Bernard Amiaud

The relationships between soil seed bank, aboveground vegetation and disturbances in old embanked marshlands of Western France

Summary The study deals with the influence of land use and abandonment on species composition of vegetation and seed bank in grasslands and oldfields. We wanted to explore: (1)How the seed bank changes when agricultural practices cease? In convergence with proposals in the literature, we addressed in particular the following two questions that have been proposed by Symonides (1986), Pickett & McDonnell (1989) and Roberts & Vankat (1991) for seed bank characteristics under secondary succession: (i) Does species richness and species diversity in the soil seed bank decrease during succession? (ii) Does the density of buried seed decline during succession? (2)What is the role played by seed bank in the recolonisation of plots disturbed by experimental disturbances? We studied species composition of vegetation and seed bank in an experiment with grassland and oldfield plots in old embanked marshlands (called “Marais Poitevin”). In these wetlands, artificial disturbances (mowing) and natural disturbances (cattle, roebucks, coypus, voles) are very frequent. In order to mimic disturbances, experimental disturbances were generated in spring after the end of the winter flooding and emerged seedlings counted three months later. Data about the seed bank, the undisturbed vegetation and seedlings emerging in disturbed quadrats were sampled. Detrended Correspondence Analysis (DCA) of the undisturbed quadrats, disturbed quadrats and seed bank samples showed significant differences of species composition. Similarity between seed bank and undisturbed aboveground vegetation was low and not very different between grassland and oldfield. Very few seedlings emerged in the undisturbed vegetation both in grassland and oldfield, which potentially indicates the importance of gaps for seed bank expression. In Marais Poitevin, the seed bank contributed very little to the seedling flora, and vegetative regrowth clearly predominated recolonisation after disturbances. In the seed bank, few species lost after succession from grassland to oldfield vegetation were still present as seeds in the soil, but in most cases species lost were not recorded in the seed bank. The results have shown that species richness and species diversity in the seed bank decrease during succession. On the other hand, the density of buried seeds did not decrease significantly from grassland to oldfield.

The relationships between soil seed bank, aboveground vegetation and disturbances in an eutrophic alluvial wetland of Western France

Summary We studied the species composition of vegetation and seed bank in an experiment with grassland and oldfield plots in an eutrophic alluvial wetland (called “Marais de Redon”) of Western France. In this wetland, artificial disturbances (mowing) and natural disturbances (cattle, roebucks, boars, voles…) are very frequent. In order to mime these natural disturbances, experimental disturbances were generated in March 1996 after the end of the winter flooding and the seedlings counted three months later. The seed bank, the undisturbed vegetation and seedlings emerging in disturbed quadrats were sampled. Detrended Correspondence Analysis (DCA) of the undisturbed quadrats, disturbed quadrats and seed bank samples showed significant differences of species composition. Similarity between seed bank and undisturbed aboveground vegetation was low and not very different between grassland and oldfield. Very few seedlings emerged in undisturbed vegetation both in grassland and oldfield, which indicates the importance of gaps for seed bank expression. The great majority of seedlings emerging after experimental disturbances were mainly recruited from the soil seed bank. This result contrasts with other studies where the seed bank contributed very little to the seedling flora and vegetative regrowth clearly predominated recolonisation after disturbances. In the seed bank, few species lost after succession from grassland to oldfield vegetation were still present as seeds in the soil, but in most cases, species lost were not recorded in the seed bank. The two hypotheses about changes in the seed bank during secondary succession, predicting decrease in species richness or species diversity and seed density were only confirmed for seed density parameter.

Spatial patterns of soil salinities in old embanked marshlands in western France

The spatial pattern of soil salinity was studied in commonly owned grazing meadows, embanked in the distant past (10th century), situated on the Atlantic coast of western France. The meadows were characterized by micro-relief, a relic of former salt marshes, with an amplitude that varied between 15 and 65 cm. The topographic sequence consisted of a mosaic of seasonally flooded depressions, of slopes, and of areas of flat, higher ground. The soils of the various topographic levels that were studied at 6 sites had different electrical conductivities and sodicities. The highest values occurred in slope soils (conductivity between 0.83 and 2.85 mS/cm), especially at the base of slopes, whereas the lowest values were typical of the soils of depressions (conductivity between 0.42 and 0.56 mS/cm). The deepest soil horizon (Cg) always had a higher sodicity and conductivity than that of the surface horizon at all topographic levels. The groundwater specific conductivity showed similar tendencies. A more intensive sampling of the spatial pattern of soil salinity at the Magnils-Reigniers site confirmed these results. In this sampling, only the conductivity of the soil-water extract was measured, as high correlations were shown at the 6 sites between the conductivity, sodicity, the exchangeable sodium content and soluble sodium content of the soil. The spatial pattern of salinity and sodicity can be related to the spatial structure of the vegetation, as salt-tolerant species (Juncus gerardi andHordeum marinum) occur on the slopes. This type of system does not seem to have been described elsewhere and appears to be related, via hydrologic mechanisms and the physical action of grazing animals, to the traditional management of the meadows for grazing.

Towards a thesaurus of plant characteristics: an ecological contribution

Ecological research produces a tremendous amount of data, but the diversity in scales and topics covered and the ways in which studies are carried out result in large numbers of small, idiosyncratic data sets using heterogeneous terminologies. Such heterogeneity can be attributed, in part, to a lack of standards for acquiring, organizing and describing data. Here, we propose a terminological resource, a Thesaurus Of Plant characteristics (TOP), whose aim is to harmonize and formalize concepts for plant characteristics widely used in ecology. TOP concentrates on two types of plant characteristics: traits and environmental associations. It builds on previous initiatives for several aspects: (i) characteristics are designed following the entity-quality (EQ) model (a characteristic is modelled as the ‘Quality’ of an ‘Entity’ ) used in the context of Open Biological Ontologies; (ii) whenever possible, the Entities and Qualities are taken from existing terminology standards, mainly the Plant Ontology (PO) and Phenotypic Quality Ontology (PATO) ontologies; and (iii) whenever a characteristic already has a definition, if appropriate, it is reused and referenced. The development of TOP, which complies with semantic web principles, was carried out through the involvement of experts from both the ecology and the semantics research communities. Regular updates of TOP are planned, based on community feedback and involvement. TOP provides names, definitions, units, synonyms and related terms for about 850 plant characteristics. TOP is available online (www.top-thesaurus.org), and can be browsed using an alphabetical list of characteristics, a hierarchical tree of characteristics, a faceted and a free-text search, and through an Application Programming Interface. Synthesis. Harmonizing definitions of concepts, as proposed by TOP, forms the basis for better integration of data across heterogeneous data sets and terminologies, thereby increasing the potential for data reuse. It also allows enhanced scientific synthesis. TOP therefore has the potential to improve research and communication not only within the field of ecology, but also in related fields with interest in plant functioning and distribution.

Filling the gap in functional trait databases: use of ecological hypotheses to replace missing data.

Functional trait databases are powerful tools in ecology, though most of them contain large amounts of missing values. The goal of this study was to test the effect of imputation methods on the evaluation of trait values at species level and on the subsequent calculation of functional diversity indices at community level using functional trait databases. Two simple imputation methods (average and median), two methods based on ecological hypotheses, and one multiple imputation method were tested using a large plant trait database, together with the influence of the percentage of missing data and differences between functional traits. At community level, the complete-case approach and three functional diversity indices calculated from grassland plant communities were included. At the species level, one of the methods based on ecological hypothesis was for all traits more accurate than imputation with average or median values, but the multiple imputation method was superior for most of the traits. The method based on functional proximity between species was the best method for traits with an unbalanced distribution, while the method based on the existence of relationships between traits was the best for traits with a balanced distribution. The ranking of the grassland communities for their functional diversity indices was not robust with the complete-case approach, even for low percentages of missing data. With the imputation methods based on ecological hypotheses, functional diversity indices could be computed with a maximum of 30% of missing data, without affecting the ranking between grassland communities. The multiple imputation method performed well, but not better than single imputation based on ecological hypothesis and adapted to the distribution of the trait values for the functional identity and range of the communities. Ecological studies using functional trait databases have to deal with missing data using imputation methods corresponding to their specific needs and making the most out of the information available in the databases. Within this framework, this study indicates the possibilities and limits of single imputation methods based on ecological hypothesis and concludes that they could be useful when studying the ranking of communities for their functional diversity indices.

After grazing exclusion, is there any modification of strategy for two guerrilla species: Elymus repens (L.) Gould and Agrostis stolonifera (L.)?

Elymus repens (L.) Gould and Agrostis stolonifera (L.), are competitive grasses with guerrilla strategy that invade grasslands with a low stocking rate. In this work, we tested the hypotheses that grazing exclusion facilitates vegetative development of rhizomes and stolons of these clonal grasses and that such change is a key mechanism for their abundance in set-aside grasslands. The competitive capacities of these two guerrilla species were characterised by samples in plant community (species richness and biomass) and on the level of individual species (morphometric measurements on stolons and rhizomes) during a growing season. Compared to grasslands where grazing was excluded for three years, species richness was higher in grazed site and the plant community structure differed. Indeed, with grazing exclusion, a shift from annual species with a diversified growth-form to perennial species with a tall tussock and graminoid growth-form was monitored. In ungrazed situation, Elymus repens and Agrostis stolonifera were the dominant grasses, and the standing biomass for the lowland community showed a significant increase compared to the grazed site. Vegetative development increased competitive capacities of these two guerrilla species and led by phenomenon of competitive exclusion to the disappearance of annuals species. With grazing cessation, Elymus repens was found to increase the size of aerial traits (shoot length and the number of leaves per shoot) and this may both be propitious for achieving dominance within plant communities and also maintaining its competitive local advantage. By contrast, Agrostis stolonifera showed an increase in a root trait, i.e. rhizome length, in the fenced site, which provide good ability for spatial propagation and then to explore adjacent patches. We concluded that Elymus repens presented a morphological capacity to change its colonising strategy from a guerrilla strategy to a phalanx strategy, by morphological variability of aerial organs, when it was submitted to competitive stress and environment modifications. Agrostis stolonifera showed a capacity to escape aerial competition resulting from grazing cessation, than to increase underground propagation capacity. The present study highlighted the capacities of Elymus repens to respond in an adaptative way to competitive pressure.

Vegetation ecology meets ecosystem science: Permanent grasslands as a functional biogeography case study

The effect of biodiversity on ecosystem functioning has been widely acknowledged, and the importance of the functional roles of species, as well as their diversity, in the control of ecosystem processes has been emphasised recently. However, bridging biodiversity and ecosystem science to address issues at a biogeographic scale is still in its infancy. Bridging this gap is the primary goal of the emerging field of functional biogeography. While the rise of Big Data has catalysed functional biogeography studies in recent years, comprehensive evidence remains scarce. Here, we present the rationale and the first results of a country-wide initiative focused on the C3 permanent grasslands. We aimed to collate, integrate and process large databases of vegetation relevés, plant traits and environmental layers to provide a country-wide assessment of ecosystem properties and services which can be used to improve regional models of climate and land use changes. We outline the theoretical background, data availability, and ecoinformatics challenges associated with the approach and its feasibility. We provide a case study of upscaling of leaf dry matter content averaged at ecosystem level and country-wide predictions of forage digestibility. Our framework sets milestones for further hypothesis testing in functional biogeography and earth system modelling.

Emergent effects of ground beetles size diversity on the strength of prey suppression

Determining how multiple predators provide better prey suppression is a key step towards developing conservation biological control strategies. While numerous previous studies have demonstrated that diverse predator assemblages can be more effective in controlling pest populations, others have shown that it is the presence or absence of competitively superior species that is critical to pest biological control (i.e. selection effect). The present study investigated how increasing ground beetle body size diversity increases prey suppression. A mesocosm experiment was conducted to compare invertebrate prey suppression between nine created ground beetle assemblages. Size diversity of these assemblages was manipulated according to three diversity levels: low, medium, and high diversity. Partitioning of the diversity effects revealed that increasing the ground beetle size diversity had no effect on the strength of prey suppression. The absence of an effect of ground beetle size diversity may be because of the absence of resource partitioning among different‐sized ground beetles. The amount and range of prey consumed increased with increasing ground beetle body size. Thus, prey suppression was strongly strengthened by the presence of large ground beetles in the assemblages. The present results suggest that for biological pest control, Agri‐managers should emphasise practices that promote the presence of large carabids. This is not only because promoting the presence of large carabids could be at least as effective as conserving a diverse ground beetle community, but also because large ground beetles are more vulnerable to environmental disturbances and to predation than ground beetles of the other size classes.

Mapping local and global variability in plant trait distributions

Significance Currently, Earth system models (ESMs) represent variation in plant life through the presence of a small set of plant functional types (PFTs), each of which accounts for hundreds or thousands of species across thousands of vegetated grid cells on land. By expanding plant traits from a single mean value per PFT to a full distribution per PFT that varies among grid cells, the trait variation present in nature is restored and may be propagated to estimates of ecosystem processes. Indeed, critical ecosystem processes tend to depend on the full trait distribution, which therefore needs to be represented accurately. These maps reintroduce substantial local variation and will allow for a more accurate representation of the land surface in ESMs. Our ability to understand and predict the response of ecosystems to a changing environment depends on quantifying vegetation functional diversity. However, representing this diversity at the global scale is challenging. Typically, in Earth system models, characterization of plant diversity has been limited to grouping related species into plant functional types (PFTs), with all trait variation in a PFT collapsed into a single mean value that is applied globally. Using the largest global plant trait database and state of the art Bayesian modeling, we created fine-grained global maps of plant trait distributions that can be applied to Earth system models. Focusing on a set of plant traits closely coupled to photosynthesis and foliar respiration—specific leaf area (SLA) and dry mass-based concentrations of leaf nitrogen (Nm) and phosphorus (Pm), we characterize how traits vary within and among over 50,000 ∼50×50-km cells across the entire vegetated land surface. We do this in several ways—without defining the PFT of each grid cell and using 4 or 14 PFTs; each model’s predictions are evaluated against out-of-sample data. This endeavor advances prior trait mapping by generating global maps that preserve variability across scales by using modern Bayesian spatial statistical modeling in combination with a database over three times larger than that in previous analyses. Our maps reveal that the most diverse grid cells possess trait variability close to the range of global PFT means.

Integrating Agricultural and Ecological Goals into the Management of Species-Rich Grasslands: Learning from the Flowering Meadows Competition in France

Current agri-environmental schemes for reconciling agricultural production with biodiversity conservation are proving ineffective Europe-wide, increasing interest in results-based schemes (RBSs). We describe here the French “Flowering Meadows” competition, rewarding the “best agroecological balance” in semi-natural grasslands managed by livestock farmers. This competition, which was entered by about a thousand farmers in 50 regional nature parks between 2007 and 2014, explicitly promotes a new style of agri-environmental scheme focusing on an ability to reach the desired outcome rather than adherence to prescriptive management rules. Building on our experience in the design and monitoring of the competition, we argue that the cornerstone of successful RBSs is a collective learning process in which the reconciliation of agriculture and environment is reconsidered in terms of synergistic relationships between agricultural and ecological functioning. We present the interactive, iterative process by which we defined an original method for assessing species-rich grasslands in agroecological terms. This approach was based on the integration of new criteria, such as flexibility, feeding value, and consistency of use, into the assessment of forage production performance and the consideration of biodiversity conservation through its functional role within the grassland ecosystem, rather than simply noting the presence or abundance of species. We describe the adaptation of this methodology on the basis of competition feedback, to bring about a significant shift in the conventional working methods of agronomists and conservationists (including researchers).The potential and efficacy of RBSs for promoting ecologically sound livestock systems are discussed in the concluding remarks, and they relate to the ecological intensification debate.