens opportunities for better understanding the magnitude of ancient human influence on Amazonia and its current state.

For more than three decades, major efforts in sampling and analyzing tree diversity in South America have focused almost exclusively on trees with stems of at least 10 and 2.5 cm diameter, showing highest species diversity in the wetter western and northern Amazon forests. By contrast, little attention has been paid to patterns and drivers of diversity in the largest canopy and emergent trees, which is surprising given these have dominant ecological functions. Here, we use a machine learning approach to quantify the importance of environmental factors and apply it to generate spatial predictions of the species diversity of all trees (dbh ≥ 10 cm) and for very large trees (dbh ≥ 70 cm) using data from 243 forest plots (108,450 trees and 2832 species) distributed across different forest types and biogeographic regions of the Brazilian Amazon. The diversity of large trees and of all trees was significantly associated with three environmental factors, but in contrasting ways across regions and forest types. Environmental variables associated with disturbances, for example, the lightning flash rate and wind speed, as well as the fraction of photosynthetically active radiation, tend to govern the diversity of large trees. Upland rainforests in the Guiana Shield and Roraima regions had a high diversity of large trees. By contrast, variables associated with resources tend to govern tree diversity in general. Places such as the province of Imeri and the northern portion of the province of Madeira stand out for their high diversity of species in general. Climatic and topographic stability and functional adaptation mechanisms promote ideal conditions for species diversity. Finally, we mapped general patterns of tree species diversity in the Brazilian Amazon, which differ substantially depending on size class., (© 2023 John Wiley & Sons Ltd.)

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 modifications 16 , 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., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Approximately 2.5 × 10 6 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.

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.

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 CO 2 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. , Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

The forests of Amazonia are among the most biodiverse plant communities on Earth. Given the immediate threats posed by climate and land-use change, an improved understanding of how this extraordinary biodiversity is spatially organized is urgently required to develop effective conservation strategies. Most Amazonian tree species are extremely rare but a few are common across the region. Indeed, just 227 'hyperdominant' species account for >50% of all individuals >10 cm diameter at 1.3 m in height. Yet, the degree to which the phenomenon of hyperdominance is sensitive to tree size, the extent to which the composition of dominant species changes with size class and how evolutionary history constrains tree hyperdominance, all remain unknown. Here, we use a large floristic dataset to show that, while hyperdominance is a universal phenomenon across forest strata, different species dominate the forest understory, midstory and canopy. We further find that, although species belonging to a range of phylogenetically dispersed lineages have become hyperdominant in small size classes, hyperdominants in large size classes are restricted to a few lineages. Our results demonstrate that it is essential to consider all forest strata to understand regional patterns of dominance and composition in Amazonia. More generally, through the lens of 654 hyperdominant species, we outline a tractable pathway for understanding the functioning of half of Amazonian forests across vertical strata and geographical locations.

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.

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 (CH 4 ) emission. To better understand the drivers of this change, we measured soil CH 4 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 CH 4 (mean: 3454.6 ± 9482.3 μg CH 4 m -2 d -1 ), consistent with previous reports, while forest soils on average emit CH 4 at modest rates (mean: 9.8 ± 120.5 μg CH 4 m -2 d -1 ), but often act as CH 4 sinks. We report that secondary forest soils tend to consume CH 4 (mean: -10.2 ± 35.7 μg CH 4 m -2 d -1 ), demonstrating that pasture CH 4 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 CH 4 directly (i.e. methanogens and methanotrophs, respectively), the vast majority of identified taxa are not known to cycle CH 4 . Each land use type had a unique subset of taxa associated with CH 4 flux, suggesting that land use change alters CH 4 cycling through shifts in microbial community composition. Taken together, we show that microbial composition is crucial for understanding the observed CH 4 dynamics and that microorganisms provide explanatory power that cannot be captured by environmental variables., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

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., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia is best approximated by a logseries with aggregated individuals, where aggregation increases with rarity. By averaging several methods to estimate total richness, we confirm that over 15,000 tree species are expected to occur in Amazonia. We also show that using ten times the number of plots would result in an increase to just ~50% of those 15,000 estimated species. To get a more complete sample of all tree species, rigorous field campaigns may be needed but the number of trees in Amazonia will remain an estimate for years to come.

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., (© 2019 by the Ecological Society of America.)

Wildfires produce substantial CO 2 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 CO 2 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 CO 2 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 CO 2 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'., (© 2018 The Author(s).)

Meteorological extreme events such as El Niño events are expected to affect tropical forest net primary production (NPP) and woody growth, but there has been no large-scale empirical validation of this expectation. We collected a large high-temporal resolution dataset (for 1-13 years depending upon location) of more than 172 000 stem growth measurements using dendrometer bands from across 14 regions spanning Amazonia, Africa and Borneo in order to test how much month-to-month variation in stand-level woody growth of adult tree stems (NPP stem ) can be explained by seasonal variation and interannual meteorological anomalies. A key finding is that woody growth responds differently to meteorological variation between tropical forests with a dry season (where monthly rainfall is less than 100 mm), and aseasonal wet forests lacking a consistent dry season. In seasonal tropical forests, a high degree of variation in woody growth can be predicted from seasonal variation in temperature, vapour pressure deficit, in addition to anomalies of soil water deficit and shortwave radiation. The variation of aseasonal wet forest woody growth is best predicted by the anomalies of vapour pressure deficit, water deficit and shortwave radiation. In total, we predict the total live woody production of the global tropical forest biome to be 2.16 Pg C yr -1 , with an interannual range 1.96-2.26 Pg C yr -1 between 1996-2016, and with the sharpest declines during the strong El Niño events of 1997/8 and 2015/6. There is high geographical variation in hotspots of El Niño-associated impacts, with weak impacts in Africa, and strongly negative impacts in parts of Southeast Asia and extensive regions across central and eastern Amazonia. Overall, there is high correlation ( r = -0.75) between the annual anomaly of tropical forest woody growth and the annual mean of the El Niño 3.4 index, driven mainly by strong correlations with anomalies of soil water deficit, vapour pressure deficit and shortwave radiation.This article is part of the discussion meeting issue 'The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications'., (© 2018 The Author(s).)

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'., (© 2018 The Author(s).)

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'., (© 2018 The Author(s).)

Science has a critical role to play in guiding more sustainable development trajectories. Here, we present the Sustainable Amazon Network (Rede Amazônia Sustentável, RAS): a multidisciplinary research initiative involving more than 30 partner organizations working to assess both social and ecological dimensions of land-use sustainability in eastern Brazilian Amazonia. The research approach adopted by RAS offers three advantages for addressing land-use sustainability problems: (i) the collection of synchronized and co-located ecological and socioeconomic data across broad gradients of past and present human use; (ii) a nested sampling design to aid comparison of ecological and socioeconomic conditions associated with different land uses across local, landscape and regional scales; and (iii) a strong engagement with a wide variety of actors and non-research institutions. Here, we elaborate on these key features, and identify the ways in which RAS can help in highlighting those problems in most urgent need of attention, and in guiding improvements in land-use sustainability in Amazonia and elsewhere in the tropics. We also discuss some of the practical lessons, limitations and realities faced during the development of the RAS initiative so far.