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.

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.

Abstract: Drought is predicted to increase in the future due to climate change, bringing with it myriad impacts on ecosystems. Plants respond to drier soils by reducing stomatal conductance in order to conserve water and avoid hydraulic damage. Despite the importance of plant drought responses for the global carbon cycle and local and regional climate feedbacks, land surface models are unable to capture observed plant responses to soil moisture stress. We assessed the impact of soil moisture stress on simulated gross primary productivity (GPP) and latent energy flux (LE) in the Joint UK Land Environment Simulator (JULES) vn4.9 on seasonal and annual timescales and evaluated 10 different representations of soil moisture stress in the model. For the default configuration, GPP was more realistic in temperate biome sites than in the tropics or high-latitude (cold-region) sites, while LE was best simulated in temperate and high-latitude (cold) sites. Errors that were not due to soil moisture stress, possibly linked to phenology, contributed to model biases for GPP in tropical savanna and deciduous forest sites. We found that three alternative approaches to calculating soil moisture stress produced more realistic results than the default parameterization for most biomes and climates. All of these involved increasing the number of soil layers from 4 to 14 and the soil depth from 3.0 to 10.8 m. In addition, we found improvements when soil matric potential replaced volumetric water content in the stress equation (the “soil14psi” experiments), when the critical threshold value for inducing soil moisture stress was reduced (“soil14p0”), and when plants were able to access soil moisture in deeper soil layers (“soil14_dr*2”). For LE, the biases were highest in the default configuration in temperate mixed forests, with overestimation occurring during most of the year. At these sites, reducing soil moisture stress (with the new parameterizations mentioned above) increased LE and increased model biases but improved the simulated seasonal cycle and brought the monthly variance closer to the measured variance of LE. Further evaluation of the reason for the high bias in LE at many of the sites would enable improvements in both carbon and energy fluxes with new parameterizations for soil moisture stress. Increasing the soil depth and plant access to deep soil moisture improved many aspects of the simulations, and we recommend these settings in future work using JULES or as a general way to improve land surface carbon and water fluxes in other models. In addition, using soil matric potential presents the opportunity to include plant functional type-specific parameters to further improve modeled fluxes.

Abstract: When ordinating plots of tropical rain forests using stand-level structural attributes such as biomass, basal area and the number of trees in different size classes, two patterns often emerge: a gradient from poorly to highly stocked plots and high positive correlations between biomass, basal area and the number of large trees. These patterns are inherited from the demographics (growth, mortality and recruitment) and size allometry of trees and tend to obscure other patterns, such as site differences among plots, that would be more informative for inferring ecological processes. Using data from 133 rain forest plots at nine sites for which site differences are known, we aimed to filter out these patterns in forest structural attributes to unveil a hidden pattern. Using a null model framework, we generated the anticipated pattern inherited from individual allometric patterns. We then evaluated deviations between the data (observations) and predictions of the null model. Ordination of the deviations revealed site differences that were not evident in the ordination of observations. These sites differences could be related to different histories of large-scale forest disturbance. By filtering out patterns inherited from individuals, our model analysis provides more information on ecological processes

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.