How are rainforest photosynthesis and turbulent fluxes influenced by clouds? To what extent are clouds affected by local processes driven by rainforest energy, water and carbon fluxes? These interrelated questions were the main drivers of the intensive field experiment CloudRoots-Amazon22 which took place at the ATTO/Campina supersites in the Amazon rainforest during the dry season, in August 2022. CloudRoots-Amazon22 collected observational data to derive causal-effect relationships between processes occurring at the leaf-level up to canopy scales in relation to the diurnal evolution of the clear-to-cloudy transition. First, we studied the impact of cloud and canopy radiation perturbations on the sub-diurnal variability of stomatal aperture. We found an asymmetry modulated by clouds that favors photosynthesis in the morning. Second, we combined 1 Hz-frequency measurements of the stable isotopologues of carbon dioxide and water vapor with measurements of turbulence to determine carbon dioxide and water vapor sources and sinks within the canopy. Using scintillometer observations, we inferred 1-minute sensible heat flux that responded within minutes to the cloud passages. Third, collocated profiles of state variables and greenhouse gases enabled us to determine the role of clouds in vertical transport. We then inferred the area fraction of cloud cover and cloud mass flux to probe the need of collecting a comprehensive data set to establish casualty between canopy and cloud processes and improve the representations in weather and climate models. Our findings contribute to advance our process knowledge of the coupling between cloudy boundary layers and primary carbon productivity of the Amazon rainforest.

Soil maps are crucial for habitat and species distribution modeling under present and future conditions, thereby providing relevant background information for conservation planning. In Amazonia, soil conditions are highly heterogeneous, which has important implications for the distribution and dynamics of the area's exceptional biodiversity. Unfortunately, available soil maps for this region suffer from inaccuracies and lack of ecologically relevant variables. Here, we develop a map of the sum of exchangeable base cation concentration (SB) in the surface soil by applying machine learning to a comprehensive set of over 10,000 field data points of SB values directly measured from soil samples or inferred using indicator plant species occurrences. As predictors, we used rasters of soil type probabilities, elevation, biomass and reflectance values from Landsat satellite images. Random Forest (RF) models were trained and tested using two different cross-validation strategies. We also assessed in which areas the map was more reliable using the area of applicability approach and compared the results with two other soil layers. The best predictors of SB variation were Landsat bands 7, 4 and 3, elevation, and proba-bility of Histosols. The regional patterns observed across Amazonia were consistent with current geological understanding; lower SB values tended to occur in central Amazonian soils and higher values in western Amazonian soils, with considerable variation within each region. The model was found applicable over most of the Amazonian biome, especially in non-inundated (terra-firme) forest, but not over coastal areas, floodplains of major rivers and wetlands, which were poorly represented in the training data. Our new SB map over performed previous SB map and represent an accurate and ecologically meaningful variable. It is available as a digital GIS layer and can be used in habitat mapping and in modeling the current or future distributions of biological communities and species. This will advance general understanding of Amazonian biogeography and help in conservation planning.

Tropical rivers such as the Rio Negro constitute a major portion of the global aquatic flux of dissolved organic carbon (DOC) entering the ocean, but the exact amount, source contributions and fate of terrestrial DOC remain unknown. We investigated the role of valley and upland whitesand ecosystems (WSEs) and terra firme plateaus in forming blackwater tributaries in the Rio Negro basin to develop novel constraints for the terrestrial export of carbon. 5709 molecular markers from ground- and surface waters of two contrasting valley and upland sites feeding Rio Negro tributaries were identified by ultrahigh resolution mass spectrometry (FT-MS), analyzed by multivariate statistics and compared to known Rio Negro markers. In a Principal Coordinates Analysis, valley and upland DOC molecular composition differed by 78% from plateau DOC, which was characterized by reworked, aliphatic and unsaturated N- and S-containing molecules, while valley and upland DOC contained mainly condensed aromatics, aromatics and oxidized unsaturated structures. Valley and upland samples differed by 10% in molecular DOC composition and by their isotopic content (14C of SPE-DOC, 18O and 2H of water) which indicated differences in hydrology and C turnover. Against expectation, markers of widespread whitesand valleys did not emerge as a major source of Rio Negro markers, but specific upland markers did. Pubchem suggested chromene and benzofuran structures as promising candidates for further study. Our findings indicate that the export of molecular markers diverges from expected transport-limited DOC behavior, and thereby opens new avenues for source annotation beyond DOC quantity. Terrestrial DOC from upland whitesand areas is a major source of specific blackwater molecules missing in the regional ecosystem C balance, whereas C export from the whitesand valleys and especially from terra firme plateaus represents mainly recycled and transformed carbon not directly affecting the ecosystem C balance and possibly, the watersheds downstream molecular signature. Our study highlights the potential of high-resolution techniques to constrain carbon balances of ecosystems and landscapes by novel molecular markers. A comparison with other terrestrial DOM datasets indicated molecular similarities with temperate acidic soils and tropical rivers that warrant further analysis of common DOM markers. Implications, limitations, and future challenges are discussed in the light of potential applications of diagnostic molecular links for DOC source annotation and estimation of terrestrial DOM export in the land-to-ocean continuum.

Response: We have made efforts to make the text more direct (especially in terms of breaking up and shortening sentences in the Results Section) and have also attended the specific points raised by both reviewers. However, we do not agree with the view that short papers are necessarily the best or only way to communicate results. In our view, a detailed and comprehensive analysis, when well supported by data, becomes a definitive reference and thus reaches out to broad audiences. Short papers can be good, but not necessarily are, the opposite also sometimes being the case. As noticed by Reviewer 1, our personal style is somewhat ‘expansive’, which so far has led us to stablish a successful publishing record. For instance, previous work published on soils of the Amazon by the lead author in Biogeosciences (Quesada et al. 2010, 2011, 2012) has had an even greater number of final pages published, but this did not stop these papers to receive over 300 citations each. We feel that the points raised by the reviewers have indeed helped to make the paper clearer and we have made changes to break up longer sentences and phrases into smaller units , but hope that there is no need for further shortening of the manuscript just for the sake of it.

The Amazon rainforest is the world's largest source of reactive volatile isoprenoids to the atmosphere. It is generally assumed that these emissions are products of photosynthetically driven secondary metabolism and released from the rainforest canopy from where they influence the oxidative capacity of the atmosphere. However, recent measurements indicate that further sources of volatiles are present. Here we show that soil microorganisms are a strong, unaccounted source of highly reactive and previously unreported sesquiterpenes (C15H24; SQT). The emission rate and chemical speciation of soil SQTs were determined as a function of soil moisture, oxygen, and rRNA transcript abundance in the laboratory. Based on these results, a model was developed to predict soil-atmosphere SQT fluxes. It was found SQT emissions from a Terra Firme soil in the dry season were in comparable magnitude to current global model canopy emissions, establishing an important ecological connection between soil microbes and atmospherically relevant SQTs.

Amazon Basin forest soils contain considerable soil organic carbon stocks; however, the contribution of soil pyrogenic carbon (PyC) to the total is unknown. PyC is derived from local fires (historical and modern) and external inputs via aeolian deposition. To establish an initial estimate of PyC stocks in non-terra preta forest with no known history of fire, to assess site and vertical variability, as well as to determine optimal sampling design, we sampled 37 one hectare forest plots in the Amazon Basin and analysed PyC via hydrogen pyrolysis of three individual samples per plot and of bulked samples to 200cm depth. Using our data and published total organic carbon stocks, we present the first field-based estimate of total PyC stock for the Amazon Basin of 1.10 Pg over 0–30cm soil depth, and 2.76 Pg over 0–100cm soil depth. This is up to 20 times higher than previously assumed. Three individual samples per 1ha are sufficient to capture the site variability of PyC in our plots. PyC showed significant, large-scale variability among plots. To capture 50% of the PyC in 200cm soil profiles, soil must be sampled to a depth of at least 71cm. PyC represents a significant (11%) portion of total organic carbon in soil profiles 0–200cm depth. This finding highlights the potentially important role that historical fire has played in modifying soil C stocks. Our data suggest that PyC is an important carbon pool for long-term storage, involved in millennial scale biogeochemical cycling, particularly in the subsurface soil.

The Amazon Basin has experienced more variable climate over the last decade, with a severe and widespread drought in 2005 causing large basin‐wide losses of biomass. A drought of similar climatological magnitude occurred again in 2010; however, there has been no basin‐wide ground‐based evaluation of effects on vegetation. We examine to what extent the 2010 drought affected forest dynamics using ground‐based observations of mortality and growth from an extensive forest plot network. We find that during the 2010 drought interval, forests did not gain biomass (net change: −0.43 Mg ha−1, confidence interval (CI): −1.11, 0.19, n = 97), regardless of whether forests experienced precipitation deficit anomalies. This contrasted with a long‐term biomass sink during the baseline pre‐2010 drought period (1998 to pre‐2010) of 1.33 Mg ha−1 yr−1 (CI: 0.90, 1.74, p < 0.01). The resulting net impact of the 2010 drought (i.e., reversal of the baseline net sink) was −1.95 Mg ha−1 yr−1 (CI:−2.77, −1.18; p < 0.001). This net biomass impact was driven by an increase in biomass mortality (1.45 Mg ha−1 yr−1 CI: 0.66, 2.25, p < 0.001) and a decline in biomass productivity (−0.50 Mg ha−1 yr−1, CI:−0.78, −0.31; p < 0.001). Surprisingly, the magnitude of the losses through tree mortality was unrelated to estimated local precipitation anomalies and was independent of estimated local pre‐2010 drought history. Thus, there was no evidence that pre‐2010 droughts compounded the effects of the 2010 drought. We detected a systematic basin‐wide impact of the 2010 drought on tree growth rates across Amazonia, which was related to the strength of the moisture deficit. This impact differed from the drought event in 2005 which did not affect productivity. Based on these ground data, live biomass in trees and corresponding estimates of live biomass in lianas and roots, we estimate that intact forests in Amazonia were carbon neutral in 2010 (−0.07 Pg C yr−1 CI:−0.42, 0.23), consistent with results from an independent analysis of airborne estimates of land‐atmospheric fluxes during 2010. Relative to the long‐term mean, the 2010 drought resulted in a reduction in biomass carbon uptake of 1.1 Pg C, compared to 1.6 Pg C for the 2005 event.

In this study, we assess the geomorphic role of a rare, large-magnitude landslide-triggering event and consider its effect on mountain forest ecosystems and the erosion of organic carbon in an Andean river catchment. Proximal triggers such as large rain storms are known to cause large numbers of landslides, but the relative effects of such low-frequency, high-magnitude events are not well known in the context of more regular, smaller events. We develop a 25-year duration, annual-resolution landslide inventory by mapping landslide occurrence in the Kosñipata Valley, Peru, from 1988 to 2012 using Landsat, QuickBird, and WorldView satellite images. Catchment-wide landslide rates were high, averaging 0.076 % yr−1 by area. As a result, landslides on average completely turn over hillslopes every ∼ 1320 years, although our data suggest that landslide occurrence varies spatially and temporally, such that turnover times are likely to be non-uniform. In total, landslides stripped 26 ± 4 tC km−2 yr−1 of organic carbon from soil (80 %) and vegetation (20 %) during the study period. A single rain storm in March 2010 accounted for 27 % of all landslide area observed during the 25-year study and accounted for 26 % of the landslide-associated organic carbon flux. An approximately linear magnitude–frequency relationship for annual landslide areas suggests that large storms contribute an equivalent landslide failure area to the sum of lower-frequency landslide events occurring over the same period. However, the spatial distribution of landslides associated with the 2010 storm is distinct. On the basis of precipitation statistics and landscape morphology, we hypothesise that focusing of storm-triggered landslide erosion at lower elevations in the Kosñipata catchment may be characteristic of longer-term patterns. These patterns may have implications for the source and composition of sediments and organic material supplied to river systems of the Amazon Basin, and, through focusing of regular ecological disturbance, for the species composition of forested ecosystems in the region.

Variations in the carbon isotopic composition of soil organic matter (SOM) in bulk and fractionated samples were used to assess the influence of C3 and C4 vegetation on SOM dynamics in semi-natural tropical ecosystems sampled along a precipitation gradient in West Africa. Differential patterns in SOM dynamics in C3/C4 mixed ecosystems occurred at various spatial scales. Relative changes in C / N ratios between two contrasting SOM fractions were used to evaluate potential site-scale differences in SOM dynamics between C3- and C4-dominated locations. These differences were strongly controlled by soil texture across the precipitation gradient, with a function driven by bulk δ13C and sand content explaining 0.63 of the observed variability. The variation of δ13C with soil depth indicated a greater accumulation of C3-derived carbon with increasing precipitation, with this trend also being strongly dependant on soil characteristics. The influence of vegetation thickening on SOM dynamics was also assessed in two adjacent, but structurally contrasting, transitional ecosystems occurring on comparable soils to minimise the confounding effects posed by climatic and edaphic factors. Radiocarbon analyses of sand-size aggregates yielded relatively short mean residence times (τ) even in deep soil layers, while the most stable SOM fraction associated with silt and clay exhibited shorter τ in the savanna woodland than in the neighbouring forest stand. These results, together with the vertical variation observed in δ13C values, strongly suggest that both ecosystems are undergoing a rapid transition towards denser closed canopy formations. However, vegetation thickening varied in intensity at each site and exerted contrasting effects on SOM dynamics. This study shows that the interdependence between biotic and abiotic factors ultimately determine whether SOM dynamics of C3- and C4-derived vegetation are at variance in ecosystems where both vegetation types coexist. The results highlight the far-reaching implications that vegetation thickening may have for the stability of deep SOM.

Sampling along a precipitation gradient in tropical South America extending from ca. 0.8 to 2.0 m a−1, savanna soils had consistently lower exchangeable cation concentrations and higher C / N ratios than nearby forest plots. These soil differences were also reflected in canopy averaged leaf traits with savanna trees typically having higher leaf mass per unit area but lower mass-based nitrogen (Nm) and potassium (Km). Both Nm and Km also increased with declining mean annual precipitation (PA), but most area-based leaf traits such as leaf photosynthetic capacity showed no systematic variation with PA or vegetation type. Despite this invariance, when taken in conjunction with other measures such as mean canopy height, area-based soil exchangeable potassium content, [K]sa , proved to be an excellent predictor of several photosynthetic properties (including 13C isotope discrimination). Moreover, when considered in a multivariate context with PA and soil plant available water storage capacity (θP) as covariates, [K]sa also proved to be an excellent predictor of stand-level canopy area, providing drastically improved fits as compared to models considering just PA and/or θP. Neither calcium, nor magnesium, nor soil pH could substitute for potassium when tested as alternative model predictors (ΔAIC > 10). Nor for any model could simple soil texture metrics such as sand or clay content substitute for either [K]sa or θP. Taken in conjunction with recent work in Africa and the forests of the Amazon Basin, this suggests – in combination with some newly conceptualised interacting effects of PA and θP also presented here – a critical role for potassium as a modulator of tropical vegetation structure and function.

Atmospheric carbon dioxide records indicate that the land surface has acted as a strong global carbon sink over recent decades, with a substantial fraction of this sink probably located in the tropics, particularly in the Amazon. Nevertheless, it is unclear how the terrestrial carbon sink will evolve as climate and atmospheric composition continue to change. Here we analyse the historical evolution of the biomass dynamics of the Amazon rainforest over three decades using a distributed network of 321 plots. While this analysis confirms that Amazon forests have acted as a long-term net biomass sink, we find a long-term decreasing trend of carbon accumulation. Rates of net increase in above-ground biomass declined by one-third during the past decade compared to the 1990s. This is a consequence of growth rate increases levelling off recently, while biomass mortality persistently increased throughout, leading to a shortening of carbon residence times. Potential drivers for the mortality increase include greater climate variability, and feedbacks of faster growth on mortality, resulting in shortened tree longevity. The observed decline of the Amazon sink diverges markedly from the recent increase in terrestrial carbon uptake at the global scale, and is contrary to expectations based on models.

Through interpretations of remote-sensing data and/or theoretical propositions, the idea that forest and savanna represent "alternative stable states" is gaining increasing acceptance. Filling an observational gap, we present detailed stratified floristic and structural analyses for forest and savanna stands located mostly within zones of transition (where both vegetation types occur in close proximity) in Africa, South America and Australia. Woody plant leaf area index variation was related to tree canopy cover in a similar way for both savanna and forest with substantial overlap between the two vegetation types. As total woody plant canopy cover increased, so did the relative contribution of middle and lower strata of woody vegetation. Herbaceous layer cover declined as woody cover increased. This pattern of understorey grasses and herbs progressively replaced by shrubs as the canopy closes over was found for both savanna and forests and on all continents. Thus, once subordinate woody canopy layers are taken into account, a less marked transition in woody plant cover across the savanna–forest-species discontinuum is observed compared to that inferred when trees of a basal diameter > 0.1 m are considered in isolation. This is especially the case for shrub-dominated savannas and in taller savannas approaching canopy closure. An increased contribution of forest species to the total subordinate cover is also observed as savanna stand canopy closure occurs. Despite similarities in canopy-cover characteristics, woody vegetation in Africa and Australia attained greater heights and stored a greater amount of above-ground biomass than in South America. Up to three times as much above-ground biomass is stored in forests compared to savannas under equivalent climatic conditions. Savanna–forest transition zones were also found to typically occur at higher precipitation regimes for South America than for Africa. Nevertheless, consistent across all three continents coexistence was found to be confined to a well-defined edaphic–climate envelope with soil and climate the key determinants of the relative location of forest and savanna stands. Moreover, when considered in conjunction with the appropriate water availability metrics, it emerges that soil exchangeable cations exert considerable control on woody canopy-cover extent as measured in our pan-continental (forest + savanna) data set. Taken together these observations do not lend support to the notion of alternate stable states mediated through fire feedbacks as the prime force shaping the distribution of the two dominant vegetation types of the tropical lands.

Repeated long-term censuses have revealed large-scale spatial patterns in Amazon basin forest structure and dynamism, with some forests in the west of the basin having up to a twice as high rate of aboveground biomass production and tree recruitment as forests in the east. Possible causes for this variation could be the climatic and edaphic gradients across the basin and/or the spatial distribution of tree species composition. To help understand causes of this variation a new individual-based model of tropical forest growth, designed to take full advantage of the forest census data available from the Amazonian Forest Inventory Network (RAINFOR), has been developed. The model allows for within-stand variations in tree size distribution and key functional traits and between-stand differences in climate and soil physical and chemical properties. It runs at the stand level with four functional traits – leaf dry mass per area (Ma), leaf nitrogen (NL) and phosphorus (PL) content and wood density (DW) varying from tree to tree – in a way that replicates the observed continua found within each stand. We first applied the model to validate canopy-level water fluxes at three eddy covariance flux measurement sites. For all three sites the canopy-level water fluxes were adequately simulated. We then applied the model at seven plots, where intensive measurements of carbon allocation are available. Tree-by-tree multi-annual growth rates generally agreed well with observations for small trees, but with deviations identified for larger trees. At the stand level, simulations at 40 plots were used to explore the influence of climate and soil nutrient availability on the gross (ΠG) and net (ΠN) primary production rates as well as the carbon use efficiency (CU). Simulated ΠG, ΠN and CU were not associated with temperature. On the other hand, all three measures of stand level productivity were positively related to both mean annual precipitation and soil nutrient status. Sensitivity studies showed a clear importance of an accurate parameterisation of within- and between-stand trait variability on the fidelity of model predictions. For example, when functional tree diversity was not included in the model (i.e. with just a single plant functional type with mean basin-wide trait values) the predictive ability of the model was reduced. This was also the case when basin-wide (as opposed to site-specific) trait distributions were applied within each stand. We conclude that models of tropical forest carbon, energy and water cycling should strive to accurately represent observed variations in functionally important traits across the range of relevant scales.

Modern land surface model simulations capture soil profile water movement through the use of soil hydraulics sub-models, but good hydraulic parameterisations are often lacking, especially in the tropics. We present much-improved gridded data sets of hydraulic parameters for surface soil for the critical area of tropical South America, describing soil profile water movement across the region to 30 cm depth. Optimal hydraulic parameter values are given for the Brooks and Corey, Campbell, van Genuchten–Mualem and van Genuchten–Burdine soil hydraulic models, which are widely used hydraulic sub-models in land surface models. This has been possible through interpolating soil measurements from several sources through the SOTERLAC soil and terrain data base and using the most recent pedotransfer functions (PTFs) derived for South American soils. All soil parameter data layers are provided at 15 arcsec resolution and available for download, this being 20x higher resolution than the best comparable parameter maps available to date. Specific examples are given of the use of PTFs and the importance highlighted of using PTFs that have been locally parameterised and that are not just based on soil texture. We discuss current developments in soil hydraulic modelling and how high-resolution parameter maps such as these can improve the simulation of vegetation development and productivity in land surface models.