|
|
Honorio Coronado, E. N., Dexter, K. G., Pennington, R. T., Chave, J., Lewis, S. L., Alexiades, M. N., et al. (2015). Phylogenetic diversity of Amazonian tree communities. Diversity and Distributions, 21(11), 1295–1307.
Abstract: Aim: To examine variation in the phylogenetic diversity (PD) of tree communities across geographical and environmental gradients in Amazonia. Location: Two hundred and eighty-three c. 1 ha forest inventory plots from across Amazonia. Methods: We evaluated PD as the total phylogenetic branch length across species in each plot (PDss), the mean pairwise phylogenetic distance between species (MPD), the mean nearest taxon distance (MNTD) and their equivalents standardized for species richness (ses.PDss, ses.MPD, ses.MNTD). We compared PD of tree communities growing (1) on substrates of varying geological age; and (2) in environments with varying ecophysiological barriers to growth and survival. Results: PDss is strongly positively correlated with species richness (SR), whereas MNTD has a negative correlation. Communities on geologically young- and intermediate-aged substrates (western and central Amazonia respectively) have the highest SR, and therefore the highest PDss and the lowest MNTD. We find that the youngest and oldest substrates (the latter on the Brazilian and Guiana Shields) have the highest ses.PDss and ses.MNTD. MPD and ses.MPD are strongly correlated with how evenly taxa are distributed among the three principal angiosperm clades and are both highest in western Amazonia. Meanwhile, seasonally dry tropical forest (SDTF) and forests on white sands have low PD, as evaluated by any metric. Main conclusions: High ses.PDss and ses.MNTD reflect greater lineage diversity in communities. We suggest that high ses.PDss and ses.MNTD in western Amazonia results from its favourable, easy-to-colonize environment, whereas high values in the Brazilian and Guianan Shields may be due to accumulation of lineages over a longer period of time. White-sand forests and SDTF are dominated by close relatives from fewer lineages, perhaps reflecting ecophysiological barriers that are difficult to surmount evolutionarily. Because MPD and ses.MPD do not reflect lineage diversity per se, we suggest that PDss, ses.PDss and ses.MNTD may be the most useful diversity metrics for setting large-scale conservation priorities. © 2015 John Wiley & Sons Ltd.
Keywords: Amazon basin; Eudicots; Magnoliids; Monocots; Phylogenetic diversity; Species richness
|
|
|
|
Courtois, E. A., Stahl, C., Van den Berge, J., Bréchet, L., Van Langenhove, L., Richter, A., et al. (2018). Spatial Variation of Soil CO2, CH4 and N2O Fluxes Across Topographical Positions in Tropical Forests of the Guiana Shield. Ecosystems, 21(7), 1445–1458.
Abstract: The spatial variation of soil greenhouse gas fluxes (GHG; carbon dioxide—CO2, methane—CH4 and nitrous oxide—N2O) remains poorly understood in highly complex ecosystems such as tropical forests. We used 240 individual flux measurements of these three GHGs from different soil types, at three topographical positions and in two extreme hydric conditions in the tropical forests of the Guiana Shield (French Guiana, South America) to (1) test the effect of topographical positions on GHG fluxes and (2) identify the soil characteristics driving flux variation in these nutrient-poor tropical soils. Surprisingly, none of the three GHG flux rates differed with topographical position. CO2 effluxes covaried with soil pH, soil water content (SWC), available nitrogen and total phosphorus. The CH4 fluxes were best explained by variation in SWC, with soils acting as a sink under drier conditions and as a source under wetter conditions. Unexpectedly, our study areas were generally sinks for N2O and N2O fluxes were partly explained by total phosphorus and available nitrogen concentrations. This first study describing the spatial variation of soil fluxes of the three main GHGs measured simultaneously in forests of the Guiana Shield lays the foundation for specific studies of the processes underlying the observed patterns.
|
|
|
|
Coutant, O., Richard-Hansen, C., de Thoisy, B., Decotte, J. - B., Valentini, A., Dejean, T., et al. (2021). Amazonian mammal monitoring using aquatic environmental DNA. Molecular Ecology Resources, 21(6), 1875–1888.
Abstract: Environmental DNA (eDNA) metabarcoding has emerged as one of the most efficient methods to assess aquatic species presence. While the method can in theory be used to investigate nonaquatic fauna, its development for inventorying semi-aquatic and terrestrial fauna is still at an early stage. Here we investigated the potential of aquatic eDNA metabarcoding for inventorying mammals in Neotropical environments, be they aquatic, semi-aquatic or terrestrial. We collected aquatic eDNA in 96 sites distributed along three Guianese watersheds and compared our inventories to expected species distributions and field observations derived from line transects located throughout French Guiana. Species occurrences and emblematic mammalian fauna richness patterns were consistent with the expected distribution of fauna and our results revealed that aquatic eDNA metabarcoding brings additional data to line transect samples for diurnal nonaquatic (terrestrial and arboreal) species. Aquatic eDNA also provided data on species not detectable in line transect surveys such as semi-aquatic, aquatic and nocturnal terrestrial and arboreal species. Although the application of eDNA to inventory mammals still needs some developments to optimize sampling efficiency, it can now be used as a complement to traditional surveys.
|
|
|
|
Almeras, T., Yoshida, M., & Okuyama, T. (2006). Strains inside xylem and inner bark of a stem submitted to a change in hydrostatic pressure. Trees-Struct. Funct., 20(4), 460–467.
Abstract: Tangential strains were measured with strain gauges at the surface of xylem and inner bark of saplings of Cryptomeria japonica D. Don. and Fagus silvatica L. during a pressurization test. The test consists in submitting the whole sapling to an artificially imposed hydrostatic pressure of increasing magnitude. The elastic response of the stems was found linear both at the surface of xylem and inner bark. A simple geometric model allows to compute radial strains in each tissue from tangential strain data. Inside inner bark, radial strains are much larger than tangential strains, because tangential strains are restrained by the core of wood. The material compliance of each tissue was computed as the ratio between the radial strain and the pressure that caused it. The material compliance of xylem is much lower than that of inner bark, but, as its thickness is much larger, its contribution to the apparent behavior of the stem is not negligible. Computation of material compliances by this pressurization test provides information about the specific behavior of each tissue in response to hydrostatic pressure. This can be used to estimate and interpret the calibration factor linking the water status of the plant to the apparent strain measured at its surface.
Keywords: diurnal strains; hydrostatic pressure; xylem; inner bark; mechanical properties
|
|
|
|
Schimann, H., Petit-Jean, C., Guitet, S., Reis, T., Domenach, A. M., & Roggy, J. - C. (2012). Microbial bioindicators of soil functioning after disturbance: The case of gold mining in tropical rainforests of French Guiana. Ecol. Indic., 20, 34–41.
Abstract: In the context of an ongoing monitoring study on the impacts of gold-mining activities on critical ecosystem processes, we explored the use of soil Denitrifying Enzyme Activity (DEA) and Substrate Induced Respiration (SIR) as ecosystem indicators in tropical rainforests of French Guiana. We also propose DEA/SIR ratio as ecosystem attribute able to describe the state of an ecosystem and to reflect changes in ecological processes. With this purpose, we measured SIR, DEA and DEA/SIR ratio in five gold-mining areas and five surrounding natural reference rainforests. We also measured indicators in two conditions of spontaneous regeneration of vegetation (stratified or not) and two conditions of soil rehabilitation (prior preparation of soils or not). We showed a high variability of DEA, SIR and DEA/SIR ratio in the natural reference forests. This pointed out the necessity to identify relevant reference systems – i.e. proving a close match in all relevant ecological dimensions – to compare with closed perturbed systems in order to assess the levels of alterations after disturbances. Results showed a high impact of gold mine on microbial processes with a strong decrease of DEA (10-fold lower), SIR (2-fold lower) and DEA/SIR ratio (8-fold lower) in perturbed areas in comparison with natural reference forests. The type of spontaneous vegetation (stratified or not) influenced the values of indicators as well as prior rehabilitation of soils, demonstrating the capacity of DEA, SIR and DEA/SIR ratio to respond in proportion to the perturbation (robustness) and to the different levels of restoration (sensitivity). The systematic decrease of the ratio DEA/SIR observed in the studied perturbed situations demonstrates clearly that the structure of microbial communities has been also modified. The ratio DEA/SIR proved to be robust and sensitive, and able to describe in fairly fine way changes of soil microbial communities in terms of structure and function in gold mine areas and during processes of restoration. We propose to use DEA, SIR and DEA/SIR ratio as bioindicators of both structural and functional aspects of C and N cycling in soils. Together with others bioindicators based on key supporting functions in soils, these indicators should accurately evaluate the ecological potential of natural ecosystems and the levels of degradation in case of land-use changes. © 2012 Elsevier Ltd.
Keywords: Bioindicators; DEA/SIR ratio; Denitrifying Enzyme Activity (DEA); Disturbance; Substrate Induced Respiration (SIR); Tropical rainforest
|
|
|
|
Barabe, D., Cuerrier, A., & Quilichini, A. (2012). Botanical gardens: Between science and commercialization. Natures Sciences Societes, 20(3), 334–342.
Abstract: Les jardins botaniques: Entre science et commercialisation.
|
|
|
|
Rowland, L., Hill, T. C., Stahl, C., Siebicke, L., Burban, B., Zaragoza-Castells, J., et al. (2014). Evidence for strong seasonality in the carbon storage and carbon use efficiency of an Amazonian forest. Global Change Biol., 20(3), 979–991.
Abstract: The relative contribution of gross primary production and ecosystem respiration to seasonal changes in the net carbon flux of tropical forests remains poorly quantified by both modelling and field studies. We use data assimilation to combine nine ecological time series from an eastern Amazonian forest, with mass balance constraints from an ecosystem carbon cycle model. The resulting analysis quantifies, with uncertainty estimates, the seasonal changes in the net carbon flux of a tropical rainforest which experiences a pronounced dry season. We show that the carbon accumulation in this forest was four times greater in the dry season than in the wet season and that this was accompanied by a 5% increase in the carbon use efficiency. This seasonal response was caused by a dry season increase in gross primary productivity, in response to radiation and a similar magnitude decrease in heterotrophic respiration, in response to drying soils. The analysis also predicts increased carbon allocation to leaves and wood in the wet season, and greater allocation to fine roots in the dry season. This study demonstrates implementation of seasonal variations in parameters better enables models to simulate observed patterns in data. In particular, we highlight the necessity to simulate the seasonal patterns of heterotrophic respiration to accurately simulate the net carbon flux seasonal tropical forest. © 2013 The Authors Global Change Biology Published by John Wiley & Sons Ltd.
Keywords: Carbon use efficiency; Dalec; Data assimilation; Ecosystem respiration; French Guiana; Seasonal carbon fluxes; Tropical forest
|
|
|
|
Talaga, S., Dezerald, O., Carteron, A., Leroy, C., Carrias, J. - F., Céréghino, R., et al. (2017). Urbanization impacts the taxonomic and functional structure of aquatic macroinvertebrate communities in a small Neotropical city. Urban Ecosystems, 20(5), 1001–1009.
Abstract: Due to habitat fragmentation, resource disruption and pollution, urbanization is one of the most destructive forms of anthropization affecting ecosystems worldwide. Generally, human-mediated perturbations dramatically alter species diversity in urban sites compared to the surroundings, thus influencing the functioning of the entire ecosystem. We investigated the taxonomic and functional diversity patterns of the aquatic macroinvertebrate communities in tank bromeliads by comparing those found in a small Neotropical city with those from an adjacent rural site. Changes in the quality of detrital inputs in relation to lower tree diversity and the presence of synanthropic species are likely important driving forces behind the observed structural changes in the urban site. Leaf-litter processors (i.e., shredders, scrapers) were positively affected in the urban site, while filter-feeders that process smaller particles produced by the activity of the shredders were negatively affected. Because we cannot ascertain whether the decline in filter-feeders is related to food web-mediated effects or to competitive exclusion (Aedes aegypti mosquitoes were present in urban bromeliads only), further studies are necessary to account for the effects of intra-guild competition or inter-guild facilitation. © 2017, Springer Science+Business Media New York.
Keywords: Aedes aegypti; Bioindicator; Diversity; Functional traits; Tank bromeliads; Urban ecology
|
|
|
|
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
|
|
|
|
Blanc, L., Echard, M., Herault, B., Bonal, D., Marcon, E., Chave, J., et al. (2009). Dynamics of aboveground carbon stocks in a selectively logged tropical forest. Ecol. Appl., 19(6), 1397–1404.
Abstract: The expansion of selective logging in tropical forests may be an important source of global carbon emissions. However, the effects of logging practices on the carbon cycle have never been quantified over long periods of time. We followed the fate of more than 60 000 tropical trees over 23 years to assess changes in aboveground carbon stocks in 48 1.56-ha plots in French Guiana that represent a gradient of timber harvest intensities, with and without intensive timber stand improvement (TSI) treatments to stimulate timber tree growth. Conventional selective logging led to emissions equivalent to more than a third of aboveground carbon stocks in plots without TSI (85 Mg C/ha), while plots with TSI lost more than one-half of aboveground carbon stocks (142 Mg C/ha). Within 20 years of logging, plots without TSI sequestered aboveground carbon equivalent to more than 80% of aboveground carbon lost to logging (-70.7 Mg C/ha), and our simulations predicted an equilibrium aboveground carbon balance within 45 years of logging. In contrast, plots with intensive TSI are predicted to require more than 100 years to sequester aboveground carbon lost to emissions. These results indicate that in some tropical forests aboveground carbon storage can be recovered within half a century after conventional logging at moderate harvest intensities.
Keywords: aboveground biomass; carbon sequestration; deforestation; French Guiana; global change; timber stand improvement; tropical forests
|
|
