Institute of Ecology and Environmental Sciences IEES-Paris

Plant domestication often alters plant traits, including chemical and physical defenses against herbivores. In squash, domestication leads to reduced levels of cucurbitacins and leaf trichomes, influencing interactions with insects. However, the impact of domestication on inducible defenses in squash remains poorly understood. Here, we investigated the chemical and physical defensive traits of wild and domesticated squash (Cucurbita argyrosperma), and compared their responses to belowground and aboveground infestation by the root-feeding larvae and the leaf-chewing adults of the banded cucumber beetle Diabrotica balteata (Coleoptera: Chrysomelidae). Wild populations contained cucurbitacins in roots and cotyledons but not in leaves, whereas domesticated varieties lacked cucurbitacins in all tissues. Belowground infestation by D. balteata larvae did not increase cucurbitacin levels in the roots but triggered the expression of cucurbitacin biosynthetic genes, irrespective of domestication status, although the response varied among different varieties. Conversely, whereas wild squash had more leaf trichomes than domesticated varieties, the induction of leaf trichomes in response to herbivory was greater in domesticated plants. Leaf herbivory varied among varieties but there was a trend of higher leaf damage on wild squash than domesticated varieties. Overall, squash plants responded to both belowground and aboveground herbivory by activating chemical defense-associated gene expression in roots and upregulating their physical defense in leaves, respectively. While domestication suppressed both chemical and physical defenses, our findings suggest that it may enhance inducible defense mechanisms by increasing trichome induction in response to herbivory.

Precise information on the location of charge in clay minerals and their charge density in smectite-dominant soils is rare. The present study was undertaken with three benchmark Vertisols to establish the relationship between the clay cation exchange capacity (CEC), charge density, as well as the location of charge in smectitic soil clay minerals and their relationship with potassium (K) fixation and release. Potassium fractions and their threshold levels in the Vertisols were determined by standard methods. Soils were segregated into silt, total clay and fine clay fractions for X-ray diffraction analysis and fine clay fractions were used to determine the CEC using standard methods. The Hofmann-Klemen effect (HK) and modified Greene-Kelly test was done with the fine clay to determine the CEC of the tetrahedral sheet. Subsequently, the CEC of the octahedral sheet was calculated as the difference between total CEC and the tetrahedral CEC. The results showed that ~60–64% of the total CEC is attributed to the tetrahedral layers. The tetrahedral CEC that is proportional to the tetrahedral charge density was significant and negatively correlated with K release threshold values and all fractions of K. The tetrahedral CEC contributed more toward the K fixation and release than the octahedral CEC. The study shows that the dominant presence of high-charge smectites in the fine clay fractions of these Vertisols contributed to the tetrahedral CEC and consequently to the charge density of these soils, which implied a tendency to fix K easily and release it with greater difficulty compared to soils with low-charge smectites.

Mangroves are one of the most carbon‐dense forests on the Earth and have been highlighted as key ecosystems for climate change mitigation and adaptation. Hundreds of studies have investigated how mangroves fix, transform, store, and export carbon. Here, we review and synthesize the previously known and emerging carbon pathways in mangroves, including gains (woody biomass accumulation, deadwood accumulation, soil carbon sequestration, root and litterfall production), transformations (food web transfer through herbivory, decomposition), and losses (respiration as CO 2 and CH 4 , litterfall export, particulate and dissolved carbon export). We then review the technologies available to measure carbon fluxes in mangroves, their potential, and their limitations. We also synthesize and compare mangrove net ecosystem productivity (NEP) with terrestrial forests. Finally, we update global estimates of carbon fluxes with the most current values of fluxes and global mangrove area. We found that the contributions of recently investigated fluxes, such as soil respiration as CH 4 , are minor (<1 Tg C year ⁻¹ ), while the contributions of deadwood accumulation, herbivory, and lateral export are significant (>35 Tg C year ⁻¹ ). Dissolved inorganic carbon exports are an order of magnitude higher than the other processes investigated and were highly variable, highlighting the need for further studies. Gross primary productivity (GPP) and ecosystem respiration (ER) per area of mangroves were within the same order of magnitude as terrestrial forests. However, ER/GPP was lower in mangroves, explaining their higher carbon sequestration. We estimate the global mean mangrove NEP of 109.1 Tg C year ⁻¹ (7.4 Mg C ha ⁻¹ year ⁻¹ ) or through a budget balance, accounting for lateral losses, a global mean of 66.6 Tg C year ⁻¹ (4.5 Mg C ha ⁻¹ year ⁻¹ ). Overall, mangroves are highly productive, and despite losses due to respiration and tidal exchange, they are significant carbon sinks.

Tropical forest root characteristics and resource acquisition strategies are underrepresented in vegetation and global models, hampering the prediction of forest–climate feedbacks for these carbon‐rich ecosystems. Lowland tropical forests often have globally unique combinations of high taxonomic and functional biodiversity, rainfall seasonality, and strongly weathered infertile soils, giving rise to distinct patterns in root traits and functions compared with higher latitude ecosystems. We provide a roadmap for integrating recent advances in our understanding of tropical forest belowground function into vegetation models, focusing on water and nutrient acquisition. We offer comparisons of recent advances in empirical and model understanding of root characteristics that represent important functional processes in tropical forests. We focus on: (1) fine‐root strategies for soil resource exploration, (2) coupling and trade‐offs in fine‐root water vs nutrient acquisition, and (3) aboveground–belowground linkages in plant resource acquisition and use. We suggest avenues for representing these extremely diverse plant communities in computationally manageable and ecologically meaningful groups in models for linked aboveground–belowground hydro‐nutrient functions. Tropical forests are undergoing warming, shifting rainfall regimes, and exacerbation of soil nutrient scarcity caused by elevated atmospheric CO2. The accurate model representation of tropical forest functions is crucial for understanding the interactions of this biome with the climate.

Adolescence is a crucial period for physical and psychological development. The impact of negative life events represents a risk factor for the onset of neuropsychiatric disorders. This study aims to investigate the relationship between negative life events and structural brain connectivity, considering both graph theory and connectivity strength. A group (n = 487) of adolescents from the IMAGEN Consortium was divided into Low and High Stress groups. Brain networks were extracted at an individual level, based on morphological similarity between grey matter regions with regions defined using an atlas-based region of interest (ROI) approach. Between-group comparisons were performed with global and local graph theory measures in a range of sparsity levels. The analysis was also performed in a larger sample of adolescents (n = 976) to examine linear correlations between stress level and network measures. Connectivity strength differences were investigated with network-based statistics. Negative life events were not found to be a factor influencing global network measures at any sparsity level. At local network level, between-group differences were found in centrality measures of the left somato-motor network (a decrease of betweenness centrality was seen at sparsity 5%), of the bilateral central visual and the left dorsal attention network (increase of degree at sparsity 10% at sparsity 30% respectively). Network-based statistics analysis showed an increase in connectivity strength in the High stress group in edges connecting the dorsal attention, limbic and salience networks. This study suggests negative life events alone do not alter structural connectivity globally, but they are associated to connectivity properties in areas involved in emotion and attention.

Emerging and endemic zoonotic diseases continue to threaten human and animal health, our social fabric, and the global economy. Zoonoses frequently emerge from congregate interfaces where multiple animal species and humans coexist, including farms and markets. Traditional food markets are widespread across the globe and create an interface where domestic and wild animals interact among themselves and with humans, increasing the risk of pathogen spillover. Despite decades of evidence linking markets to disease outbreaks across the world, there remains a striking lack of pathogen surveillance programs that can relay timely, cost-effective, and actionable information to decision-makers to protect human and animal health. However, the strategic incorporation of environmental surveillance systems in markets coupled with novel pathogen detection strategies can create an early warning system capable of alerting us to the risk of outbreaks before they happen. Here, we explore the concept of “smart” markets that utilize continuous surveillance systems to monitor the emergence of zoonotic pathogens with spillover potential. IMPORTANCE Fast detection and rapid intervention are crucial to mitigate risks of pathogen emergence, spillover and spread—every second counts. However, comprehensive, active, longitudinal surveillance systems at high-risk interfaces that provide real-time data for action remain lacking. This paper proposes "smart market" systems harnessing cutting-edge tools and a range of sampling techniques, including wastewater and air collection, multiplex assays, and metagenomic sequencing. Coupled with robust response pathways, these systems could better enable Early Warning and bolster prevention efforts.

Grassland management effects on soil organic carbon storage under future climate are unknown. Here we examine the impact of ley grassland durations in crop rotations on soil organic carbon in temperate climate from 2005 to 2100, considering two IPCC scenarios, RCP4.5 and RCP8.5, with and without atmospheric CO2 enhancements. We used the DailyDayCent model and a long-term experiment to show that ley grasslands increase soil organic carbon storage by approximately 10 Mg ha⁻¹ over 96 years compared with continuous cropping. Surprisingly, extending ley duration from 3 to 6 years does not enhance soil organic carbon. Furthermore, in comparison with non-renewed grasslands, those renewed every three years demonstrated a notable increase in soil organic carbon storage, by 0.3 Mg ha⁻¹ yr⁻¹. We concluded that management of ploughing and renewal intervals is crucial for maximizing soil organic carbon stocks, through balancing biomass carbon inputs during regrowth and carbon losses through soil respiration.

Bacterial diversity analyses often suffer from a bias due to sampling only from a limited number of hosts or narrow geographic locations. This was the case for the phytopathogenic species Dickeya solani, whose members were mainly isolated from a few hosts–potato and ornamentals–and from the same geographical area–Europe and Israel, which are connected by seed trade. Most D. solani members were clonal with the notable exception of the potato isolate RNS05.1.2A and two related strains that are clearly distinct from other D. solani genomes. To investigate if D. solani genomic diversity might be broadened by analysis of strains isolated from other environments, we analysed new strains isolated from ornamentals and from river water as well as strain CFBP 5647 isolated from tomato in the Caribbean island Guadeloupe. While water strains were clonal to RNS05.1.2A, the Caribbean tomato strain formed a third clade. The genomes of the three clades are highly syntenic; they shared almost 3900 protein families, and clade-specific genes were mainly included in genomic islands of extrachromosomal origin. Our study thus revealed both broader D. solani diversity with the characterisation of a third clade isolated in Latin America and a very high genomic conservation between clade members.

Diversity and taxonomic revision of methanogens and other archaea in the intestinal tract of terrestrial arthropods. Methane emission by terrestrial invertebrates is restricted to millipedes, termites, cockroaches, and scarab beetles. The arthropod-associated archaea known to date belong to the orders Methanobacteriales, Methanomassiliicoccales, Methanomicrobiales, and Methanosarcinales, and in a few cases also to non-methanogenic Nitrososphaerales and Bathyarchaeales. However, all major host groups are severely undersampled, and the taxonomy of existing lineages is not well developed. Full-length 16S rRNA gene sequences and genomes of arthropod-associated archaea are scarce, reference databases lack resolution, and the names of many taxa are either not validly published or under-classified and require revision. Here, we investigated the diversity of archaea in a wide range of methane-emitting arthropods, combining phylogenomic analysis of isolates and metagenome-assembled genomes (MAGs) with amplicon sequencing of full-length 16S rRNA genes. Our results allowed us to describe numerous new species in hitherto undescribed taxa among the orders Methanobacteriales (Methanacia, Methanarmilla, Methanobaculum, Methanobinarius, Methanocatella, Methanoflexus, Methanorudis, and Methanovirga, all gen. nova), Methanomicrobiales (Methanofilum and Methanorbis, both gen. nova), Methanosarcinales (Methanofrustulum and Methanolapillus, both gen. nova), Methanomassiliicoccales (Methanomethylophilaceae fam. nov., Methanarcanum, Methanogranum, Methanomethylophilus, Methanomicula, Methanoplasma, Methanoprimaticola, all gen. nova), and the new family Bathycorpusculaceae (Bathycorpusculum gen. nov.). Reclassification of amplicon libraries from this and previous studies using this new taxonomic framework revealed that arthropods harbor only CO2 and methyl-reducing hydrogenotrophic methanogens. Numerous genus-level lineages appear to be present exclusively in arthropods suggesting long evolutionary trajectories with their termite, cockroach, and millipede hosts, and a radiation into various microhabitats and ecological niches provided by their digestive tracts (e.g., hindgut compartments, gut wall, or anaerobic protists). The distribution patterns among the different host groups are often complex, indicating a mixed mode of transmission and a parallel evolution of invertebrate and vertebrate-associated lineages.

Isotopes are widely used in ecology to study food webs and physiology. The fractionation observed between trophic levels in nitrogen and carbon isotopes, explained by isotopic biochemical selectivity, is subject to important within-trophic level variations, leading to imprecision in trophic level estimation. Understanding the drivers of these variations is thus important to improve the study of food webs. In this study, we characterized this variation by submitting Spodoptera littoralis larvae to a gradient of starvation levels, a factor that we hypothesized would change the trophic fractionation between individuals. The various growth rates that were induced from these starvation levels resulted in a ∼ 1-1.5‰ within-trophic level variation of the trophic fractionation in both carbon and nitrogen, which is substantial compared to the 3-4‰ classically associated with between-trophic levels variations. Hence starved animals sampled in natura may be ranked at a higher trophic level than they really are. We were able to gain an understanding of the effect of growth rate on isotopes fluxes between three easy-to-measure biological materials, food, the organism and its wastes (frass), giving insight into physiological processes at play but also conveying helpful information to the sampling framework of field studies.

Mangrove sediments are known to be potentially active reducing zones for nitrogen removal. The goal of this work was to investigate the potential for nitrate reduction in marine mangrove sediments along a canal impacted by anthropogenic activity (Guadeloupe, Lesser Antilles). To this end, the effect of nitrate concentration, organic carbon load, and hydraulic retention time was assessed as factors affecting these nitrate reduction rates. Nitrate reduction potential was determined using flow‐through reactors in marine mangrove sediments collected along “The Canal des Rotours” in Guadeloupe. Potential nitrate reduction rates, in the presence of indigenous organic carbon, generally increased upon increasing nitrate supply from around 120 nmol cm⁻³ h⁻¹ (low nitrate) up to 378 nmol cm⁻³ h⁻¹ (high nitrate). The potential for nitrate reduction increased significantly with the addition of mangrove leaves, whereas the addition of simple, easily degradable carbon (acetate) resulted in an almost fivefold increase in nitrate reduction rates (up to 748 nmol cm⁻³ h⁻¹). The hydraulic retention time also had an impact on the nitrate reducing capacity due to an increased contact time between nitrate and the benthic microbial community. Marine mangrove sediments have a high potential to mitigate nitrogen pollution, mainly governed by the presence of large amounts of degradable carbon in the form of litter. The mangrove sediments from this Caribbean island, currently exposed to a small tidal effect, could increase their nitrate elimination capacities due to prolonged water retention via engineering.

Context Farmland on steep slopes is increasingly abandoned because it is unsuitable for most forms of modern agriculture. Succession back to forest is often slow or inexistent due to over-exploitation. Observations and measurements in Dong Cao catchment 47.9 ha Vietnam, started under farming and continued after abandonment: 20 years of uninterrupted monitoring of soil, water, land use and vegetation were integrated in this study. Objective Our aim is to identify the specific combination of soil features and agricultural practices that are responsible for fast, slow or blocked succession. We differentiate between the recovery of forest structure, relatively easy, and recovery of the original species composition, more difficult. Methods Multivariate analysis of vegetation data produced plant communities in a gradient of complexity. Using classic statistics, we sought relationships between environmental variables, land use and vegetation. Results Forest recovery failed the first 10 years, then part of the catchment developed forest. Land use explained best the distribution of plant communities over the catchment, slope and soil features were less related. Cassava cropping seriously slowed down the succession to closed forest. During abandonment soil carbon stocks (0–15 cm depth) increased with about 3% per year. Conclusion Starting from weedy thickets (2002) we distinguished two successional pathways: a positive pathway towards increased resemblance with the original Lowland forest via broken forest to closed deciduous to closed evergreen forest; a negative pathway away from the original forest species composition to degraded shrub land and low grass. Livestock was related to the negative pathway.

The tree flora of the Mediterranean Basin contains an outstanding taxonomic richness and a high proportion of endemic taxa. Contrary to other regions of the Mediterranean biome, a comprehensive phylogenetic analysis of the relationship between phylogenetic diversity, trait diversity and environmental factors in a spatial ecological context is lacking. We inferred the first calibrated phylogeny of 203 native tree species occurring in the European Mediterranean Basin based on 12 DNA regions. Using a set of four functional traits, we computed phylogenetic diversity for all 10,042 grid cells of 10 × 10 km spatial resolution to completely cover Mediterranean Europe. Then, we tested the spatial influence of environmental factors on tree diversity. Our results suggest that the nature of the relationship between traits and phylogeny varies among the different studied traits and according to the evolutionary distance considered. Phylogenetic diversity and functional diversity of European Mediterranean trees correlated strongly with species richness. High values of these diversity indices were located in the north of the study area, at high altitude, and minimum temperature of the coldest month. In contrast, the two phylogenetic indices that were not correlated with species richness (Mean Phylogenetic Distance, Phylogenetic Species Variability) were located in the south of the study area and were positively correlated with high altitude, soil organic carbon stock and sand soil texture. Our study provides support for the use of phylogenies in conservation biology to assess ecosystem functioning, and provides insights for the implementation of sustainable forest ecosystem management.

Mangroves are among the most carbon-dense ecosystems worldwide. Most of the carbon in mangroves is found belowground, and root production might be an important control of carbon accumulation, but has been rarely quantified and understood at the global scale. Here, we determined the global mangrove root production rate and its controls using a systematic review and a recently formalised, spatially explicit mangrove typology framework based on geomorphological settings. We found that global mangrove root production averaged ~770 ± 202 g of dry biomass m-2 y-1 globally, which is much higher than previously reported and close to the root production of the most productive tropical forests. Geomorphological settings exerted marked control over root production together with air temperature and precipitation (r2 ≈ 30%, p < 0.001). Our review shows that individual global changes (e.g. warming, eutrophication, drought) have antagonist effects on root production, but they have rarely been studied in combination. Based on this newly established root production rate, root-derived carbon might account for most of the total carbon buried in mangroves, and 19 Tg C lost in mangroves each year (e.g. as CO2 ). Inclusion of root production measurements in understudied geomorphological settings (i.e. deltas), regions (Indonesia, South America and Africa) and soil depth (> 40 cm), as well as the creation of a mangrove root traits database will push forward our understanding of the global mangrove carbon cycle for now and the future. Overall, this review presents a comprehensive analysis of root production in mangroves, and highlights the central role of root production in the global mangrove carbon budget.

The response of insect pollinator communities to increasing urbanization is shaped by landscape and local factors. But what about habitats that are already highly artificial? We investigated the drivers of pollinator diversity in a dense urban matrix, the city of Paris. We monitored insect pollinator communities monthly (March-October) for two consecutive years in 12 green spaces that differed in their management practices, focusing on four insect orders (Hymenoptera, Diptera, Lepidoptera, Coleoptera). Pollinator abundance and species richness were both positively tied to green space size and flowering plant species richness, but negatively linked to surrounding impervious surfaces. In addition, environmental features at both the local and landscape scales influenced the composition and functional diversity of wild bee communities. Indeed, small and large bees responded differently, with the occurrence of large-bodied species being impaired by the proportion of impervious surfaces but strongly enhanced by plant species richness. Also, sites with a majority of spontaneous plant species had more functionally diverse bee communities, with oligolectic species more likely to be found. These results, consistent with the literature, can guide the design and management practices of urban green spaces to promote pollinator diversity and pollination function, even in dense urban environments.

There is growing concern on the survival of Mediterranean forests under the projected near-future droughts as a result of anthropogenic climate change. Here we determine the resilience of Mediterranean forests across the entire range of climatic boundary conditions realized during the past 500 kyrs based on continuous pollen and geochemical records of (sub)centennial-scale resolution from drillcores from Tenaghi Philippon, Greece. Using convergent cross-mapping we provide empirical confirmation that global atmospheric carbon dioxide (CO2) may affect Mediterranean vegetation through forcing on moisture availability. Our analysis documents two stable vegetation regimes across the wide range of CO2 and moisture levels realized during the past four glacial-interglacial cycles, with abrupt shifts from forest to steppe biomes occurring when a threshold in precipitation is crossed. Our approach highlights that a CO2-driven moisture decrease in the near future may bear an impending risk for abrupt vegetation regime shifts prompting forest loss in the Mediterranean region.

The integration of ecosystem processes over large spatial extents is critical to predicting whether and how global changes may impact biodiversity and ecosystem functions. Yet, there remains an important gap in meta-ecosystem models to predict multiple functions (e.g., carbon sequestration, elemental cycling, trophic efficiency) across ecosystem types (e.g., terrestrial-aquatic, benthic-pelagic). We derive a flexible meta-ecosystem model to predict ecosystem functions at landscape extents by integrating the spatial dimension of natural systems as spatial networks of different habitat types connected by cross-ecosystem flows of materials and organisms. We partition the physical connectedness of ecosystems from the spatial flow rates of materials and organisms, allowing the representation of all types of connectivity across ecosystem boundaries as well as the interaction(s) between them. Through simulating a forest-lake-stream meta-ecosystem, our model illustrated that even if spatial flows induced significant local losses of nutrients, differences in local ecosystem efficiencies could lead to increased secondary production at regional scale. This emergent result, which we dub the ‘cross-ecosystem efficiency hypothesis’, emphasizes the importance of integrating ecosystem diversity and complementarity in meta-ecosystem models to generate empirically testable hypotheses for ecosystem functions.