Ecological change increases malaria risk in the Brazilian Amazon.

Ecological change in the Brazilian Amazon is closely linked to human mobility and health. Mining, agriculture, logging, and other activities alter highly diverse ecological and demographic contexts and subsequent exposure to diseases such as malaria. Studies that have attempted to quantify the impact of deforestation on malaria in the Brazilian Amazon have produced conflicting results. However, they varied in methodology and data sources. Most importantly, all studies used annual data, neglecting the subannual seasonal dynamics of malaria. Here, we fill the knowledge gap on the subannual relationship between ecological change in the Brazilian Amazon and malaria transmission. Using the highest spatiotemporal resolution available, we estimated the effect of deforestation on malaria cases between 2003 and 2022 using a stratified Bayesian spatiotemporal hierarchical zero-inflated Poisson model fitted with the Integrated Nested Laplace Approximation. The model was also stratified by state. We found that a 1% increase in 1-mo lagged deforestation increased malaria cases in a given month and municipality by 6.3% [95% credible interval (Crl): 6.2, 6.5%]. Based on an interaction term included in the model, the effect of deforestation on malaria was even larger in areas with higher forest cover. We found that the coefficients for deforestation and mobility were highly variable when stratified by state. Our results provide detailed evidence that, on average, deforestation increases malaria transmission, but that the relationship is not spatiotemporally uniform. These results have implications for stratifying malaria control interventions based on ecological dynamics to help Brazil achieve its goal of malaria elimination by 2035.

The Andes-Amazon-Atlantic pathway: A foundational hydroclimate system for social-ecological system sustainability.

The Amazon River Basin's extraordinary social-ecological system is sustained by various water phases, fluxes, and stores that are interconnected across the tropical Andes mountains, Amazon lowlands, and Atlantic Ocean. This "Andes-Amazon-Atlantic" (AAA) pathway is a complex hydroclimatic system linked by the regional water cycle through atmospheric circulation and continental hydrology. Here, we aim to articulate the AAA hydroclimate pathway as a foundational system for research, management, conservation, and governance of aquatic systems of the Amazon Basin. We identify and describe the AAA pathway as an interdependent, multidirectional, and multiscale hydroclimate system. We then present an assessment of recent (1981 to 2020) changes in the AAA pathway, primarily reflecting an acceleration in the rates of hydrologic fluxes (i.e., water cycle intensification). We discuss how the changing AAA pathway orchestrates and impacts social-ecological systems. We conclude with four recommendations for the sustainability of the AAA pathway in ongoing research, management, conservation, and governance.

A large net carbon loss attributed to anthropogenic and natural disturbances in the Amazon Arc of Deforestation.

The Amazon forest contains globally important carbon stocks, but in recent years, atmospheric measurements suggest that it has been releasing more carbon than it has absorbed because of deforestation and forest degradation. Accurately attributing the sources of carbon loss to forest degradation and natural disturbances remains a challenge because of the difficulty of classifying disturbances and simultaneously estimating carbon changes. We used a unique, randomized, repeated, very high-resolution airborne laser scanning survey to provide a direct, detailed, and high-resolution partitioning of aboveground carbon gains and losses in the Brazilian Arc of Deforestation. Our analysis revealed that disturbances directly attributed to human activity impacted 4.2% of the survey area while windthrows and other disturbances affected 2.7% and 14.7%, respectively. Extrapolating the lidar-based statistics to the study area (544,300 km2), we found that 24.1, 24.2, and 14.5 Tg C y-1 were lost through clearing, fires, and logging, respectively. The losses due to large windthrows (21.5 Tg C y-1) and other disturbances (50.3 Tg C y-1) were partially counterbalanced by forest growth (44.1 Tg C y-1). Our high-resolution estimates demonstrated a greater loss of carbon through forest degradation than through deforestation and a net loss of carbon of 90.5 ± 16.6 Tg C y-1 for the study region attributable to both anthropogenic and natural processes. This study highlights the role of forest degradation in the carbon balance for this critical region in the Earth system.

Double stress of waterlogging and drought drives forest-savanna coexistence.

Forest-savanna boundaries are ecotones that support complex ecosystem functions and are sensitive to biotic/abiotic perturbations. What drives their distribution today and how it may shift in the future are open questions. Feedbacks among climate, fire, herbivory, and land use are known drivers. Here, we show that alternating seasonal drought and waterlogging stress favors the dominance of savanna-like ecosystems over forests. We track the seasonal water-table depth as an indicator of water stress when too deep and oxygen stress when too shallow and map forest/savanna occurrence within this double-stress space in the neotropics. We find that under a given annual precipitation, savannas are favored in landscape positions experiencing double stress, which is more common as the dry season strengthens (climate driver) but only found in waterlogged lowlands (terrain driver). We further show that hydrological changes at the end of the century may expose some flooded forests to savanna expansion, affecting biodiversity and soil carbon storage. Our results highlight the importance of land hydrology in understanding/predicting forest-savanna transitions in a changing world.

High rates of rock organic carbon oxidation sustained as Andean sediment transits the Amazon foreland-floodplain.

The oxidation of organic carbon contained within sedimentary rocks ("petrogenic" carbon, or hereafter OCpetro) emits nearly as much CO2 as is released by volcanism, thereby playing a key role in the long-term global C budget. High erosion rates in mountains have been shown to increase OCpetro oxidation. However, these settings also export unweathered material that may continue to react in downstream floodplains. The relative importance of OCpetro oxidation in mountains versus floodplains remains difficult to assess as disparate methods have been used in the different environments. Here, we investigate the sources and fluxes of rhenium (Re) in the Rio Madre de Dios to quantify OCpetro oxidation from the Andes to the Amazon floodplain using a common approach. Dissolved rhenium concentrations (n = 131) range from 0.01 to 63 pmol L-1 and vary depending on lithology and geomorphic setting. We find that >75% of the dissolved Re derives from OCpetro oxidation and that this proportion increases downstream. We estimate that in the Andes, OCpetro oxidation releases 11.2+4.5/-2.8 tC km-2 y-1 of CO2, which corresponds to ~41% of the total OCpetro denudation (sum of oxidized and solid OCpetro). A Re mass balance across the Rio Madre de Dios shows that 46% of OCpetro oxidation takes place in the Andes, 14% in the foreland-lowlands, and 40% in the Andean-fed floodplains. This doubling of OCpetro oxidation flux downstream of the Andes demonstrates that, when present, floodplains can greatly increase OCpetro oxidation and CO2 release.

Estimating the spatial amplification of damage caused by degradation in the Amazon.

The Amazon rainforests have been undergoing unprecedented levels of human-induced disturbances. In addition to local impacts, such changes are likely to cascade following the eastern-western atmospheric flow generated by trade winds. We propose a model of spatial and temporal interactions created by this flow to estimate the spread of effects from local disturbances to downwind locations along atmospheric trajectories. The spatial component captures cascading effects propagated by neighboring regions, while the temporal component captures the persistence of local disturbances. Importantly, all these network effects can be described by a single matrix, acting as a spatial multiplier that amplifies local forest disturbances. This matrix holds practical implications for policymakers as they can use it to easily map where the damage of an initial forest disturbance is amplified and propagated to. We identify regions that are likely to cause the largest impact throughout the basin and those that are the most vulnerable to shocks caused by remote deforestation. On average, the presence of cascading effects mediated by winds in the Amazon doubles the impact of an initial damage. However, there is heterogeneity in this impact. While damage in some regions does not propagate, in others, amplification can reach 250%. Since we only account for spillovers mediated by winds, our multiplier of 2 should be seen as a lower bound.

Collective property rights lead to secondary forest growth in the Brazilian Amazon.

Forests serve a crucial role in our fight against climate change. Secondary forests provide important potential for conservation of biodiversity and climate change mitigation. In this paper, we explore whether collective property rights in the form of indigenous territories (ITs) lead to higher rates of secondary forest growth in previously deforested areas. We exploit the timing of granting of property rights, the geographic boundaries of ITs and two different methods, regression discontinuity design and difference-in-difference, to recover causal estimates. We find strong evidence that indigenous territories with secure tenure not only reduce deforestation inside their lands but also lead to higher secondary forest growth on previously deforested areas. After receiving full property rights, land inside ITs displayed higher secondary forest growth than land outside ITs, with an estimated effect of 5% using our main RDD specification, and 2.21% using our difference-in-difference research design. Furthermore, we estimate that the average age of secondary forests was 2.2 y older inside ITs with secure tenure using our main RDD specification, and 2.8 y older when using our difference-in-difference research design. Together, these findings provide evidence for the role that collective property rights can play in the push to restore forest ecosystems.

Advancing convergence research: Renewable energy solutions for off-grid communities.

Millions of people across the world live off-grid not by choice but because they live in rural areas, have low income, and have no political clout. Delivering sustainable energy solutions to such a substantial amount of the world's population requires more than a technological fix; it requires leveraging the knowledge of underserved populations working together with a transdisciplinary team to find holistically derived solutions. Our original research has resulted in an innovative Convergence Framework integrating the fields of engineering, social sciences, and communication, and is based on working together with communities and other stakeholders to address the challenges posed by delivering clean energy solutions. In this paper, we discuss the evolution of this Framework and illustrate how this Framework is being operationalized in our on-going research project, cocreating hybrid renewable energy systems for off-grid communities in the Brazilian Amazon. The research shows how this Framework can address clean energy transitions, strengthen emerging industries at local level, and foster Global North-South scholarly collaborations. We do so by the integration of social science and engineering and by focusing on community engagement, energy justice, and governance for underserved communities. Further, this solution-driven Framework leads to the emergence of unique approaches that advance scientific knowledge, while at the same time addressing community needs.

Recurrent droughts increase risk of cascading tipping events by outpacing adaptive capacities in the Amazon rainforest.

Tipping elements are nonlinear subsystems of the Earth system that have the potential to abruptly shift to another state if environmental change occurs close to a critical threshold with large consequences for human societies and ecosystems. Among these tipping elements may be the Amazon rainforest, which has been undergoing intensive anthropogenic activities and increasingly frequent droughts. Here, we assess how extreme deviations from climatological rainfall regimes may cause local forest collapse that cascades through the coupled forest-climate system. We develop a conceptual dynamic network model to isolate and uncover the role of atmospheric moisture recycling in such tipping cascades. We account for heterogeneity in critical thresholds of the forest caused by adaptation to local climatic conditions. Our results reveal that, despite this adaptation, a future climate characterized by permanent drought conditions could trigger a transition to an open canopy state particularly in the southern Amazon. The loss of atmospheric moisture recycling contributes to one-third of the tipping events. Thus, by exceeding local thresholds in forest adaptive capacity, local climate change impacts may propagate to other regions of the Amazon basin, causing a risk of forest shifts even in regions where critical thresholds have not been crossed locally.

Changing Clinical Epidemiology of Plasmodium vivax Malaria as Transmission Decreases: Population-Based Prospective Panel Survey in the Brazilian Amazon.

BACKGROUND: Malarial infections are often missed by microscopy, and most parasite carriers are asymptomatic in low-endemicity settings. Whether parasite detectability and its ability to elicit symptoms change as transmission declines remains unclear. METHODS: We performed a prospective panel survey with repeated measurements on the same participants over 12 months to investigate whether Plasmodium vivax detectability by microscopy and risk of symptoms upon infection varied during a community-wide larviciding intervention in the Amazon basin of Brazil that markedly reduced vector density. We screened 1096 to 1400 residents in the intervention site for malaria by microscopy and quantitative TaqMan assays at baseline and twice during intervention. RESULTS: We found that more P vivax infections than expected from their parasite densities measured by TaqMan assays were missed by microscopy as transmission decreased. At lower transmission, study participants appeared to tolerate higher P vivax loads without developing symptoms. We hypothesize that changes in the ratio between circulating parasites and those that accumulate in the bone marrow and spleen, by avoiding peripheral blood microscopy detection, account for decreased parasite detectability and lower risk of symptoms under low transmission. CONCLUSIONS: P vivax infections are more likely to be subpatent and remain asymptomatic as malaria transmission decreases.

Molecular Epidemiology of Mayaro Virus among Febrile Patients, Roraima State, Brazil, 2018-2021.

We detected Mayaro virus (MAYV) in 3.4% (28/822) of febrile patients tested during 2018-2021 from Roraima State, Brazil. We also isolated MAYV strains and confirmed that these cases were caused by genotype D. Improved surveillance is needed to better determine the burden of MAYV in the Amazon Region.

Co-Circulation of 2 Oropouche Virus Lineages, Amazon Basin, Colombia, 2024.

In early 2024, explosive outbreaks of Oropouche virus (OROV) linked to a novel lineage were documented in the Amazon Region of Brazil. We report the introduction of this lineage into Colombia and its co-circulation with another OROV lineage. Continued surveillance is needed to prevent further spread of OROV in the Americas.

Lower Microscopy Sensitivity with Decreasing Malaria Prevalence in the Urban Amazon Region, Brazil, 2018-2021.

Malaria is increasingly diagnosed in urban centers across the Amazon Basin. In this study, we combined repeated prevalence surveys over a 4-year period of a household-based random sample of 2,774 persons with parasite genotyping to investigate the epidemiology of malaria in Mâncio Lima, the main urban transmission hotspot in Amazonian Brazil. We found that most malarial infections were asymptomatic and undetected by point-of-care microscopy. Our findings indicate that as malaria transmission decreases, the detection threshold of microscopy rises, resulting in more missed infections despite similar parasite densities estimated by molecular methods. We identified genetically highly diverse populations of Plasmodium vivax and P. falciparum in the region; occasional shared lineages between urban and rural residents suggest cross-boundary propagation. The prevalence of low-density and asymptomatic infections poses a significant challenge for routine surveillance and the effectiveness of malaria control and elimination strategies in urbanized areas with readily accessible laboratory facilities.

Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Work-Flow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana.

French Guiana, located in the Guiana Shield, is a natural reservoir for many zoonotic pathogens that are of considerable medical or veterinary importance. Until now, there has been limited data available on the description of parasites circulating in this area, especially on protozoan belonging to the phylum Apicomplexa; conversely, the neighbouring countries describe a high parasitic prevalence in animals and humans. Epidemiological surveillance is necessary, as new potentially virulent strains may emerge from these forest ecosystems, such as Amazonian toxoplasmosis. However, there is no standard tool for detecting protozoa in wildlife. In this study, we developed Meat-Borne-Parasite, a high-throughput meta-barcoding workflow for detecting Apicomplexa based on the Oxford Nanopore Technologies sequencing platform using the 18S gene of 14 Apicomplexa positive samples collected in French Guiana. Sequencing reads were then analysed with MetONTIIME pipeline. Thanks to a scoring rule, we were able to classify 10 samples out of 14 as Apicomplexa positive and reveal the presence of co-carriages. The same samples were also sequenced with the Illumina platform for validation purposes. For samples identified as Apicomplexa positive by both platforms, a strong positive correlation at up to the genus level was reported. Overall, the presented workflow represents a reliable method for Apicomplexa detection, which may pave the way for more comprehensive biomonitoring of zoonotic pathogens.

An Elevational Phylogeographic Diversity Gradient in Neotropical Birds Is Decoupled from Speciation Rates.

AbstractA key question about macroevolutionary speciation rates is whether they are controlled by microevolutionary processes operating at the population level. For example, does spatial variation in population genetic differentiation underlie geographical gradients in speciation rates? Previous work suggests that speciation rates increase with elevation in Neotropical birds, but underlying population-level gradients remain unexplored. Here, we characterize elevational phylogeographic diversity between montane and lowland birds in the megadiverse Andes-Amazonian system and assess its relationship to speciation rates to evaluate the link between population-level differentiation and species-level diversification. We aggregated and georeferenced nearly 7,000 mitochondrial DNA sequences across 103 species or species complexes in the Andes and Amazonia and used these sequences to describe phylogeographic differentiation across both regions. Our results show increased levels of both discrete and continuous metrics of population structure in the Andean mountains compared with the Amazonian lowlands. However, higher levels of population differentiation do not predict higher rates of speciation in our dataset. Multiple potential factors may lead to our observed decoupling of initial population divergence and speciation rates, including the ephemerality of incipient species and the multifaceted nature of the speciation process, as well as methodological challenges associated with estimating rates of population differentiation and speciation.

Habitat use of Amazonian birds varies by age and foraging guild along a disturbance gradient.

Patterns of habitat use directly influence a species' fitness, yet for many species an individual's age can influence patterns of habitat use. However, in tropical rainforests, which host the greatest terrestrial species diversity, little is known about how age classes of different species use different adjacent habitats of varying quality. We use long-term mist net data from the Amazon rainforest to assess patterns of habitat use among adult, adolescent (teenage) and young understory birds in forest fragments, primary and secondary forest at the Biological Dynamics of Forest Fragments Project in Brazil. Insectivore adults were most common in primary forest, adolescents were equally likely in primary and secondary forest, and all ages were the least common in forest fragments. In contrast to insectivores, frugivores and omnivores showed no differences among all three habitat types. Our results illustrate potential ideal despotic distributions among breeding populations of some guilds of understory birds where adult insectivores may competitively exclude adolescent individuals from primary forest. Secondary forest recovery appears to hold promise as a breeding habitat for frugivore and omnivore species but only as a pre-breeding habitat for insectivores, but as the forest ages, the demographic structure of bird populations should match that of primary forest.

Amazonian rivers are leaky barriers to gene flow in forest understory birds.

Ever since Alfred Russel Wallace's nineteenth-century observation that related terrestrial species are often separated on opposing riverbanks, major Amazonian rivers have been recognized as key drivers of speciation. However, rivers are dynamic entities whose widths and courses may vary through time. It thus remains unknown how effective rivers are at reducing gene flow and promoting speciation over long timescales. We fit demographic models to genomic sequences to reconstruct the history of gene flow in three pairs of avian taxa fully separated by different Amazonian rivers, and whose geographic ranges do not make contact in headwater regions where rivers may cease to be barriers. Models with gene flow were best fit but still supported an initial period without any gene flow, which ranged from 187 000 to over 959 000 years, suggesting that rivers are capable of initiating speciation through long stretches of allopatric divergence. Allopatry was followed by either bursts or prolonged episodes of gene flow that retarded genomic differentiation but did not fully homogenize populations. Our results support Amazonian rivers as key barriers that promoted speciation and the build-up of species richness, but they also suggest that river barriers are often leaky, with genomic divergence accumulating slowly owing to episodes of substantial gene flow.

Widespread cultural change in declining populations of Amazon parrots.

Species worldwide are experiencing anthropogenic environmental change, and the long-term impacts on animal cultural traditions such as vocal dialects are often unknown. Our prior studies of the yellow-naped amazon (Amazona auropalliata) revealed stable vocal dialects over an 11-year period (1994-2005), with modest shifts in geographic boundaries and acoustic structure of contact calls. Here, we examined whether yellow-naped amazons maintained stable dialects over the subsequent 11-year time span from 2005 to 2016, culminating in 22 years of study. Over this same period, this species suffered a dramatic decrease in population size that prompted two successive uplists in IUCN status, from vulnerable to critically endangered. In this most recent 11-year time span, we found evidence of geographic shifts in call types, manifesting in more bilingual sites and introgression across the formerly distinct North-South acoustic boundary. We also found greater evidence of acoustic drift, in the form of new emerging call types and greater acoustic variation overall. These results suggest cultural traditions such as dialects may change in response to demographic and environmental conditions, with broad implications for threatened species.

Quantifying past forest cover and biomass changes in the Ecuadorian Amazon.

Here, we developed and applied models to quantitatively reconstruct forest cover and biomass changes at three lakes in northwestern Amazonia over the past > 1500 yr. We used remotely sensed data and a modern dataset of 50 Amazonian lakes to develop generalized linear models that predict aboveground biomass, using phytolith morphotypes and forest cover as predictor variables. Also, we applied a published beta regression model to predict forest cover within 200 m of each lake, using Poaceae phytoliths. Charcoal and maize phytoliths were analysed to identify past land use. Results showed forest cover and biomass changes at our study sites ranged between 48-84% and 142-438 Mg ha-1, respectively. Human occupation was discontinuous, with major changes in forest cover and biomass coinciding with periods of land use. Forest cover and biomass decreased notably after fire (at all sites) or cultivation events (Lakes Zancudococha, Kumpaka). The timing and ecological impact of past land use were spatially and temporally variable. Our results suggest past human impact was small-scaled and heterogenous in northwestern Amazonia, with a significant impact of fire on forest cover and biomass changes.

Leaf thermal safety margins decline at hotter temperatures in a natural warming 'experiment' in the Amazon.

The threat of rising global temperatures may be especially pronounced for low-latitude, lowland plant species that have evolved under stable climatic conditions. However, little is known about how these species may acclimate to elevated temperatures. Here, we leveraged a strong, steep thermal gradient along a natural geothermal river to assess the ability of woody plants in the Amazon to acclimate to elevated air temperatures. We measured leaf traits in six common tropical woody species along the thermal gradient to investigate whether individuals of these species: acclimate their thermoregulatory traits to maintain stable leaf temperatures despite higher ambient temperatures; acclimate their photosynthetic thermal tolerances to withstand hotter leaf temperatures; and whether acclimation is sufficient to maintain stable leaf thermal safety margins (TSMs) across different growth temperatures. Individuals of three species acclimated their thermoregulatory traits, and three species increased their thermal tolerances with growth temperature. However, acclimation was generally insufficient to maintain constant TSMs. Notwithstanding, leaf health was generally consistent across growth temperatures. Acclimation in woody Amazonian plants is generally too weak to maintain TSMs at high growth temperatures, supporting previous findings that Amazonian plants will be increasingly vulnerable to thermal stress as temperatures rise.