Variabilité trophique chez la truite marbrée (Salmo marmoratus) : déterminismes ontogénétiques et environnementaux

La variabilité au sein des populations naturelles est un facteur primordial de maintien de la diversité fonctionnelle dans les communautés et les écosystèmes. Présente dans une aire géographique restreinte, la truite marbrée (Salmo marmoratus) est une espèce aujourd'hui menacée par les effets du changement climatique (augmentation de la fréquence et de l'intensité des crues) et par les invasions biologiques. Seules quelques populations persistent dans le bassin adriatique. Les objectifs de cette thèse sont de quantifier la variabilité trophique de cette espèce dans des populations naturelles de l'échelle populationnelle à l'échelle individuelle et d'en identifier les mécanismes. Le régime alimentaire de 1523 individus issus des sept populations du bassin de la Soca (Slovénie) échantillonnées entre 2011 et 2013 a été analysé à l'aide des isotopes stables (d15N et d13C). Les résultats mettent en évidence une forte variabilité trophique entre les individus et au sein des individus au cours de leur ontogénie. Cette variabilité trophique également observée à l'échelle populationnelle, dépend d'une part de la structure en taille des populations et d'autre part des effets des variables environnementales à la fois sur la physiologie des organismes et sur la disponibilité des ressources alimentaires. Les résultats indiquent un fort taux de cannibalisme chez cette espèce (de 6 à 32 % à l'échelle de la population) survenant par opportunisme et favorisé par la densité des proies. Le cannibalisme est un comportement permanent qui va affecter la dynamique des populations. L'étude des interactions trophiques entre la truite marbrée et une truite exotique (la truite arc-en-ciel, Oncorhynchus mykiss) montre que la compétition entre ces deux Salmonidés engendre un déplacement de niches trophiques de l'espèce native. Cependant, nos résultats suggèrent que le comportement piscivore de la truite marbrée, rarement observé chez des Salmonidés de rivière, confère à l'espèce une résistance biologique face aux invasions biologiques. L'ensemble des résultats démontre la forte plasticité trophique, à la fois individuelle et populationnelle, de ce prédateur aquatique, qui pourrait constituer un avantage adaptatif dans un contexte de changement climatique.Variability within natural populations plays a major role in maintaining functional diversity in communities and ecosystems. The marble trout (Salmo marmoratus) is a species of great conservation concern given its restricted geographical area. Few populations persist in the Adriatic basin, threatened by the impacts of global change (increase of the frequency and intensity of flood events) and by biological invasions. In this thesis, we aimed to quantify trophic variability of this species both at the population and individual levels and to understand the underlying mechanisms. The diet of 1523 marble trout from the seven remnant populations persisting in the Soca River basin (Slovenia) were sampled between 2011 and 2013 and were analyzed with stable isotopes (d15N and d13C). Our results show strong variability through ontogeny within as well as between individuals. This intraspecific variation was observed at the population level and was determined by both environmental variables and size-structured demography effects on fish physiology and ecological opportunities. Results indicate a high rate of opportunistic cannibalism (from 6 to 32 % in populations) promoted by prey densities. This permanent behavior may lead to modification of the populations' size structures and dynamics. Studying trophic interactions between the marble trout and an invasive salmonid species (rainbow trout, Oncorhynchus mykiss), we showed that trophic niches of the native trout shifted because of interspecific competition. However, our results suggest that the piscivorous behavior of the marble trout, rare for stream-dwelling salmonids, would be a strong advantage for biotic resistance against biological invaders. This thesis demonstrates the high trophic plasticity, both at the individual and population levels, in this freshwater predator that could be an adaptative advantage in a global change context

Fortes densités de la Gorgebleue endémique du littoral français (Cyanecula svecica namnetum) révélées dans les roselières intertidales et perspectives de conservation au regard de l’élévation du niveau marin

Notre étude porte sur l’estimation de la densité au sein des roselières intertidales de l’estuaire de la Gironde (France) de la sous-espèce de Gorgebleue à miroir endémique du littoral atlantique français (Cyanecula svecica namnetum). Nous avons analysé des données de points d’écoute collectées durant le début de période de reproduction grâce à 94 stations distribuées sur 100 hectares. L’analyse des données intégrant la probabilité de détection des oiseaux en fonction de la distance de détection (distance sampling) nous a permis d’estimer une densité moyenne de 20,5 ± 3,7 mâles pour 10 hectares (14,4 – 29.5 dans l’IC à 95 %). Jusqu’à ce jour, de telles densités n’ont jamais été documentées pour ce taxon endémique au statut de conservation préoccupant compte-tenu de son relatif haut degré de spécialisation en termes de ressources trophiques exploitées, de son aire de répartition et de ses effectifs limités. Malgré leur singularité compte tenu de la taille limitée de la zone d’étude, nos résultats confirment l’importance des marais côtiers pour C. s. namnetum. Au vu des importantes altérations des habitats littoraux inhérentes à la montée du niveau marin déjà observées sur les zones de reproduction de C. s. namnetum, nos résultats mettent en lumière l’intérêt à développer des stratégies de conservation pour les habitats exploités par le taxon, intégrant les rôles-clés potentiels des zones arrière-littorales pour compenser les pertes d’habitats inhérentes aux effets des changements globaux en cours et à venir.Our study deals with density estimation in intertidal reed beds of the Gironde estuary (France) of the French endemic subspecies of Bluethroat breeding along the Atlantic coast (Cyanecula svecica namnetum). We analysed count point data collected during the beginning of the breeding period, with information gathered from 94 stations distributed over 100 hectares. Analysis of data integrating bird detection probability as a function of the detection distance (distance sampling) allowed us to estimate an average density of 20.5 ± 3.7 males for 10 hectares (14.4 – 29.5 within the 95 % CI). Up to now, no equivalent densities have been documented for this endemic taxa which is of conservation concern given its relatively high degree of specialization in terms of ecological resources exploited and its limited range and numbers. Despite their singularity given the limited size of the study area, our results confirm the particular importance of coastal marshes for C. s. namnetum. In view of strong alterations of coastal habitats due to the rise in sea level already observed in the breeding grounds of C. s. namnetum, our results highlight the interest in developing conservation strategies for habitats exploited by the taxa, integrating the potential key roles of back littoral areas

A conceptual map of invasion biology: Integrating hypotheses into a consensus network

Background and aims Since its emergence in the mid‐20th century, invasion biology has matured into a productive research field addressing questions of fundamental and applied importance. Not only has the number of empirical studies increased through time, but also has the number of competing, overlapping and, in some cases, contradictory hypotheses about biological invasions. To make these contradictions and redundancies explicit, and to gain insight into the field’s current theoretical structure, we developed and applied a Delphi approach to create a consensus network of 39 existing invasion hypotheses. Results The resulting network was analysed with a link‐clustering algorithm that revealed five concept clusters (resource availability, biotic interaction, propagule, trait and Darwin’s clusters) representing complementary areas in the theory of invasion biology. The network also displays hypotheses that link two or more clusters, called connecting hypotheses, which are important in determining network structure. The network indicates hypotheses that are logically linked either positively (77 connections of support) or negatively (that is, they contradict each other; 6 connections). Significance The network visually synthesizes how invasion biology’s predominant hypotheses are conceptually related to each other, and thus, reveals an emergent structure – a conceptual map – that can serve as a navigation tool for scholars, practitioners and students, both inside and outside of the field of invasion biology, and guide the development of a more coherent foundation of theory. Additionally, the outlined approach can be more widely applied to create a conceptual map for the larger fields of ecology and biogeography

The Ecologist's Career Compass: A game to explore career paths

One of the most challenging endeavors for students is choosing a career path that best fits their interests, wills and skills, and setting their professional goals accordingly. Such decisions are often made from within the culture of academia, in which mentors and peers are mainly familiar with the academic job market and lack the knowledge necessary to consult about other types of careers. We aimed to address this gap for ecology and related fields by creating an engaging and effective tool to help students and professionals to familiarize themselves with the diversity of potential career paths available to ecologists. The tool is an applied card game – the Ecologist's Career Compass – which is provided here freely. The game is played as a trump card game and includes 33 cards, each representing a combination of one of four job-market sectors and one of nine types of positions. Each card indicates the level of seven skill categories required to likely be hired and succeed in the focal position at the focal sector, as well as more specific examples for typical jobs in the focal combination. The information in the game largely relies on input from a global survey we conducted among 315 ecologists from 35 countries. While the challenges faced by early-career ecologists in developing their professional path are substantial and diverse, this game can assist in gaining a broad comparative overview of the whole ecology job market and the skills required to likely excel in different paths. We hope this applied game will act as a conversation starter about the diversity of aspirations and opportunities in ecology classrooms and labs.Alexander von Humboldt‐Stiftung http://dx.doi.org/10.13039/100005156Deutsche Bundesstiftung Umwelt http://dx.doi.org/10.13039/100007636Peer Reviewe

Direct and indirect effects of environmental factors on dietary niches in size-structured populations of a wild salmonid

Dietary plasticity of populations can be associated to ontogenetic diet preferences and depends on the size-structure of populations. Dietary niche characterizes the functional role of organisms in a food web, as it reflects both resources' diversity used by a consumer and trophic interactions in the system. Dietary niches are controlled both by biotic and abiotic factors, but their interactions in natural systems remain poorly studied. Here, we investigated the variability of dietary niche in salmonid wild populations focusing both on inter-population and intra-population (through time) trophic changes, using marble trout (Salmo marmoratus) living in Slovenian headwater streams as a model system. Stable isotope analysis showed high variability of dietary niche and trophic diversity among six of the seven remnant marble trout populations. We observed substantial differences in dietary niche width among populations and within populations through time. Results of partial least square path modelling highlighted opposite effects of immature and mature trout on trophic niche structure. Direct effects of temperature and slope (stream and watershed) were opposite; temperature narrowed dietary niches while slope increased them. Environmental factors (e.g., temperature, stream and watershed slope) had indirect effects on trophic niches after accounting for fish density. Our results showed that size-distribution and sexual maturity are key determinants of the dietary niche width in a population. Increasing density of immature trout tended to widen the dietary niche while increasing density of mature trout tended to narrow it. Environmental factors had direct effects both on resources and consumers densities and indirect effects. Direct and indirect effects were often antagonistic

Nonlinear effects of environmental drivers shape macroinvertebrate biodiversity in an agricultural pondscape

Agriculture is a leading cause of biodiversity loss and significantly impacts freshwater biodiversity through many stressors acting locally and on the landscape scale. The individual effects of these numerous stressors are often difficult to disentangle and quantify, as they might have nonlinear impacts on biodiversity. Within agroecosystems, ponds are biodiversity hotspots providing habitat for many freshwater species and resting or feeding places for terrestrial organisms. Ponds are strongly influenced by their terrestrial surroundings, and understanding the determinants of biodiversity in agricultural landscapes remains difficult but crucial for improving conservation policies and actions. We aimed to identify the main effects of environmental and spatial variables on α-, β-, and γ-diversities of macroinvertebrate communities inhabiting ponds (n = 42) in an agricultural landscape in the Northeast Germany, and to quantify the respective roles of taxonomic turnover and nestedness in the pondscape. We disentangled the nonlinear effects of a wide range of environmental and spatial variables on macroinvertebrate α- and β-biodiversity. Our results show that α-diversity is impaired by eutrophication (phosphate and nitrogen) and that overshaded ponds support impoverished macroinvertebrate biota. The share of arable land in the ponds' surroundings decreases β-diversity (i.e., dissimilarity in community), while β-diversity is higher in shallower ponds. Moreover, we found that β-diversity is mainly driven by taxonomic turnover and that ponds embedded in arable fields support local and regional diversity. Our findings highlight the importance of such ponds for supporting biodiversity, identify the main stressors related to human activities (eutrophication), and emphasize the need for a large number of ponds in the landscape to conserve biodiversity. Small freshwater systems in agricultural landscapes challenge us to compromise between human demands and nature conservation worldwide. Identifying and quantifying the effects of environmental variables on biodiversity inhabiting those ecosystems can help address threats impacting freshwater life with more effective management of pondscapes

High temperature perception in leaves promotes vascular regeneration and graft formation in distant tissues

Cellular regeneration in response to wounding is fundamental to maintain tissue integrity. Various internal factors including hormones and transcription factors mediate healing, but little is known about the role of external factors. To understand how the environment affects regeneration, we investigated the effects of temperature upon the horticulturally relevant process of plant grafting. We found that elevated temperatures accelerated vascular regeneration in Arabidopsis thaliana and tomato grafts. Leaves were crucial for this effect, as blocking auxin transport or mutating PHYTOCHROME INTERACTING FACTOR 4 (PIF4) or YUCCA2/5/8/9 in the cotyledons abolished the temperature enhancement. However, these perturbations did not affect grafting at ambient temperatures, and temperature enhancement of callus formation and tissue adhesion did not require PIF4, suggesting leaf-derived auxin specifically enhanced vascular regeneration in response to elevated temperatures. We also found that elevated temperatures accelerated the formation of inter-plant vascular connections between the parasitic plant Phtheirospennum japonicum and host Arabidopsis, and this effect required shoot-derived auxin from the parasite. Taken together, our results identify a pathway whereby local temperature perception mediates long distance auxin signaling to modify regeneration, grafting and parasitism.This article has an associated 'The people behind the papers' interview

From microbes to mammals: Pond biodiversity homogenization across different land-use types in an agricultural landscape

Local biodiversity patterns are expected to strongly reflect variation in topography, land use, dispersal boundaries, nutrient supplies, contaminant spread, management practices, and other anthropogenic influences. Contrary to this expectation, studies focusing on specific taxa revealed a biodiversity homogenization effect in areas subjected to long-term intensive industrial agriculture. We investigated whether land use affects biodiversity levels and community composition (α- and β-diversity) in 67 kettle holes (KH) representing small aquatic islands embedded in the patchwork matrix of a largely agricultural landscape comprising grassland, forest, and arable fields. These KH, similar to millions of standing water bodies of glacial origin, spread across northern Europe, Asia, and North America, are physico-chemically diverse and differ in the degree of coupling with their surroundings. We assessed aquatic and sediment biodiversity patterns of eukaryotes, Bacteria, and Archaea in relation to environmental features of the KH, using deep-amplicon-sequencing of environmental DNA (eDNA). First, we asked whether deep sequencing of eDNA provides a representative picture of KH aquatic biodiversity across the Bacteria, Archaea, and eukaryotes. Second, we investigated if and to what extent KH biodiversity is influenced by the surrounding land use. We hypothesized that richness and community composition will greatly differ in KH from agricultural land use compared with KH in grasslands and forests. Our data show that deep eDNA amplicon sequencing is useful for in-depth assessments of cross-domain biodiversity comprising both micro- and macro-organisms, but has limitations with respect to single-taxa conservation studies. Using this broad method, we show that sediment eDNA, integrating several years to decades, depicts the history of agricultural land-use intensification. Aquatic biodiversity was best explained by seasonality, whereas land-use type explained little of the variation. We concluded that, counter to our hypothesis, land use intensification coupled with landscape wide nutrient enrichment (including atmospheric deposition), groundwater connectivity between KH and organismal (active and passive) dispersal in the tight network of ponds, resulted in a biodiversity homogenization in the KH water, leveling off today's detectable differences in KH biodiversity between land-use types. These findings have profound implications for measures and management strategies to combat current biodiversity loss in agricultural landscapes worldwide

A proposed unified framework to describe the management of biological invasions

Managing the impacts of invasive alien species (IAS) is a great societal challenge. A wide variety of terms have been used to describe the management of invasive alien species and the sequence in which they might be applied. This variety and lack of consistency creates uncertainty in the presentation and description of management in policy, science and practice. Here we expand on the existing description of the invasion process to develop an IAS management framework. We define the different forms of active management using a novel approach based on changes in species status, avoiding the need for stand-alone descriptions of management types, and provide a complete set of potential management activities. We propose a standardised set of management terminology as an emergent feature of this framework. We identified eight key forms of management: (1) pathway management, (2) interception, (3) limits to keeping, (4) secure keeping, (5) eradication, (6) complete reproductive removal, (7) containment and (8) suppression. We recognise four associated terms: prevention; captive management; rapid eradication; and long-term management, and note the use of impact mitigation and restoration as associated forms of management. We discuss the wider use of this framework and the supporting activities required to ensure management is well-targeted, cost-effective and makes best use of limited resources

Hypotheses in urban ecology: building a common knowledge base

Urban ecology is a rapidly growing research field that has to keep pace with the pressing need to tackle the sustainability crisis. As an inherently multi-disciplinary field with close ties to practitioners and administrators, research synthesis and knowledge transfer between those different stakeholders is crucial. Knowledge maps can enhance knowledge transfer and provide orientation to researchers as well as practitioners. A promising option for developing such knowledge maps is to create hypothesis networks, which structure existing hypotheses and aggregate them according to topics and research aims. Combining expert knowledge with information from the literature, we here identify 62 research hypotheses used in urban ecology and link them in such a network. Our network clusters hypotheses into four distinct themes: (i) Urban species traits & evolution, (ii) Urban biotic communities, (iii) Urban habitats and (iv) Urban ecosystems. We discuss the potentials and limitations of this approach. All information is openly provided as part of an extendable Wikidata project, and we invite researchers, practitioners and others interested in urban ecology to contribute additional hypotheses, as well as comment and add to the existing ones. The hypothesis network and Wikidata project form a first step towards a knowledge base for urban ecology, which can be expanded and curated to benefit both practitioners and researchers