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International audience

L'écopastoralisme est une pratique de gestion écologique en plein essor, dont les bienfaits pour le maintien ou la restauration des milieux naturels ont été largement démontrés. Mais cette solution alternative de gestion obtient-elle les mêmes résultats sur des milieux fortement anthropisés et artificialisés ? Une étude menée sur les digues artificielles du Rhône de la réserve de chasse de Donzère-Mondragon s'est intéressée aux impacts des différents troupeaux sur les communautés végétales d’écosystèmes récents. Grâce à un suivi botanique sur plusieurs années, les scientifiques ont pu démontrer que la gestion par les herbivores s'avérait efficace pour maintenir l'ouverture des milieux et augmenter significativement le nombre et la diversité des espèces par rapport à l’absence de gestion ou aux interventions mécaniques.

International audience

4 páginas.- 14 referencias.- Free Access, Soil can be seen as an important and delicate interfacebetween the biosphere, hydrosphere, atmosphere andlithosphere. Biogeochemical processes occurring at thisinterface are crucial for maintaining soil ecosystem func-tion, plant productivity and water quality. Aside fromcontrolling the fate of pollutants, this interface plays akey role in the biogeochemical cycles and thus has a rolein soils acting as a source or sink of greenhouse gases.With this in mind, we decided to organize the 8thInternational Symposium on Interactions of Soil Mineralswith Organic Components and Microorganisms (ISMOM2019), with the focus on “Understanding Soil Interfacial Reactions for Sustainable Soil Management and Climatic Change Mitigation”. This meeting took place in Seville,Spain, during 23–28 June 2019, and was organized by Heike Knicker and Francisco J. González-Vila from the IRNAS-CSIC, Seville, as a part of the interCongress series of international symposia of Commission 2.5 (Soil chemical, physical and biological interfacial reactions) of theInternational Union of Soil Sciences (IUSS).During the meeting, we had the pleasure of presenting the contributions of 170 participants from 33 countries. In total, 185 abstracts were submitted, of which 157 were finally presented as plenary (two), keynote (five) or oral (54) talks along with 96 posters. The number, diversity and quality of the submitted abstracts, as well as the excellent work of the scientific committee, provided an interesting and well‐balanced scientific programme. The contributions were presented during the following six sessions. Soil as a C and N sink: Who is the major player – soil minerals, soil organic matter quality, microbial activity or their interplay? New physical, chemical and biological analytical approaches: How can they lead us to a better understanding of soil interfaces? Ecological disturbances: How do mismanagement of soils (overgrazing, erosion, etc.) and natural disasters (fire, flooding, etc.) affect the interplay between soil minerals, SOM and microorganisms? Dynamics of pollutants at soil interfaces: What is new and how can environmental biotechnology be beneficial for soil restoration and bioremediation? Soil amendments (biochar, composts and digestates): How do they affect interactions at soil interfaces? Nutrient availability in soils: Can our knowledge on soil interfaces improve biotechnological approaches or soil management to decrease the need for artificial fertilizers? In order to increase the visibility of posters, a part of the time for the poster session was dedicated to a “pico‐session” during which poster presenters had a maximum of 2 min to advertise their work. This offer was well appreciated both by presenters, in particular by young researchers, and interested participants and greatly stimulated the following discussions at the poster boards. Considerable time for discussion and remaining questions was also provided after each session, an offer that was also well accepted by the audience. A special highlight was the Dr P.M. Huang Prize awarded to Dr. Rota Wagai from the National Institute for Agro‐Environmental Sciences, NIAES, Japan, for his outstanding and unique contributions to our understanding of the interaction of organic matter, minerals and microorganisms in the soil. Generous sponsorship from the IUSS Stimulus Fund, Commission 2.5 of the IUSS, the International Humic Substance Society (IHSS) and the University of Seville allowed travel grants to be awarded to young scientists and scientists from under‐funded countries, in addition to keynote speakers. The support by the IRNAS‐CSIC, as well as the sponsoring by Agrana AG, Bruker BioSpin GmbH, Analisis Vinicos, Abogase Legal SI and AMC Chemical & TRICHODEX, contributed to successfully providing this international platform for fruitful discussions between scientists and students from soil sciences, chemistry, biology, biochemistry, physics, ecology or environmental sciences., The papers collected together in this special issue of the European Journal of Soil Science reflect the diversity of communications at the conference. The following special issue contains a small collection of 14 papers based on presentations made at the meeting. As part of the section Soil as a C and N sink, the contribution of Briedis et al. (2021) describes a study dealing with the effects of land‐use types (native vegetation [NV] vs. no‐till system [NT]) on organic carbon (OC) stocks and on the chemical composition of organic matter (OM), seeking a better understanding of the OC build‐up in no‐till areas and the mechanisms that govern OC protection in highly weathered soils in Brazil. Applying solid‐state 13C nuclear magnetic resonance (NMR) spectroscopic analyses in soils fractionated into coarse and fine fractions by sieving, they concluded that “maintaining continuous NT is a sine qua non condition” to improve SOM contents. They confirmed further that the interactions of labile compounds with soil minerals can be seen as the driving factor for OM protection in soil. The article by Cissé, van Oort, Chenu, Essi, and Staunton (2021) shifts the focus to the soil organic nitrogen fraction and investigates the relative enrichment of SOM in the operationally defined fraction, glomalin‐related soil protein. This study relied on the “42‐Plots” long‐term bare fallow trial in Versailles, France, and challenged hypotheses on the fungal origin and intrinsic stability of this fraction. It was concluded that GRSP is continually produced by the recycling of soil organic matter, with no evidence that it is of predominantly arbuscular fungal origin. Soil pH and availability of sources of N contributed to the complex balance between protein synthesis and accumulation. The work by Le Bayon et al. (2021) introduced the use of X‐ray microcomputed tomography for characterizing earthworm‐derived belowground soil aggregates. It was presented in the section dedicated to New physical, chemical and biological analytical approaches. The calculation of density and size (down to 30 μm) allowed the authors to distinguish mineral and light organic and void spaces, and to compare pore size distribution in soils after the action of different earthworms. This major advance opens exciting possibilities for the study of organo‐mineral interfaces. A more pedogenesis‐related approach is presented by Pospíšilová and her coworkers (Pospíšilová et al., 2021). Applying X‐ray diffraction (XRD) on the fine earth and clay fractions of soils from the Litovelské Pomoraví (Czech Republic), they identified hydroxy‐interlayered vermiculites (HIV). Such minerals appear not to have been found in Bohemian and Moravian loess before. Based on their findings, they concluded that HIV and even vermiculite are pedogenic clay minerals. The paper by Wu, Wu, Huang, and Cai (2021) demonstrates how the interaction with mineral or organo‐mineral surfaces may have an important impact on molecular reactions. This study reports that one mineral in particular, birnessite, facilitates the conjugate transfer of plasmids and may initiate the formation of intracellular reactive oxygen species. Clay minerals may contribute to the global dissemination of antimicrobial resistance. The goal of the session Ecological disturbances was to present some new insights on the impact of (mis)management of soils or natural disasters and how they affect the interplay between soil minerals, SOM and microorganisms. Towards this goal, Escobar Ortega, Aguilar Vásquez, Ávila Alba, and García de Salamone (2021) evaluated the impact on the rhizosphere microbial communities of inclusion of cover crops in succession with soybean and plant growth‐promoting rhizobacteria (PGPR) inoculation. The underlying assumption of this work is that the inclusion of cover crops adds, through the input of crop residues to the soil, to the preservation of soil quality. However, using glyphosate to interrupt the growth of the cover crop is supposed to have a negative impact on the microbial rhizosphere communities that should be better understood. Therefore, they assessed whether the inoculation of two cover crops with A. brasilense and P. fluorescens, their growth interruption with glyphosate and the fertilization of cover crops at sowing, modify the functional and structural diversity of rhizosphere microbial communities. The study of the response of the microbial communities to changing management practices was also the objective of the work by Navas, Martín‐Lammerding, Hontoria, Ulcuango, and Mariscal‐Sancho (2021). They hypothesized that tillage type affects the abundance and size of macroaggregates, which in turn changes the microenvironment and the total abundances of fungi and bacteria within them. Evaluating the total abundance of bacteria (based on 16S rRNA analysis) and fungi (based on internal transcribed spacer analysis) inhabiting each aggregate fraction, they found that bacteria and fungi respond differently to changes in the distribution of aggregates induced by management practices. They further observed that in contrast to the fungal abundance, the distribution of bacteria in the aggregates was closely related to C and N concentrations. Another paper from Navas, Pérez‐Esteban, Torres, Hontoria, and Moliner (2021) investigated microbial communities along a gradient of metal contamination in a former copper mining area. Their underlying objective is to identify and exploit the metal resistance properties of microorganisms to use as biofertilizers to improve the efficiency of phytoremediation. Marked differences in abundances of species were observed along the contamination gradient and metal‐resistant genes were identified. Contaminated soils may be an important reservoir for useful microorganisms, notably Bradyrhizobium diazoefficiens and Pseudomonas aeruginosa, capable of both resisting large metal contents and also improving nutrient availability. Studying the fate of pollutants in soils is strongly associated with the study and understanding of their sorption behaviour. In line with this and within the fourth session Dynamics of pollutants at soil interfaces, Mikhail Borisover (2021) introduced a new approach to quantify sorption–desorption hysteresis using single‐point desorption isotherms in liquid‐phase sorption experiments in terms of the Gibbs free energy of non‐relaxed states. The study by Evans and Jacobs (2021) investigates the complexity of tertiary anion exchange reactions in soils from different horizons of alpine tundra soils in order to assess their impact on aluminium biogeochemistry. A combination of batch and column experimental approaches was used to follow oxalate/hydroxide/fluoride exchange along with aluminium solubilization. In recent years, concerns about the application of glyphosate have considerably increased. As a consequence, the behaviour of this widely used herbicide in soils has also been an issue discussed at the ISMOM after the presentation of Galicia‐Andrés, Tunega, Gerzabek, and Oostenbrink (2021), who investigate the molecular basis of the interactions between glyphosate and kaolinite, a clay mineral with high abundances in subtropical and tropical soils. Applying force‐field molecular dynamics simulation together with first principle calculations using a density functional theory‐based approach, they were in particular interested in the role of H‐bond formation as the precursor stage. They confirmed that kaolinite has an important contribution to the overall adsorption capacity of soils for glyphosate, specifically in its anionic form. Another study of an agrochemical was presented in the session dedicated to Soil amendments; the contribution of Aldana, Hazlerigg, Lopez‐Capel, and Werner (2021) presents results of batch studies in which the sorption and retention of atrazine, diuron, enrofloxacin, oxytetracycline and biochar applied in different doses to tropical soils with different texture was investigated. They identified rice husk biochar as an amendment that can efficiently reduce the leaching of the selected agrochemicals. However, because changes in soil properties due to the amendment may inadvertently lead to increased leaching, the authors conclude that the implementation of this approach should be conducted carefully and that field studies evaluating the long‐term effects of biochar‐amended soils on the fate of agrochemicals are still needed. Leiva‐Suárez et al. (2021) suggested the use of biochar, rich in nitrogen, as a slow‐release fertilizer, and studied the long‐term availability of N and P in sewage sludge‐derived hydrochars and pyrochars during a second cropping period. They prepared a soil that was previously amended with 13C‐ and 15N‐enriched hydrochars and pyrochars and was subjected to a first cropping period. After a second cropping period with Lolium perenne, the distribution of the isotopic labels between crop and soil was monitored. Hydrochars were identified as good candidates for long‐term fertilization and all amendments were reported to have comparable turnover rates in the long term, independently of their aromaticity and the native SOM. In another work presented in the session Nutrient availability in soils, Liu et al. (2021) tested the hypothesis that the efficiency of nitrification inhibitors can be increased by enhancing the nitrogen application rate. To test the hypothesis, field experiments with different N fertilization rates and the addition of nitrification inhibitor 3,4‐dimethylpyrazole phosphate (DMPP) were conducted and the respective efficacy of DMPP addition in reducing soil N2O emissions was determined. They suggest that ammonia‐oxidizing bacteria could be the dominant N2O emission contributors in nitrogen‐treated soils. They further reported that DMPP was more efficient at high nitrogen rates and concluded that DMPP application can be an efficient strategy to mitigate environmental risks related to N2O emissions from soils. We would like to thank EJSS for providing the opportunity for this special issue and acknowledge the great help and support of the Editor in Chief Professor Jennifer Dungait and the EJSS publication staff. Finally, we wish to thank the contributing authors and offer our sincere gratitude to all the reviewers, without whom this special issue could not have been completed. Last but not least, we thank all the participants of the 8th ISMOM for their activity, which turned the meeting into a lively and successful event. We are looking forward to continuing the discussions and interactions initiated at this meeting at the 9th ISMOM in 2024.

International audience; Cats Felis catus, in all their forms (domestic, free-roaming/stray and feral), have been identified as a major global threat to biodiversity, especially birds and small mammals. However, there has been little previous consideration of the extent and impact of predation of bats by cats, or of whether specific characteristics make certain species of bats particularly vulnerable to predation by cats. We reviewed the impact of cats on bats, based on a collation of scientific literature and the International Union for Conservation of Nature (IUCN) Red List database. Our aim was to produce a synthesis of the extent to which cats prey upon and threaten bats. We also collated available data on cat diet, which provide information on predation rates of bats by cats. Few studies (n = 44) have identified bat species preyed upon or threatened by cats, with a disproportionate number of studies from islands. In these studies, 86 bat species (about 7% of the global extant tally) are reported as preyed upon or threatened by cats, and about one quarter of these species are listed as Near Threatened or threatened (IUCN categories Critically Endangered, Endangered, or Vulnerable). In IUCN Red List assessments, cats are more frequently mentioned as a threat to threatened or Near Threatened bat species than to non-threatened species (IUCN category Least Concern). In studies reporting on the incidence of bats in cat dietary samples (scats, stomachs and guts), the frequency of occurrence of bats in samples averaged 0.7 ± 2.1% (mean ± standard deviation; n = 102). Many studies had sample sizes that were too small to be likely to detect bats. All forms of cat are reported to kill bats, and such predation has been reported in all major terrestrial habitats. We conclude that predation by cats is an under-appreciated threat to the world’s bat species.

Transfer efficiency is the proportion of energy passed between nodes in food webs. It is an emergent, unitless property that is difficult to measure, and responds dynamically to environmental and ecosystem changes. Because the consequences of changes in transfer efficiency compound through ecosystems, slight variations can have large effects on food availability for top predators. Here, we review the processes controlling transfer efficiency, approaches to estimate it, and known variations across ocean biomes. Both process-level analysis and observed macroscale variations suggest that ecosystem-scale transfer efficiency is highly variable, impacted by fishing, and will decline with climate change. It is important that we more fully resolve the processes controlling transfer efficiency in models to effectively anticipate changes in marine ecosystems and fisheries resources.

International audience

International audience; Biological nitrification inhibition (BNI) has already led to several studies mainly focused on underlying molecular mechanisms and applications to agriculture. We argue that it is also important to study BNI more systematically from the ecological and evolutionary points of view to understand its implications for plants and soil nitrifiers as well as its consequences for ecosystems. Therefore, we propose here a dedicated research agenda identifying the most critical research questions: (1) How is BNI distributed across plant phylogeny and why has it been selected? (2) What are the costs-to-benefits balance of producing BNI compounds and the relative impacts on BNI evolution? (3) Can we understand the evolutionary pressures leading to BNI and identify the environmental conditions favorable to BNI plants? (4) How has BNI coevolved with plant preference for ammonium vs. nitrate? (5) Diverse BNI compounds and various inhibition mechanisms have been described, but implications of this diversity are not understood. Does it allow inhibition of various groups of nitrifiers? (6) Does this diversity of BNI compounds increase the efficiency, spatial extension, and duration of BNI effect? (7) What are the impacts of BNI compounds on other soil functions? (8) Can field experiments, coupled to scanning of the diversity of BNI capabilities within plant communities, evaluate whether BNI influences plant-plant competition and plant coexistence? (9) Can field quantification of various nitrogen (N) fluxes assess whether BNI lead to more efficient N cycling with lower losses and hence increased primary production? (10) Can the impact of BNI on N budgets and climate (through its impact on N2O emissions and its indirect impact on carbon budget) be evaluated at the regional scale? We discuss why implementing this research program is crucial both for the sake of knowledge and to develop applications of BNI for agriculture.

National audience

To understand how and to what extent single or multiple perturbations can alter the relationships between the abundances of different nitrifier groups and nitrification, soil microcosms were exposed to six disturbance treatments: a heat shock, cold shock, or control conditions applied to undisturbed soils or to soils that had previously been subjected to a first heat shock. We monitored the recovery of the abundances of four main nitrifier groups (ammonia-oxidizing archaea and bacteria, AOA and AOB, respectively, and Nitrobacter and Nitrospira nitrite oxidizers) as well as nitrification activity for 25 days. AOA were sensitive to cold shocks, whereas AOB were not; the latter were sensitive to heat shock. Despite the variations, both groups were resilient to the first disturbance. In contrast, Nitrobacter was affected by both disturbances, whereas Nitrospira was resistant to both shocks. Prior exposure to a heat shock affected each group’s responses as well as the relationships between them. For example, AOB were more vulnerable to heat shock in pre-exposed soils, whereas under the same circumstances, AOA were resilient. Nitrification activity was resistant to the first disturbances, but a legacy effect was observed, and nitrification was highest in Heat-Heat and lowest in Heat-Cold treatments. Overall, our study shows that within soil nitrifiers, temporal patterns and legacy effects interact to result in complex disturbance responses.

International audience

International audience; Air pollution is a public health issue and the toxicity of ambient particulate matter (PM) is well-recognized. Although it does not mostly contribute to the total mass of PM, increasing evidence indicates that the ultrafine fraction has generally a greater toxicity than the others do. A better knowledge of the underlying mechanisms involved in the pathological disorders related to nanoparticles (NPs) remains essential. Hence, the goal of this study was to determine better whether the exposure to a relatively low dose of well-characterized iron-rich NPs (Fe-NPs) might alter some critical toxicological endpoints in a relevant primary culture model of human bronchial epithelial cells (HBECs). We sought to use Fe-NPs representative of those frequently found in the industrial smokes of metallurgical industries. After having noticed the effective internalization of Fe-NPs, oxidative, inflammatory, DNA repair, and apoptotic endpoints were investigated within HBECs, mainly through transcriptional screening. Taken together, these results revealed that, despite it only produced relatively low levels of reactive oxygen species without any significant oxidative damage, low-dose Fe-NPs quickly significantly deregulated the transcription of some target genes closely involved in the proinflammatory response. Although this inflammatory process seemed to stay under control over time in case of this acute scenario of exposure, the future study of its evolution after a scenario of repeated exposure could be very interesting to evaluate the toxicity of Fe-NPs better. K E Y W O R D S gene expression profiling, human bronchial epithelial cells, inflammation, iron nanoparticles, oxidative stress, physicochemical characterization 1 | INTRODUCTION Air pollution still constitutes the major threat to human health, whereas the adverse impacts and the underlying mechanisms of air pollution-derived particulate matter (PM) are not clearly defined

Plants can detect cues associated with the risk of future herbivory and modify defence phenotypes accordingly; however, our current understanding is limited both with respect to the range of early warning cues to which plants respond and the nature of the responses. Here we report that exposure to volatile emissions from plant tissues infested with herbivore eggs promotes stronger defence responses to subsequent herbivory in two Brassica species. Furthermore, exposure to these volatile cues elicited an apparent shift from growth to reproduction in Brassica nigra, with exposed plants exhibiting increased flower and seed production, but reduced leaf production, relative to unexposed controls. Our results thus document plant defence priming in response to a novel environmental cue, oviposition-induced plant volatiles, while also showing that plant responses to early warning cues can include changes in both defence and life-history traits.

Contexte et objectifs – La conservation durable de la biodiversité requiert une bonne compréhension des causes de son déclin. Mis à part les activités humaines, les changements climatiques se révèlent comme la principale menace qui pèse sur la biodiversité au 21ème siècle. Notre étude vise à déterminer l’impact du changement climatique sur les Ptéridophytes au Togo.Méthodologie – En se basant sur 2865 occurrences de Ptéridophytes couvrant toute l’Afrique de l’Ouest et regroupés en 5 groupes écologiques, les distributions actuelle et future des Ptéridophytes ont été modélisées grâce à Maxent. La capacité de conservation des aires protégées du Togo vis-à-vis de ces plantes a été évaluée.Résultats clés – Nos résultats montrent que 9,81% du pays peut abriter simultanément l’ensemble des groupes de ptéridophytes. Les précipitations des périodes sèches, l’isothermalité et la saisonnalité de la température sont les variables climatiques qui contraignent le plus leurs niches en Afrique de l’Ouest et particulièrement au Togo. Exceptés les taxons thermophiles dont les zones climatiquement favorables devraient quasiment doubler à l’horizon 2070, les niches des autres groupes devraient se restreindre drastiquement au Togo. Seules les aires protégées du tiers sud des Monts Togo pourront garantir la conservation des niches climatiques actuelles et futures des ptéridophytes dans le pays.Conclusions – Le sud des Monts Togo constituera probablement un refuge climatique pour les ptéridophytes au Togo. Toutefois, la faiblesse de l’étendue des aires protégées dans cette partie du pays pourrait constituer une source de vulnérabilité pour ces plantes. Vulnerability of pteridophytes to climate change and implications for their conservation in Togo (west Africa) Background and aims – The sustainable conservation of biodiversity requires a good understanding of the causes of its decline. Apart from human activities, climate change is the major threat to global biodiversity during the 21st century. Our study aims to determine the impact of climate change on pteridophytes in Togo.Methods – Based on 2865 occurrences of pteridophytes covering West Africa and grouped into 5 ecological groups, current and future distributions of pteridophytes were modelized using Maxent. The conservation capacity of Togolese protected areas for these plants was assessed.Key results – Our results show that 9.81% of the country can shelter simultaneously all groups of pteridophytes. Precipitations of the driest periods, isothermality and temperature seasonality are the climatic variables which constrain the most their niche in West Africa and particularly in Togo. Apart from thermophilic taxa whose climatically suitable niche is expected to nearly double by 2070, niche of all other group should be drastically restricted in Togo. Only protected areas in the southern third of Togo Mountains would guarantee current and future climatic niches for pteridophytes in the country.Conclusions – Southern Togo Mountains will probably constitute a climatic refugium for Pteridophytes in Togo. However, the small extent of protected areas in this part of the country would be a source of vulnerability for these plants.

There are many studies devoted to the negative impact of conventional pesticides that effectively control pests, but cause widespread environmental pollution. As a result, interest is growing in pesticides of a natural origin with a lower environmental impact. Among them, azadirachtin, sold under various formulations (neem oil, Neem-Azal, Bioneem, etc.), is still the most widely recommended molecule in agricultural ecosystems. Azadirachtin has also been used in traditional medicine for centuries, and studies published over the past few years have tended to support its therapeutic use. Yet the argument that azadirachtin is harmless to the environment has been offset by its notable collateral and controversial effects on non-target organisms. The present paper summarizes the work already done in this field.

International audience; Agroforestry and, more precisely, the integration of animals into orchards, represent an interesting source of income diversification for fruit growers who are confronted with rising climatic and economic risks. Besides farm resilience and optimisation of land use, this association seems to provide reciprocal benefits for both trees and animals, such as: nutrient cycling, weed management, natural protection and pest control. In particular, poultry and, more specifically, chickens, have caught the attention of numerous fruit growers in search of simple and time-saving agroecological solutions to regulate pests and weeds in their orchards. Yet, whereas traditional silvopastoral systems involving livestock have been extensively studied, the advantages and disadvantages of introducing chickens into orchards have been overlooked.

International audience; Context: There is a long-standing quest in landscape ecology for holistic biodiversity metrics accounting for multi-taxa diversity in heterogeneous habitat mosaics. Passive acoustic monitoring of biodiversity may provide integrative indices allowing to investigate how soundscapes are shaped by compositional and configurational heterogeneity of mosaic landscapes.Objectives: We tested the effects of dominant habitat and landscape heterogeneity on acoustic diversity indices across a large range of mosaic landscapes from two long-term socio-ecological research areas in Occitanie, France and Arizona, USA.Methods: We assessed acoustic diversity by automated recording for 44 landscapes distributed along gradients of compositional and configurational heterogeneity. We analyzed the responses of six acoustic indices and a composite multiacoustic index to habitat type and multi-scale landscape metrics for three time periods: 24 h-diel cycles, dawns and nights.Results: Landscape mosaics dominated by permanent grasslands in Occitanie and woodlands in Arizona produced the highest values of acoustic diversity. Moreover, several indices including H, ADI, NDSI, NP and the multiacoustic index consistently responded to edge density in both study regions, but with contrasting patterns, increasing in Occitanie and decreasing in Arizona. Landscape configuration was a key driver of acoustic diversity for diel and nocturnal soundscapes, while dawn soundscapes depended more on landscape composition.Conclusions: Acoustic diversity was correlated more with configurational than compositional heterogeneity in both regions, with contrasting effects explained by the interplay between biogeography and land use history. We suggest that multiple acoustic indices are needed to properly account for complex responses of soundscapes to large-scale habitat heterogeneity in mosaic landscapes.

International audience

International audience

16 pages, 4 figures, 2 tables, Increasing interest in the acquisition of biotic and abiotic resources from within the deep sea (e.g., fisheries, oil–gas extraction, and mining) urgently imposes the development of novel monitoring technologies, beyond the traditional vessel-assisted, time-consuming, high-cost sampling surveys. The implementation of permanent networks of seabed and water-column-cabled (fixed) and docked mobile platforms is presently enforced, to cooperatively measure biological features and environmental (physicochemical) parameters. Video and acoustic (i.e., optoacoustic) imaging are becoming central approaches for studying benthic fauna (e.g., quantifying species presence, behavior, and trophic interactions) in a remote, continuous, and prolonged fashion. Imaging is also being complemented by in situ environmental-DNA sequencing technologies, allowing the traceability of a wide range of organisms (including prokaryotes) beyond the reach of optoacoustic tools. Here, we describe the different fixed and mobile platforms of those benthic and pelagic monitoring networks, proposing at the same time an innovative roadmap for the automated computing of hierarchical ecological information on deep-sea ecosystems (i.e., from single species’ abundance and life traits to community composition, and overall biodiversity), This work was developed within the framework of the Tecnoterra (ICM-CSIC/UPC) and the following project activities: ARIM (Autonomous Robotic sea-floor Infrastructure for benthopelagic Monitoring; MartTERA ERA-Net Cofound), ARCHES (Autonomous Robotic Networks to Help Modern Societies; German Helmholtz Association), RESBIO (Grant TEC2017-87861-R; Ministerio de Ciencia, Innovación y Universidades), RESNEP (Grant CTM2017-82991-C2-1-R; Ministerio de Ciencia, Innovacion y Universidades), MERCES (Marine Ecosystem Restoration in Changing European Seas - GA No. 689518), and IDEM (Implementing the MSFD to the Deep Mediterranean Sea, GA No. 11.0661/2017/750680/SUB/ENV.C2)

International audience

The extend of biogeochemical cycling of nickel (Ni) by tropical hyperaccumulator plants in their native habitat is largely unknown, although these unusual plants are suspected to play a major role in the recycling of this element in ultramafic ecosystems. In this study, we have assessed the biogeochemical cycling of Ni (and other elements, including mineral nutrients) by a tropical Ni hyperaccumulator plant, i.e., Phyllanthus rufuschaneyi, which is one of the most promising species for tropical Ni agromining. The study site was a young secondary forest in Sabah (Malaysia) where Phyllanthus rufuschaneyi occurs as the dominant species on an ultramafic Cambisol. For 2 years, we monitored a 100-m2 plot and collected information on weather, biomass increase, soil fertility, water fluxes to the soil and litter fluxes for a wide range of elements, including Ni. The Ni cycle is mainly driven by internal fluxes, notably the degradation and recycling of Ni-rich litter. Over the period of investigation, the Ni litter flux corresponded to the total Ni stock of the litter (5.2 g m−2 year−1). The results further show that Ni turnover varies significantly with the accumulation properties of the plant cover. This points to the major influence of Ni hyperaccumulator plants in building up Ni available stocks in the topsoils, as has also been shown in temperate ultramafic systems. Litterfall and throughfall contribute substantially to the cycling of phosphorus, sulphur and potassium in this ecosystem, with throughfall contributing 2-, 220- and 20-fold higher to the respective nutrient fluxes relative to litterfall. The magnesium:calcium ratio far exceeded 1 in the soil, but was < 1 in the leaves of Phyllanthus rufuschaneyi. The insights from this study should be taken into account when designing tropical agromining operations; as Ni stocks could be more labile than initially thought. The removal of Ni- and nutrients-rich biomass will likely affect available Ni (and major nutrients) for the next cropping seasons, and requires sustainable fertilisation, to be utilized to replenish depleted major nutrients. These findings also have major ecological implications.

Sex-related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determinationsystems might drive lifespan evolution, sex chromosome influence on aging rates have not been investigated so far, likely due toan apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (heterogametic females)systems. Taking advantage of a unique collection of capture–recapture datasets in amphibians, a vertebrate group where XY andZW systems have repeatedly evolved over the past 200 million years, we examined whether sex heterogamy can predict sexdifferences in aging rates and lifespans. We showed that the strength and direction of sex differences in aging rates (and notlifespan) differ between XY and ZW systems. Sex-specific variation in aging rates was moderate within each system, but agingrates tended to be consistently higher in the heterogametic sex. This led to small but detectable effects of sex chromosome systemon sex differences in aging rates in our models. Although preliminary, our results suggest that exposed recessive deleteriousmutations on the X/Z chromosome (the “unguarded X/Z effect”) or repeat-rich Y/W chromosome (the “toxic Y/W effect”) couldaccelerate aging in the heterogametic sex in some vertebrate clades., C was supported asa postdoctoral researcher by the Vanier-Banting postdoctoral fellowship program and the Swiss National Science Foundation (SNF grant number 31003A_182265).

Chloromethane (CH3Cl) is an important source of chlorine in the stratosphere, but detailed knowledge of the magnitude of its sources and sinks is missing. Here, we measured the stable chlorine isot...

The sterile insect technique is an environment friendly control tactic and is very species specific. It is not a stand-alone technique and has been used mostly in combination with other control tactics within an area-wide integrated pest management strategy. For a period of eight years, the direct impact of a campaign to eradicate a population of the tsetse fly Glossina palpalis gambiensis in Senegal was monitored using a set of fruit-feeding insect species (Cetoniinae and Nymphalidae) that served as ecological indicators of the health of the ecosystem. Here we show that the eradication campaign had very limited impacts on the apparent densities of the most frequent species as well as three diversity indexes during the reduction phase involving insecticides but reverted to pre-intervention levels as soon as the release of the sterile male insects started. These results greatly expand our understanding of the impact of vector eradication campaigns on non-target species.

International audience

International audience

International audience

International audience

International audience

International audience

The species of Eleotris from Indonesia are reviewed and compared to the known species described from the area. Nine species are recognized including three new species in the ‘melanosoma’ neuromast pattern group. These are described using genetic and morpho-meristic approaches. The new species differ by a high percentage of genetic divergence in partial COI gene (652 bp) and by several characters including the number of pectoral fin rays, the number of scales in lateral, predorsal, forward and zigzag series. The main characteristics of the other known species in the area in the ‘melanosoma’ group, Eleotris melanosoma Bleeker, 1853 and Eleotris macrolepis (Bleeker, 1875), both belonging to this group, are given for comparison. A key for Eleotris species from Indonesia is provided.

International audience

In the environment, abiotic (climatic conditions, physico-chemical parameters), biotic (interactions between microorganisms, vegetation and fauna), and anthropogenic (stress, pollution) filters are driving the microbial diversity observed locally. A key question in microbial ecology is to understand the impact of these filters on bacterial diversity and ecosystem functioning. To highlight the responses of bacterial assemblages to these ecological filters, a new approach based on bacterial functional traits has been developed. This approach provides a functional picture of bacterial assemblages using morphological, physiological, and genomic traits as proxies of functions, and leads to a generalizable approach over a larger range of ecosystems with different bacterial diversities. We have created a user-friendly database of bacterial functional traits, thanks to the properties of 19,455 bacterial strains. This database has been called BactoTraits. For example, oxygen preference, size and shape of bacteria, motility, optimum and range of pH and temperature, genome GC percent and trophic type are among the 19 traits included in BactoTraits. Based on the best-informed strains in the database, we identified five functional groups (i.e. mesophiles, competitors, colonizers, stress-sensitives and stress-tolerants) exhibiting a wide strain taxonomic diversity but with quite similar trait profile combinations. As an example of application, BactoTraits was used to characterize the traits and functional diversity of bacterial assemblages in soil samples from 10 sites with different physico-chemical properties and various levels of metal and polycyclic aromatic hydrocarbon (PAH) contaminations. Inference of functional traits was based on taxonomic diversity information obtained by high-throughput sequencing of 16S rDNA. This trait-based approach has allowed to discriminate soils according to their physico-chemical properties and levels of contamination and to go further into the description of the bacterial assemblages. Several bacterial traits were identified as indicators of specific contaminants such as metals (e.g. filament shape, microaerophile and temperature optimum/range higher than 40 °C) or PAHs (e.g. spherical shape, facultative anaerobe/aerobe, no spore production, pH optimum ≥ 8, low temperature optimum but high temperature variation tolerance). Inferring trait values from a taxonomy-based approach can be extended readily to other microbial systems and contexts such as (i) studies on soils and aquatic ecosystems, (ii) microbial ecology along various environmental gradients, (iii) human, plant and animal microbiotes, as well as (iv) trophic interactions between bacterial communities and their predators.

Disease ecology and disease biogeography are complementary fields for the study of infectious diseases, both fields focus on the distribution and abundance of pathogens across scales. While disease ecology focuses on the study of disease systems at the local level and during short periods, disease biogeography expands the study of disease systems over large areas and prolonged periods. What is local vs. regional extents and what is short vs. prolonged periods is debatable. We propose that the study of the ecology and biogeography of disease systems takes place along a continuum, were the limits of ecology and biogeography are blurred. To demonstrate that disease systems operate from the local to the global and can be tracked from the fine to the coarse, this Research Topic compiles study cases that highlight concepts, methods, and applications of ecology and biogeography to untangle spatial patterns of disease phenomena across scales and for diverse infectious diseases.

International audience; Conflicts are ubiquitous in forest management because of several overlapping temporal and spatial issues (see examples in tropical and temperate areas [...]

International audience; Changes in temperature affect consumer-resource interactions which underpin the functioning of ecosystems. However, existing studies report contrasting predictions regarding the impacts of warming on biological rates and community dynamics. To improve prediction accuracy and comparability, we develop a framework that combines two approaches: sensitivity analysis and aggregate parameters. The former determines which biological parameters impact the community most strongly. The use of aggregate parameters (i.e., maximal energetic efficiency, ρ, and interaction strength, κ), that combine multiple biological parameters, increases explanatory power and reduces the complexity of theoretical analyses. We illustrate the framework using empirically-derived thermal dependence curves of biological rates and applying it to consumer-resource biomass ratio and community stability. Based on our analyses, we present four predictions: 1) resource growth rate regulates biomass distributions at mild temperatures, 2) interaction strength alone determines the thermal boundaries of the community, 3) warming destabilises dynamics at low and mild temperatures only, 4) interactions strength must decrease faster than maximal energetic efficiency for warming to stabilise dynamics. We argue that directly measuring the aggregate parameters should increase the accuracy of predictions on warming impacts on food webs and promote cross-system comparisons.

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Intertidal seagrass meadows are exposed to both marine and terrestrial environmental constraints. Seagrass vulnerability to climate changes in these highly dynamic and thermally stressful environments is concerning. Using broad scale monitoring data covering contrasted intertidal environments, this study aims to provide a comprehensive view of the extent, drivers and potential limits of Zostera marina phenotypic responses. The links between phenotypic and reproductive strategies are also explored. Across 500km of coastline, Z. marina exhibited extensive variations of density, morphology, above- and belowground biomass, and rates of clonality. Variance partitioning of phenotypic traits confirmed the strong link between intertidal seagrass populations and broad-scale climate variability. However, it also highlighted a non-negligeable role of local factors such as exposure regime, substrate and tidal cycles. In its response to the environment, Z. marina displayed a trade-off between the density and size of shoots, leading to two distinct phenotypic types: high densities and low above-to-belowground biomass ratios (Type 1) in response to both high hydrodynamic and temperature stress; and low densities, high aboveground biomass per shoot and developed leaves and sheaths (Type 2) in the most stable and less stressful intertidal environments. We argue that Type 1 maximizes self-facilitation whereas Type 2 minimizes intra-specific competition, and that their occurrence matches predictions from the stress-gradient hypothesis (SGH). Building on the SGH, we propose a generalized response of seagrass to environmental changes and discuss the role of light as a potential limiting resource for intertidal meadows. Synthesis – Here, we show how the SGH can explain seagrass phenotypic responses, drawing on previous experimental results to provide relevant predictions across different stress gradients. We also show that Zostera marina responds to strong hydrodynamics and thermal constraints, both likely to increase in the intertidal with climate changes, with a facilitation-maximizing phenotypic type (Type 1). This strategy appears incompatible with the competition-minimizing Type 2 found when seagrass face resource limitation, such as light limitation induced by water quality degradation. This potential limit to the resilience of intertidal seagrass populations in the face of cumulative stressors raises concern about their vulnerability regarding future climate scenarios.

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International audience; Oyster farming for black pearl production is central in French Polynesia. It is the second source of national income and provides substantial job opportunities, notably in remote atolls. However, this sector has been undermined by successive crises, such as mass-mortalities of wild and farmed oyster stocks that have impacted entire lagoons. An option to revive the activity consists of reintroducing oysters in strategic benthic locations selected to maximize reproduction and dispersal of larvae throughout the lagoon, hence promoting recolonization and spat collection for farming. For Takaroa, a Tuamotu atoll recently impacted by mortalities, a systematic prioritization approach identified these restocking sites, using environmental and socio-economic criteria such as: location of suitable habitats for oyster settlement, larval connectivity estimated from hydrodynamic circulation model, farming waste accumulation, and opportunity cost to fishers and farmers who lose access to restocking areas. This approach provides managers with a portfolio of restocking options.

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Pristine environmental conditions and wide biodiversity are the best evidence of pre-colonial times, before anthropic interference in the Anthropocene. The Galeao shell mound represents the main example of an insular archaeological site located in the context of the Guanabara Bay in the Middle Holocene. The faunal remains from this shell mound were identified through comparative anatomy, to access the ichthyofauna and also amphibian, reptile and mammal paleodiversity. The diagnostic elements revealed the presence of predominantly demersal teleost fish, typical inhabitants of estuarine and marine systems, along with the usual species inhabiting rocky shores and rocky bottoms. Additionally, it revealed an exceptional diversity of sharks, including the presence of pelagic taxa, as well as stingrays. The local wildlife consists of species commonly found in swampy, mangrove, Brazilian restinga and Atlantic forest biomes. This study shows widely practiced fishery and hunting by the Amerindian using the resources of the Guanabara Bay and indicates specific targets during the Middle Holocene. Degradation of coastal environments and/or overfishing threaten the local biodiversity, with species now absent and some with statuses which go from Vulnerable to Critically Endangered.

Anthropogenic climate change is causing a severe impact on the survival of organisms (Brondizio et al., 2019; Shukla et al., 2019). Climate is one of the major drivers of species distributions, and the velocity at which the cur- rent climate is changing, owing to human activities, already induces a redistribution of life on Earth at an unprecedented speed, especially in the oceans where marine life is shifting towards the poles six times faster than the velocity at which terrestrial life is shifting pole- ward on land (Lenoir et al., 2020). Besides, biodiversity redistribution may enhance climate warming through positive feedback loops (e.g., the shrubification of the Arctic altering the surface albedo), thus indirectly affect- ing human well-being (Pecl et al., 2017). For this reason, both essential climate variables (ECVs) and essential bio- diversity variables (EBVs) have been developed as proxies for the early detection of climate change and biodiversity redistribution (Bojinski et al., 2014; Pereira et al., 2013; Schmeller et al., 2018).

Manure application to land and deposition of urine and dung by grazing animals are major sources of ammonia (NH3 ) and nitrous oxide (N2 O) emissions. Using data on NH3 and N2 O emissions following land-applied manures and excreta deposited during grazing, emission factors (EFs) disaggregated by climate zone were developed, and the effects of mitigation strategies were evaluated. The NH3 data represent emissions from cattle and swine manures in temperate wet climates, and the N2 O data include cattle, sheep, and swine manure emissions in temperate wet/dry and tropical wet/dry climates. The NH3 EFs for broadcast cattle solid manure and slurry were 0.03 and 0.24 kg NH3 -N kg-1 total N (TN), respectively, whereas the NH3 EF of broadcast swine slurry was 0.29. Emissions from both cattle and swine slurry were reduced between 46 and 62% with low-emissions application methods. Land application of cattle and swine manure in wet climates had EFs of 0.005 and 0.011 kg N2 O-N kg-1 TN, respectively, whereas in dry climates the EF for cattle manure was 0.0031. The N2 O EFs for cattle urine and dung in wet climates were 0.0095 and 0.002 kg N2 O-N kg-1 TN, respectively, which were three times greater than for dry climates. The N2 O EFs for sheep urine and dung in wet climates were 0.0043 and 0.0005, respectively. The use of nitrification inhibitors reduced emissions in swine manure, cattle urine/dung, and sheep urine by 45-63%. These enhanced EFs can improve national inventories; however, more data from poorly represented regions (e.g., Asia, Africa, South America) are needed.

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BACKGROUND Pyrethroid insecticides such as deltamethrin have been massively used against Aedes aegypti leading to the spread of resistance alleles worldwide. In an insecticide resistance management context, we evaluated the temporal dynamics of deltamethrin resistance using two distinct populations carrying resistant alleles at different frequencies. Three different scenarios were followed: a continuous selection, a full release of selection, or a repeated introgression with susceptible individuals. The responses of each population to these selection regimes were measured across five generations by bioassays and by monitoring the frequency of knockdown resistance (kdr) mutations and the transcription levels and copy number variations of key detoxification enzymes. RESULTS Knockdown resistance mutations, overexpression and copy number variations of detoxification enzymes as a mechanism of metabolic resistance to deltamethrin was found and maintained under selection across generations. On comparison, the release of insecticide pressure for five generations did not affect resistance levels and resistance marker frequencies. However, introgressing susceptible alleles drastically reduced deltamethrin resistance in only three generations. CONCLUSION The present study confirmed that strategies consisting to stop deltamethrin spraying are likely to fail when the frequencies of resistant alleles are too high and the fitness cost associated to resistance is low. In dead-end situations like in French Guiana where alternative insecticides are not available, alternative control strategies may provide a high benefit for vector control, particularly if they favor the introgression of susceptible alleles in natural populations. © 2021 Society of Chemical Industry.

International audience; Understanding the natural state of coral reefs is paramount to evaluate the response of these ecosystems to local and global human impacts as well as management and conservation strategies. In French Polynesia, some islands are still pristine or uninhabited, such as Tupai atoll. Tupai has been uninhabited, with access to the lagoon prohibited since 2010. However, fishers from nearby islands often take from the outer reef slope at Tupai. Our marine biodiversity survey (coral, macro-invertebrates, and fish) conducted in 2019 highlighted a low density of commercial fish species and top-predators on the outer slope in comparison to the lagoon, where the top-predators represented 16% (of the density) of functional trophic groups. Our surveys also showed a high living coral cover (46%) on the outer slope of Tupai, perhaps due to the absence of both touristic sub-aquatic activities and local pollution from private and commercial activities. Overall, this initial scientific assessment of Tupai has granted an understanding of the spatial patterns of coral, macro-invertebrates, and fish assemblages in the absence of human impacts (i.e., in the lagoon), representing an ecological baseline that could inform conservation management strategies to ensure the preservation of coral reef ecosystem.