Predicting spatial patterns of soil bacteria under current and future environmental conditions

Soil bacteria are largely missing from future biodiversity assessments hindering comprehensive forecasts of ecosystem changes. Soil bacterial communities are expected to be more strongly driven by pH and less by other edaphic and climatic factors. Thus, alkalinisation or acidification along with climate change may influence soil bacteria, with subsequent influences for example on nutrient cycling and vegetation. Future forecasts of soil bacteria are therefore needed. We applied species distribution modelling (SDM) to quantify the roles of environmental factors in governing spatial abundance distribution of soil bacterial OTUs and to predict how future changes in these factors may change bacterial communities in a temperate mountain area. Models indicated that factors related to soil (especially pH), climate and/or topography explain and predict part of the abundance distribution of most OTUs. This supports the expectations that microorganisms have specific environmental requirements (i.e., niches/envelopes) and that they should accordingly respond to environmental changes. Our predictions indicate a stronger role of pH over other predictors (e.g. climate) in governing distributions of bacteria, yet the predicted future changes in bacteria communities are smaller than their current variation across space. The extent of bacterial community change predictions varies as a function of elevation, but in general, deviations from neutral soil pH are expected to decrease abundances and diversity of bacteria. Our findings highlight the need to account for edaphic changes, along with climate changes, in future forecasts of soil bacteria.

Soil protist function varies with elevation in the Swiss Alps

Protists are abundant and play key trophic functions in soil. Documenting how their trophic contributions vary across large environmental gradients is essential to understand and predict how biogeochemical cycles will be impacted by global changes. Here, using amplicon sequencing of environmental DNA in open habitat soil from 161 locations spanning 2600 m of elevation in the Swiss Alps (from 400 to 3000 m), we found that, over the whole study area, soils are dominated by consumers, followed by parasites and phototrophs. In contrast, the proportion of these groups in local communities shows large variations in relation to elevation. While there is, on average, three times more consumers than parasites at low elevation (400–1000 m), this ratio increases to 12 at high elevation (2000–3000 m). This suggests that the decrease in protist host biomass and diversity toward mountains tops impact protist functional composition. Furthermore, the taxonomic composition of protists that infect animals was related to elevation while that of protists that infect plants or of protist consumers was related to soil pH. This study provides a first step to document and understand how soil protist functions vary along the elevational gradient.

Greater topoclimatic control of above- versus below-ground communities

Assessing the degree to which climate explains the spatial distributions of different taxonomic and functional groups is essential for anticipating the effects of climate change on ecosystems. Most effort so far has focused on above-ground organisms, which offer only a partial view on the response of biodiversity to environmental gradients. Here including both above- and below-ground organisms, we quantified the degree of topoclimatic control on the occurrence patterns of >1,500 taxa and phylotypes along a c. 3,000 m elevation gradient, by fitting species distribution models. Higher model performances for animals and plants than for soil microbes (fungi, bacteria and protists) suggest that the direct influence of topoclimate is stronger on above-ground species than on below-ground microorganisms. Accordingly, direct climate change effects are predicted to be stronger for above-ground than for below-ground taxa, whereas factors expressing local soil microclimate and geochemistry are likely more important to explain and forecast the occurrence patterns of soil microbiota. Detailed mapping and future scenarios of soil microclimate and microhabitats, together with comparative studies of interacting and ecologically dependent above- and below-ground biota, are thus needed to understand and realistically forecast the future distribution of ecosystems.

Archaeorhizomycetes Spatial Distribution in Soils Along Wide Elevational and Environmental Gradients Reveal Co-abundance Patterns With Other Fungal Saprobes and Potential Weathering Capacities

Archaeorhizomycetes, a widespread fungal class with a dominant presence in many soil environments, contains cryptic filamentous species forming plant-root associations whose role in terrestrial ecosystems remains unclear. Here, we apply a correlative approach to identify the abiotic and biotic environmental variables shaping the distribution of this fungal group. We used a DNA sequencing dataset containing Archaeorhizomycetes sequences and environmental variables from 103 sites, obtained through a random-stratified sampling in the Western Swiss Alps along a wide elevation gradient (>2,500 m). We observed that the relative abundance of Archaeorhizomycetes follows a "humped-shaped" curve. Fitted linear and quadratic generalized linear models revealed that both climatic (minimum temperature, precipitation sum, growing degree-days) and edaphic (carbon, hydrogen, organic carbon, aluminum oxide, and phyllosilicates) factors contribute to explaining the variation in Archaeorhizomycetes abundance. Furthermore, a network inference topology described significant co-abundance patterns between Archaeorhizomycetes and other saprotrophic and ectomycorrhizal fungal taxa. Overall, our results provide strong support to the hypothesis that Archaeorhizomycetes in this area have clear ecological requirements along wide, elevation-driven abiotic and biotic gradients. Additionally, correlations to soil redox parameters, particularly with phyllosilicates minerals, suggest Archaeorhizomycetes might be implied in biological rock weathering. Such soil taxa-environment studies along wide gradients are thus a useful complement to latitudinal field observations and culture-based approaches to uncover the ecological roles of cryptic soil organisms.

Generalizing soil properties in geographic space: Approaches used and ways forward

Soil is one of the most complex systems on Earth, functioning at the interface between the lithosphere, biosphere, hydrosphere, and atmosphere and generating a multitude of functions. Moreover, soil constitutes the belowground environment from which plants capture water and nutrients. Despite their great importance, soil properties are often not sufficiently considered in other disciplines, especially in spatial studies of plant distributions. Most soil properties are available as point data and, to be used in spatial analyses, need to be generalised over entire regions (i.e. digital soil mapping). Three categories of statistical approaches can be used for such purpose: geostatistical approaches (GSA), predictive-statistical approaches (PSA), and hybrid approaches (HA) that combine the two previous ones. How then to choose the best approach in a given soil study context? Does it depend on the soil properties to be spatialized, the study area's characteristics, and/or the availability of soil data? The main aims of this study was to review the use of these three approaches to derive maps of soil properties in relation to the soil parameters, the study area characteristics, and the number of soil samples. We evidenced that the approaches that tend to show the best performance for spatializing soil properties were not necessarily the ones most used in practice. Although PSA was the most widely used, it tended to be outperformed by HA in many cases, but the latter was far less used. However, as the study settings were not always properly described and not all situations were represented in the set of papers analysed, more comparative studies would be needed across a wider range of regions, soil properties, and spatial scales to provide robust conclusions on the best spatialization methods in a specific context.

Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps

Mountain ecosystems are characterized by a diverse range of climatic and topographic conditions over short distances and are known to shelter a high biodiversity. Despite important progress, still little is known on bacterial diversity in mountain areas. Here, we investigated soil bacterial biogeography at more than 100 sampling sites randomly stratified across a 700-km² area with 2,200-m elevation gradient in the western Swiss Alps. Bacterial grassland communities were highly diverse, with 12,741 total operational taxonomic units (OTUs) across 100 sites and an average of 2,918 OTUs per site. Bacterial community structure was correlated with local climatic, topographic, and soil physicochemical parameters with high statistical significance. We found pH (correlated with % CaO and % mineral carbon), hydrogen index (correlated with bulk gravimetric water content), and annual average number of frost days during the growing season to be among the groups of the most important environmental drivers of bacterial community structure. In contrast, bacterial community structure was only weakly stratified as a function of elevation. Contrasting patterns were discovered for individual bacterial taxa. Acidobacteria responded both positively and negatively to pH extremes. Various families within the Bacteroidetes responded to available phosphorus levels. Different verrucomicrobial groups responded to electrical conductivity, total organic carbon, water content, and mineral carbon contents. Alpine grassland bacterial communities are thus highly diverse, which is likely due to the large variety of different environmental conditions. These results shed new light on the biodiversity of mountain ecosystems, which were already identified as potentially fragile to anthropogenic influences and climate change.

IMPORTANCE

This article addresses the question of how microbial communities in alpine regions are dependent on local climatic and soil physicochemical variables. We benefit from a unique 700-km² study region in the western Swiss Alps region, which has been exhaustively studied for macro-organismal and fungal ecology, and for topoclimatic modeling of future ecological trends, but without taking into account soil bacterial diversity. Here, we present an in-depth biogeographical characterization of the bacterial community diversity in this alpine region across 100 randomly stratified sites, using 56 environmental variables. Our exhaustive sampling ensured the detection of ecological trends with high statistical robustness. Our data both confirm previously observed general trends and show many new detailed trends for a wide range of bacterial taxonomic groups and environmental parameters.

Sol-gel synthesis, structure and bioactivity of polycaprolactone/CaO . SiO2 hybrid material

A method has been developed to cast novel organic/inorganic polymer hybrids from multicomponent solutions containing tetramethyl orthosilicate, calcium nitrate tetrahydrate, polycaprolactone, water, and methylethyketone via sol-gel process. The existence of the hydrogen bonds between organic and inorganic components of the hybrid and hydroxyapatite formation on the surface was proved by Fourier transform infrared analysis. The morphology of the hybrid material was studied by scanning electron microscopy. The structure of a molecular level dispersion was disclosed by atomic force microscopy, pore size distribution, and surface measurements. The infrared spectra of the hybrid relative to sample soaked in a fluid simulating the composition of human blood plasma suggests that polycaprolactone/CaO * SiO(2) hybrid material synthesised via sol-gel process is bioactive as well as the CaO * SiO(2) gel glass.

Effect of the substitution of Y2O3 for CaO on the bioactivity of 2.5CaO.2SiO2 glass

Glasses were prepared whose composition is defined by the following general formula: (2.5-x)CaO.x/3Y2O3.2SiO2 (0 < or = x < or = 1). Their behaviour when they were soaked in a simulated body fluid (SBF) and their thermal properties (glass transformation and softening temperatures, Tg and Ts respectively) were studied Tg and Ts increase with the Y2O3 content. The trend can be explained on the basis of the increased structural rigidity when Ca2+ ions are substituted by Y2+ ions, because of the formation of stronger bonds to the oxygen. The bioactivity was studied by means of electron microscopy equipped with an energy dispersive system for elemental analysis and IR spectroscopy. All the glasses studied except the one with the greatest amount of Y2O3. x = 1.0, reacted with SBF by forming a calcium phosphate layer. The experimental results suggest that the bioactivity is negatively influenced by the Y2O3 content: the tendency to form a calcium phosphate layer is reduced the greater the amount of CaO substituted. A comparison with literature data indicates that the amount of Y2O3 that can be substituted depends on the CaO content of the base CaO-SiO2 glass. The experimental results are in good agreement with the mechanism reported in the literature. After 7 days soaking, crystalline hydroxyapatite is formed in the Y2O3-free glass and in the glasses of low Y2O3 content (x-0.2).

Bioactivity of 1.25CaO.SiO2 glass: an FTIR and X-ray study on powdered samples

Powdered samples (170-230 mesh) of a glass of composition 1.25CaO.SiO2 were soaked in a simulated body fluid (SBF). The powders were submitted to Fourier transform infrared transmission spectroscopy as coarse powders (such as drawn out from the SBF) and as fine powders (soaked and subsequently ground). Soaked samples were submitted to differential thermal analysis (DTA) and the crystalline phases formed during heating in the DTA apparatus were identified by means of X-ray diffraction analysis. The method appears to be useful in studying the mechanism of deposition of the hydroxyapatite layer. It is documented, by using the same method, that the mechanism involves the reactions of hydrolysis and successive condensation and repolymerization of the silicate substrate. These reactions are very fast. Extensive Ca2+ cation depletion occurs, but appears to be slower.

Effect of the substitution of La2O3 for CaO on the bioactivity of 2.5CaO.2SiO2 glass

Glasses of the following composition were prepared: (2.5-x)CaO.x/3La2O3.2SiO2 (0 < or = x < or = 1). Their behavior when soaked in a simulated body fluid (SBF) was studied by means of electron microscopy (EM) equipped with an energy-dispersive system (EDS) for elemental analysis, IR spectroscopy, and x-ray diffraction. All the studied glasses react with SBF by forming a calcium phosphate layer. This layer appears to be increasingly thinner with increasing amounts of La2O3 substituted. The experimental results are in good agreement with mechanisms reported in the literature. Moreover they suggest that lanthanum oxide is retained in the layer below the phosphate. After 6 days of soaking, crystalline hydroxyapatite is formed in the case of La2O3 free glass.

Apatite formation on (2-x)CaO.x/3 M2O3 x 2SiO2 glasses (M = La, Y; 0 < or = x < or = 0.6) in a simulated body fluid

Glasses were prepared by substituting La2O3 or Y2O3 for CaO in glassy wollastonite composition (CaO.SiO2). Their behaviour when they are soaked in a simulated body fluid (SBF) was studied by means of an electron microscope equipped with an energy dispersive system for elemental analysis, and by means of IR spectroscopy. Electron microscopy and energy dispersive microanalysis were performed on samples soaked as polished bulk samples, and IR analysis was on samples soaked as fine powders. A carbonate-containing hydroxyapatite layer is formed when glasses of low La2O3 content are soaked in SBF. When Y2O3-containing glasses are considered, even in the case of small substitution for CaO, the same layer forms only on fracture surfaces. The experimental results agree with the mechanism reported in the literature.

The regulation of intracellular Mg2+ in guinea-pig heart, studied with Mg(2+)-selective microelectrodes and fluorochromes

Because of the reported presence of a Na(+)-Mg2+ exchanger in guinea-pig but not in ferret myocardium, the Mg2+ extrusion mechanism in guinea-pig myocardium has been reinvestigated using Mg(2+)- and Na(+)- selective microelectrodes and the fluorochromes mag-fura-2 and -5. The mean [Mg2+]i measured with microelectrodes in trabeculae or papillary muscles was 0.72 mmol/l (n = 22, thirteen experiments; range 0.42-1.23 mmol/l). Increasing [Mg2+]o from 0.5 mmol/l to either 10.5 or 20 mmol/l caused small increases in [Mg2+]i. Decreasing [Na+]o by 50% had no effect on the [Mg2+]i and there was no change in [Na+]i on increasing [Mg2+]o from 0.5 to 10.5 mmol/l. Varying pHo or changing pHi with NH4Cl did not influence the [Mg2+]i. In vitro calibration of mag-fura-2 and -5 using the ratio method gave values for K'd (experimentally determined dissociation constant) of 22.2 +/- 2.7 (mean +/- S.D., n = 7) and 25.7 +/- 1.3 (n = 4) mmol/l respectively. Mag-fura-2 reacted to physiological concentrations of Ca2+ and mag-fura-5 to changes in pH. In isolated myocytes, Na+ removal gave an apparent increase of [Mg2+]i with mag-fura-2 but not with mag-fura-5. However, when the pHi was altered with NH4Cl mag-fura-5 showed an apparent decrease in [Mg2+]i on application and an apparent increase on removal, with a time course similar to the pHi changes. It is concluded that Mg2+ extrusion in guinea-pig myocardium is not via a Na(+)-Mg2+ exchanger. The use of mag-fura-2 and -5 are limited in their application because of Ca2+ and H+ sensitivity respectively.

Calcium buffer solutions and how to make them: a do it yourself guide

In measurements of the intracellular free calcium concentration ([Ca2+]) using either microelectrodes or fluorescent probes, calibration is normally carried out in EGTA calcium buffer solutions. In the first part of the article the general properties of calcium buffer solutions are discussed, the equations used to calculate the apparent calcium binding constant (Kapp) are derived, and the difficulties in the calculation are discussed. The effects of the purity of EGTA as well as the influence of calcium contamination on the buffer solutions are explained. Because of the difficulties in calculating Kapp, and the importance of EGTA purity and calcium contamination, it is suggested that it is easier to measure all three under the appropriate experimental conditions using the method of Bers (1982). In the second part a do-it-yourself guide to the preparation of EGTA calcium buffer solutions is given. An experimental example is provided using the Bers method to measure purity, contamination, and Kapp. It is concluded that unless all three factors are known it is not possible to prepare accurate EGTA calcium buffer solutions.

Intracellular free magnesium and its regulation, studied in isolated ferret ventricular muscle with ion-selective microelectrodes

Intracellular free magnesium ([Mg2+]i) was measured in isolated ferret papillary muscles using ion-selective microelectrodes filled with the new magnesium sensor ETH 5214. This new sensor, unlike its predecessor ETH 1117, does not react to marked changes in K+, Na+ or pH. Reducing Ca2+ from 20 microM to around 10 nM also did not affect the response so these electrodes are ideally suited to study intracellular Mg2+ and its regulation. The mean value for the [Mg2+]i from thirty-two experiments (forty-two impalements) was 0.85 mM, confirming previous estimates from this laboratory. Intracellular Mg2+ is not passively distributed and the possibility that Mg2+ is transported out of the cell by a Na(+)-Mg2+ exchanger was investigated. An increase in [Mg2+]o caused an increase in [Mg2+]i, as did stepwise reduction in the [Na+]o. However, this increase in [Mg2+]i on Na+ reduction also occurred in Mg2(+)-free solution suggesting that the increase in [Mg2+]i was due to the increase in intracellular Ca2+ on Na+ reduction. Moreover, increasing [Na+]i by strophanthidin did not change the [Mg2+]i and on increasing [Mg2+]o there was no reduction in the [Na+]i. Blocking ATP production lead to small increases in the [Mg2+]i. These results are not consistent with a Na(+)-Mg2+ exchanger as being the main outward transport mechanism for Mg2+ in this tissue.