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Zinger, L., Donald, J., Brosse, S., Gonzalez, M. A., Iribar, A., Leroy, C., et al. (2020). Advances and prospects of environmental DNA in neotropical rainforests. Adv. Ecol. Res., 62, 331–373.
Abstract: The rainforests of the Neotropics shelter a vast diversity of plant, animal and microscopic species that provide critical ecosystem goods and services for both local and worldwide populations. These environments face a major crisis due to increased deforestation, pollution, and climate change, emphasizing the need for more effective conservation efforts. The adequate monitoring of these ecosystems has proven a complex and time consuming endeavour, which depends on ever dwindling taxonomic expertise. To date, many species remain undiscovered, let alone described, with otherwise limited information regarding known species population distributions and densities. Overcoming these knowledge shortfalls and practical limitations is becoming increasingly possible through techniques based on environmental DNA (eDNA), i.e., DNA that can be obtained from environmental samples (e.g. tissues, soil, sediment, water, etc.). When coupled with high-throughput sequencing, these techniques now enable realistic, cost-effective, and standardisable biodiversity assessments. This opens up enormous opportunities for advancing our understanding of complex and species-rich tropical communities, but also in facilitating large-scale biomonitoring programs in the neotropics. In this review, we provide a brief introduction to eDNA methods, and an overview of their current and potential uses in both terrestrial and aquatic ecosystems of neotropical rainforests. We also discuss the limits and challenges of these methods for our understanding and monitoring of biodiversity, as well as future research and applied perspectives of these techniques in neotropical rainforests, and beyond. © 2020 Elsevier Ltd
Keywords: Biomonitoring; Conservation biology; DNA metabarcoding; eDNA; Environmental genomics; Neotropics; Rainforests
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Aubry-Kientz, M., Laybros, A., Weinstein, B., Ball, J. G. C., Jackson, T., Coomes, D., et al. (2021). Multisensor data fusion for improved segmentation of individual tree crowns in dense tropical forests. IEEE Journal of Selected topics in Applied Earth Observations and Remote Sensing, 14, 3927–3936.
Abstract: Automatic tree crown segmentation from remote sensing data is especially challenging in dense, diverse, and multilayered tropical forest canopies, and tracking mortality by this approach is even more difficult. Here, we examine the potential for combining airborne laser scanning (ALS) with multispectral and hyperspectral data to improve the accuracy of tree crown segmentation at a study site in French Guiana. We combined an ALS point cloud clustering method with a spectral deep learning model to achieve 83% accuracy at recognizing manually segmented reference crowns (with congruence >0.5). This method outperformed a two-step process that involved clustering the ALS point cloud and then using the logistic regression of hyperspectral distances to correct oversegmentation. We used this approach to map tree mortality from repeat surveys and show that the number of crowns identified in the first that intersected with height loss clusters was a good estimator of the number of dead trees in these areas. Our results demonstrate that multisensor data fusion improves the automatic segmentation of individual tree crowns and presents a promising avenue to study forest demography with repeated remote sensing acquisitions.
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Amani, B. H. K., N'Guessan, A. E., Derroire, G., N'dja, J. K., Elogne, A. G. M., Traoré, K., et al. (2021). The potential of secondary forests to restore biodiversity of the lost forests in semi-deciduous West Africa. Biological Conservation, 259.
Abstract: In West Africa, more than 80% of the original forest cover has disappeared due to the exponential growth of human populations in a recurrent search for new agricultural land. Once the fertility of the land is exhausted, these areas are abandoned and left to be reforested through natural succession. Despite the widespread presence of secondary forests of various ages in West African landscapes, little is known about the trajectories of recovery and the environmental factors that influence recovery rates. We set up 96 0.2 ha forest plots, along a chronosequence of 1 to 40 years and including 7 controls, on which all trees larger than 2.5 cm in diameter at breast height were inventoried. We modelled the recovery trajectories of four complementary dimensions of biodiversity (richness, diversity, composition, indicators of old-growth forest) in a Bayesian framework. Our results show that the four dimensions of biodiversity recover at different rates, with composition recovering much faster than floristic diversity. Among the local, landscape, and historical factors studied, the number of remnants and proximity to old-growth forests have a positive impact on recovery rates, with, under good environmental conditions, the composition, richness, and diversity being almost completely recovered in less than 25 years. Our results demonstrate the very high resilience of the composition of the semi-deciduous forests of West Africa, but also suggest that the management of these post-forest areas must be differentiated according to the landscape context and the presence of isolated trees, which are the last vestiges of the former forest. In unfavourable conditions, natural dynamics should be assisted by agroforestry practices and local tree planting to allow for a rapid restoration of forest goods and services to local populations.
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Sayer, E. J., Rodtassana, C., Sheldrake, M., Bréchet, L. M., Ashford, O. S., Lopez-Sangil, L., et al. (2020). Revisiting nutrient cycling by litterfall—Insights from 15 years of litter manipulation in old-growth lowland tropical forest. Adv. Ecol. Res., 62, 173–223.
Abstract: The crucial role of tropical forests in the global carbon balance is underpinned by their extraordinarily high biomass and productivity, even though the majority of tropical forests grow on nutrient-poor soils. Nutrient cycling by litterfall has long been considered essential for maintaining high primary productivity in lowland tropical forests but few studies have tested this assumption experimentally. We review and synthesise findings from the Gigante Litter Manipulation Project (GLiMP), a long-term experiment in lowland tropical forest in Panama, Central America, in which litter has been removed from or added to large-scale plots for 15 years. We assessed changes in soil and litter nutrient concentrations in response to the experimental treatments and estimated nutrient return and nutrient use efficiency to indicate changes in nutrient cycling. The soil concentrations of most nutrients increased with litter addition and declined with litter removal. Litter removal altered nitrogen, potassium, manganese and zinc cycling, demonstrating the importance of litter inputs for maintaining the availability of these elements to plants. By contrast, litter addition only altered nitrogen cycling and, despite low concentrations of available soil phosphorus, the effects of litter manipulation on phosphorus cycling were inconsistent. We discuss potential mechanisms underlying the observed changes, and we emphasise the importance of decomposition processes in the forest floor for retaining nutrient elements, which partially decouples nutrient cycling from the mineral soil. Finally, by synthesising GLiMP studies conducted during 15 years of litter manipulation, we highlight key knowledge gaps and avenues for future research into tropical forest nutrient cycling. © 2020 Elsevier Ltd
Keywords: Forest floor; Litter addition; Litter removal; Litterfall; Nutrient cycling; Nutrient use efficiency; Soil fertility; Trace elements; Tropical lowland forest
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Heu, K., Romoli, O., Schonbeck, J. C., Ajenoe, R., Epelboin, Y., Kircher, V., et al. (2021). The Effect of Secondary Metabolites Produced by Serratia marcescens on Aedes aegypti and Its Microbiota. Frontiers in Microbiology, 12, 645701.
Abstract: Serratia marcescens is a bacterial species widely found in the environment, which very efficiently colonizes mosquitoes. In this study, we isolated a red-pigmented S. marcescens strain from our mosquito colony (called S. marcescens VA). This red pigmentation is caused by the production of prodigiosin, a molecule with antibacterial properties. To investigate the role of prodigiosin on mosquito- S. marcescens interactions, we produced two white mutants of S. marcescens VA by random mutagenesis. Whole genome sequencing and chemical analyses suggest that one mutant has a nonsense mutation in the gene encoding prodigiosin synthase, while the other one is deficient in the production of several types of secondary metabolites including prodigiosin and serratamolide. We used our mutants to investigate how S. marcescens secondary metabolites affect the mosquito and its microbiota. Our in vitro tests indicated that S. marcescens VA inhibits the growth of several mosquito microbiota isolates using a combination of prodigiosin and other secondary metabolites, corroborating published data. This strain requires secondary metabolites other than prodigiosin for its proteolytic and hemolytic activities. In the mosquito, we observed that S. marcescens VA is highly virulent to larvae in a prodigiosin-dependent manner, while its virulence on adults is lower and largely depends on other metabolites
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Leponce, M., Corbara, B., Delabie, J. H. C., Orivel, J., Aberlenc, H. - P., Bail, J., et al. (2021). Spatial and functional structure of an entire ant assemblage in a lowland Panamanian rainforest. Basic and Applied, 56, 32–44.
Abstract: Ants are a major ecological group in tropical rainforests. Few studies in the Neotropics have documented the distribution of ants from the ground to the canopy, and none have included the understorey. A previous analysis of an intensive arthropod study in Panama, involving 11 sampling methods, showed that the factors influencing ant β diversity (i.e., changes in assemblage composition) were, in decreasing order of importance, the vertical (height), temporal (season), and horizontal (geographic distance) dimensions. In the present study, we went one step further and aimed (1) to identify the best sampling methods to study the entire ant assemblage across the three strata, (2) to test if all strata show a similar horizontal β diversity and (3) to analyze the functional structure of the entire ant assemblage. We identified 405 ant species from 11 subfamilies and 68 genera. Slightly more species were sampled in the canopy than on the ground; they belonged to distinct sub-assemblages. The understorey fauna was mainly a mixture of species found in the other two strata. The horizontal β diversity between sites was similar for the three strata. About half of the ant species foraged in two (29%) or three (25%) strata. A single method, aerial flight interception traps placed alongside tree trunks, acting as arboreal pitfall traps, collected half of the species and reflected the vertical stratification. Using the functional traits approach, we observed that generalist species with mid-sized colonies were by far the most numerous (31%), followed by ground- or litter-dwelling species, either specialists (20%), or generalists (16%), and arboreal species, either generalists (19%) or territorially dominant (8%), and finally army ants (5%). Our results reinforce the idea that a proper understanding of the functioning of ant assemblages requires the inclusion of arboreal ants in survey programs.
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Chanson, A., Moreau, C. S., & Duplais, C. (2021). Assessing Biosynthetic Gene Cluster Diversity of Specialized Metabolites in the Conserved Gut Symbionts of Herbivorous Turtle Ants. Frontiers in Microbiology, 12, 678100.
Abstract: Cephalotes are herbivorous ants (>115 species) feeding on low-nitrogen food sources, and they rely on gut symbionts to supplement their diet by recycling nitrogen food waste into amino acids. These conserved gut symbionts, which encompass five bacterial orders, have been studied previously for their primary nitrogen metabolism; however, little is known about their ability to biosynthesize specialized metabolites which can play a role in bacterial interactions between communities living in close proximity in the gut. To evaluate the biosynthetic potential of their gut symbionts, we mine 14 cultured isolate genomes and gut metagenomes across 17 Cephalotes species to explore the biodiversity of biosynthetic gene clusters (BGCs) producing specialized metabolites. The diversity of BGCs across Cephalotes phylogeny was analyzed using sequence similarity networking and BGC phylogenetic reconstruction. Our results reveal that the conserved gut symbionts involved in the nutritional symbiosis possess 80% of all the 233 BGCs retrieved in this work. Furthermore, the phylogenetic analysis of BGCs reveals different patterns of distribution, suggesting different mechanisms of conservation. A siderophore BGC shows high similarity in a single symbiont across different ant host species, whereas a BGC encoding the production of non-ribosomal peptides (NRPs) found different symbionts within a single host species. Additionally, BGCs were abundant in four of the five bacterial orders of conserved symbionts co-occurring in the hindgut. However, one major symbiont localized alone in the midgut lack BGCs. Because the spatial isolation prevents direct interaction with other symbionts, this result supports the idea that BGCs are maintained in bacteria living in close proximity but are dispensable for an alone-living symbiont. These findings together pave the way for studying the mechanisms of BGC conservation and evolution in gut bacterial genomes associated with Cephalotes. This work also provides a genetic background for further study, aiming to characterize bacterial specialized metabolites and to understand their functional role in multipartite mutualisms between conserved gut symbionts and Cephalotes turtle ants.
Keywords: insect-microbe mutualism, ants, metagemonic, biosynthetic gene cluster, gut bacteria, Cephalotes
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de Thoisy, B., Duron, O., Epelboin, L., Musset, L., Quénel, P., Roche, B., et al. (2021). Ecology, evolution, and epidemiology of zoonotic and vector-borne infectious diseases in French Guiana: Transdisciplinarity does matter to tackle new emerging threats. Infection, Génétics and Evolution, 93, 104916.
Abstract: French Guiana is a European ultraperipheric region located on the northern Atlantic coast of South America. It constitutes an important forested region for biological conservation in the Neotropics. Although very sparsely populated, with its inhabitants mainly concentrated on the Atlantic coastal strip and along the two main rivers, it is marked by the presence and development of old and new epidemic disease outbreaks, both research and health priorities. In this review paper, we synthetize 15 years of multidisciplinary and integrative research at the interface between wildlife, ecosystem modification, human activities and sociodemographic development, and human health. This study reveals a complex epidemiological landscape marked by important transitional changes, facilitated by increased interconnections between wildlife, land-use change and human occupation and activity, human and trade transportation, demography with substantial immigration, and identified vector and parasite pharmacological resistance. Among other French Guianese characteristics, we demonstrate herein the existence of more complex multi-host disease life cycles than previously described for several disease systems in Central and South America, which clearly indicates that today the greater promiscuity between wildlife and humans due to demographic and economic pressures may offer novel settings for microbes and their hosts to circulate and spread. French Guiana is a microcosm that crystallizes all the current global environmental, demographic and socioeconomic change conditions, which may favor the development of ancient and future infectious diseases.
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Diatta, B. D., Niass, O., Diouf, M., Guéye, M., Houel, E., & Boetsch, G. (2021). Diversité et composition phytochimique des bâtonnets frotte-dents (cure-dents) proposés chez les Peul de la commune de Tessékéré (Ferlo Nord, Sénégal). Journal of Applied Biosciences, 158, 16267–16281.
Abstract: Objectifs : Le but de cette étude était de déterminer la composition phytochimique et la teneur en grandes classes chimiques des tiges les plus utilisées comme bâtonnets frotte-dents chez les peul de Widou Thiengoli au Nord Ferlo (Sénégal). Méthodes et résultats : Des entretiens ouverts semi structurés ont permis de recueillir les plantes les plus utilisées. L’indice de fidélité renseigne sur la convergence des usages quant à l’emploi des plantes comme bâtonnets frotte-dent comparé aux autres pratiques cosmétiques. L’étude de la composition phytochimique des tiges a ciblé 8 classes chimiques. Les tanins et les saponines sont très fréquents ; les terpénoïdes et les leuco-anthocyanines presque inexistants. Un dosage des flavonoïdes, alcaloïdes et polyphénols, réalisé chez des extraits aqueux, a porté sur 12 plantes. Les meilleures teneurs en polyphénols et alcaloïdes sont recueillies chez Anogeissus leiocarpa, et la meilleure en flavonoïdes chez Commiphora africana. Conclusion et applicabilité des résultats : Ces résultats permettent de sélectionner à travers la composition phytochimique des plantes, les espèces présentant de potentielles activités antimicrobiennes, car renfermant des composés phytochimique doués de fonctions germicides, au- delà de la fonction mécanique connue des bâtonnets dans l’élimination de la plaque dentaire.
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Maggia, M. - E., Decaëns, T., Lapied, E., Dupont, L., Roy, V., Schimann, H., et al. (2021). At each site its diversity: DNA barcoding reveals remarkable earthworm diversity in neotropical rainforests of French Guiana. Applied Soil Ecology, 164, 103932.
Abstract: Despite their recognized essential role in soil, earthworms in tropical environments are still understudied. The aim of this study was to re-evaluate the diversity at the regional scale, as well as to investigate the environmental and spatial drivers of earthworm communities. We sampled earthworm communities across a range of habitats at six localities in French Guiana using three different sampling methods. We generated 1675 DNA barcodes and combined them with data from a previous study. Together, all sequences clustered into 119 MOTUs which were used as proxy to assess species richness. Only two MOTUs were common between the six localities and 20.2% were singletons, showing very high regional species richness and a high number of rare species. A canonical redundancy analysis was used to identify key drivers of the earthworm community composition. The RDA results and beta-diversity calculations both show strong species turnover and a strong spatial effect, resulting from dispersal limitations that are responsible for the current community composition. Sampling in different microhabitats allowed the discovery of 23 MOTUs that are exclusively found in decaying trunks and epiphytes, highlighting hidden diversity of earthworms outside of soil.
Keywords: DNA barcoding Tropical rainforest Community ecology Diversity level Sampling methods
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