Jean-Michel Gobat

Ecology of testate amoebae (Protozoa : Rhizopoda) in Sphagnum peatlands in the Jura mountains, Switzerland and France

Testate amoebae (Protozoa) living in Sphagnum peatlands are important environmental and paleoecological indicators. The distribution of these animals is closely related to soil moisture variables. This study examines the ecology of sphagnicolous testate amoebae near the southern limit of bogs in Europe. A total of 64 samples were collected for analysis of testate amoebae from six peatlands in the Jura region of Switzerland and France. Eleven site-specific ecological variables, six of which were soil-moisture related variables, were measured at each site. The data were subjected to weighted averaging, jack-knifing, cluster analysis, canonical correspondence analysis, and the indicator value method to model relationships between testate amoebae distributions and environmental variables. Testate amoebae abundance showed a direct relationship with pear pH and depth to water table. Strong relationships were with sites that had a water table less than 41 cm deep. In drier sites with water table depth greater than 41 cm, other factors such as soil porosity and water holding capacity were more important compared to the wetter sites. Though there was a strong relationship between restate amoebae faunas and soil moisture content and porosity, these two variables could not be confidently predicted. Testate amoebae in peatlands in this region appear to be sensitive to peat pH and water tables. Further work is needed to explore relationships between restate amoebae, soil moisture, and porosity.

Structure of microbial communities in Sphagnum peatlands and effect of atmospheric carbon dioxide enrichment

In laboratory experiments, bacterioplankton were incubated under different nutrient conditions, and the percentage of bacteria exhibiting a polysaccharidic capsule (capsulated bacteria) and that of CTC (cyanotetrazolium chloride)-positive and therefore metabolically highly active bacteria were determined. In these seawater cultures amended with nutrients more than 95% of the CTC-positive cells exhibited a capsule. During two cruises, one to the North Atlantic and one to the North Sea, we investigated the distribution of capsulated bacteria throughout the water column. Capsulated bacteria were generally more abundant in eutrophic surface waters than in deeper layers or more oligotrophic regions. In the upper 100 m of the North Atlantic, about 6–14% of the total bacterioplankton community was capsulated, while in the layers below 100 m depth, 97% of the bacteria lacked a visible capsule. The percentage of capsulated bacteria correlated with bacterial abundance and production, and chlorophyll a concentration. Also, the bioavailability of DOC (dissolved organic carbon), estimated by the ratio between bacterial production and DOC concentration, significantly correlated with the percentage of capsulated bacteria. In the North Sea, the contribution of capsulated bacteria to the total number of bacteria decreased from the surface (3 m depth) to the near-bottom (25–35 m) layers from 20% to 14% capsulated bacteria. In the nearshore area of the North Sea, about 27% of the bacteria exhibited a capsule. Overall, a pronounced decrease in the contribution of capsulated bacteria to the total bacterial abundance was detectable from the eutrophic coastal environment to the open North Atlantic. Using this epifluorescence-based technique to enumerate capsulated bacterioplankton thus allowed us to routinely assess the number of capsulated bacteria even in the oceanic water column. Based on the data obtained in this study we conclude that almost all metabolically highly active bacteria exhibit a capsule, but also some of the metabolically less active cells express a polysaccharide capsule detectable with this method.

The palaeoecological history of the Praz-Rodet bog (Swiss Jura) based on pollen, plant macrofossils and testate amoebae (Protozoa)

Stratigraphy, radiocarbon dating and analyses of pollen, plant macrofossils and testate amoebae were used to reconstruct the development and ecology of a small raised bog in a karst-dominated landscape in the Swiss Jura Mountains. Special focus was on past vegetation and on the history of Pinus rotundata in relation to anthropogenic and climatic influences. Testate amoebae were used to reconstruc-t past local soil pH and water-table depth. The inferred development of the Praz-Rodet bog typifies a classic hydroseral tefrestrialization of a small basin. Two features are specific for this site. First, the bog was much wetter than today for a long period; according to our hypothesis, this only changed as a consequence of human activities. Second, two hiatuses are present at the coring location (Younger Dryas--early Preboreal, and 4700-2800 cal. yr BP), the former probably caused by low lake productivity due to cold temperatures and the latter by the erosional activity of the adjacent small river. The date of 2800 cal. yr BP for renewed peat accumulation may be related to climatic change (Subboreal-Subatlantic transition). Pollen indicators failed to show one hiatus: an apparently complete pollen sequence is therefore no guarantee of an uninterrupted sediment accumulation. Evidence of early minor human impact on the vegetation in the Joux Valley dates back to c. 6850 calendar years, congruous with the early Neolithic in the Jura Mountains. The history of Pinuis rotindata appears to be more complex than previously believed. Human activity is clearly responsible for the present abundance of this species, but the tree was naturally present on the bog long before the first evidence of important human disturbance of the site (1500 cal. yr BP). It is suggested that, in karst-dominated landscapes, dense forests growing on mineral soils around raised bogs may significantly reduce summer evapotranspiration by acting as windbreaks. Forest clearance results in increased evapotranspiration, causing a lowering of the water table on the bog and a modification of the vegetation cover. This hypothesis has implications for the management of similar small raised bogs in karst-dominated landscape.

Root, mycorrhiza and earthworm interactions: their effects on soil structuring processes, plant and soil nutrient concentration and plant biomass

Earthworms, arbuscular mycorrhiza fungi (AMF) and roots are important components of the belowground part of terrestrial ecosystem. However, their interacting effects on soil properties and plant growth are still poorly understood. A compartmental experimental design was used in a climate chamber in order to investigate, without phosphorus (P) addition, the single and combined effects of earthworms (Allolobophora chlorotica), AMF (Glomus intraradices) and roots (Allium porrum) on soil structure, nutrient concentration and plant growth. In our experimental conditions, plant roots improved soil structure stability (at the level of macroaggregates) whereas earthworms decreased it. AMF had no effect on soil structure stability but increased P transfer from the soil to the plant and significantly increased plant biomass. Earthworms had no direct influence on P uptake or plant biomass, and the N/P ratio measured in the shoots indicated that P was limiting. Interactions between AMF and earthworms were also observed on total C and N content in the soil and on total root biomass. Their effects varied temporally and between the different soil compartments (bulk soil, rhizosphere and drilosphere). After comparison with other similar studies, we suggest that effects of earthworms and AMF on plant production may depend on the limiting factors in the soil, mainly N or P. Our experiment highlights the importance of measuring physical and chemical soil parameters when studying soil organism interactions and their influence on plant performance.

Effect of cattle activities on gap colonization in mountain pastures

Cattle influences gap dynamics in pastures in two ways: (1) by creating gaps and (2) by affecting the colonization process. This effect of cattle activity on gap revegetation can be subdivided in three main factors: herbage removal, trampling and dung and urine deposition. The objective of this study was to assess how these three effects moderate the plant succession following gap creation.In an exclosure, four controlled treatments simulating cattle activity (repeated mowing, trampling, manuring and untreated control) were applied on plots of 2 × 2 m. In the centre of each plot, one artificial gap of 60 × 60 cm was created. During three years, vegetation changes were monitored in spring and in autumn, with a square grid of 100 cells of 0.01 m2 centred on the gap.Our experiment confirmed that fine-scale gap creation may have a high impact on relative abundances of species in the community. The gap environment acts on species as a filter and this filtering was described in terms of regenerative attributes. Colonizers were species with small seeds, unspecialized seed dispersal, persistent seed bank and high vegetation spread. However, the role of dung deposition, herbage removal or trampling by cattle did not seem to be of primary importance in the revegetation process, but could moderate vegetation response. Therefore, the different cattle effects act as secondary filters that selectively favoured or disadvantaged different species from the gap-regenerating community. These complex interactions are probably keys to understand plant coexistence in perennial grasslands.

European Humus Forms Reference Base

In Europe an abundance of humus taxonomies exists starting with early approaches in the late 19th century. Frequently used in an international context, they do not cover all site conditions in the European area. Although having basic concepts and general lines, the European (and North American, Canadian) classification systems differ in important parameters used for the description and classification of humus forms. These discrepancies result in incongruities, so require adjustments when exchanging partially compatible soil data, even between nearby countries. In 2003, 26 European specialists in humus forms met in Trento (Italy) and decided to formulate rules of classification based on morphogenetic descriptions and diagnostic horizons, adapted to European ecological conditions. Taking into account old and new European and North American systems of humus forms classification, six main references (Anmoor, Mull, Moder, Mor, Amphi and Tangel) were defined, each of them further dividing into detailed categories. This inventory assigned a strong discriminatory power to the action of the pedofauna. Both semiterrestrial (anoxic) and terrestrial (aerated) topsoils were classified. The descriptors of the diagnostic horizons were conceived in accordance with the spirit of recent international soil classifications. Assigning an “ecological value” to each main humus form along a gradient dividing those characterized by accumulation of poorly transformed organic matter, from very biologically active forms degrading and incorporating all organic remains, this European system of classification avoids a hierarchical structure and allows an elastic approach open to additional ecological contributions and renditions.

Soil microbial community changes in wooded mountain pastures due to simulated effects of cattle grazing

The effect of cattle activity on pastures can be subdivided into three categories of disturbances: herbage removal, dunging and trampling. The objective of this study was to assess separately or in combination the effect of these factors on the potential activities of soil microbial communities and to compare these effects with those of soil properties and plant composition or biomass. Controlled treatments simulating the three factors were applied in a fenced area including a light gradient (sunny and shady situation): (i) repeated mowing; (ii) trampling; (iii) fertilizing with a liquid mixture of dung and urine. In the third year of the experiment, community level physiological profiles (CLPP) (Biolog Ecoplates™) were measured for each plots. Furthermore soil chemical properties (pH, total organic carbon, total nitrogen and total phosphorus), plant species composition and plant biomass were also assessed. Despite differences in plant communities and soil properties, the metabolic potential of the microbial community in the sunny and in the shady situations were similar. Effects of treatments on microbial communities were more pronounced in the sunny than in the shady situation. In both cases, repeated mowing was the first factor retained for explaining functional variations. In contrast, fertilizing was not a significant factor. The vegetation explained a high proportion of variation of the microbial community descriptors in the sunny situation, while no significant variation appeared under shady condition. The three components of cattle activities influenced differently the soil microbial communities and this depended on the light conditions within the wooded pasture. Cattle activities may also change spatially at a fine scale and short-term and induce changes in the microbial community structure. Thus, the shifting mosaic that has been described for the vegetation of pastures may also apply for below-ground microbial communities.

Influence of tree cover on the diversity of herbaceous communities in subalpine wooded pastures

. The relationships between several diversity indices and tree cover in subalpine wooded pastures with Larix de-cidua were analysed at two spatial scales: phytocoenoses (2500-m2 plots) and herbaceous synusia (1-m2 quadrats). Diversity indices have a non-linear relationship to Larix cover; the best fit was obtained with Gaussian regressions. Species richness was influenced by Larix cover more than evenness. At the phytocoenosis level, the optimum for species and synusial richness in the herb layer was near 25 % tree cover. At the synusia level, species richness of the herb layer showed an optimum when mean distance to the four nearest Larix trees was ca. 30 m, or when the potential number of sunshine hours between April and September was close to 1250 h. Canonical Correspondence Analysis confirmed the influence of Larix cover on the composition of phytocoenoses and herbaceous synusiae, but included also the role of altitude, slope and aspect.

PATUMOD: a compartment model of vegetation dynamics in wooded pastures

A system of wooded pasture can be described by seven biological state variables (trees, shrubs, underwood grasslands, fallows, eutrophic meadows, oligrotrophic lawns and cattle) linked by a network of dynamic interactions, which are controlled by altitude and human activities. PATUMOD is a spatially implicit compartment model designed to simulate vegetation dynamics in such silvopastoral ecosystems at community level and according to an equilibrium paradigm. Computer simulations show that the state variables generally end up on a steady-state (one-point attractor), independent on their initial values but strongly dependent on cattle load. At a given altitude, to each value of the stock density is corresponding a stable equilibrium characterised by a given relative cover of each vegetation component. If the initial values are very far of the attractor, a long succession of intermediate stages is required before leading to the steady-state. A remarkable exception to this rule can occur at low altitude, with a repellor between switching trajectories towards two attractors, corresponding to a threshold between scarcely and densely wooded pastures. PATUMOD can be applied to simulate different management scenarios, which include changing global stock density and cutting trees or shrubs.

Impact of two root systems, earthworms and mycorrhizae on the physical properties of an unstable silt loam Luvisol and plant production

Background and aimsSoil organisms are known to engineer the soil physical properties, but their impact is difficult to assess and poorly documented. Shrinkage analysis has a good potential for such assessment. This study analyses the effects of mycorrhizae (Glomus intraradices), earthworms (Allolobophora chlorotica) and two plants, Allium porrum (leek) and Petunia hybrida (petunia), on the physical properties of an unstable loamy Luvisol, as well as the biological interactions between the soil organisms.MethodsIn addition to soil organism biomass, shrinkage analysis and soil aggregate stability analysis were used to characterize the soil physical properties.ResultsThe soil aggregate stability, specific volume and structural pores volumes were increased with plant roots compared to control. The drilling effect of roots could not explain the pore volume increase, which was several orders of magnitude larger than the volume of the roots. Leek had larger impact on volumes while petunia mostly increased soil aggregate stability. Mycorrhizae increased the soil stability and the soil volume. Earthworms alone decreased the pore volumes at any pore size, and plant roots mitigated this.ConclusionsOur results highlight (1) the large impact of soil biota on soil physical properties, (2) that their separated effects can either combine or mitigate each other and (3) that the observed changes are varying in intensity according to soil type and plant type.