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Koenig, Isabelle
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Koenig, Isabelle
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- PublicationAccès libreSoil chemistry changes beneath decomposing cadavers over a one-year period(2018-3-6)
; ; ; Decomposing vertebrate cadavers release large, localized inputs of nutrients. These temporally limited resource patches affect nutrient cycling and soil organisms. The impact of decomposing cadavers on soil chemistry is relevant to soil biology, as a natural disturbance, and forensic science, to estimate the postmortem interval. However, cadaver impacts on soils are rarely studied, making it difficult to identify common patterns. We investigated the effects of decomposing pig cadavers (Sus scrofa domesticus) on soil chemistry (pH, ammonium, nitrate, nitrogen, phosphorous, potassium and carbon) over a one-year period in a sprucedominant forest. Four treatments were applied, each with five replicates: two treatments including pig cadavers (placed on the ground and hung one metre above ground) and two controls (bare soil and bags filled with soil placed on the ground i.e. “fake pig” treatment). In the first two months (15–59 days after the start of the experiment), cadavers caused significant increases of ammonium, nitrogen, phosphorous and potassium (p < 0.05) whereas nitrate significantly increased towards the end of the study (263–367 days; p < 0.05). Soil pH increased significantly at first and then decreased significantly at the end of the experiment. After one year, some markers returned to basal levels (i.e. not significantly different from control plots), whereas others were still significantly different. Based on these response patterns and in comparison with previous studies, we define three categories of chemical markers that may have the potential to date the time since death: early peak markers (EPM), late peak markers (LPM) and late decrease markers (LDM). The marker categories will enhance our understanding of soil processes and can be highly useful when changes in soil chemistry are related to changes in the composition of soil organism communities. For actual casework further studies and more data are necessary to refine the marker categories along a more precise timeline and to develop a method that can be used in court. - PublicationAccès libreUsing testate amoeba community structure and functional diversity to assess the impact of climate changes on ecosystem functioning: finding relevant and convenient tools for bio-monitoring of "Sphagnum" peatlands evolution or recoveryL’impact grandissant de l’homme sur les écosystèmes et les changements climatiques en cours font disparaître nombre de milieux naturels dans le monde. Il est aujourd’hui acquis que les écosystèmes naturels et la biodiversité ont un rôle important dans le bien-être de l’humanité et que les services qu’ils rendent ont une valeur monétaire qui peut être estimée (services écosystémiques). Parmi ces écosystèmes, les zones humides et les tourbières ont une importance particulière, liée autant à la flore très spécifique qui y vit qu’à leur rôle de puits de carbone. En effet, leurs sols, détrempés une grande partie de l’année, sont anoxiques et la matière organique s’y décompose très lentement. Elle s’y accumule, permettant de fixer dans le sol (la tourbe) du carbone atmosphérique. Mais cette fonction est liée directement à l’engorgement en eau, qui dépend du régime des précipitations et donc du climat. Dans un contexte de changement climatiques, mais aussi à une pression anthropique croissante, les tourbières sont partout dans le monde en voie de régression. En Suisse, par exemple, il ne reste actuellement que 10% des zones humides existantes au XIXème siècle. Dès lors, il est urgent de développer des outils qui permettent de suivre leur évolution.
L’objectif de cette thèse est de mettre au point des indicateurs permettant de suivre l’état des tourbières ainsi que leur fonctionnement en tant qu’écosystème. Les relevés de végétation utilisés depuis longtemps permettent de suivre les changements sur le long à très long terme ; cependant, cet outil est insuffisant pour documenter des changements rapides de l’ordre de quelques mois. En particulier, lors de travaux de revitalisation, il est difficile d’estimer l’impact des mesures prises (comme par exemple : manipulation de la nappe d’eau, réintroduction d’espèces végétales, etc.) sur le fonctionnement général de la tourbière. Si la végétation prendrait des années à se modifier, les communautés de micro-organismes vont réagir en effet beaucoup plus rapidement. Parmi ces micro-organismes, les amibes à thèques, un groupe de protistes unicellulaires se protégeant dans une coquille (appelé thèque), jouent un rôle prépondérant dans le réseau trophique des sols de tourbière et sont aujourd’hui reconnues comme étant de bonnes indicatrices de divers gradients tel l’humidité, le pH, les nutriments ou les polluants. Les thèques de ces organismes ont une forme caractéristique qui permet leur identification au niveau de l’espèce. Des traits morphologiques ont été corrélés aux préférences écologiques des espèces, et il est possible, en les observant, de mettre en évidence des filtres environnementaux. La définition des traits fonctionnels nécessite des expérimentations en milieu contrôlé pour définir clairement les corrélations entre les traits morphologiques et le fonctionnement de l’écosystème.
Le premier article (chapitre 2) a permis de montrer qu’une sélection d’espèces d’amibes à thèque est plus finement corrélée aux changements de micro-gradients (humidité) que la végétation dans un gradient altitudinal de tourbières naturelles relativement préservées. En effet, dans cette étude, nous montrons qu’un pool de dix espèces d’amibes à thèque faciles à identifier, permettent de suivre la profondeur de la nappe le long du gradient gouille – buttes, à diverses altitudes alors que la végétation (globale ou séparée entre plantes vasculaires et bryophytes) est plutôt mieux corrélée à l’altitude et autocorrélée au site lui-même. Dès lors, ces dix espèces d’amibes sont de meilleures indicatrices de l’état et du fonctionnement de la tourbière.
Dans le second article (chapitre 3), nous comparons la structure de la communauté d’amibes ainsi que la moyenne pondérée des traits fonctionnels entre une tourbière artificielle créée au Jardin Botanique de Neuchâtel (d’une surface d’environ 100m2) avec une tourbière naturelle en cours de régénération (Bois des Lattes, NE). Recréer une tourbière fonctionnelle à basse altitude est un solide défi, surtout lorsque la météo impose une longue sécheresse la première année. Nos résultats indiquent que la population d’amibes à thèque à fortement changé durant cette première année et semble indiquer que le fonctionnement de la tourbière a été profondément perturbé. En effet, la comparaison entre les communautés d’amibes sur le site de référence et les deux échantillonnages du jardin botanique (2015 et 2016) montrent des différences significatives ; alors que Corythion dubium représente environ 1/5-1/3 de tous les individus vivants rencontrés au jardin botanique, cette communauté est dominée par Difflugia sp. et Phryganella acropodia sur le site de référence (Bois des Lattes, NE). Par contre, sur la base des traits fonctionnels, le fonctionnement semble assez proche entre les sites, avec des signes indiquant un stress hydrique important mais comparable entre le site de référence (sphaignes sur tourbe nue) et le jardin botanique.
La troisième partie de cette thèse nous a permis de corréler les traits fonctionnels avec la fluctuation de la nappe d’eau dans une situation contrôlée en mésocosmes. Dans la première phase de l’expérimentation (article 3, chapitre 4) le niveau d’eau a été réglé à −4cm (humide), −15cm (contrôle) et −25cm (sec) depuis le sommet des capitulums et plusieurs échantillonnages ont été réalisés durant 18 mois. Les traitements mouillés et contrôle ont peu changé durant cette phase, restant largement dominés par Hyalosphenia papilio, une espèce mixotrophe fréquente en tourbière et avec une bonne tolérance aux variations de la nappe. Dans les réplicas secs, nos résultats montrent que la population d’amibes à thèque répond rapidement au traitement en basculant vers des espèces connues pour mieux tolérer les conditions sèches (groupe de Nebela tincta, Corythion dubium). Les traits fonctionnels mis en évidence dans le traitement sec sont un biovolume plus petit, un pseudostome caché (ventral ou ventral-central) et étroit ainsi que la perte de la mixotrophie. Dans la seconde phase (papier 4, chapitre 5), nous avons simulé une situation de régénération en remontant le niveau d’eau à −10cm de la surface de la sphaigne. Quatre échantillonnages ont été pris en compte, le premier et le dernier de la première phase, ainsi que deux échantillons 2 et 6 mois après l’égalisation du niveau d’eau. Dans le traitement sec, la population d’amibes à thèque revient progressivement à son état du début de l’expérimentation avec une diminution des taxa adaptés aux conditions sèches et la réapparition de taxa corrélés à des conditions humides (et en particulier Hyalosphenia papilio). La moyenne pondérée des traits fonctionnels se modifie indiquant des contraintes environnementales moins drastiques. De façon intéressante, certains échantillons des traitements humides et contrôle ont vu leur communauté d’amibes ainsi que leur moyenne pondérée de traits indiquer que la situation locale était plus sèche et reflétait ainsi l’état de la sphaigne dans laquelle l’échantillonnage s’est fait.
Cette thèse permet de montrer le potentiel de bio-indication des amibes à thèque et de leurs traits fonctionnels dans le suivi des tourbières, que ce soit pour suivre des mesures de revitalisation ou pour faire un diagnostic de leur état et de leur fonctionnement. L’approche par les traits, en contournant la difficulté d’une identification des taxa très précise et en mettant en évidence les mécanismes en cours, permettrait de créer un outil de bio-indication basé sur des classes de traits et des proportions, ne nécessitant pas l’utilisation de statistiques complexes., Human activity and ongoing climate changes have an increasing impact on ecosystems and lead to the loss of several natural habitats. Ecosystems provide functions contributing to human well-being and these functions could be estimated based on a monetary value. Among these ecosystems, wetlands and peatlands are of primary importance, by hosting a specific flora and acting as a carbon sink. Their waterlogged soils are anoxic, and the mineralisation of the organic matter is slow. Organic matter accumulates in the peat and thus fixes atmospheric carbon in soil. But this function is directly linked to the humidity content, which depends on precipitation rate and local climate. With ongoing climate changes and human pressure on peatlands, these ecosystems are regressing all over the world. In Switzerland for example only 10% of the wetlands, that still existed in the 19th century, remained until now. Henceforth, developing tools that allow the monitoring of peatlands has become a key priority.
The aim of this thesis was to develop bio-indicators that can be used to monitor the status and functioning of Sphagnum peatlands. Until now, monitoring of Sphagnum peatlands was mainly conducted through vegetation surveys. However, as vegetation responds to perturbation with a delay, its power to assess short term changes is limited. Particularly, it is difficult to estimate the impact of revitalisation actions (i.e. manipulation of water table, introduction of vegetation, etc.) on the global functioning of the peatland. While vegetation takes years to reflect changes, micro-organismal communities will react sooner. Among these micro-organisms, testate amoebae, a group of unicellular protists building a shell (test), play an important role in food web functioning in Sphagnum peatland’s soils and are well correlated to local changes. They are now used to monitor various gradients like humidity, pH, nutrients contents and pollutants. The shell is characteristic and allows the identification to species level. Recently morphological traits were correlated to ecological preferences of taxa and studies use them to underline environmental gradients. However, studies in control conditions are needed to define functional traits i.e. traits that are correlated with environmental filters. Therefore a clear definition of the correlation between morphological traits and ecosystem functioning is necessary.
In this thesis we showed that a group of selected testate amoeba taxa is more precisely correlated to microgradient (humidity content) than vegetation along an altitudinal gradient of Sphagnum peatlands in Switzerland. We demonstrated that these ten selected taxa, which were easy to determine, allow to monitor the water table depth along the pool – hummock gradient at each elevation while vegetation (global or vascular plant and bryophytes separately) was better correlated to elevation or autocorrelated to the site itself. Henceforth, these ten testate amoeba taxa describe the status and functioning of the bogs more precisely. In addition we compared the structure of testate amoeba community and community weighted mean of functional traits between an artificial peatbog (covering an area of 100m2) set up in the Botanical Garden in Neuchâtel and a regenerated bog in Bois des Lattes (NE). Rebuilding a fully functional Sphagnum peatbog at low elevation is challenging, especially with long warm and dry periods during the first year. Our results showed that testate amoeba community structure changed drastically during this first year and seemed to indicate that the bog functioning was deeply disturbed. Henceforth, the comparison between the community structure found on bare peat in Bois des Lattes and the living community structure found in both samplings (2015 and 2016) in the Botanical Garden was significantly different. In the Botanical Garden, Corythion dubium represented ca. 20% to 30% of the whole living population while the Difflugia genus and Phryganella acropodial dominated sampling in Bois des Lattes (ca. 25%). On the other hand, the global functioning of both sites appeared to be quite similar based on functional traits and indicated a water stressed situation. Thus, even if the community structure was relatively different between the Botanical Garden bog and Bois des Lattes, the global functioning remained in the same range in both sites.
We also monitored the changes in testate amoeba community structure and correlated functional traits with water table fluctuations in a controlled experiment i.e. mesocosms. We assessed the response of testate amoeba community structure and weighted mean of traits to three levels of water tables, wet (-4cm), intermediate (-15cm, taken as control) and dry (-25cm). In wet and intermediate plots, little changes occurred over 18 months and the community stayed largely dominated by Hyalosphenia papilio, a mixotrophic taxa common in Sphagnum peatlands and with a relatively wide tolerance to fluctuation in water level depths. In dry plots, the shift in community structure occurred rapidly and taxa related to dryer conditions dominated the community (Nebela tincta group, Corythion dubium). In these plots, the shift in community weighted mean of functional traits went towards small taxa, with a small hidden pseudostome (ventral and ventral-central) and the loss of mixotrophy. In the follow-up of this experiment, we simulated a regeneration situation by putting the water level at -10cm in all plots. Four samplings were taken into account, the first and the last of the previous experiment and two additional samplings were done, two and six months after the rewetting. Our results showed that, during the recovery period, the community structure of testate amoebae reflected the change in water level, in the former dry treatment. Taxa living in more humid conditions like H. papilio, recovered whereas N. tincta, and C. dubium, taxa related to dry conditions, regressed in community structure. The community weighted mean of traits shifted and indicated that the environmental constraints were less drastic in theses plots. Interestingly, the community structure and the weighted mean of traits in some former wet and intermediate plots indicated that the local conditions should be dryer and, indeed, this reflected the state of Sphagnum stems which was very dry in these plots.
This thesis confirms the bio-indication potential of testate amoeba communities and functional traits in Sphagnum peatlands monitoring. This can be used either for a follow- up of the revitalisation measures or to diagnose their functioning. The trait based approach, by circumventing the difficulties of precise identification and by highlighting ongoing processes, provide cues to build bio-indication tools based on functional trait classes and proportion without the need of complex statistics. Moreover, assessing the success of restoration measures is important to assess the role of peatlands in the carbon cycle. In this context, easy to handle bio-monitoring tools better correlated to very local hydrologic conditions are needed and testate amoeba community structure and community weighted mean of functional traits could play this role. - PublicationAccès libreComparative ecology of vascular plant, bryophyte and testate amoeba communities in four Sphagnum peatlands along an altitudinal gradient in Switzerland(2015-3-4)
; - PublicationAccès libreComparative ecology of vascular plant, bryophyte and testate amoeba communities in four Sphagnum peatlands along an altitudinal gradient in Switzerland
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We compared the relationships of testate amoebae, bryophytes, and vascular plants with soil temperature, water table depth, micro-habitats and the carbon and nitrogen content of Sphagnum mosses in four peatlands along a 1300 m altitudinal gradient in Switzerland. We used the full diversity of vascular plants and bryophyte but only a selection of ten easily identifiable testate amoeba morpho-taxa (i.e. species or species-complexes).
Indirect and direct gradient ordinations, multiple factor analysis (MFA) and transfer function models for inferring water table depth showed that a selection of ten testate amoeba taxa are more powerful (% variance explained in RDA) and accurate (discrimination among habitats) indicators of local conditions (micro-habitat type, water table depth and Sphagnum C/N ratio) than the vegetation (vascular plants and bryophytes either individually or combined and considering the full diversity).
Our study showed that a limited list of ten easily identifiable testate amoeba taxa have higher bioindication value than the full bryophytes and vascular plants. Furthermore, testate amoebae can be analyzed on samples collected at any season (accessibility allowing and if precise sampling sites are well marked) – a clear advantage for biomonitoring and can be used to infer past changes from the peat record at the same taxonomic resolution. This simple approach could therefore be very useful for biomonitoring of peatlands. - PublicationAccès libreSoil chemistry changes beneath decomposing cadavers over a one-year period
; ; Decomposing vertebrate cadavers release large, localized inputs of nutrients. These temporally limited resource patches affect nutrient cycling and soil organisms. The impact of decomposing cadavers on soil chemistry is relevant to soil biology, as a natural disturbance, and forensic science, to estimate the postmortem interval. However, cadaver impacts on soils are rarely studied, making it difficult to identify common patterns.
We investigated the effects of decomposing pig cadavers (Sus scrofa domesticus) on soil chemistry (pH, ammonium, nitrate, nitrogen, phosphorous, potassium and carbon) over a one-year period in a sprucedominant forest. Four treatments were applied, each with five replicates: two treatments including pig cadavers (placed on the ground and hung one metre above ground) and two controls (bare soil and bags filled with soil placed on the ground i.e. “fake pig” treatment). In the first two months (15–59 days after the start of the experiment), cadavers caused significant increases of ammonium, nitrogen, phosphorous and potassium (p <0.05) whereas nitrate significantly increased towards the end of the study (263–367 days; p <0.05). Soil pH increased significantly at first and then decreased significantly at the end of the experiment. After one year, some markers returned to basal levels (i.e. not significantly different from control plots), whereas others were still significantly different. Based on these response patterns and in comparison with previous studies, we define three categories of chemical markers that may have the potential to date the time since death: early peak markers (EPM), late peak markers (LPM) and late decrease markers (LDM).
The marker categories will enhance our understanding of soil processes and can be highly useful when changes in soil chemistry are related to changes in the composition of soil organism communities. For actual casework further studies and more data are necessary to refine the marker categories along a more precise timeline and to develop a method that can be used in court. - PublicationAccès libreImpact of two hot and dry summers on the community structure and functional diversity of testate amoebae in an artificial bog, illustrating their use as bioindicators of peatland health
; - PublicationAccès libreResponse of Sphagnum Testate Amoebae to Drainage, Subsequent Re-wetting and Associated Changes in the Moss Carpet: Results from a Three Year Mesocosm Experiment
; ; Sphagnum peatlands represent a globally significant pool and sink of carbon but these functions are threatened by ongoing climate change. Testate amoebae are useful bioindicators of hydrological changes, but little experimental work has been done on the impact of water table changes on communities.
Using a mesocosm experimental setting that was previously used to assess the impact of drought disturbance on communities and ecosystem processes with three contrasted water table positions: wet (–4 cm), intermediate (–15 cm) and dry (–25 cm), we studied the capacity of testate amoeba communities to recover when the water table was kept at –10 cm for all plots. The overall experiment lasted three years. We assessed the taxonomic and functional trait responses of testate amoeba communities. The selected traits were hypothesised to be correlated to moisture content (response traits: shell size, aperture position) or trophic role (effect traits: mixotrophy, aperture size controlling prey range).
During the disturbance phase, the mixotrophic species Hyalosphenia papilio dominated the wet and intermediate plots, while the community shifted to a dominance of “dry indicators” (Corythion dubium, Nebela tincta, Cryptodifflugia oviformis) and corresponding traits (loss of mixotrophy, and dominance of smaller taxa with ventral or ventral-central aperture) in dry plots. During the recovery phase we observed two contrasted trends in the previously wet and intermediate plots: communities remained similar where the Sphagnum carpet remained intact but species and traits indicators of drier conditions increased in plots where it had degraded. In the former dry plots, indicators and traits of wet conditions increased by the end of the experiment.
This is one of the first experiment simulating a disturbance and subsequent recovery in ex-situ mesocosms of Sphagnum peatland focusing on the response of testate amoebae community structure as well as functional traits to water table manipulation. The results generally confirmed that testate amoebae respond within a few months to hydrological changes and thus represent useful bioindicators for assessing current and past hydrological changes in Sphagnum peatlands. - PublicationAccès libreCreation of a raised bog in the Botanical garden of Neuchâtel: a tool for research, collections and public information
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This object corresponds to the three missions of the garden : 1) to inform the public as well as students about these unusual, fragile and threatened ecosystems, 2) to present characteristic peatland plants from the Jura Mountains (Sphagnum, Drosera, Eriophorum, Betula nana, etc.), and 3) to conduct research projects.
During the winter 2014-15, the snow remained longer on the peatbog that on the adjacent path and meadow, thus providing evidence for a microclimatic effect of the bog. The excessively dry and hot summer 2015 allowed testing the resistance of the newly established bog vegetation. Most plants resisted well, including graminoids Eriophorum vaginatum, Trichophorum cespitosum or Carex sp., ericaceous (Vaccinium oxycoccos, myrtillus and vitis-idea) and mosses (especially Sphagnum). This living laboratory provides a unique opportunity to inform the public about the characteristics and functions of these ecosystems and the challenges of conserving and restoring them in a warmer world. - PublicationAccès libreTaxonomic and functional traits responses of Sphagnum peatland testate amoebae to experimentally manipulated water table
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Testate amoebae are good indicators of surface moisture conditions in Sphagnum peatlands and are routinely used in palaeoecology. Their shells (tests), on which identification is based, can also be used to define functional traits and thus to infer changes in ecosystem functioning.
We investigated the response of testate amoeba communities to manipulated water table depth (wet: −4 cm, intermediate: −15 cm, and dry: −25 cm) over time (seven time points, 19 months) using mesocosms by comparing two approaches: community structure and functional traits responses, using a combination of morphological (biovolume, length, aperture size and position) and physiological (mixotrophy/heterotrophy, shell material) traits.
This is the first study investigating the effect of water table depth on testate amoeba assemblages over time using a mesocosm approach. Taxonomical and functional approaches showed similar response patterns, confirming that water level acted as a strong environmental filter. After one year Hyalosphenia papilio decreased in the dry treatment, and the community structure shifted towards a dominance of dry indicators (Nebela tincta complex, Corythion dubium, Euglypha compressa) and the selected functional traits (smaller, heterotrophic, compressed species, with a ventral aperture) corresponded to drought adaptations.
In line with recent observational and transfer function studies exploring the use of testate amoebae functional traits, our experimental results illustrate how well-selected traits could be used to monitor the impact of present and past climatic changes on Sphagnum peatlands.