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  • Publication
    Métadonnées seulement
    Toward the use of testate amoeba functional traits as indicator of floodplain restoration success
    (2012) ;
    Malysheva, Elena
    ;
    Mazei, Yuri
    ;
    Moretti, Marco
    ;
    Functional traits (FT) offer a new framework to understand the ecology of organisms and overcome taxonomic difficulties that currently limit the study of minute soil taxa. FT are likely to be selected by environmental filters and hence they may provide more direct information on ecosystem characteristics than the species composition of a community. We tested the potential of testate amoeba (TA) functional traits as bioindicators of selected ecosystem processes in the context of a restored floodplain in north-western Switzerland. The floodplain was divided into six functional process zones (FPZs) associated to distinct post-restoration successional stages. We selected TA FT and computed three functional indices: functional richness (FRic), divergence (FDiv), evenness (FEve), and dispersion (FDis). We then compared the patterns of functional indices and classical diversity indices such as species richness, diversity and evenness. We assessed whether traits converged or were over-dispersed in the different FPZs using a randomization procedure. Finally, we related environmental variables and functional traits using the "Fourth Corner" statistic. This procedure enabled us to highlight relations that can potentially be used for bioindication. Promising candidates include the relationships between shell biovolume and vegetation structure and between shell compression and plant litter input variables. (C) 2011 Elsevier Masson SAS. All rights reserved.
  • Publication
    Métadonnées seulement
    Relationships between testate amoeba communities and water quality in Lake Donghu, a large alkaline lake in Wuhan, China
    (2013) ; ; ;
    Gu, Yansheng
    ;
    Wang, Hongmei
    ;
    Cui, Yongde
    ;
    Zhang, Xiaoke
    ;
    The middle Yangtze Reach is one of the most developed regions of China. As a result, most lakes in this area have suffered from eutrophication and serious environmental pollution during recent decades. The aquatic biodiversity in the lakes of the area is thus currently under significant threat from continuous human activities. Testate amoebae (TA) are benthic (rarely planktonic) microorganisms characterized by an agglutinated or autogenous shell. Owing to their high abundance, preservation potential in lacustrine sediments, and distinct response to environmental stress, they are increasingly used as indicators for monitoring water quality and reconstructing palaeoenvironmental changes. However this approach has not yet been developed in China. This study presents an initial assessment of benthic TA assemblages in eight lakes of Lake Donghu in the region of Wuhan, China. Testate amoeba community structure was most strongly correlated to water pH. In more alkaline conditions, communities were dominated by Centropyxis aculeata, Difflugia oblonga, Pontigulasia compressa, Pon. elisa and Lesquereusia modesta. These results are consistent with previous studies and show that TA could be useful for reconstructing past water pH fluctuations in China. To achieve this, the next step will be to expand the database and build transfer function models.
  • Publication
    Métadonnées seulement
    Response of forest soil euglyphid testate amoebae (Rhizaria: Cercozoa) to pig cadavers assessed by high-throughput sequencing
    Decomposing cadavers modify the soil environment, but the effect on soil organisms and especially on soil protists is still poorly documented. We conducted a 35-month experiment in a deciduous forest where soil samples were taken under pig cadavers, control plots and fake pigs (bags of similar volume as the pigs). We extracted total soil DNA, amplified the SSU ribosomal RNA (rRNA) gene V9 region and sequenced it by Illumina technology and analysed the data for euglyphid testate amoebae (Rhizaria: Euglyphida), a common group of protozoa known to respond to micro- environmental changes. We found 51 euglyphid operational taxonomic units (OTUs), 45 of which did not match any known sequence. Most OTUs decreased in abundance underneath cadavers between days 0 and 309, but some responded positively after a time lag. We sequenced the full-length SSU rRNA gene of two common OTUs that responded positively to cadavers; a phylogenetic analysis showed that they did not belong to any known euglyphid family. This study confirmed the existence of an unknown diversity of euglyphids and that they react to cadavers. Results suggest that metabarcoding of soil euglyphids could be used as a forensic tool to estimate the post-mortem interval (PMI) particularly for long-term (>2 months) PMI, for which no reliable tool exists.
  • Publication
    Métadonnées seulement
    Can soil testate amoebae be used for estimating the time since death? A field experiment in a deciduous forest
    Estimation of the post-mortem interval (PMI, the time interval between death and recovery of a body) can be crucial in solving criminal cases. Today minimum PMI calculations rely mainly on medical and entomological evidence. However, beyond 4-6 weeks even entomological methods become less accurate. Thus additional tools are needed. Cadaveric fluids released by decomposing cadavers modify the soil environment and thus impact soil organisms, which may thus be used to estimate the PMI. Although the response of bacteria or fungi to the presence of a corpse has been studied, to the best of our knowledge nothing is known about other soil organisms. Testate amoebae, a group of shelled protozoa, are sensitive bioindicators of soil physico-chemical and micro-climatic conditions and are therefore good potential PMI indicators. We investigated the response of testate amoebae to three decomposing pig cadavers, and compared the pattern to two controls each, bare soils and fake cadavers, in a beach-oak forest near Neuchatel, Switzerland. Forest litter samples collected in the three treatments over 10 months were analysed by microscopy. The pig treatment significantly impacted the testate amoeba community: after 22 and 33 days no living amoeba remained underneath the pig cadavers. Communities subsequently recovered but 10 months after the beginning of the experiment recovery was not complete. The fake cadavers also influenced the testate amoeba communities by altering the soil microclimate during a dry hot period, but less than the cadavers. These results confirm the sensitivity of soil testate amoebae to micro-climatic conditions and show that they respond fast to the presence of cadavers -and that this effect although decreasing over time lasts for months, possibly several years. This study therefore confirms that soil protozoa could potentially be useful as forensic indicators, especially in cases with a longer PMI. (C) 2014 Elsevier Ireland Ltd. All rights reserved.
  • Publication
    Métadonnées seulement
    Spatio-temporal heterogeneity of riparian soil morphology in a restored floodplain
    (2013) ;
    Guenat, C.
    ;
    Bullinger-Weber, G.
    ;
    Floodplains have been intensively altered in industrialized countries, but are now increasingly being restored. It is therefore important to assess the effect of these restoration projects on the aquatic and terrestrial components of ecosystems. However, despite being functionally crucial components of terrestrial ecosystems, soils are generally overlooked in floodplain restoration assessments. We studied the spatio-temporal heterogeneity of soil morphology in a restored (riverbed widening) river reach along the River Thur (Switzerland) using three criteria (soil diversity, dynamism and typicality) and their associated indicators. We hypothesized that these criteria would correctly discriminate the post-restoration changes in soil morphology, and that these changes correspond to patterns of vascular plant diversity. Soil diversity and dynamism increased 5 yr after the restoration, but some typical soils of braided rivers were still missing. Soil typicality and dynamism were correlated to vegetation changes. These results suggest a limited success of the project, in agreement with evaluations carried out at the same site using other, more resource-demanding, methods (e.g., soil fauna, fish diversity, ecosystem functioning). Soil morphology provides structural and functional information on floodplain ecosystems. The spatio-temporal heterogeneity of soil morphology represents a cost-efficient ecological indicator that could easily be integrated into rapid assessment protocols of floodplain and river restoration projects. The follow-up assessment after several major floods (>= HQ20) should take place to allow for testing the longerterm validity of our conclusion for the River Thur site. More generally, it would be useful to apply the soil morphology indicator approach in different settings to test its broader applicability.
  • Publication
    Accès libre
    Functional responses of multi-taxa communities to disturbance and stress gradients in a restored floodplain
    1. Trait-based approaches can reveal the mechanisms through which disturbances or stress impact communities, allowing comparisons of the role of different mechanisms in shaping communities among taxonomic groups. Such information can lead to higher comparability, transferability and predictability of the outcome of restoration projects. However, multitaxa trait-based approaches were rarely used in the context of ecosystem restoration. 2. We investigated the responses to environmental gradients of seven taxa (vascular plants, staphylinid and carabid beetles, spiders, isopods, diplopods and earthworms) in a restored floodplain using a species traits approach. We assessed the impact of flood disturbances and soil hydric stress on the functional diversity (FD) and community-weighted mean (CWM) response of traits for each taxon. 3. Ordination of hydrological variables revealed two main gradients. The first was related to the spatiotemporal dynamics of flood disturbances and the second to the average changes in soil hydric conditions. 4. The analysis of CWM revealed that larger, poorly mobile species with narrow ecological tolerances were filtered by regular floods and/or changes in soil hydric conditions. 5. Functional diversity patterns differed between the two gradients: decreasing with increasing flood disturbance, but increasing along the soil hydric stress gradient. This suggests that the mechanisms shaping community composition differ between the two gradients with environmental filtering being dominant with increasing flood disturbances and competition decreasing with more soil hydric stress. 6. Synthesis and applications. Our study shows that the impact of restored flood disturbances and soil hydric stress on plant and invertebrate functional diversity and community- weighted mean can be positive, negative or more complex depending on the taxonomic group and environmental gradient considered. The patterns can to some extent be explained by the specific characteristics of each group. Larger, poorly mobile species with narrow ecological tolerances were particularly vulnerable to changes in disturbance and stress regime following floodplain restoration. These species may therefore be lost in the initial phases of restoration projects, but other more characteristic species of dynamic floodplains will be favoured. Understanding the consequences of these contrasted responses for biodiversity conservation and ecosystem functioning constitutes the next challenge for ecosystem restoration.
  • Publication
    Accès libre
    Patterns of earthworm communities and species traits in relation to the perturbation gradient of a restored floodplain
    (2012-3-29) ; ;
    Shrestha, J
    ;
    Mitchell, E.A.D.
    ;
    Little is known about the diversity and ecology of earthworms in floodplains, as well as their response to natural and anthropic perturbations (e.g. floods, river channelisation, floodplain restoration). We characterised the patterns of earthworm communities and species traits in the different habitats of a lowland restored floodplain in Switzerland. In addition to classical species-based metrics, such as species richness and Shannon diversity, species traits were used to calculate the community weighted means (CWMs) of traits and functional dispersion (FDis). We hypothesised that trait-based metrics would reveal clearer patterns than classical approaches. The distribution of earthworm traits varied among habitats in relation to changes in flooding frequency: poorly developed gravel bar soils most exposed to flooding were characterised by high abundance of small epigeic species and low abundance of large anecic species. Differences in anecic and endogeic earthworm community structure matched flood frequency. In agreement with our hypothesis, CWMs were more strongly correlated to environmental variables than species composition, diversity, or functional diversity. Based on these results, the ratio of the relative abundances of epigeic and anecic species, and the differences in species composition within anecic and endogeic ecological types of earthworms were identified as indicators of soil development in floodplains.
  • Publication
    Accès libre
    Patterns of earthworm, enchytraeid and nematode diversity and community structure in urban soils of different ages
    (2016-1-9) ;
    Dozsa-Farkas, Klara
    ;
    Boros, Gergely
    ;
    Rochat, Guy
    ;
    Sandoz, Gauthier
    ;
    ; ;
    Annelids (Lumbricidae and Enchytraeidae) and nematodes are common soil organisms and play important roles in organic matter decomposition, nutrient cycling and creation of soil structure and porosity. However, these three groups have rarely been studied together and only few studies exist for urban soils. We studied the diversity and community composition of annelids and nematodes in soils spanning more than two centuries of urban soil development in Neuch^atel (Switzerland) and assessed the relationships 1) among these three groups and 2) between each group and environmental (physical, chemical and functional) characteristics of soils and soil age. While the groups of environmental variables were correlated (Mantel tests) no correlation was found between pairs of soil fauna groups and between each soil fauna group and environmental variables. More specifically, redundancy analyses showed that earthworm assemblages were best correlated with soil bulk density and with soil depth, the latter being positively correlated with soil age. Enchytraeid assemblages and the proportion of enchytraeid r-strategists were respectively best correlated with soil carbonate content and negatively correlated with soil age. Nematodes assemblages were best correlated with soil water content. Moreover, relationships between pairs of soil biota groups, and between each group and environmental (physical, chemical and functional) variables, varied along the soil age gradient (moving window analysis). This study provides new knowledge on urban soil biodiversity and how environmental conditions can influence soil diversity and community patterns in the urban context. The contrasted community patterns of earthworms, enchytraeids and nematodes in urban soils of different ages and their different ecological roles suggest that they represent potential complementary indicators of soil quality and functioning such as soil formation and organic matter dynamics.
  • Publication
    Accès libre
    Response of Sphagnum Peatland Testate Amoebae to a 1-Year Transplantation Experiment Along an Artificial Hydrological Gradient
    (2014-2-1)
    Marcisz, Katarzyna
    ;
    ;
    Gilbert, Daniel
    ;
    Lamentowicz, Mariusz
    ;
    Peatland testate amoebae (TA) are well-established bioindicators for depth to water table (DWT), but effects of hydrological changes on TA communities have never been tested experimentally. We tested this in a field experiment by placing Sphagnum carpets (15 cm diameter) collected in hummock, lawn and pool microsites (origin) at three local conditions (dry, moist and wet) using trenches dug in a peatland. One series of samples was seeded with microorganism extract from all microsites. TA community were analysed at T0: 8–2008, T1: 5–2009 and T2: 8–2009. We analysed the data using conditional inference trees, principal response curves (PRC) and DWT inferred from TA communities using a transfer function used for paleoecological reconstruction. Density declined from T0 to T1 and then increased sharply by T2. Species richness, Simpson diversity and Simpson evenness were lower at T2 than at T0 and T1. Seeded communities had higher species richness in pool samples at T0. Pool samples tended to have higher density, lower species richness, Simpson diversity and Simpson Evenness than hummock and/or lawn samples until T1. In the PRC, the effect of origin was significant at T0 and T1, but the effect faded away by T2. Seeding effect was strongest at T1 and lowest vanished by T2. Local condition effect was strong but not in line with the wetness gradient at T1 but started to reflect it by T2. Likewise, TA-inferredDWTstarted to match the experimental conditions by T2, but more so in hummock and lawn samples than in pool samples. This study confirmed that TA responds to hydrological changes over a 1-year period. However, sensitivity of TA to hydrological fluctuations, and thus the accuracy of inferred DWT changes, was habitat specific, pool TA communities being least responsive to environmental changes. Lawns and hummocks may be thus better suited than pools for paleoecological reconstructions. This, however, contrasts with the higher prediction error and species’ tolerance for DWT with increasing dryness observed in transfer function models.
  • Publication
    Accès libre
    Above- and below-ground aspects of floodplain restoration: from biodiversity to ecosystem functions
    La biodiversité est le moteur du fonctionnement des écosystèmes. Elle est directement responsable des services fournis par les écosystèmes aux sociétés humaines. Cependant, la diversité de certains taxa dont beaucoup d'organismes du sol reste peu connue; et les processus qui créent, maintiennent et détruisent cette biodiversité ne sont que très partiellement compris. De ce fait, il est extrêmement difficile de restaurer la biodiversité dans les écosystèmes perturbés.
    Les zones alluviales cristallisent ces problèmes. Elles accueillent une extraordinaire biodiversité qui est souvent mal caractèrisée; elles sont mondialement menacées; et il n'y a que peu de consensus en ce qui concerne les méthodes pour revitaliser leur biodiversité
    Dans le but d'améliorer notre compréhension des écosystèmes dynamiques et de la multitude d'interactions écologiques qu'ils hébergent, cette thèse se concentre sur trois aspects des zones alluviales: les sols alluviaux, la biodiversité hébergée par ces sols et les changements de biodiversité entre les différents groupes étudiés le long des gradients environnementaux.
    Les résultats obtenus lors de cette thèse comblent plusieurs lacunes dans la connaissance écosystémique des zones alluviales et fournissent des perspectives pour améliorer la gestion de ces écosystèmes. En effet, l'hétérogénéité spatio-temporelle de la morphologie des sols fournit des informations structurelles et fonctionnelles sur les zones alluviales qui peuvent être inclues dans les protocoles des projets de revitalisation. De plus, les conditions environnementales influencent fortement les caractéristiques fonctionnelles des communautés. Ces caractéristiques peuvent donc être exploitées comme outil de bioindication. Finalement, les résultats du présent travail ont démontré le rôle de la diversité en tant qu'assurance pour le maintient du fonctionnement des communautés dans les écosystèmes récemment revitalisés.
    Les prochains défis à relever consistent à adopter une approche holistique des réseaux trophiques du sol, et définir l'importance des processus écologiques dans la structuration de la biodiversité des écosystèmes dynamiques., Biodiversity sustains ecosytem functioning and services to human societies. However, the diversity of certain taxa including many soil organisms remains poorly known and the processes creating, sustaining, and destroying biodiversity are only partially understood. As a result, restoring diversity in disturbed ecosystem remains a challenging task.
    Floodplains cristallize these issues. They host an extraordinary biodiversity that is often poorly charaterized, they are threathen worldwide, and there is little agreement about the ways to restore their biodiversity.
    Aiming at improving our understanding of disturbed ecosystems and the many ecological interactions they host, this PhD thesis focuses on three aspects of floodplain ecosystems: floodplain soils, below-ground biodiversity, and the changes in biodiversity among taxonomic groups and along environmental gradients.
    With this respect, the results obtained during this PhD thesis fulfil several gaps in the knowledge of riparian ecosystems and provide perspectives for improved management of floodplains and riverine ecosystems. For instance, the spatio-temporal heterogeneity of soil morphology provides structural and functional information on floodplain ecosystems that can be included into restoration project protocols. Moreover, the strong impacts of environmental conditions on community functional characteristics can be developed into bioindication tools. Finally, the results of this PhD thesis revealed the role of diversity as an insurance to community functioning in recently restored ecosystems.
    Future challenges include using holistic approaches for the study of the diversity and the functioning of the soil foodwebs, and disentangling the importance of assembly processes in structuring biodiversity patterns in disturbed ecosystems.