Declining Amazon biomass due to deforestation and subsequent degradation losses exceeding gains

In the Amazon, deforestation and climate change lead to increased vulnerability to forest degradation, threatening its existing carbon stocks and its capacity as a carbon sink. We use satellite L-Band Vegetation Optical Depth (L-VOD) data that provide an integrated (top-down) estimate of biomass carbon to track changes over 2011–2019. Because the spatial resolution of L-VOD is coarse (0.25°), it allows limited attribution of the observed changes. We therefore combined high-resolution annual maps of forest cover and disturbances with biomass maps to model carbon losses (bottom-up) from deforestation and degradation, and gains from regrowing secondary forests. We show an increase of deforestation and associated degradation losses since 2012 which greatly outweigh secondary forest gains. Degradation accounted for 40% of gross losses. After an increase in 2011, old-growth forests show a net loss of above-ground carbon between 2012 and 2019. The sum of component carbon fluxes in our model is consistent with the total biomass change from L-VOD of 1.3 Pg C over 2012-2019. Across nine Amazon countries, we found that while Brazil contains the majority of biomass stocks (64%), its losses from disturbances were disproportionately high (79% of gross losses). Our multi-source analysis provides a pessimistic assessment of the Amazon carbon balance and highlights the urgent need to stop the recent rise of deforestation and degradation, particularly in the Brazilian Amazon.     

Regional species gains outpace losses across North American continental shelf regions

Aim

Although species richness globally is likely to be declining, patterns in diversity at the regional scale depend on species gains within new habitats and species losses from previously inhabited areas. Our understanding of the processes associated with gains or losses remains poor, including whether these events exhibit immediate or delayed responses to environmental change.

Location

The study focuses on nine temperate marine ecosystems in North America.

Time period

The study period varies by region, but overall encompasses observations from 1970 to 2014.

Major taxa studied

We identified regional gains and losses for 577 marine fish and invertebrate species.

Methods

From a total of 166,213 sampling events from bottom trawls across North America that informed 17,997 independent observations of species gains and losses, we built generalized linear mixed effects models to test whether lagged temperature can explain instances of gains and losses of marine fishes and invertebrates in North American continental shelf habitats.

Results

We found that gains were less likely in years with high seasonality, consistent with seasonal extremes as a strong constraint on species occurrence. Losses were also negatively associated with high seasonality, but the response was delayed by 3 years.

Main conclusions

Environmental conditions play a role in species occupancy across diverse temperate marine ecosystems. Immediate gains paired with delayed losses can drive transient increases in species richness during times of environmental change. Identifying the dynamics behind regional species gains and losses is an important step towards prediction of biodiversity changes across ecosystems.     

Surficial gains and subsoil losses of soil carbon and nitrogen during secondary forest development

Reforestation of formerly cultivated land is widely understood to accumulate above‐ and belowground detrital organic matter pools, including soil organic matter. However, during 40 years of study of reforestation in the subtropical southeastern USA, repeated observations of above‐ and belowground carbon documented that significant gains in soil organic matter (SOM) in surface soils (0–7.5 cm) were offset by significant SOM losses in subsoils (35–60 cm). Here, we extended the observation period in this long‐term experiment by an additional decade, and used soil fractionation and stable isotopes and radioisotopes to explore changes in soil organic carbon and soil nitrogen that accompanied nearly 50 years of loblolly pine secondary forest development. We observed that accumulations of mineral soil C and N from 0 to 7.5 cm were almost entirely due to accumulations of light‐fraction SOM. Meanwhile, losses of soil C and N from mineral soils at 35 to 60 cm were from SOM associated with silt and clay‐sized particles. Isotopic signatures showed relatively large accumulations of forest‐derived carbon in surface soils, and little to no accumulation of forest‐derived carbon in subsoils. We argue that the land use change from old field to secondary forest drove biogeochemical and hydrological changes throughout the soil profile that enhanced microbial activity and SOM decomposition in subsoils. However, when the pine stands aged and began to transition to mixed pines and hardwoods, demands on soil organic matter for nutrients to support aboveground growth eased due to pine mortality, and subsoil organic matter levels stabilized. This study emphasizes the importance of long‐term experiments and deep measurements when characterizing soil C and N responses to land use change and the remarkable paucity of such long‐term soil data deeper than 30 cm.     

Groundwater nitrogen dynamics at the terrestrial-lotic interface of a small catchment in the Central Amazon basin

Processes operating at the terrestrial-lotic interface may significantly alter dissolved nitrogen concentrations in groundwater as a result of shifting redox conditions and microbial communities. We monitored concentrations of total dissolved nitrogen, NO ₄ ^– , NH ₄ ^– , O₂ and Fe²⁺ for 10 months along two transects tracing groundwater flow from an upland (terra firme) forest, beneath the riparian forest, and into the stream channel of a small Central Amazonian catchment. Our aim was to examine the role of near-stream processes in regulating groundwater transfers of dissolved nitrogen from terrestrial to lotic ecosystems in the Central Amazon. We found pronounced compositional differences in inorganic nitrogen chemistry between upland, riparian, and stream hydrologic compartments. Nitrate dominated (average 89% of total inorganic nitrogen; TIN) the inorganic nitrogen chemistry of oxygenated upland groundwater but decreased markedly upon crossing the upland-riparian margin. Conversely, NH ₄ ^– dominated (average 93% of TIN) the inorganic chemistry of apparently anoxic riparian groundwater; NH ₄ ^– and TIN concentrations decreased markedly across the riparian-stream channel margin. In the oxygenated streamwater, NO ₃ ^– again dominated (average 82% of TIN) inorganic nitrogen chemistry. Denitrification followed by continued ammonification is hypothesized to effect the shift in speciation observed at the upland-riparian margin, while a combination of several processes may control the shift in speciation and loss of TIN observed at the riparian-stream margin. Dissolved organic nitrogen concentrations did not vary significantly between upland and riparian groundwater, but decreased across the riparian-stream margin. Our data suggest that extensive transformation reactions focused at the upland and stream margins of the riparian zone strongly regulate and diminish transfers of inorganic nitrogen from groundwater to streamwater in the catchment. This suggestion questions the veracity of attempts in the literature to link stream nitrogen chemistry with nutrient status in adjacent forests of similar catchments in the Central Amazon. It also complicates efforts to model nitrogen transfers across terrestrial-lotic interfaces in response to deforestation and changing climate.     

Biophysical stratification of the Amazon basin

In field measurement programmes, stratified sampling can optimize sampling efficiency, but stratification is often undertaken subjectively, and is frequently based on a priori classification schemes such as those used for vegetation maps. In order to avoid the problems associated with a priori subjective schemes, we explore here an objective procedure, Regression Tree Analysis (RTA). RTA has previously been used in local-scale studies, but here we apply it to a very large study domain, namely the entire humid tropical zone of South America. The aim of the study was to develop an optimal sampling design in preparation for the Large Scale Biosphere-Atmosphere Experiment in Amazonia (LBA). Co-registered spatially continuous fields of rainfall, temperature, photosynthetically active radiation (PAR), the normalized difference index (NDVI), an index of surface moisture, and other independent variables were used to predict three dependent variables, annual net radiation (Rn), latent heat (LE) and net primary production (NPP). Rather than simply dividing the study area based on differing levels of the three dependent variables, empirical models were developed using RTA to indicate how the relationships between these and possible forcing variables vary across the study area. For each variable long-term seasonal indices such as annual average, monthly minimum and amplitude were used to exclude effects of temporal phase differences between the hemispheres. The resulting hierarchical models revealed variations in the interdependence of the forcing variables throughout the study area and therefore provided a basis for a stratified sampling and identifying the most important variables to be collected in LBA for the Amazon basin as a whole as well as optimizing the sampling scheme for scaling up findings from the field scale to larger areas.     

Distribution of aboveground live biomass in the Amazon basin

The amount and spatial distribution of forest biomass in the Amazon basin is a major source of uncertainty in estimating the flux of carbon released from land‐cover and land‐use change. Direct measurements of aboveground live biomass (AGLB) are limited to small areas of forest inventory plots and site‐specific allometric equations that cannot be readily generalized for the entire basin. Furthermore, there is no spaceborne remote sensing instrument that can measure tropical forest biomass directly. To determine the spatial distribution of forest biomass of the Amazon basin, we report a method based on remote sensing metrics representing various forest structural parameters and environmental variables, and more than 500 plot measurements of forest biomass distributed over the basin. A decision tree approach was used to develop the spatial distribution of AGLB for seven distinct biomass classes of lowland old‐growth forests with more than 80% accuracy. AGLB for other vegetation types, such as the woody and herbaceous savanna and secondary forests, was directly estimated with a regression based on satellite data. Results show that AGLB is highest in Central Amazonia and in regions to the east and north, including the Guyanas. Biomass is generally above 300 Mg ha⁻¹ here except in areas of intense logging or open floodplains. In Western Amazonia, from the lowlands of Peru, Ecuador, and Colombia to the Andean mountains, biomass ranges from 150 to 300 Mg ha⁻¹. Most transitional and seasonal forests at the southern and northwestern edges of the basin have biomass ranging from 100 to 200 Mg ha⁻¹. The AGLB distribution has a significant correlation with the length of the dry season. We estimate that the total carbon in forest biomass of the Amazon basin, including the dead and belowground biomass, is 86 Pg C with ±20% uncertainty.     

Oncogenic mutations in B-Raf: some losses yield gains

A study by Wan et al. in this issue of Cell demonstrates that the majority of oncogenic mutations in the B-Raf protein kinase result in increased catalytic activity, through disruption of the autoinhibited state of the kinase domain. Surprisingly, several mutations lead to impaired B-Raf kinase activity, yet these mutants are nevertheless capable of stimulating downstream signaling through transactivation of C-Raf.     

Extensive gains and losses of olfactory receptor genes in mammalian evolution

Odor perception in mammals is mediated by a large multigene family of olfactory receptor (OR) genes. The number of OR genes varies extensively among different species of mammals, and most species have a substantial number of pseudogenes. To gain some insight into the evolutionary dynamics of mammalian OR genes, we identified the entire set of OR genes in platypuses, opossums, cows, dogs, rats, and macaques and studied the evolutionary change of the genes together with those of humans and mice. We found that platypuses and primates have <400 functional OR genes while the other species have 800-1,200 functional OR genes. We then estimated the numbers of gains and losses of OR genes for each branch of the phylogenetic tree of mammals. This analysis showed that (i) gene expansion occurred in the placental lineage each time after it diverged from monotremes and from marsupials and (ii) hundreds of gains and losses of OR genes have occurred in an order-specific manner, making the gene repertoires highly variable among different orders. It appears that the number of OR genes is determined primarily by the functional requirement for each species, but once the number reaches the required level, it fluctuates by random duplication and deletion of genes. This fluctuation seems to have been aided by the stochastic nature of OR gene expression.     

Group sizes and compositions of monkeys in the upper Amazon basin

Eleven species of New World monkeys inhabit the basin of the upper Amazon. Twice, for a total 16 months, the author studied the group sizes and compositions of these species in the basin of the Rivers Caquetá and Putumayo, particularly in the two study areas established in the basin of the River Peneya, a tributary of the River Caquetá. Data obtained by the author were compared with those on the same and close relative species living in other places. And the author could conclude that each species, showing a considerable range of variation in group size and composition, has a common specificity for the social structure of the unit group.     

A method for calling gains and losses in array CGH data

Array CGH is a powerful technique for genomic studies of cancer. It enables one to carry out genome-wide screening for regions of genetic alterations, such as chromosome gains and losses, or localized amplifications and deletions. In this paper, we propose a new algorithm 'Cluster along chromosomes' (CLAC) for the analysis of array CGH data. CLAC builds hierarchical clustering-style trees along each chromosome arm (or chromosome), and then selects the 'interesting' clusters by controlling the False Discovery Rate (FDR) at a certain level. In addition, it provides a consensus summary across a set of arrays, as well as an estimate of the corresponding FDR. We illustrate the method using an application of CLAC on a lung cancer microarray CGH data set as well as a BAC array CGH data set of aneuploid cell strains.     

Foods and feeding behavior of monkeys in the upper Amazon basin

Eleven species of the New World monkeys inhabit the basin of the River Caquetá in the upper Amazon. Twice for a total of 16 months the author studied the foods and feeding behaviors of 10 species of monkeys in the basin of the River Caquetá, particularly in the two study areas established in the basin of the River Peneya, a tributary of the River Caquetá. Sixty-seven adult monkeys of 10 species were collected, mainly in the basin of the River Peneya, for morphological study, so that the author had a chance to analyze their stomach contents. Some characteristics of the food habits of 10 species of the New World monkeys inhabiting the same area were made clear by means of direct observations in the wild and the analysis of the stomach contents.     

Mapping gains and losses in woody vegetation across global tropical drylands

Woody vegetation in global tropical drylands is of significant importance for both the interannual variability of the carbon cycle and local livelihoods. Satellite observations over the past decades provide a unique way to assess the vegetation long‐term dynamics across biomes worldwide. Yet, the actual changes in the woody vegetation are always hidden by interannual fluctuations of the leaf density, because the most widely used remote sensing data are primarily related to the photosynthetically active vegetation components. Here, we quantify the temporal trends of the nonphotosynthetic woody components (i.e., stems and branches) in global tropical drylands during 2000–2012 using the vegetation optical depth (VOD), retrieved from passive microwave observations. This is achieved by a novel method focusing on the dry season period to minimize the influence of herbaceous vegetation and using MODerate resolution Imaging Spectroradiometer (MODIS) Normalized Difference Vegetation Index (NDVI) data to remove the interannual fluctuations of the woody leaf component. We revealed significant trends (P < 0.05) in the woody component (VOD_wood) in 35% of the areas characterized by a nonsignificant trend in the leaf component (VOD_leaf modeled from NDVI), indicating pronounced gradual growth/decline in woody vegetation not captured by traditional assessments. The method is validated using a unique record of ground measurements from the semiarid Sahel and shows a strong agreement between changes in VOD_wood and changes in ground observed woody cover (r² = 0.78). Reliability of the obtained woody component trends is also supported by a review of relevant literatures for eight hot spot regions of change. The proposed approach is expected to contribute to an improved assessment of, for example, changes in dryland carbon pools.     

A neurochemical approach to valuation sensitivity over gains and losses

Prospect theory proposes the hypothesis that people have diminishing sensitivity in valuing increases in the size of monetary outcomes, for both gains and losses. For decision-making under risk, this implies a tendency to be risk-tolerant over losses while being generally risk averse over gains. We offer a neurochemistry-based model of the diminishing valuation sensitivity hypothesis. Specifically, we propose that dopamine tone modulates the sensitivity towards valuation of gains while serotonin tone modulates the sensitivity towards valuation of losses. Consequently, higher dopamine tone would yield a more concave valuation function over gains while higher serotonin tone would yield a more convex valuation function over losses. Using a neurogenetics strategy to test our neurochemical model, we find that subjects with the 9-repeat allele of DAT1 (lower DA tone) are more risk-tolerant over gains than subjects with the 10-repeat allele, and that subjects with the 10-repeat allele of STin2 (higher 5HT tone) are more risk-tolerant over losses than subjects with the 12-repeat allele. Overall, our results support the implications of our model and provide the first neurogenetics evidence that risk attitudes are partially hard-wired in differentiating between gain- and loss-oriented risks.     

Isolation of fungi from bats of the Amazon basin

A total of 2,886 bats captured in the Amazon Basin of Brazil were processed for the isolation of fungi. From the livers, spleens, and lungs of 155 bats (5.4%), 186 fungal isolates of the genera Candida (123 isolates), Trichosporon (26 isolates), Torulopsis (25 isolates), Kluyveromyces (11 isolates), and Geotrichum (1 isolate) were recovered. Seven known pathogenic species were present: Candida parapsilosis, C. guilliermondii, C. albicans, C. stellatoidea, C. pseudotropicalis, Trichosporon beigelii, and Torulopsis glabrata. Twenty-three culture-positive bats showed identical fungal colonization in multiple organs or mixed colonization in a single organ. The fungal isolation rates for individual bat species varied from 1 fungus per 87 bats to 3 fungi per 13 bats, and the mycoflora diversity for members of an individual fungus-bearing bat species varied from 16 fungi per 40 bats to 7 fungi per 6 bats. Of the 38 fungal species isolated, 36 had not been previously described as in vivo bat isolates. Of the 27 culture-positive bat species, 21 had not been previously described as mammalian hosts for medically or nonmedically important fungi.     

Plankton and primary production in aquatic systems of the Central Amazon basin

• 1. Three aquatic environments of the Central Amazon Basin were sampled during the low water phase: Rio Solimo˜es (Amazon), Rio Negro and Lago Junauaca´.
• 2. In the nutrient-rich Rio Solimo˜es, primary productivity averaged 0.063 g C/m² per day, but net growth of phytoplankton is impossible because of the depth, poor light penetration and current-driven turbulence.
• 3. In the chemically-poor Rio Negro, a daily cycle of ΣCO₂ was caused by photosynthetic demand in surface waters, and primary productivity averaged 0.19 g C/m² per day.
• 4. In Lago Janauaca´. a lake bordering the Solimo˜es, nutrients were low in concentration and intensively recycled; large phytoplankton populations produced up to 3.5 g C/m² per day (average = 2.2).
• 5. The 10 m annual change in water level of the Amazon River provides and drains most of the water in lakes along the river. During storage of river water in the lakes the particulates settle and the dissolved inorganic nutrients are converted to organic forms by intense phytoplankton growth. These lakes may be a major source of organic matter for the river ecosystem.