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Dessert, C., Clergue, C., Rousteau, A., Crispi, O., & Benedetti, M. F. (2020). Atmospheric contribution to cations cycling in highly weathered catchment, Guadeloupe (Lesser Antilles). Chem. Geol., 531(119354).
Abstract: The important fertilizing role of atmospheric dust, and particularly African dust, in tropical rainforests is increasingly recognized but still poorly quantified. To better evaluate dust input into the Caribbean basin, we sampled critical zone compartments of a small forested volcanic catchment in Guadeloupe (soils, parent rock, atmospheric dust, plants, soil solutions, stream and rain waters). The aims of this study are to track sources of cation nutrients (Ca, Mg, K, Sr) developed on highly weathered soil in the rainforest of Guadeloupe, to quantify plant recycling of these nutrients, and to identify constraints on regolith development and its associated nutrient pool. In the Quiock Creek catchment, a large isotopic range of 87Sr/86Sr and eNd values was observed despite the small scale of observation. Sr isotopic composition of the dissolved load varied from 0.7084 in rainfall to 0.7110 in soil solution, whereas it ranges between 0.7068 and 0.7153 for soil samples and between 0.7096 and 0.7102 for plants. The Nd isotopic composition varied between -8.39 in near-surface soil samples to 2.71 in deeper soil. All samples had an intermediate signature between that of the bedrock endmember (87Sr/86Sr = 0.7038; eNd = 4.8) and the atmospheric endmember (sea salt: 87Sr/86Sr = 0.7092 and Saharan dust: 87Sr/86Sr = 0.7187, eNd=-11.5). The regolith was built on pyroclastic deposits, but, because of extreme leaching, the regolith has lost its original bedrock signature and inherited an exogenous atmospheric signature. Our results show that only the chemical weathering of the fresh near-surface minerals can provide nutrients to the ecosystem (first 30 cm). However, this dust weathering is too low to sustain the tropical forest ecosystem on its own. The cationic mass balance at the catchment scale, as well as the Sr isotopic signature, show that cation and Sr fluxes are of atmospheric origin only and that original bedrock no longer participates in nutrient cycles. The vegetation reflects the 87Sr/86Sr of the dissolved pool of atmospheric Sr. At the soil-plant scale, the cation-nutrient fluxes provided by vegetation (litter fall + leaf excretion) are major compared to input and output fluxes. The annual Ca, K, Sr and Mg fluxes within the vegetation are, respectively, 31, 28, 20 and 3 times greater than the exported fluxes at the outlet of the basin. The residence time of nutrients in the vegetation is 16 years for K and close to 45 years for Sr, Ca and Mg. These results emphasize the highly efficient vegetative turnover that dominates the nutrient cycle in the Quiock Creek catchment. This first characterization of biogeochemical cycles in the Guadeloupean rainforest suggests that the forest community of Quiock Creek is sustained by a small near-surface nutrient pool disconnected from the deep volcanic bedrock. We also demonstrated that, even with efficient nutrient recycling, Saharan dust plays a significant role in maintaining ecosystem productivity in Guadeloupe over long-time scales.
Keywords: Atmospheric deposit; Cation-nutrient recycling; Critical Zone; Saharan dust; Sr and Nd isotopes; Atmospheric chemistry; Biogeochemistry; Catchments; Deposits; Dust; Ecosystems; Forestry; Isotopes; Lakes; Positive ions; Rain; Recycling; Runoff; Soil moisture; Soil surveys; Tropics; Vegetation; Volcanoes; Weathering; Atmospheric deposits; Critical zones; Nutrient recycling; Saharan dust; Sr and Nd isotopes; Nutrients; catchment; cation; dust; isotopic composition; neodymium isotope; regolith; strontium isotope; trace element; water chemistry; water quality; Guadeloupe; Leeward Islands [Lesser Antilles]; Sahara
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Sommeria-Klein, G., Zinger, L., Coissac, E., Iribar, A., Schimann, H., Taberlet, P., et al. (2020). Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA-based census of soil biodiversity from a tropical forest. Mol. Ecol. Resour., 20(2), 371–386.
Abstract: High-throughput sequencing of amplicons from environmental DNA samples permits rapid, standardized and comprehensive biodiversity assessments. However, retrieving and interpreting the structure of such data sets requires efficient methods for dimensionality reduction. Latent Dirichlet Allocation (LDA) can be used to decompose environmental DNA samples into overlapping assemblages of co-occurring taxa. It is a flexible model-based method adapted to uneven sample sizes and to large and sparse data sets. Here, we compare LDA performance on abundance and occurrence data, and we quantify the robustness of the LDA decomposition by measuring its stability with respect to the algorithm's initialization. We then apply LDA to a survey of 1,131 soil DNA samples that were collected in a 12-ha plot of primary tropical forest and amplified using standard primers for bacteria, protists, fungi and metazoans. The analysis reveals that bacteria, protists and fungi exhibit a strong spatial structure, which matches the topographical features of the plot, while metazoans do not, confirming that microbial diversity is primarily controlled by environmental variation at the studied scale. We conclude that LDA is a sensitive, robust and computationally efficient method to detect and interpret the structure of large DNA-based biodiversity data sets. We finally discuss the possible future applications of this approach for the study of biodiversity. © 2019 John Wiley & Sons Ltd
Keywords: community ecology; environmental DNA; metabarcoding; OTU presence–absence; soil microbiome; topic modelling; bacterium; biodiversity; biology; classification; eukaryote; fungus; genetics; high throughput sequencing; isolation and purification; microbiology; parasitology; procedures; soil; Bacteria; Biodiversity; Computational Biology; Eukaryota; Fungi; High-Throughput Nucleotide Sequencing; Soil; Soil Microbiology
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Schimann, H., Vleminckx, J., Baraloto, C., Engel, J., Jaouen, G., Louisanna, E., et al. (2020). Tree communities and soil properties influence fungal community assembly in neotropical forests. Biotropica, 52(3), 444–456.
Abstract: The influence exerted by tree communities, topography, and soil chemistry on the assembly of macrofungal communities remains poorly understood, especially in highly diverse tropical forests. Here, we used a large dataset that combines inventories of macrofungal Basidiomycetes fruiting bodies, tree species composition, and measurements for 16 soil physicochemical parameters, collected in 34 plots located in four sites of lowland rain forests in French Guiana. Plots were established on three different topographical conditions: hilltop, slope, and seasonally flooded soils. We found hyperdiverse Basidiomycetes communities, mainly comprising members of Agaricales and Polyporales. Phosphorus, clay contents, and base saturation in soils strongly varied across plots and shaped the richness and composition of tree communities. The latter composition explained 23% of the variation in the composition of macrofungal communities, probably through high heterogeneity of the litter chemistry and selective effects of biotic interactions. The high local heterogeneity of habitats influenced the distribution of both macrofungi and trees, as a result of diversed local soil hydromorphic conditions associated with contrasting soil chemistry. This first regional study across habitats of French Guiana forests revealed new niches for macrofungi, such as ectomycorrhizal ones, and illustrates how macrofungi inventories are still paramount to can be to understand the processes at work in the tropics. Abstract in Spanish is available with online material. © 2020 The Association for Tropical Biology and Conservation
Keywords: communities; composition; diversity; habitat; lowland neotropical rain forest; macrofungi; soil properties; trees; ectomycorrhiza; fungus; heterogeneity; Neotropical Region; physicochemical property; rainforest; species inventory; species richness; tree; tropical forest; French Guiana; Agaricales; Aphyllophorales; Basidiomycota
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Legeay, J., Husson, C., Boudier, B., Louisanna, E., Baraloto, C., Schimann, H., et al. (2020). Surprising low diversity of the plant pathogen Phytophthora in Amazonian forests. Environ. Microbiol., 22(12), 5019–5032.
Abstract: The genus Phytophthora represents a group of plant pathogens with broad global distribution. The majority of them cause the collar and root-rot of diverse plant species. Little is known about Phytophthora communities in forest ecosystems, especially in the Neotropical forests where natural enemies could maintain the huge plant diversity via negative density dependence. We characterized the diversity of soil-borne Phytophthora communities in the North French Guiana rainforest and investigated how they are structured by host identity and environmental factors. In this little-explored habitat, 250 soil cores were sampled from 10 plots hosting 10 different plant families across three forest environments (Terra Firme, Seasonally Flooded and White Sand). Phytophthora diversity was studied using a baiting approach and metabarcoding (High-Throughput Sequencing) on environmental DNA extracted from both soil samples and baiting-leaves. These three approaches revealed very similar communities, characterized by an unexpected low diversity of Phytophthora species, with the dominance of two cryptic species close to Phytophthora heveae. As expected, the Phytophthora community composition of the French Guiana rainforest was significantly impacted by the host plant family and environment. However, these plant pathogen communities are very small and are dominated by generalist species, questioning their potential roles as drivers of plant diversity in these Amazonian forests. © 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.
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Privet, K., Vedel, V., Fortunel, C., Orivel, J., Martinez, Q., Cerdan, A., et al. (2020). Relative effciency of pitfall trapping vs. nocturnal hand collecting in assessing soil-dwelling spider diversity along a structural gradient of neotropical habitats. Diversity, 12(2), 81.
Abstract: Assessing spider diversity remains a great challenge, especially in tropical habitats where dozens of species can locally co-occur. Pitfall trapping is one of the most widely used techniques to collect spiders, but it suffers from several biases, and its accuracy likely varies with habitat complexity. In this study, we compared the efficiency of passive pitfall trapping versus active nocturnal hand collecting (\"HC) to capture low understory-dwelling spider taxonomical (morpho-species) and functional (hunting guilds) diversity along a structural gradient of habitats in French Guiana. We focused on four habitats describing a structural gradient: garden to the orchard to the forest edge to the undisturbed forest. Overall, estimated morpho-species richness and composition did not vary consistently between habitats, but abundances of ground-hunting spiders decreased significantly with increasing habitat complexity. We found habitat-dependence differences in taxonomic diversity between sampling strategies: NHC revealed higher diversity in the orchard, whereas pitfalls resulted in higher diversity in the forest. Species turnover resulted in high dissimilarity in species composition between habitats using either method. This study shows how pitfall trapping is influenced by habitat structure, rendering this sampling method incomplete for complex, tropical environments. However, pitfall traps remain a valuable component of inventories because they sample distinct assemblage of spiders. © 2020 by the authors.
Keywords: Araneae; Diversity indices; Functional diversity; Guiana shield; Sampling methods; Species richness; Turnover; Araneae
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Honorio Coronado, E. N., Blanc-Jolivet, C., Mader, M., García-Dávila, C. R., Gomero, D. A., del Castillo Torres, D., et al. (2020). SNP markers as a successful molecular tool for assessing species identity and geographic origin of trees in the economically important South American legume genus Dipteryx. J. Hered., 111(4), 346–356.
Abstract: Dipteryx timber has been heavily exploited in South America since 2000s due to the increasing international demand for hardwood. Developing tools for the genetic identification of Dipteryx species and their geographical origin can help to promote legal trading of timber. A collection of 800 individual trees, belonging to 6 different Dipteryx species, was genotyped based on 171 molecular markers. After the exclusion of markers out of Hardy-Weinberg equilibrium or with no polymorphism or low amplification, 83 nuclear, 29 chloroplast, 13 mitochondrial single nucleotide polymorphisms (SNPs), and 2 chloroplast and 5 mitochondrial INDELS remained. Six genetic groups were identified using Bayesian Structure analyses of the nuclear SNPs, which corresponded to the different Dipteryx species collected in the field. Seventeen highly informative markers were identified as suitable for species identification and obtained self-assignment success rates to species level of 78-96%. An additional set of 15 molecular markers was selected to determine the different genetic clusters found in Dipteryx odorata and Dipteryx ferrea, obtaining self-assignment success rates of 91-100%. The success to assign samples to the correct country of origin using all or only the informative markers improved when using the nearest neighbor approach (69-92%) compared to the Bayesian approach (33-80%). While nuclear and chloroplast SNPs were more suitable for differentiating the different Dipteryx species, mitochondrial SNPs were ideal for determining the genetic clusters of D. odorata and D. ferrea. These 32 selected SNPs will be invaluable genetic tools for the accurate identification of species and country of origin of Dipteryx timber. © The American Genetic Association 2020. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com
Keywords: Cumaru; Genetic assignment; Leguminosae; Timber verification; article; chloroplast; genetic association; genetic marker; geographic origin; indel mutation; nonhuman; single nucleotide polymorphism; species identification; structure analysis; tonka bean; Dipteryx; Fabaceae
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ter Steege, H., Prado, P. I., Lima, R. A. F., Pos, E., de Souza Coelho, L., de Andrade Lima Filho, D., et al. (2020). Biased-corrected richness estimates for the Amazonian tree flora. Sci. Rep., 10(10130).
Abstract: Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia is best approximated by a logseries with aggregated individuals, where aggregation increases with rarity. By averaging several methods to estimate total richness, we confirm that over 15,000 tree species are expected to occur in Amazonia. We also show that using ten times the number of plots would result in an increase to just ~50% of those 15,000 estimated species. To get a more complete sample of all tree species, rigorous field campaigns may be needed but the number of trees in Amazonia will remain an estimate for years to come. © 2020, The Author(s).
Keywords: adult; article; averaging; flora; forest; population abundance
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Romero, G. Q., Marino, N. A. C., MacDonald, A. A. M., Céréghino, R., Trzcinski, M. K., Mercado, D. A., et al. (2020). Extreme rainfall events alter the trophic structure in bromeliad tanks across the Neotropics. Nat. Commun., 11(3215).
Abstract: Changes in global and regional precipitation regimes are among the most pervasive components of climate change. Intensification of rainfall cycles, ranging from frequent downpours to severe droughts, could cause widespread, but largely unknown, alterations to trophic structure and ecosystem function. We conducted multi-site coordinated experiments to show how variation in the quantity and evenness of rainfall modulates trophic structure in 210 natural freshwater microcosms (tank bromeliads) across Central and South America (18°N to 29°S). The biomass of smaller organisms (detritivores) was higher under more stable hydrological conditions. Conversely, the biomass of predators was highest when rainfall was uneven, resulting in top-heavy biomass pyramids. These results illustrate how extremes of precipitation, resulting in localized droughts or flooding, can erode the base of freshwater food webs, with negative implications for the stability of trophic dynamics. © 2020, The Author(s).
Keywords: fresh water; rain; fresh water; agricultural intensification; angiosperm; biomass; climate change; ecosystem function; extreme event; food web; freshwater ecosystem; Neotropic Ecozone; precipitation intensity; rainfall; trophic structure; Article; biomass; Central America; controlled study; detritivore; drought; flooding; food web; hydrology; microcosm; Neotropics; nonhuman; precipitation; predator; South America; trophic level; animal; biodiversity; Bromelia; climate change; ecosystem; flooding; food chain; Central America; South America; Animals; Biodiversity; Biomass; Bromelia; Climate Change; Droughts; Ecosystem; Floods; Food Chain; Fresh Water; Hydrology; South America
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Kattge, J., Bönisch, G., Díaz, S., Lavorel, S., Prentice, I. C., Leadley, P., et al. (2020). TRY plant trait database – enhanced coverage and open access. Global Change Biol., 26(1), 119–188.
Abstract: Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
Keywords: data coverage; data integration; data representativeness; functional diversity; plant traits; TRY plant trait database; biodiversity; data processing; database; ecological modeling; environmental factor; growth; intraspecific competition; access to information; biodiversity; ecology; ecosystem; plant; Access to Information; Biodiversity; Ecology; Ecosystem; Plants
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Thomas, H. J. D., Bjorkman, A. D., Myers-Smith, I. H., Elmendorf, S. C., Kattge, J., Diaz, S., et al. (2020). Global plant trait relationships extend to the climatic extremes of the tundra biome. Nat. Commun., 11(1351).
Abstract: The majority of variation in six traits critical to the growth, survival and reproduction of plant species is thought to be organised along just two dimensions, corresponding to strategies of plant size and resource acquisition. However, it is unknown whether global plant trait relationships extend to climatic extremes, and if these interspecific relationships are confounded by trait variation within species. We test whether trait relationships extend to the cold extremes of life on Earth using the largest database of tundra plant traits yet compiled. We show that tundra plants demonstrate remarkably similar resource economic traits, but not size traits, compared to global distributions, and exhibit the same two dimensions of trait variation. Three quarters of trait variation occurs among species, mirroring global estimates of interspecific trait variation. Plant trait relationships are thus generalizable to the edge of global trait-space, informing prediction of plant community change in a warming world. © 2020, Crown.
Keywords: biome; climate change; extreme event; global change; growth; interspecific interaction; plant community; tundra; article; plant community; prediction; tundra; warming; classification; climate; ecosystem; genetics; plant; plant development; Climate; Ecosystem; Plant Development; Plants; Tundra
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