Intraspecific alternative phenotypes contribute to variation in species' strategies for growth

Ecologists have historically sought to identify the mechanisms underlying the maintenance of local species diversity. High-dimensional trait-based relationships, such as alternative phenotypes, have been hypothesized as important for maintaining species diversity such that phenotypically dissimilar individuals compete less for resources but have similar performance in a given environment. The presence of alternative phenotypes has primarily been investigated at the community level, despite the importance of intraspecific variation to diversity maintenance. The aims of this research are to (1) determine the presence or absence of intraspecific alternative phenotypes in three species of tropical tree seedlings, (2) investigate if these different species use the same alternative phenotypes for growth success, and (3) evaluate how findings align with species co-occurrence patterns. We model species-specific relative growth rate with individual-level measurements of leaf mass per area (LMA) and root mass fraction (RMF), environmental data, and their interactions. We find that two of the three species have intraspecific alternative phenotypes, with individuals within species having different functional forms leading to similar growth. Interestingly, individuals within these species use the same trait combinations, high LMA × low RMF and low LMA × high RMF, in high soil nutrient environments to acquire resources for higher growth. This similarity among species in intraspecific alternative phenotypes and variables that contribute most to growth may lead to their negative spatial co-occurrence. Overall, we find that multiple traits or interactions between traits and the environment drive species-specific strategies for growth, but that individuals within species leverage this multi-dimensionality in different ways for growth success.

Soil microbial community response to ectomycorrhizal dominance in diverse neotropical montane forests

Ectomycorrhizal (EM) associations can promote the dominance of tree species in otherwise diverse tropical forests. These EM associations between trees and their fungal mutualists have important consequences for soil organic matter cycling, yet the influence of these EM-associated effects on surrounding microbial communities is not well known, particularly in neotropical forests. We examined fungal and prokaryotic community composition in surface soil samples from mixed arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) stands as well as stands dominated by EM-associated Oreomunnea mexicana (Juglandaceae) in four watersheds differing in soil fertility in the Fortuna Forest Reserve, Panama. We hypothesized that EM-dominated stands would support distinct microbial community assemblages relative to the mixed AM-EM stands due to differences in carbon and nitrogen cycling associated with the dominance of EM trees. We expected that this microbiome selection in EM-dominated stands would lead to lower overall microbial community diversity and turnover, with tighter correspondence between general fungal and prokaryotic communities. We measured fungal and prokaryotic community composition via high-throughput Illumina sequencing of the ITS2 (fungi) and 16S rRNA (prokaryotic) gene regions. We analyzed differences in alpha and beta diversity between forest stands associated with different mycorrhizal types, as well as the relative abundance of fungal functional groups and various microbial taxa. We found that fungal and prokaryotic community composition differed based on stand mycorrhizal type. There was lower prokaryotic diversity and lower relative abundance of fungal saprotrophs and pathogens in EM-dominated than AM-EM mixed stands. However, contrary to our prediction, there was lower homogeneity for fungal communities in EM-dominated stands compared to mixed AM-EM stands. Overall, we demonstrate that EM-dominated tropical forest stands have distinct soil microbiomes relative to surrounding diverse forests, suggesting that EM fungi may filter microbial functional groups in ways that could potentially influence plant performance or ecosystem function.

Biochar effects on NTFP-enriched secondary forest growth and soil properties in Amazonian Ecuador

Deforestation in the Amazon has resulted in large areas of depleted soils on abandoned pastures and agricultural sites that present a restoration challenge central to protecting biodiversity and ecosystem function in the region. Biochar - charcoal made from waste materials - can improve soil physical, chemical, and biological properties, but the few tropical field trials to date do not give consistent results regarding tree growth. This study presents three years of soil performance and tree growth of a secondary forest shading nontimber forest product (NTFP) plantations of Ocotea quixos (Lauraceae), Myroxylon balsamum (Fabaceae), and their mixture. Open kiln and traditional mound biochars were added at 10 t ha-1 at two sites with contrasting soil types. Biochar additions resulted in pronounced effects on soil properties that varied over time and with depth in the soil profile. Biochar additions generally increased soil organic matter, electrical conductivity, and plant nutrients (in particular K, Ca, and N), but there were interactive effects of NTFP treatments, and stronger responses on the poorer soil type. Biochar amendments resulted in increased tree growth, with a 29 ± 12% increase in aboveground biomass (AGB) on plots amended with kiln biochar and a 23 ± 9% increase in plots with mound biochar compared to controls. Tree species also varied in growth responses to biochar additions, with the largest increases observed in Jaccaranda copaia and Piptocoma discolor. Significant interactions between biochar and NTFP treatments were also seen for tree growth responses, such as Cecropia spp., which only showed increased biomass on mound biochar plots planted with Ocotea quixos. Overall, our results demonstrate a stronger effect of biochar in less favorable soil conditions, and an overriding effect of the legume NTFP in richer soils, and suggest that additions of biochar and legumes are important options to increase productivity and ecological resilience in tropical forest restoration.

Ecosystem carbon storage considering combined environmental and land-use changes in the future and pathways to carbon neutrality in developed regions

Assessing the carbon storage capacity of terrestrial ecosystems is crucial for land management and carbon reduction policymaking. There is still a knowledge gap regarding how ecosystem carbon storage will be impacted by combined environmental and land-use factors and their spatial-temporal changes, especially in developed regions where urbanization has slowed down. This study investigated how developed regions in subtropical and tropical areas might increase carbon storage and achieve carbon neutrality, using Guangdong Province in South China as an example. Based on the sustainable development assumption, three land-management scenarios were developed and simulated for 2020-2060 using the Patch-generating Land Use Simulation model. Without considering disturbance and natural losses, carbon storage was estimated by net ecosystem productivity (NEP)-the difference between net primary productivity (NPP) and heterotrophic respiration (HR). NPP was predicted using an artificial neural network model trained by historical NPP data and 16 environmental and land-use variables. HR was predicted using soil respiration models from previous research. Based on the balance between carbon storage and emissions, we predicted the allowable fossil fuel consumption to achieve net-zero CO2 emissions in 2060. The results show that Guangdong's total carbon storage changes from 73.7 MtC in 2020 to 70.6-74.8 MtC in 2060 under different scenarios. Nonlinear relationships exist between the carbon stored and the areas of different land-use types. Topography, temperatures, and land-use configurations jointly lead to significantly varied carbon storage between croplands and between forests in space and time. Protecting and regenerating forests in subtropical areas and forest edges is more effective than afforestation in lowland tropical areas for storing carbon. Net-zero CO2 emissions rely more on reducing emissions than land management. To achieve this, the proportion of fossil energy in total energy consumption should be lowered from 75.5 % in 2020 to ~25 % in 2060.

Biting rhythms and infection rates of anthropophilic sand fly species (Diptera: Phlebotominae) in sites with different land use in southern Mexico

Could tropical forest conversion shape sand fly (Diptera: Phlebotominae) biting rhythms and Leishmania infection rates? Using a Shannon trap, we estimated the bite rate and infection prevalence among anthropophilic sand flies at sites with different land use in southern Mexico. We estimated the expected monthly infection rate of the Leishmania parasite along the gradient and generated information on the biting rhythm of sand flies in a poorly characterized cutaneous leishmaniasis endemic region. We used generalized mixed linear and mixed additives models to evaluate differences in the biting rate, nocturnal activity, and inoculation rate of female sand flies, as well as their relationship with the loss of forest cover and environmental disparities recorded throughout the study area. Our results show that the loss of forest cover influences the biting rhythm of sand fly species and the potential number of infectious bites with Leishmania, but the greatest entomological and potential epidemiological risk continues to be associated with sylvatic areas (amplification events). Despite this, we detected that the effect of forest cover (%) on the entomological exposure seems to be also dependent on the sand fly species, and that, albeit to a lesser extent, Leishmania parasite is circulating in disturbed landscapes through generalist and competent sand fly vector species. We also found that land use change did not affect the nocturnal activity, however we detected that important vector species were active most of the time. Contrary to our expectation, temperature and humidity did not shape the biting rhythm of sand fly species. We discuss the limitations and epidemiological implications of our findings regarding the risk of contracting leishmaniasis in southern Mexico.

Co-occurring tree species drive arbuscular mycorrhizal fungi diversity in tropical forest

It is still uncertain whether environment or host plant species is more important in determining AMF diversity; although, plant roots are usually associated with abundant AMF species in different environments. This study explored the effect of plant species and environmental factors on AMF diversity based on three co-occurring tree species (Glochidion coccineum, Schefflera octophylla, and Schima superba) on six elevations of Mt. Jianfengling. A total of 185 OTUs (operational taxonomic units) of AMF were found in the three co-occurring dominant tree species. Of which 109 unique OTUs were identified in the three co-occurring plant species, which accounted for the total number of 58.92%. Forty-five OTUs were shared by the three co-occurring tree species, accounting for a total number of 24.32%. The plant species of Schefflera octophylla was identified as having the highest AMF diversity with the largest number of OTUs of 143. The fungi in the genus of Glomus were the dominant AMF species in the three co-occurring tree species. AMF communities and diversity are quite different, either within different plant species at the same elevation or within the same plant species at different elevations. However, the altitude had no significant effect on the ACE index. Therefore, the results suggest that plant species have a more important effect on AMF diversity and community composition.

Depth-driven responses of microbial residual carbon to nitrogen addition approaches in a tropical forest: Canopy addition versus understory addition

Canopies play an important role in nitrogen (N) redistribution in forest ecosystems, and ignoring the canopy's role might bias estimates of the ecological consequences of anthropogenic atmospheric N deposition. We investigated the effects of the approach of N addition (Canopy addition vs. Understory addition) and level of N addition (25 kg N ha^-1yr^-1 vs. 50 kg N ha^-1yr^-1) on microbial residual carbon (MRC) accumulation in topsoil and subsoil. We found that the response of MRC to both approach and level of N addition varied greatly with soil depth in a tropical forest over eight years of continuous N addition. Specifically, N addition enhanced the accumulation of fungal and total MRC and their contribution to soil organic C (SOC) pools in the topsoil, whereas it decreased the contribution of fungal and total MRC to SOC in the subsoil. The contrasting effects of N addition on MRC contribution at varying soil depths were associated with the distinct response of microbial residues production. Understory N addition showed overall greater effects on MRC accumulation than canopy N addition did. Our results suggest that the canopy plays an important role in buffering the impacts of anthropogenic atmospheric N deposition on soil C cycling in tropical forests. The depth-dependent response of microbial residues to N addition also highlights the urgent need for further studies of different response mechanisms at different soil depths.

Carbon sink and source function of Eastern Himalayan forests: implications of change in climate and biotic variables

Forests serve as a sink and source of carbon and play a substantial role in regional and global carbon cycling. The Himalayan forests act as climate regulators of the Hindukush region, which is experiencing climate change at a high pace, and a proper understanding of these systems is necessary to mitigate this problem. We hypothesize that the variance of abiotic factors and vegetation will influence the carbon sink and source function of the different forest types of the Himalayas. Carbon sequestration was computed from the increment of carbon stocks estimated allometrically using Forest Survey of India equations, and soil CO₂ flux was determined by the alkali absorption method. The carbon sequestration rate and CO₂ flux by the different forests exhibited a negative relation. The carbon sequestration rate was highest with minimum emission in the temperate forest, while the tropical forest recorded the least sequestration and maximum carbon flux rate. The Pearson correlation test between carbon sequestration and tree species richness and diversity revealed a positive-significant influence but negative relation with climatic factors. An analysis of variance indicated significant seasonal differences between the rate of soil carbon emissions due to variations in the forest. A multivariate regression analysis of the monthly soil CO₂ emission rate shows high variability (85%) due to fluctuations of climatic variables in the Eastern Himalayan forests. Results of the present study revealed that the carbon sink and source function of forests respond to changes in forest types, climatic variables, and edaphic factors. Tree species and soil nutrient content influenced carbon sequestration, while shifts in climatic factors influenced soil CO₂ emission rate. Increased temperature and rainfall may further change the soil quality by enhancing soil CO₂ emission and reducing soil organic carbon, thereby impacting this region's carbon sink and source function. Enhancing tree diversity in the forests of this region may be beneficial for retarding this impact.

Long-term phosphorus addition alleviates CO2 and N2O emissions via altering soil microbial functions in secondary rather primary tropical forests

Tropical forests, where the soils are nitrogen (N) rich but phosphorus (P) poor, have a disproportionate influence on global carbon (C) and N cycling. While N deposition substantially alters soil C and N retention in tropical forests, whether P input can alleviate these N-induced effects by regulating soil microbial functions remains unclear. We investigated soil microbial taxonomy and functional traits in response to 10-year independent and interactive effects of N and P additions in a primary and a secondary tropical forest in Hainan Island. In the primary forest, N addition boosted oligotrophic bacteria and phosphatase and enriched genes responsible for C-, P-mineralization, nitrification and denitrification, suggesting aggravated P limitation while N excess. This might stimulate P excavation via organic matter mineralization, and enhance N losses, thereby increasing soil CO₂ and N₂O emissions by 86% and 110%, respectively. Phosphorus and NP additions elevated C-mining enzymes activity mainly due to intensified C limitation, causing 82% increase in CO₂ emission. In secondary forest, P and NP additions reduced phosphatase activity, enriched fungal copiotrophs and increased microbial biomass, suggesting removal of nutrient deficiencies and stimulation of fungal growth. Meanwhile, soil CO₂ emission decreased by 25% and N₂O emission declined by 52-82% due to alleviated P acquisition from organic matter decomposition and increased microbial C and N immobilization. Overall, N addition accelerates most microbial processes for C and N release in tropical forests. Long-term P addition increases C and N retention via reducing soil CO₂ and N₂O emissions in the secondary but not primary forest because of strong C limitation to microbial N immobilization. Further, the seasonal and annual variations in CO₂ and N₂O emissions should be considered in future studies to test the generalization of these findings and predict and model dynamics in greenhouse gas emissions and C and N cycling.

Agroforestry orchards support greater butterfly diversity than monoculture plantations in the tropics

Large-scale deforestation in the tropics, triggered by logging and subsequent agricultural monoculture has a significant adverse impact on biodiversity due to habitat degradation. Here, we measured the diversity of butterfly species in three agricultural landscapes, agroforestry orchards, oil palm, and rubber tree plantations. Butterfly species were counted at 127 sampling points over the course of a year using the point count method. We found that agroforestry orchards supported a greater number of butterfly species (74 species) compared to rubber tree (61 species) and oil palm plantations (54 species) which were dominated by generalist (73%) followed by forest specialists (27%). We found no significant difference of butterfly species composition between agroforestry orchards and rubber tree plantation, with both habitats associated with more butterfly species compared to oil palm plantations. This indicates butterflies were able to persist better in certain agricultural landscapes. GLMMs suggested that tree height, undergrowth coverage and height, and elevation determined butterfly diversity. Butterfly species richness was also influenced by season and landscape-level variables such as proximity to forest, mean NDVI, and habitat. Understanding the factors that contributed to butterfly species richness in an agroecosystem, stakeholders should consider management practices to improve biodiversity conservation such as ground vegetation management and retaining adjacent forest areas to enhance butterfly species richness. Furthermore, our findings suggest that agroforestry system should be considered to enhance biodiversity in agricultural landscapes.

Chytrid fungus in amphibians from the lowland Brazilian Amazon

Infectious diseases are one of the main threats to biodiversity. The fungus Batrachochytrium dendrobatidis (Bd) is associated with several amphibian losses around the globe, and environmental conditions may dictate the success of pathogen spread. The Brazilian Amazon has been considered climatically unsuitable for chytrid fungus, but additional information on Bd dynamics in this ecoregion is still lacking. We sampled 462 amphibians (449 anurans, 4 caudatans and 9 caecilians), representing 57 species from the Brazilian Amazon, and quantified Bd infections using qPCR. We tested whether abiotic variables predicted the risk of Bd infections, and tested for relationships between biotic variables and Bd. Finally, we experimentally tested the effects of Bd strains CLFT 156 and CLFT 102 (from the southern and northern Atlantic Forest, respectively) on Atelopus manauensis. We detected higher Bd prevalence than those previously reported for the Brazilian Amazon, and positive individuals in all 3 orders of amphibians sampled. Both biotic and abiotic predictors were related to prevalence, and no variable explained infection load. Moreover, we detected higher Bd prevalence in forested than open areas, while the host's reproductive biology was not a factor. We detected higher mortality in the experimental group infected with CLFT 156, probably because this strain was isolated from a region characterized by discrepant climatic conditions (latitudinally more distant) when compared with the host's sampling site in Amazon. The lowland Brazilian Amazon is still underexplored and future studies targeting all amphibian orders are essential to better understand Bd infection dynamics in this region.

Land-planning management based on multiple ecosystem services and simulation in tropical forests

Forest losses can lead to severe damage to ecosystem services (ESs), especially in the tropics. Tropical forests are widespread in southwestern China, and they experience continual effects of human activities (e.g., rubber boom). However, forest simulations of land planning have not yet been systematically conducted. Based on a future land-use simulation model, here, the spatio-temporal characteristics of four ES (i.e., soil retention, water yield, carbon fixation, and habitat quality) were examined, and three scenarios (i.e., natural development, rubber development, and ecological protection) were designed and evaluated during 2000 for Xishuangbanna (XSBN), southwestern China. The results showed that: (1) from 2000 to 2020, the average values of the ESs declined by 449.1 t for soil retention, 13.4 mm for water yield, 0.1 for habitat quality, and 0.1 kg C/m² for carbon fixation; (2) the four ESs, with the exception of water yield, had synergistic relationships, and trade-off appeared on the margins of these synergistic relationships; (3) compared with the scenarios of natural development and rubber development, the environmental protection scenario was found to have high efficiency for protecting nature reserves and reducing fragmentation; and (4) the intensity of land-use change will accelerate the decrease of ESs, and it is essential for nature reserves and areas of northern XSBN to improve their level of environmental protection. This work not only further enriches the ES research from the ecological environment and land-planning points of view, but it also provides different planning perspectives for ES and forest scenarios. This is useful in methodical approaches to forest sustainability.

Hot spots and anomalies of CO2 over eastern Amazonia, Brazil: A time series from 2015 to 2018

The easternmost Amazon, located in the Maranhão State, in Brazil, has suffered massive deforestation in recent years, which has devastated almost 80% of the original vegetation. We aim to characterize hot spots, hot moments, atmospheric carbon dioxide anomalies (Xco₂, ppm), and their interactions with climate and vegetation indices in eastern Amazon, using data from NASA's Orbiting Carbon Observatory-2 (OCO-2). The study covered the period from January 2015 to December 2018. The data were subjected to regression, correlation, and temporal analysis, identifying the spatial distribution of hot/cold moments and hot/cold spots. In addition, anomalies were calculated to identify potential CO₂ sources and sinks. Temporal changes indicate atmospheric Xco₂ in the range from 362.2 to 403.4 ppm. Higher Xco₂ values (hot moments) were concentrated between May and September, with some peaks in December. The lowest values (cold moments) were concentrated from November to April. SIF 771 W m^-2 sr^-1 μm^-1 explained the temporal changes of Xco₂ in 58% (R² adj = 0.58; p < 0.001) and precipitation in 27% (R² adj = 0.27; p ≤ 0.001). Spatial hot spots with 90% confidence were more representative in 2016. The maximum and minimum Xco₂ (ppm) anomalies were 6.19 ppm (source) and -6.29 ppm (sink), respectively. We conclude that the hot moments of Xco₂ in the eastern Amazon rainforest are concentrated in the dry season of the year. Xco₂ spatial hot spots and anomalies are concentrated in the southern region and close to protected areas of the Amazon rainforest.

Spatial pattern of functional genes abundance reveals the importance of PhoD gene harboring bacterial community for maintaining plant growth in the tropical forest of Southwestern China

The concept of microbial functional genes has added a new dimension to microbial ecology research by improving the model of microbial community-ecosystem functions relationship. However, our knowledge vis-à-vis fine-scale spatial distribution pattern of functional genes and their probable impact on plant community in the hyper-diverse tropical forest ecosystem is very limited. Here, we investigated the spatial pattern of functional genes abundance (NirK, AOA, AOB, and PhoD), identified key influencing factors, and distinguished the key functional group supporting the plant community in a tropical rainforest located in Xishuangbanna. In total, 200 soil samples and vegetation data of ~4800 individuals of plants across a 1 ha study area were collected. Our results detected higher spatial variability with a maximum magnitude of abundance for PhoD gene (4.53 × 10⁷ copies) followed by NirK (2.71 × 10⁶ copies), AOA (1.97 × 10⁶ copies), and AOB (7.38 × 10⁴ copies). A strong spatial dependence was observed for PhoD and NirK over the distance of 17 and 18 m, respectively. Interestingly, the N:P stoichiometry played a critical role in structuring the spatial pattern of the most abundant PhoD gene. The significant positive and negative relationship of PhoD with N:P ratio and available phosphorus, respectively, indicated that the P-limiting environment was a driving factor for recruitment of PhoD gene community. The structural equation modeling ascertained the direct positive impact of PhoD on plant biomass and high demand of available P by plants suggesting that the organic phosphorus mineralization process is essential to maintain plant productivity by re-establishing the availability of the most limiting P nutrient. Our preliminary study improves our understanding of how microbial functional genes-environment associations could be used for monitoring soil health and its overall impact on ecosystem multifunctionality. Finally, we intend to conduct the study at a large spatial scale for achieving a holistic view.

Liana functional assembly along the hydrological gradient in Central Amazonia

Soil hydrology, nutrient availability, and forest disturbance determine the variation of tropical tree species composition locally. However, most habitat filtering is explained by tree species' hydraulic traits along the hydrological gradient. We asked whether these patterns apply to lianas. At the community level, we investigated whether hydrological gradient, soil fertility, and forest disturbance explain liana species composition and whether liana species-environment relationships are mediated by leaf and stem wood functional traits. We sampled liana species composition in 18 1-ha plots across a 64 km² landscape in Central Amazonia and measured eleven leaf and stem wood traits across 115 liana species in 2000 individuals. We correlated liana species composition, summarized using PCoA with the functional composition summarized using principal coordinate analysis (PCA), employing species mean values of traits at the plot level. We tested the relationship between ordination axes and environmental gradients. Liana species composition was highly correlated with functional composition. Taxonomic (PCoA) and functional (PCA) compositions were strongly associated with the hydrological gradient, with a slight influence from forest disturbance on functional composition. Species in valley areas had larger stomata size and higher proportions of self-supporting xylem than in plateaus. Liana species on plateaus invest more in fast-growing leaves (higher SLA), although they show a higher wood density. Our study reveals that lianas use different functional solutions in dealing with each end of the hydrological gradient and that the relationships among habitat preferences and traits explain lianas species distributions less directly than previously found in trees.

Seasonal Variation of Soil Quality in a Semi-deciduous Northern Tropical Forest of Nagaland, India

To assess the seasonal changes in soil parameters and the soil quality of a semi-deciduous forest in Nagaland, tropical forest soil samples were tested for 10 physical and chemical variables. Apart from clay content, EC, and CEC, the rest of the parameters showed a seasonal mean significant difference at p < .05 level. Based on the principal component analysis, available nitrogen (N_av) and electrical conductivity (EC) were included in a minimum data set and are regarded to best represent the system attributes. In both additive and weighted soil quality method, maximum SQI was recorded in autumn season. The research summarized that seasonal variations can influence soil characteristics and soil quality through its aggregate effects. Considering the result obtained from the present study, the approach we have used in soil quality assessment would be suitable for primarily screening the tropical forest soil status. This would ultimately pave ways for future management and mitigation plans to facilitate the improvement of forest health and aid to biodiversity conservation.

Carbon payments can cost-effectively improve logging sustainability in the Amazon

Selective logging is pervasive across the tropics and unsustainable logging depletes forest biodiversity and carbon stocks. Improving the sustainability of logging will be crucial for meeting climate targets. Carbon-based payment for ecosystem service schemes, including REDD+, give economic value to standing forests and can protect them from degradation, but only if the revenue from carbon payments is greater than the opportunity cost of forgone or reduced logging. We currently lack understanding of whether carbon payments are feasible for protecting Amazonian forests from logging, despite the Amazon holding the largest unexploited timber reserves and an expanding logging sector. Using financial data and inventories of >660,000 trees covering 52,000 ha of Brazilian forest concessions, we estimate the carbon price required to protect forests from logging. We estimate that a carbon price of $7.90 per tCO₂ is sufficient to match the opportunity costs of all logging and fund protection of primary forest. Alternatively, improving the sustainability of logging operations by ensuring a greater proportion of trees are left uncut requires only slightly higher investments of $7.97-10.45 per tCO₂. These prices fall well below the current compliance market rate and demonstrate a cost-effective opportunity to safeguard large tracts of the Amazon rainforest from further degradation.

AMAZONIA CAMTRAP: A dataset of mammal, bird, and reptile species recorded with camera traps in the Amazon forest

The Amazon forest has the highest biodiversity on earth. However, information on Amazonian vertebrate diversity is still deficient and scattered across the published, peer-reviewed and grey literature and in unpublished raw data. Camera traps are an effective non-invasive method of surveying vertebrates, applicable to different scales of time and space. In this study, we organized and standardized camera trap records from different Amazon regions to compile the most extensive dataset of inventories of mammal, bird and reptile species ever assembled for the area. The complete dataset comprises 154,123 records of 317 species (185 birds, 119 mammals and 13 reptiles) gathered from surveys from the Amazonian portion of eight countries (Brazil, Bolivia, Colombia, Ecuador, French Guiana, Peru, Suriname and Venezuela). The most frequently recorded species per taxa were: mammals - Cuniculus paca (11,907 records); birds - Pauxi tuberosa (3,713 records); and reptiles - Tupinambis teguixin (716 records). The information detailed in this data paper opens-up opportunities for new ecological studies at different spatial and temporal scales, allowing for a more accurate evaluation of the effects of habitat loss, fragmentation, climate change and other human-mediated defaunation processes in one of the most important and threatened tropical environments in the world. The dataset is not copyright restricted; please cite this data-paper when using its data in publications and we also request that researchers and educators inform us of how they are using this data.

Latitudinal gradient for mercury accumulation and isotopic evidence for post-depositional processes among three tropical forests in Southwest China

Tropical forest contributes to > 50% of global litterfall mercury (Hg) inputs and surface soil Hg storage, while with limited understanding of Hg biogeochemical processes. In this study, we displayed the 5-m resolution of Hg spatial distribution in three 1-ha tropical forest plots across the latitudinal gradient in Southwest China, and determined Hg isotopic signatures to understand factors driving Hg spatial distribution and sequestration processes. Our results show that tropical forest at the lowest latitude has the highest litterfall Hg input (74.95 versus 34.14-56.59 μg m^-2 yr^-1 at higher latitude plots), but the smallest surface soil Hg concentration (2-3 times smaller than at higher latitude sites). Hg isotopic evidence indicates that the decreasing climate mediated microbial Hg reduction in forest floor leads to the increasing Hg accumulation along the latitudinal gradient in three tropical forests. The terrain induced indirect effects by influencing litterfall Hg inputs, soil organic matters distribution and interplays between surface and deep soils drive the heterogeneity of surface soil Hg distribution within each sampling plot. Our results highlight though the elevated litterfall Hg inputs, the distinct post-depositional reductions induced Hg loss would remarkedly decrease atmospheric Hg net sink in tropical forest.

Loss of soil microbial residue carbon by converting a tropical forest to tea plantation

Land-use change can lead to profound changes in the storage of soil organic carbon (SOC) in the tropics. Soil microbial residues make up the majority of persistent SOC pools, yet the impact of land-use change on microbial residue C accumulation in the tropics is not well understood. Here, we investigated how the conversion of tropical primary montane rainforest to secondary forest and the conversions of secondary forest to Prunus salicina plantation and tea plantation, influence the accumulation of soil microbial residue C (indicated by amino sugars). Our results showed that the secondary forest had a higher SOC than that of the primary forest (+63%), while they had no difference in microbial residue C concentration, indicating a relatively slow microbial-derived C accrual during secondary succession. Moreover, the P. salicina plantation and tea plantation had lower SOC than the secondary forest (-53% and -57%, respectively). A decrease in fungal biomass (-51%) resulted in less fungal and total residue C concentrations in the tea plantation than in the secondary forest (-38% and -35%, respectively), indicating microbial-derived C loss following the forest conversion. The change in microbial residue C depended on litter standing crop rather than soil nutrient and root biomass. Litter standing crop affected microbial residue C concentration by regulating fungal biomass and hydrolytic enzyme activities. Taken together, our results highlight that litter-microbe interactions drive microbial residue C accumulation following forest conversions in the tropics.

Estimating the potential of wild foods for nutrition and food security planning in tropical areas: Experimentation with a method in Northwestern Colombia

Wild foods contribute to the food security of multiple communities in tropical areas of Africa, Asia and Latin America. However, wild foods are not regularly considered in the planning of strategies for food and nutrition security mainly due to the lack of technical and/or scientific knowledge so that they can be considered suitable for human consumption. This paper proposes a multidisciplinary method that estimates the potential of wild foods as alternative resources when planning interventions in favour of food and nutrition security in tropical forest territories. When designing the method, four dimensions were identified in science, technology and innovation (STI) that define this potential as well as ten assessment criteria. The wild foods chosen for applying the method were Alibertia patinoi (a fruit commonly known as Borojó) and Proechimys semispinosus (Mouse of thorns), which are two of the main wild foods traditionally used by human communities in a tropical forest territory in the northwest of Colombia. In both cases, although there are significant advances in STI, compliance with some criteria is still required to regard them as viable alternatives for nutrition and food security within this territory. This research is useful for promoting the inclusion of wild food in food security programmes for communities where this food is already included in their traditional pattern of consumption and identifies the progress needed in STI to achieve this purpose. It may also promote the early recognition of possible traditional and cultural practices with high risk of transmission of pathogenic elements by the handling and/or inadequate consumption of wild foods. This early recognition could contribute to the prevention of diseases of wild animal origin, including those of rapid global spread.

Land use intensity determines soil properties and biomass recovery after abandonment of agricultural land in an Amazonian biodiversity hotspot

There has been widespread clearance of tropical forests for agriculture, but in many cases the cultivation phase is only transient. The secondary forests recovering on these abandoned sites may contribute to mitigation of greenhouse gas emissions and protection of biodiversity, but the rates of recovery may be dependent on land-use intensity and changes in soil properties during cultivation. However fine-scale details on these changes are poorly known for many tropical forest locations. We quantified soil properties and recovery of woody biomass in 42 tropical forest fragments representing a chronosequence following two types of agricultural land-uses, and in 15 comparable reference old growth forests, between the Andes and the Amazon in Peru. Soil fertility, particularly base cation concentrations, responded negatively to increasing intensity of agricultural land-use, and either decreased or increased with time after abandonment dependent on prior land-use. The predicted mean recovery rate of woody biomass over the first 20 years following abandonment matched that predicted by a general model for the Neotropics, but recovery was three-fold higher on sites abandoned following traditional agriculture than on sites recovering from intensive agriculture. Estimated total biomass recovered to just above half that of reference old growth forests within 71 years. The inclusion of the biomass of lianas and smaller tree stems did not modify the apparent rate of ecosystem biomass recovery, however the proportion of the total biomass stored in small stems was greater following intensive than traditional agriculture, which suggests that patterns of stand structural development are sensitive to land-use history. We conclude that effects of historic land use on soil nutrient concentrations and their changes through time are required for a more complete interpretation of variation in biomass recovery rates at local scales. These results also highlight the critical importance of contemporary agricultural intensification for carbon storage in tropical forests.

Degradation activity of fungal communities on avocado peel (Persea americana Mill.) in a solid-state process: mycobiota successions and trophic guild shifts

To explore the capability of soil mycobiota to degrade avocado peel waste and identify relevant successions and trophic guild shifts, fungal communities from three environments with different land uses were evaluated in a solid-state process. Soil samples used as inoculum were collected from a pristine mature tropical forest, a traditionally managed Mayan land, and an intensively managed monospecific avocado plantation. Soil-substrate mixes were evaluated for 52 weeks to evaluate organic matter decay and the carbon-to-nitrogen ratio. Amplicon-based high-throughput sequencing from internally transcribed spacer (ITS) analysis revealed significant differences in fungal communities widely dominated by Fusarium sp. and Clonostachys sp.; however, less represented taxa showed relevant shifts concomitantly with organic matter content drops. Trophic guild assignment revealed different behaviors in fungal communities between treatments over the 52 weeks, suggesting distinct preconditioning of fungal communities in these environments. Overall, the results lead to the identification of promising degradation moments and inoculum sources for further consortia enrichment or bioprospecting efforts.

Long-term fertilization modifies the mineralization of soil organic matter in response to added substrate

The turnover of SOC in soils is strongly influenced by the availability of substrate and nutrients, especially nitrogen (N) and phosphorus (P). Here, we assessed how long-term fertilization modified SOM mineralization in response to added substrate in a tropical forest. We carried out a 90-day incubation study in which we added two structurally similar compounds which differed in microbial metabolic availability: corn cellulose or corn starch to soils collected from a long-term (11 years) factorial N and P fertilization experiment site in a tropical forest in south China. We measured total soil mineralization rate (CO₂ efflux) to characterize SOM mineralization and using ¹³C isotope signatures to determine the source of the CO₂ (original soil C or added substrate) and assessed changes in extracellular enzyme activities: acid phosphomonoesterase (AP), β-1,4-glucosidase (BG), β-1,4- N-acetaminophen glucosidase (NAG), phenol oxidase (PHO) and peroxidase (PER), and microbial biomarkers to determine whether nutrient stoichiometry and decomposer communities explain differences in SOM mineralization rates. Total C mineralization increased substantially with substrate addition, particularly cellulose (5.38, 7.13, 5.58 and 5.37 times for N, P, NP fertilization and CK, respectively) compared to no substrate addition, and original soil C mineralization was further enhanced in long-term N (3.40% and 5.18% for cellulose and starch addition, respectively) or NP (35.11% for cellulose addition) fertilized soils compared to control treatment. Enzyme activities were stimulated by the addition of both substrates but suppressed by P-fertilization. Addition of both substrates increased microbial investment in P-acquisition, but only starch addition promoted C investment in N-acquisition. Finally, fungal abundance increased with substrate addition to a greater extent than bacterial abundance, particularly in cellulose-amended soils, and the effect was amplified by long-term fertilization. Our findings indicate that SOM mineralization might be enhanced in N and P enrichment ecosystems, since the litter input can liberate microbes from C limitation and stimulate SOM mineralization if N and P are sufficient. Our study further demonstrates that structurally similar substrates can have distinct effects on SOM mineralization and the extent of SOM mineralization is strongly dependent on elemental stoichiometry, as well as the resource requirements of microbial decomposers.

The stability of soil organic carbon across topographies in a tropical rainforest

Mechanisms of soil organic carbon (SOC) stability are still unclear in forest ecosystems. In order to unveil the influences of topography on the SOC stability, a 60ha dynamic plot of a tropical montane rainforest was selected in Jianfengling, in Hainan Island, China and soil was sampled from 60 quadrats. The chemical fractions of the SOC were detected with 13C CPMAS/NMR and path analyses explore the mechanisms of SOC stability in different topographies. The chemical fractions of the SOC comprised alkyl carbon > O-alkyl carbon > carboxyl carbon > aromatic carbon. The decomposition index (DI) values were greater than 1 in the different topographies, with an average DI value was 1.29, which indicated that the SOC in the study area was stable. Flat and top areas (together named RF) had more favorable nutrients and silt contents compared with steep and slight steep areas (together named RS). The influencing factors of SOC stability varied across the topographies, where SOC, soil moisture (SM) and ammoniacal nitrogen (NH₄⁺-N, AN) were the main influencing factors in the RF, while SM and AN were the main factors in the RS. Greater SOC and AN strengthened the SOC stability, while higher soil moisture lowered SOC stability. The inertia index was higher in the RS than the RF areas, indicating that local topography significantly affects SOC content and SOC stability by changing soil environmental factors. Topography cannot be neglected in considering SOC stability and future C budgets.

Modeling canopy interception under drought conditions: The relevance of evaporation and extra sources of energy

Modeling canopy interception is fundamental for understanding the forests' role in local and regional hydrology. In this study, canopy interception (CI), throughfall (TF), and stemflow (SF) were evaluated for a semi-deciduous Atlantic Forest (AFR) from 2013 to 2019, where a prolonged dry period occurred. The Gash and Liu models were analyzed in detail to determine the most appropriate for modeling CI throughout drought conditions. Thus, the climatic parameters were retrieved annually by a modified TF-based method (E_I%), whereas the structural parameters represented the entire period. The contribution of the energy stored in the forest (i.e. air and biomass; Q) to CI was also assessed in the AFR stand. Both models performed well when using E_I%, as the Gash model overestimated CI by 71 mm (4.6%), whereas the Liu model underestimated it by only 13 mm (0.85%). This performance is due to an increased Q and turbulent mechanisms (such as advection and strong updrafts) that occur in drought conditions and are indirectly accounted for in E_I%. However, the Liu model stood out for modeling CI under a prolonged dry period, as the exponential wetting approach better represents the complex canopies of the semi-deciduous forests. Thus, we recommend the Liu model and additional energy sources when dealing with prolonged droughts, as in the case of climate change scenarios projected to the studied region.

Optimizing forest road planning in a sustainable forest management area in the Brazilian Amazon

The construction of forest roads in Brazilian Amazon is costly and has a significant environmental impact. Several practices and principles must be observed to comply with legislation, to preserve the remaining forest, and to ensure sustainable exploitation. Road planning is complex in this context, based on the number of aspects and variables that must be considered. This research aimed to evaluate computational methods' effectiveness in planning forest roads, optimizing resources to reduce damage to the remaining forest, compared to traditional planning methods. The study area was a native forest under a sustainable forest management regime located in municipalities of Terra Santa and Oriximiná, in Pará, in Brazilian Amazon. Data obtained from area made it possible formulate six instances of different sizes. A binary integer linear programming model was used, solved using CPLEX software, and Dijkstra, Bellman-Ford, Dial, and D'Esopo-Pape shortest path algorithm, implemented in C programming language. During processing of instances, the time taken to obtain the solution increased according to size of instance, however, time difference was not significant. Among the evaluated algorithms, the D'Esopo-Pape algorithm showed the best performance. The evaluated methods were effective in obtaining an optimal solution for proposed forest road planning. The solutions obtained using computational methods more effectively considered the restrictions associated with sustainable forest management, in contrast to those derived from the traditional planning by forestry company.

A new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from Northern Thailand, with its genetic relationship in the S. asakoae species-group

A new black fly species, Simulium (Gomphostilbia) kiewlomense, is described from females, males, pupae and mature larvae in Thailand. This new species is placed in the S. asakoae species-group and is characterized by having a combination of the elongate female sensory vesicle, widened male hind basitarsus, which is much wider than the hind femur, small pupal terminal hooks, and light greenish larval abdominal segments 1-3. Taxonomic notes are given to separate this new species from other related species. A DNA analysis using the COI gene shows that this new species has two genoforms with 1.21% difference. This is the 28th species of the S. asakoae species-group in Thailand, strengthening the evidence for high species diversity of this species-group.

Ranavirus is widespread in Costa Rica and co-occurs with threatened amphibians

Amphibians are globally threatened by emerging infectious diseases, and ranaviruses are among the most concerning pathogens to threaten species in the wild. We sampled for ranaviruses in wild amphibians at 8 sites in Costa Rica, spanning broad climatic zones and taxonomic associations. Seven of these sites are inhabited by highly threatened amphibian species that persist at low global population sizes after population declines due to amphibian chytridiomycosis. One of the surveyed sites is occupied by an introduced amphibian species, which is relatively rare in Central America but may be an important pathway for long-distance transport of ranaviruses. We detected ranavirus using quantitative polymerase chain reaction in 16.3% of the 243 individuals and among 5 of our 8 sites, but not at the site with the introduced species. Infection prevalence varied among species and sites, but not with mean annual temperature or mean annual precipitation. Infection intensity did not vary with species, site, temperature, or precipitation. Our results show that ranavirus infection is spatially widespread in Costa Rica, affecting a broad range of host species, and occurs across climatic zones-though we encountered no mortality or morbidity in our sampled species. Ranaviruses are known to cause intermittent mass mortality in amphibian populations, and the threatened species sampled here are likely vulnerable to population impacts from emerging ranaviruses. Therefore, we believe the potential impacts of ranaviruses on amphibian populations in tropical regions have likely been underestimated, and that they should be viewed as a potential major stressor to threatened amphibians in tropical regions.

Amphibian chytrid infections along the highest elevational gradient of the Brazilian Atlantic Forest

Environmental variation along elevational gradients shapes conditions for pathogen development, which influences disease outcomes. Chytridiomycosis is a non-vectored disease caused by the aquatic fungus Batrachochytrium dendrobatidis (Bd) and is responsible for massive declines of amphibian populations all over the world. Several biotic and abiotic factors are known to influence Bd infection dynamics in amphibians, including temperature and host species richness. Here, we quantified Bd prevalence and load along an elevational gradient in the Caparaó National Park (CNP), Brazil, and tested for associations of Bd infections with elevation, temperature, and species richness. We hypothesized that Bd infections would increase as local species richness decreased with elevation. We detected Bd along the entire elevational gradient and found a negative association between infection load and elevation. We did not detect significant associations between infection prevalence and elevation. Our findings are consistent with other wide elevational gradient studies, but are contrary to 2 other studies performed in the Atlantic Forest. We did not find the minimum elevational range that should be sampled to detect the influence of elevation on Bd variation. Our study represents the widest elevational gradient that has been sampled in Brazil and contributes to a better understanding of Bd distribution and dynamics in natural systems.

Spatial distribution of six managed tree species is influenced by topography conditions in the Central Amazon

In tropical forests, the spatial distribution of trees may present random, uniform, or grouped patterns that can simultaneously be affected by site and species characteristics. In Central Amazon, topographic gradients and soil water levels drive differences in tree species distribution and in forest dynamics at local scales. Knowing this kind of information can be useful for a forest manager to plan harvesting operations considering the microhabitat preference of merchantable species to reduce the disturbances caused by logging activities. Thus, the spatial variation of tree species is an important information to be considered to support the planning process of forest logging. The present study aims to evaluate the spatial distribution pattern of six species and analyze the relationship between the topography and the population densities and stem size of those species. The study was carried out in a forest production compartment managed by a private company located in the municipality of Silves, state of Amazonas, Brazil. The spatial pattern of the six species was characterized by Ripley's K function. Spatial distribution of diameter at breast height (DBH) and tree density based on kernel incidence calculation were evaluated for topographic classes of slope, elevation, and distance from streams, which were mapped using geographic information systems (GIS). The means of DBH and density of each species were compared among topographic classes by ANOVA and Tukey's test. The results demonstrated the predominance of the aggregate distribution pattern for the six species up to 1105 m (p < 0.01). The tree species Minquartia guianensis Aubl., Protium puncticulatum J.F.Macbr, Manilkara elata (Allemão ex Miq.) Monach, and Caryocar glabrum Aubl. Pers showed an increase in the tree density as the distance from the streams and elevation increased, standing spatially incident on plateaus. Kernel densities of Dinizia excelsa Ducke and Goupia glabra Aubl. were higher closer to streams. The DBH averages followed similar trends of population density for M. guianensis, M. elata, and C. glabrum, and the opposite pattern for D. excelsa, which presented larger individuals in less densely populated areas. P. puncticulatum and G. glabra mean DBH distribution was not affected by the topographic variables analyzed. Topography-related variables showed effects on variations of density and tree size, suggesting that species may be spatially sensitive to the habitat variability available in the study area. In view of logging planning, spatial distribution must be considered in decisions related to cutting down trees and maintenance of remaining trees, especially because some species are more aggregated in smaller scales. Moreover, as topographic variations affect the spatial distribution of size and density, the timber yield will vary spatially in the area, bringing implications for planning logging intensities, roads, skid trails and forest operations. Finally, the procedures and information generated in this study can be reproduced and applied to other species and managed areas to support the planning toward minimizing impacts on the spatial structure of commercial species, as well as to increase the chances of future stock recovery of managed forests in the Amazon.

Habitat loss and canopy openness mediate leaf trait plasticity of an endangered palm in the Brazilian Atlantic Forest

Forest cover and light availability comprise key factors for plant establishment in tropical forests. In the Brazilian Atlantic Forest (AF), Euterpe edulis (Areacaceae) is an endangered and keystone food resource contributing to forest functionality. We investigated the influence of forest loss and light availability on leaf traits and acclimatization of young individuals of E. edulis in AF fragments. We aimed to understand (i) how canopy openness and transmitted light are affected by forest cover at the landscape scale and the individual palm level; and (ii) how local and landscape features, combined and separately, affect key leaf traits widely known to be related to plant growth. The study was carried out in 15 forest fragments, ranging from 16 to 97% of surrounding forest cover. In each fragment, we sampled 10-20 individuals of E. edulis and analyzed nine leaf traits related to morphological, biochemical and chemical aspects. We also took hemispherical photographs to estimate canopy openness on the top of each E. edulis and also within fragment plots. We found that young plants predominantly occurred in more shaded environments. Additionally, E. edulis succeeded to acclimate in six of the nine traits analyzed, with most traits being affected by local and landscape features. It is likely that the lack of variation in traits related to protection against herbivory are limiting the species establishment in highly deforested landscapes. Our results provide novel evidence that both landscape and local contexts affect the leaf traits of E. edulis young plants leading to biochemical, chemical and morphological adjustments.

Rodent suppression of seedling establishment in tropical pasture

Grasses are recognized as a critical regeneration barrier in tropical pastures, yet the effects of rodents and rodent-grass interactions are not well understood. As selective foragers, rodents could shape tree communities, moderating biodiversity in regenerating tropical landscapes. We utilized a fully crossed two-way factorial design to examine the effect that grasses, rodents, and their interaction had on tree seedling establishment in pasture habitat. We followed two separate tree cohorts for 1 year each within the experimental framework. Multiple cohorts were used to better represent successional tree species variation and responses. Trees species were characterized by a gradient of seed masses and as pioneer or persistent successional type. Both cohort seedlings were altered when rodents were present compared to control treatments. In Cohort 1, rodents adversely affected seedlings of persistent tree species only in the absence of grass. In Cohort 2, seedlings of persistent tree species were decimated by rodents in the absence or presence of grass. In both cohorts, seedlings of persistent species established better in grass treatments, while seedlings of pioneer tree species were strongly suppressed. Tree species seed mass positively correlated with seedling establishment across all treatments except no grass-rodent treatments. Strong suppression of tree seedlings by rodents (Sigmodon toltecus) is a novel result in tropical land recently released from agriculture. One implication is that selective foraging by rodents on large-seeded persistent tree species may be facilitated by the removal of grass. Another implication is that temporary rodent control in pastures may permit higher establishment of deep-forest persistent species.

Spatial and environmental constraints on natural forest regeneration in the degraded landscape of Hong Kong

Tropical forests are the main reservoirs for global biodiversity and climate control. As secondary forests are now more widespread than primary forests, understanding their functioning and role in the biosphere is increasingly important. This includes understanding how they achieve stability, how they accumulate species and build biodiversity and how they cycle nutrients and carbon. This study investigates how we can restore tropical secondary forests to resemble high biomass, highly biodiverse and stable ecosystems seen today only in primary, undisturbed forests. The study used historic aerial photographs and recent high-resolution satellite images from 1945 to 2014 to map forest patches with five age categories, from 14-years to over 70-years, in Hong Kong's degraded tropical landscape. A forest inventory comprising 28 quadrats provided a rare opportunity to relate patterns of species composition at different stages during the succession with topographic and soil characteristics. The topographic variables accounted for 15% of the variance in species abundance, and age of forest stands explained 29%. Species richness rapidly increased after the first 15 years, but was lower in old-growth, than in medium age forest. This is attributed to the inability of late-successional species to disperse into the young forests as the natural dispersal agents (birds, mammals) have been lost. Light-loving pioneers which are unable to tolerate the shade of older forests, cannot regenerate in their own shade, therefore species diversity declines after a few decades. For ecosystem restoration in tropical secondary forests, introduction of late-successional species is necessary to assist natural succession, given the absence of native fauna, seed dispersal agents, and the surrounding altered environment. We also show that remote sensing can play a pivotal role in understanding the recovery and functioning of secondary forest regeneration as its contribution to the biosphere is increasingly important.

Deforestation Trajectories on a Development Frontier in the Brazilian Amazon: 35 Years of Settlement Colonization, Policy and Economic Shifts, and Land Accumulation

We examine deforestation processes in Apuí, a deforestation hotspot in Brazil's state of Amazonas and present processes of land-use change on this Amazonian development frontier. Settlement projects attract agents whose clearing reflects land accumulation and the economic importance of deforestation. We used a mixed-method approach in the Rio Juma Settlement to examine colonization and deforestation trajectories for 35 years at three scales of analysis: the entire landscape, cohorts of settlement lots divided by occupation periods, and lots grouped by landholding size per household. All sizes of landholdings are deforesting much more than before, and current political and economic forces favoring the agribusiness sector foreshadow increasing rates of forest clearing for pasture establishment in Apuí. The area cleared per year over the 2013-2018 period in Apuí grew by a percentage more than twice the corresponding percentage for the Brazilian Amazon as a whole. With the national congress and presidential administration signaling impunity for illegal deforestation, wealthy actors, and groups are investing resources in land grabbing and land accumulation, with land speculation being a crucial deforestation factor. This paper is unique in providing causal explanations at the decision-maker's level on how deforestation trajectories are linked to economic and political events (period effects) at the larger scales, adding to the literature by showing that such effects were more important than aging and cohort effects as explanations for deforestation trajectories. Additional research is needed to deepen our understanding of relations between land speculation, illegal possession of public lands, and the expansion of agricultural frontiers in Amazonia.

Functional traits of broad-leaved monocot herbs in the understory and forest edges of a Costa Rican rainforest

Broad-leaved monocot herbs are widespread and dominant components of the shaded understories of wet neotropical forests. These understory habitats are characterized by light limitation and a constant threat of falling branches. Many shaded understory herb species have close relatives that occupy forest edges and gaps, where light availability is higher and defoliation threat is lower, creating an opportunity for comparative analysis of functional traits in order to better understand the evolutionary adaptations associated with this habitat transition. We documented ecological, morphological and ecophysiological traits of multiple herb species in six monocot families from each of these two habitats in the wet tropical rainforest at the La Selva Biological Station, Costa Rica. We found that a mixture of phylogenetic canalization and ecological selection for specific habitats helped explain patterns of functional traits. Understory herbs were significantly shorter and had smaller leaves than forest edge species. Although the mean number of leaves per plant and specific leaf area did not differ between the two groups, the larger leaf size of forest edge species gave them more than three times the mean plant leaf area. Measures of leaf water content and nitrogen content varied within both groups and mean values were not significantly different. Despite the high leaf nitrogen contents, the maximum photosynthetic rates of understory herbs were quite low. Measures of δ¹³C as an analog of water use efficiency found significantly lower (more negative) values in understory herbs compared to forest edge species. Clonality was strongly developed in several species but did not show strong phylogenetic patterns. This study highlights many functional traits that differ between broad-leaved monocot species characteristic of understory and forest edge habitats, as well as traits that vary primarily by phylogenetic relatedness. Overall, plant functional traits do not provide a simple explanation for the relative differences in abundance for individual understory and forest edge species with some occurring in great abundance while others are relatively rare.

Metaheuristics applied for storage yards allocation in an Amazonian sustainable forest management area

In the sustainable management of Amazonian forests, it is essential to carry out the optimal planning of logging infrastructures to reduce costs and environmental impacts. However, there is a high degree of complexity due to the number of variables involved. Among these infrastructures, wood storage yards are of utmost importance as they directly influence the opening of forest roads and trails. The objective of this research was to evaluate the allocation of wood storage yards through exact solution and metaheuristics in a forest management area. The study area was a native forest under sustainable forest management regime located in the Brazilian Amazon. Three instances were formulated involving 5947 trees and 3172 wood storage yards facilities. We used a binary integer programming model solved by CPLEX and the metaheuristics Greedy Randomized Adaptive Search Procedure (GRASP), Tabu Search (TS), Variable Neighborhood Search (VNS) and Simulated Annealing (SA). GAP values increased as a function of instances. Although all metaheuristics obtained significant solutions with shorter processing times, only SA obtained feasible solutions in all executions for all three instances. In general, the metaheuristics were efficient in obtaining feasible solutions faster than CPLEX, which represents the feasibility of the planning of allocation storage large areas, and without significant losses of best-known solution. The SA presented the best performance in the three evaluated instances. Contribution of this study can be highlighted: evaluation of alternative computational methods for planning the allocation of wooden storage yards; evidence was obtained of effectiveness and efficiency of assessed metaheuristics and, the applicability of approximate methods in this problem was evaluated.

High moon brightness and low ambient temperatures affect sloth predation by harpy eagles

Background

Climate plays a key role in the life histories of tropical vertebrates. However, tropical forests are only weakly seasonal compared with temperate and boreal regions. For species with limited ability to control core body temperature, even mild climatic variation can determine major behavioural outcomes, such as foraging and predator avoidance. In tropical forests, sloths are the arboreal vertebrate attaining the greatest biomass density, but their capacity to regulate body temperature is limited, relying on behavioural adaptations to thermoregulate. Sloths are largely or strictly nocturnal, and depend on crypsis to avoid predation. The harpy eagle (Harpia harpyja) is a sloth-specialist and exerts strong top-down control over its prey species. Yet the role of environmental variables on the regulation of predator-prey interactions between sloths and harpy eagles are unknown. The harpy eagle is considered Near Threatened. This motivated a comprehensive effort to reintroduce this species into parts of Mesoamerica. This effort incidentally enabled us to understand the prey profile of harpy eagles over multiple seasons.

Methods

Our study was conducted between 2003 and 2009 at Soberanía National Park, Panamá. Telemetered harpy eagles were seen hunting and feeding on individual prey species. For each predation event, field assistants systematically recorded the species killed. We analysed the effects of climatic conditions and vegetation phenology on the prey species profile of harpy eagles using generalised linear mixed models.

Results

Here we show that sloth predation by harpy eagles was negatively affected by nocturnal ambient light (i.e. bright moonshine) and positively affected by seasonally cool temperatures. We suggest that the first ensured low detectability conditions for sloths foraging at night and the second posed a thermally unsuitable climate that forced sloths to forage under riskier daylight. We showed that even moderate seasonal variation in temperature can influence the relationship between a keystone tropical forest predator and a dominant prey item. Therefore, predator-prey ecology in the tropics can be modulated by subtle changes in environmental conditions. The seasonal effects shown here suggest important demographic consequences for sloths, which are under top-down regulation from harpy eagle predation, perhaps limiting their geographic distribution at higher latitudes.

Shifts in foraging behaviour of heterospecific flocking birds in a lowland Malaysian rainforest

Mixed-species flocks (MSFs) serve important roles in bird communities, especially in tropical forests. Although structure of mixed-species bird flocks and its benefits has been intensively studied globally, the foraging plasticity of a species when joining MSFs has rarely been evaluated. The present study examines foraging strategies of the Rufous-crowned Babbler (Malacopteron magnum), Chestnut-winged Babbler (Cyanoderma erythropterum) and Black-naped Monarch (Hypothymis azurea) when participating in MSFs in the Krau Wildlife Reserve, central Peninsular Malaysia. These species exhibit active foraging shifts in utilisation of vertical strata, foraging substrate, attack manoeuvres and foliage density, when foraging in MSFs, compared to when foraging outside MSFs. While the Rufous-crowned Babbler and Chestnut-winged Babbler commonly used gleaning and stretching (to completely extend the legs or neck to reach the food items) manoeuvres when foraging outside MSFs, respectively, they adopted probing manoeuvre and frequently used higher strata upon joining MSFs. The Chestnut-winged Babbler tended to forage on the underside of leaves and the Black-naped Monarch frequently utilised branches when joining MSFs, while they exclusively used aerial leaf litter and live green leaves, respectively, when foraging with conspecifics. The monarch also adopted the hovering manoeuvre and frequently foraged within denser foliage cover when joining MSFs. This study demonstrated that flock members exhibits foraging plasticity either through an expansion or active shift in foraging niches when participating in MSFs, thus suggesting the occurrence of possible foraging improvement and/or reductions in predation risk.

Spatiotemporal evolution of tropical forest degradation and its impact on ecological sensitivity: A case study in Jinghong, Xishuangbanna, China

Due to rapid urbanization and a growing population, the tropical forest in southwestern China has experienced a dramatic shrinkage, which threatens its biodiversity and imposes limitations to sustainable development. Spatiotemporal change analysis and ecological sensitivity assessment are the important prerequisites for investigating the relationship between eco-environmental quality and human activities. In this study, the tropical forest and other land cover types in Jinghong, China were firstly classified by a machine learning classification algorithm (support vector machine, SVM) with 7 pairs of remote sensing (RS) data (from 1989 to 2018). Then the spatiotemporal change patterns were analyzed. The ecological sensitivity was evaluated based on an index system method (ISM) in which a weighted combination of eleven indicators were produced using an analytic hierarchy process (AHP) method and GIS. Meanwhile four individual sensitivity indicators, including biodiversity sensitivity (BS), water resources sensitivity (WRS), geological hazard sensitivity (GHS) and soil erosion sensitivity (SES) were assessed respectively to create a multi-perspective understanding of the entire ecological sensitivity. The results suggest that the tropical forest experienced a continual decrease from 5631.78 km² in 1999 to 4216.23 km² in 2018 with an average change rate of -1.49%. The decreased area was mainly encroached on by human settlements and agriculture, particularly in the south of Jinghong. Furthermore, it could be seen that urbanization is the key driver for the changes to ecological sensitivity with both positive and negative impacts. In Jinghong, the region covered by a tropical forest has a relatively higher comprehensive ecological sensitivity (CES) than that of an urban area. This work shows RS and GIS to be powerful tools providing profound insights to researchers with regard to the spatiotemporal evolution of tropical forests and ecological sensitivity. The results are significant for improving policies in order to keep a sustainable balance in regional ecosystem management.

Seasonal shifts of arbuscular mycorrhizal fungi in Cocos nucifera roots in Yucatan, Mexico

The diversity and community structure of arbuscular mycorrhizal fungi (AMF) associated with coconut (Cocos nucifera) roots was evaluated by next generation sequencing (NGS) using partial sequences of the 18S rDNA gene and by spore isolation and morphological identification from rhizosphere soil. Root samples from six different Green Dwarf coconut plantations and from one organic plantation surrounded by tropical dry forest along the coastal sand dunes in Yucatan, Mexico, were collected during the rainy and dry seasons. In total, 14 root samples were sequenced with the Illumina MiSeq platform. Additionally, soil samples from the dry season were collected to identify AMF glomerospores. Based on a 95-97% similarity, a total of 36 virtual taxa (VT) belonging to nine genera were identified including one new genus-like clade. Glomus was the most abundant genus, both in number of VT and sequences. The comparison of dry and rainy season samples revealed differences in the richness and composition of AMF communities colonizing coconut roots. Our study shows that the main AMF genera associated with coconut tree roots in all samples were Glomus, Sclerocystis, Rhizophagus, Redeckera, and Diversispora. Based on glomerospore morphology, 22 morphospecies were recorded among which 14 were identified to species. Sclerocystis sinuosa, Sclerocystis rubiformis, Glomus microaggregatum, and Acaulospora scrobiculata were dominant in field rhizosphere samples. This is the first assessment of the composition of AMF communities colonizing coconut roots in rainy and dry seasons. It is of importance for selection of AMF species to investigate for their potential application in sustainable agriculture of coconut.

Metagenomic 16S rDNA amplicon data on bacterial diversity profiling and its predicted metabolic functions of varillales in Allpahuayo-Mishana National Reserve

The white-sands forests or varillales of the Peruvian Amazon are characterized by their distinct physical characteristics, patchy distribution, and endemism [1, 2]. Much research has been conducted on the specialized plant and animal communities that inhabit these ecosystems, yet their soil microbiomes have yet to be studied. Here we provide metagenomic 16S rDNA amplicon data of soil microbiomes from three types of varillales in Allpahuayo-Mishana National Reserve near Iquitos, Peru. Composite soil samples were collected from very low varillal, high-dry varillal, and high-wet varillal. Purified metagenomic DNA was used to prepare and sequence 16S rDNA metagenomic libraries on the Illumina MiqSeq platform. Raw paired-endsequences were analyzed using the Metagenomics RAST server (MG-RAST) and Parallel-Meta3 software and revealed the existence of a high percentage of undiscovered sequences, potentially indicating specialized bacterial communities in these forests. Also, were predicted several metabolic functions in this dataset. The raw sequence data in fastq format is available in the public repository Discover Mendeley Data (https://data.mendeley.com/datasets/syktzxcnp6/2). Also, is available at NCBI's Sequence Read Archive (SRA) with accession numbers SRX7891206 (very low varillal), SRX7891207 (high-dry varillal), and SRX7891208 (high-wet varillal).

Development of a portable leaf photosynthesis and volatile organic compounds emission system

Understanding how plant carbon metabolism responds to environmental variables such as light is central to understanding ecosystem carbon cycling and the production of food, biofuels, and biomaterials. Here, we couple a portable leaf photosynthesis system to an autosampler for volatile organic compounds (VOCs) to enable field observations of net photosynthesis simultaneously with emissions of VOCs as a function of light. Following sample collection, VOCs are analyzed using automated thermal desorption-gas chromatograph-mass spectrometry (TD-GC-MS). An example is presented from a banana plant in the central Amazon with a focus on the response of photosynthesis and the emissions of eight individual monoterpenes to light intensity. Our observations reveal that banana leaf emissions represent a 1.1 +/- 0.1% loss of photosynthesis by carbon. Monoterpene emissions from banana are dominated by trans-β-ocimene, which accounts for up to 57% of total monoterpene emissions at high light. We conclude that the developed system is ideal for the identification and quantification of VOC emissions from leaves in parallel with CO2 and water fluxes.The system therefore permits the analysis of biological and environmental sensitivities of carbon metabolism in leaves in remote field locations, resulting in the emission of hydrocarbons to the atmosphere.•A field-portable system is developed for the identification and quantification of VOCs from leaves in parallel with leaf physiological measurements including photosynthesis and transpiration.•The system will enable the characterization of carbon and energy allocation to the biosynthesis and emission of VOCs linked with photosynthesis (e.g. isoprene and monoterpenes) and their biological and environmental sensitivities (e.g. light, temperature, CO2).•Allow the development of more accurate mechanistic global VOC emission models linked with photosynthesis, improving our ability to predict how forests will respond to climate change. It is our hope that the presented system will contribute with critical data towards these goals across Earth's diverse tropical forests.

Temporal changes in the most effective pollinator of a bromeliad pollinated by bees and hummingbirds

A generalist pollination system may be characterized through the interaction of a plant species with two or more functional groups of pollinators. The spatiotemporal variation of the most effective pollinator is the factor most frequently advocated to explain the emergence and maintenance of generalist pollination systems. There are few studies merging variation in floral visitor assemblages and the efficacy of pollination by different functional groups. Thus, there are gaps in our knowledge about the variation in time of pollinator efficacy and frequency of generalist species. In this study, we evaluated the pollination efficacy of the floral visitors of Edmundoa lindenii (Bromeliaceae) and their frequency of visits across four reproductive events. We analyzed the frequency of the three groups of floral visitors (large bees, small bees, and hummingbirds) through focal observations in the reproductive events of 2015, 2016, 2017, and 2018. We evaluated the pollination efficacy (fecundity after one visit) through selective exposure treatments and the breeding system by manual pollinations. We tested if the reproductive success after natural pollination varied between the reproductive events and also calculated the pollen limitation index. E. lindenii is a self-incompatible and parthenocarpic species, requiring the action of pollinators for sexual reproduction. Hummingbirds had higher efficacy than large bees and small bees acted only as pollen larcenists. The relative frequency of the groups of floral visitors varied between the reproductive events. Pollen limitation has occurred only in the reproductive event of 2017, when visits by hummingbirds were scarce and reproductive success after natural pollination was the lowest. We conclude that hummingbirds and large bees were the main and the secondary pollinators of E. lindenii, respectively, and that temporal variations in the pollinator assemblages had effects on its reproductive success. Despite their lower pollination efficacy, large bees ensured seed set when hummingbirds failed. Thus, we provide evidence that variable pollination environments may favor generalization, even under differential effectiveness of pollinator groups if secondary pollinators provide reproductive assurance.

Potential role in seed dispersal revealed by experimental trials with captive southern muriquis (Brachyteles arachnoides)

Primates are great fruit consumers and disperse intact seeds from most of the plants they consume, but effective seed dispersal depends, amongst other factors, on handling behavior. Likewise, the treatment in gut and mouth may alter seed fate. Overall, frugivore and folivore-frugivore primates are recognized to provide beneficial gut treatment for Neotropical plant species, but this effect might be overlooked at species-specific levels. In this study, we assessed the role of the southern muriqui (Brachyteles arachnoides), an endangered and endemic primate living in restricted fragments of the Brazilian Atlantic Forest, on potential quality of seed dispersal of native plants. Our main goals were to understand the effect of seed ingestion by this large-bodied atelid on germination of defecated seeds and in seed recovery by offering wild fruits of native species to captive individuals. We found that seven out of nine plant species were defecated intact and were able to germinate. Of those seven, one species showed enhanced and another showed decreased germination potential after defecation, while three species germinated faster after being defecated. The remaining species showed no differences from control seeds. The two non-germinating species were heavily predated, and average seed recovery was lower than expected, suggesting high levels of seed predation. The largest species offered (Inga vulpina) showed the highest dispersal potential. Our data support an overall neutral or potentially positive role of southern muriquis in seed dispersal quality for seven out of nine Atlantic Forest plant species, highlighting these primates' potential to produce an effective seed rain.

Understanding the relationship between soil properties and litter chemistry in three forest communities in tropical forest ecosystem

In this study, we investigated the relationship between soil properties and litter chemistry in three forest communities, i.e., Sal mixed forest (SMF), dry mixed forest (DMF), and teak plantation forest (TPF), in tropical deciduous forest ecosystem in North India. Fresh leaf litter and soil samples were collected at two soil depths (0-15 and 15-30 cm) from all these three forest communities. Litter bag experiment was also conducted to know differences in litter nutrients after its decomposition. The concentrations (mg kg^-1) of different nutrients such as sodium (Na) 2.6, potassium (K) 38.5, calcium (Ca) 425, and carbon (C) 45.54% were highest in fresh litter collected from DMF. Total organic carbon (g kg^-1) was significantly higher in SMF (19.23) in comparison to DMF (18.41) and TPF (13.61) at 0-15-cm soil depth. Na, K, Ca, available P, total P, available N, and total N were highest in DMF soil. We observed significantly positive correlation between all nutrients of litter and soil. Although soil bulk density (BD) and particle density (PD) showed their significant negative correlation with litter C, total porosity was positively correlated. Similarly, litter Na has its significant negative correlation with BD and positive correlation with PD. The litter chemistry played a significant role in changing soil pH and TOC. All litter nutrients, except total P, have their significant positive correlation with soil pH. Total P, C, and N of litter have their significant positive correlation with total soil organic carbon. This indicates that litter chemistry and soil properties have specific relation among them despite unique species composition in each forest community.

Regulation of nitrogen fixation from free-living organisms in soil and leaf litter of two tropical forests of the Guiana shield

BACKGROUND AND AIMS

Biological fixation of atmospheric nitrogen (N₂) is the main pathway for introducing N into unmanaged ecosystems. While recent estimates suggest that free-living N fixation (FLNF) accounts for the majority of N fixed in mature tropical forests, the controls governing this process are not completely understood. The aim of this study was to quantify FLNF rates and determine its drivers in two tropical pristine forests of French Guiana.

METHODS

We used the acetylene reduction assay to measure FLNF rates at two sites, in two seasons and along three topographical positions, and used regression analyses to identify which edaphic explanatory variables, including carbon (C), nitrogen (N), phosphorus (P) and molybdenum (Mo) content, pH, water and available N and P, explained most of the variation in FLNF rates.

RESULTS

Overall, FLNF rates were lower than measured in tropical systems elsewhere. In soils seasonal variability was small and FLNF rates differed among topographies at only one site. Water, P and pH explained 24% of the variation. In leaf litter, FLNF rates differed seasonally, without site or topographical differences. Water, C, N and P explained 46% of the observed variation. We found no regulatory role of Mo at our sites.

CONCLUSIONS

Rates of FLNF were low in primary rainforest on poor soils on the Guiana shield. Water was the most important rate-regulating factor and FLNF increased with increasing P, but decreased with increasing N. Our results support the general assumption that N fixation in tropical lowland forests is limited by P availability.

Forest filter effect for polybrominated diphenyl ethers in a tropical watershed

There is limited research characterizing the fates of persistent organic pollutants in tropical multi-use watersheds. This study aimed to evaluate the role of forests in the environmental fates of select polybrominated diphenyl ethers (PBDEs) for a case study tropical drainage basin, the Rio Cobre watershed. Field samples of deposition, soil, litterfall and the atmosphere of a forest and nearby clearing were analyzed for the presence of the PBDEs (PBDE-28, 47, 99, 100, 153, 154, 183 and 209), which are routinely detected in the environment. The mean air and litterfall concentrations of these PBDEs were generally lower in the forest than in the clearing, whereas the deposition flux rate and soil concentrations were higher in the forest. The results suggest that the forest filtered the PBDEs by transferring them from the atmosphere to the soil, despite the tropical nature of the study site.

Comparison of malaria incidence rates and socioeconomic-environmental factors between the states of Acre and Rondônia: a spatio-temporal modelling study

BACKGROUND

Plasmodium falciparum malaria is a threat to public health, but Plasmodium vivax malaria is most prevalent in Latin America, where the incidence rate has been increasing since 2016, particularly in Venezuela and Brazil. The Brazilian Amazon reported 193,000 cases in 2017, which were mostly confirmed as P. vivax (~ 90%). Herein, the relationships among malaria incidence rates and the proportion of accumulated deforestation were contrasted using data from the states of Acre and Rondônia in the south-western Brazilian Amazon. The main purpose is to test the hypothesis that the observed difference in incidence rates is associated with the proportion of accumulated deforestation.

METHODS

An ecological study using spatial and temporal models for mapping and modelling malaria risk was performed. The municipalities of Acre and Rondônia were the spatial units of analysis, whereas month and year were the temporal units. The number of reported malaria cases from 2009 until 2015 were used to calculate the incidence rate per 1000 people at risk. Accumulated deforestation was calculated using publicly available satellite images. Geographically weighted regression was applied to provide a local model of the spatial heterogeneity of incidence rates. Time-series dynamic regression was applied to test the correlation of incidence rates and accumulated deforestation, adjusted by climate and socioeconomic factors.

RESULTS

The malaria incidence rate declined in Rondônia but remained stable in Acre. There was a high and positive correlation between the decline in malaria and higher proportions of accumulated deforestation in Rondônia. Geographically weighted regression showed a complex relationship. As deforestation increased, malaria incidence also increased in Acre, while as deforestation increased, malaria incidence decreased in Rondônia. Time-series dynamic regression showed a positive association between malaria incidence and precipitation and accumulated deforestation, whereas the association was negative with the human development index in the westernmost areas of Acre.

CONCLUSION

Landscape modification caused by accumulated deforestation is an important driver of malaria incidence in the Brazilian Amazon. However, this relationship is not linearly correlated because it depends on the overall proportion of the land covered by forest. For regions that are partially degraded, forest cover becomes a less representative component in the landscape, causing the abovementioned non-linear relationship. In such a scenario, accumulated deforestation can lead to a decline in malaria incidence.

Photosynthetic heat tolerance of shade and sun leaves of three tropical tree species

Previous studies of heat tolerance of tropical trees have focused on canopy leaves exposed to full sunlight and high temperatures. However, in lowland tropical forests with leaf area indices of 5-6, the vast majority of leaves experience varying degrees of shade and a reduced heat load compared to sun leaves. Here we tested whether heat tolerance is lower in shade than in sun leaves. For three tropical tree species, Calophyllum inophyllum, Inga spectabilis, and Ormosia macrocalyx, disks of fully developed shade and sun leaves were subjected to 15-min heat treatments, followed by measurement of chlorophyll a fluorescence after 48 h of recovery. In two of the three species, the temperature causing a 50% decrease of the fluorescence ratio F_v/F_m (T₅₀) was significantly lower (by ~ 1.0 °C) in shade than in sun leaves, indicating a moderately decreased heat tolerance of shade leaves. In shade leaves of these two species, the rise in initial fluorescence, F₀, also occurred at lower temperatures. In the third species, there was no shade-sun difference in T₅₀. In situ measurements of photosynthetic CO₂ assimilation showed that the optimum temperature for photosynthesis tended to be lower in shade leaves, although differences were not significant. At supra-optimal temperatures, photosynthesis was largely constrained by stomatal conductance, and the high-temperature CO₂ compensation point, T_Max, occurred at considerably lower temperatures than T₅₀. Our study demonstrates that the temperature response of shade leaves of tropical trees differs only marginally from that of sun leaves, both in terms of heat tolerance and photosynthetic performance.