Co-occurring grass species differ in their associated microbial community composition in a temperate native grassland

Background and aims

Specific associations exist between plant species and the soil microbial community and these associations vary between habitat types and different plant groups. However, there is evidence that the associations are highly specific. Hence, we aimed to determine the specificity of plant-microbe relationships amongst co-occurring grass species in a temperate grassland.

Methods and results

We examined the broad microbial groups of bacteria and fungi as well as a specific fungal group, the arbuscular mycorrhizal community amongst two dominant C₃ and C₄ species and one sub-dominant C₃ species using terminal restriction fragment length polymorphism (T-RFLP) analysis. We found that the two dominant species were more similar to each other in their bacterial and arbuscular mycorrhizal community composition than either was to the sub-dominant species, but not in their fungal community composition. We also found no clear evidence that those differences were directly linked to soil chemical properties.

Conclusions

Our results demonstrate that co-occurring grass species have a distinct soil microbial community and T-RFLP analysis is able to detect plant species effect on the microbial community composition on an extremely local scale, providing an insight into the differences in the response of bacterial, fungal and arbuscular mycorrhizal communities to different, but similar and co-occurring, plant species.     

Impacts of Myriophyllum aquaticum invasion in a Mediterranean wetland on plant and macro-arthropod communities

The invasion by alien macrophytes in aquatic ecosystems may produce a strong alteration of the native aquatic vegetation leading to heavy impacts for both plant and faunal native diversity. Myriophyllum aquaticum is an aquatic plant native of Southern America, invasive in several part of the world. We studied the effects of M. aquaticum invasion on plant and macro-arthropod communities in the canals around a protected wetland in the Mediterranean basin. We sampled plant and macro-arthropod communities in 10 transects in invaded and non-invaded tracts of the canals. We assessed the differences in plant and macro-arthropod species richness, diversity, taxonomic diversity and species composition between invaded and non-invaded habitats by means of univariate and multivariate analyses. Our study shows a significant loss of plant diversity between non-invaded to invaded sites, leading to communities numerically and taxonomically impoverished and highly divergent in the species composition. We also detected significant differences in arthropod species composition between invaded and non-invaded transects. Some taxa such as mosquitoes and malacostraca were more frequent in the M. aquaticum-dominated stands. Furthermore, the study shows a positive relation between invaded habitats and juvenile individuals of the invasive alien crayfish Procambarus clarkii.     

Water velocity regulates macro‐consumer herbivory on the benthic macrophyte Podostemum ceratophyllum Michx.

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Exploration of bacterial community classes in major human habitats

Background

Determining bacterial abundance variation is the first step in understanding bacterial similarity between individuals. Categorization of bacterial communities into groups or community classes is the subsequent step in describing microbial distribution based on abundance patterns. Here, we present an analysis of the groupings of bacterial communities in stool, nasal, skin, vaginal and oral habitats in a healthy cohort of 236 subjects from the Human Microbiome Project.

Results

We identify distinct community group patterns in the anterior nares, four skin sites, and vagina at the genus level. We also confirm three enterotypes previously identified in stools. We identify two clusters with low silhouette values in most oral sites, in which bacterial communities are more homogeneous. Subjects sharing a community class in one habitat do not necessarily share a community class in another, except in the three vaginal sites and the symmetric habitats of the left and right retroauricular creases. Demographic factors, including gender, age, and ethnicity, significantly influence community composition in several habitats. Community classes in the vagina, retroauricular crease and stool are stable over approximately 200 days.

Conclusion

The community composition, association of demographic factors with community classes, and demonstration of community stability deepen our understanding of the variability and dynamics of human microbiomes. This also has significant implications for experimental designs that seek microbial correlations with clinical phenotypes.     

Influence of salinity on bacterioplankton communities from the Brazilian rain forest to the coastal Atlantic Ocean

Background

Planktonic bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems, however, the taxa that make up these communities are poorly known. The aim of this study was to investigate bacterial communities in aquatic ecosystems at Ilha Grande, Rio de Janeiro, Brazil, a preserved insular environment of the Atlantic rain forest and how they correlate with a salinity gradient going from terrestrial aquatic habitats to the coastal Atlantic Ocean.

Methodology/Principal Findings

We analyzed chemical and microbiological parameters of water samples and constructed 16S rRNA gene libraries of free living bacteria obtained at three marine (two coastal and one offshore) and three freshwater (water spring, river, and mangrove) environments. A total of 836 sequences were analyzed by MOTHUR, yielding 269 freshwater and 219 marine operational taxonomic units (OTUs) grouped at 97% stringency. Richness and diversity indexes indicated that freshwater environments were the most diverse, especially the water spring. The main bacterial group in freshwater environments was Betaproteobacteria (43.5%), whereas Cyanobacteria (30.5%), Alphaproteobacteria (25.5%), and Gammaproteobacteria (26.3%) dominated the marine ones. Venn diagram showed no overlap between marine and freshwater OTUs at 97% stringency. LIBSHUFF statistics and PCA analysis revealed marked differences between the freshwater and marine libraries suggesting the importance of salinity as a driver of community composition in this habitat. The phylogenetic analysis of marine and freshwater libraries showed that the differences in community composition are consistent.

Conclusions/Significance

Our data supports the notion that a divergent evolutionary scenario is driving community composition in the studied habitats. This work also improves the comprehension of microbial community dynamics in tropical waters and how they are structured in relation to physicochemical parameters. Furthermore, this paper reveals for the first time the pristine bacterioplankton communities in a tropical island at the South Atlantic Ocean.     

Effects of desiccation on the toxicant sensitivity of rotifers

Non-native aquatic macrophytes have invaded different types of ecosystems all over the world. The exotic submersed macrophyte Hydrilla verticillata recently invaded the Paraná basin, Brazil, being recorded by the first time in the natural habitats of this river in 2005. We investigated the effects of this species on ostracod assemblages and compared the abundance, richness, and Shannon–Wiener diversity of ostracod assemblages that colonize the invading species with those that colonize Egeria najas, a native submersed species with similar architecture and physical complexity. Fragments of these two species were left for 28 days in tanks to root and grow and then they were transferred to a floodplain lake where they remained in pairs (one plant of each species; N = 7) during 30 days for colonization by ostracods. A detrented correspondence analysis was used to summarize ostracod assemblage composition. Although there were no significant differences in ostracod abundance, richness and Shannon diversity when analyzed separately, cumulative curves, which permit to eliminate effects of abundance on richness, indicated a significantly higher number of ostracod species on H. verticillata. Assemblage composition was significantly different between both plant species, as shown by the first DCA axis. Our results show that H. verticillata might provide favorable habitats for native ostracod assemblages.     

Influences of aquatic macrophytes on invertebrate community structure,guild structure,and microdistribution in streams

The aquatic macrophytes Ranunculus aquatilis and Rorippa nasturtium-aquaticum were transplanted into substrate trays and placed in a stream alongside unvegetated substrate. Macrophytes were observed to have significant effects on 1) invertebrate community structure, 2) guild structure, and 3) microdistribution. 1) Significantly higher taxa richness and community abundances were associated with macrophytes. 2) Significantly higher abundances of shredder, scraper, and predator guilds were associated with macrophytes in fall, and all guilds had higher abundances in macrophytes in spring. However, guild frequency distributions did not differ among habitats except in spring. 3) Enallagma, Gammarus, Gyraulus, Physa, and Pisidium exhibited a strong association with macrophytes, while Hydropsyche, Simulium, Baetis tricaudatus, Glossosoma velona, and Helicopsyche borealis appeared to avoid them. A strong correlation appeared to exist between current velocity preferences of these taxa and their selection or avoidance of vegetated habitat. Thus, the effect of macrophytes in reducing current velocities appeared to be the most important influence on invertebrate microdistribution. However, macrophytes also increase physical heterogeneity and their large surface areas benefit invertebrate community abundances by creating additional living spaces in the water column where none exist above unvegetated substrate.     

Diversity and composition of bacterial community in the rhizosphere sediments of submerged macrophytes revealed by 454 pyrosequencing

Freshwater lake sediments support a variety of submerged macrophytes that may host groups of bacteria exerting important ecological functions. We collected three kinds of commonly found submerged macrophyte species (Ceratophyllum demersum, Vallisneria spiralis and Elodea nuttallii) to investigate the bacterial community associated with their rhizosphere sediments. High-throughput 454 pyrosequencing and bioinformatics analyses were performed to examine the diversity and composition of the bacterial community. The results obtained indicated that the diversity of the bacterial community associated with the rhizosphere sediments of submerged macrophytes was significantly lower than that of the bulk sediment. Remarkable differences in the bacterial community composition between the rhizosphere and bulk sediments were also observed.     

Solid state fermentation of aquatic macrophytes for crude protein extraction

Aquatic macrophytes such as Elodea nuttalli, Vallisneria natans, Alterranthera philoxerides that are widely distributed in water environments of Lake Taihu basin were used as substrate of solid state fermentation to produce crude protein extraction. The effects of single-strain fermentation and mixed strains fermentation of aquatic macrophytes on the production of crude protein extraction and cellulase activity are analyzed, respectively. The experimental results showed that the crude protein content of products with mixed strains fermentation is higher than that with single-strain fermentation. The crude protein content of V. natans fermented by Aspergillus niger and Candida utilis is the highest among the aquatic macrophytes examined in this study. V. natans is used as the substrate to be fermented by C. utilis and A. niger; their ratio is 1:1 at 28 ± 1 °C for 72 h. The crude protein of fermented V. natans is as high as 49.54%, with 128.82% of its increase rate. The cellulose activity reaches a maximum of 4.21 μ/ml at 84 h of fementation of V. natans. Thus, the solid state fermentation of aquatic macrophytes to produce crude protein extraction is promising, which make aquatic macrophytes a potential resource and thus is beneficial to the long-term ecological restoration of eutrophic lakes.     

An invasive fish promotes invasive plants in Minnesota lakes

1. Biological invasions can greatly alter ecological communities, affecting not only the diversity and abundance but also composition of invaded assemblages. This is because invaders’ impacts are mediated by characteristics of resident species: some may be highly sensitive to invader impacts while others are unaffected or even facilitated. In some cases, this can result in invasive species promoting further invasions; in particular, herbivory by introduced animals has been shown to disproportionately harm native plants, which can indirectly benefit non-native plants. Here, we investigated whether such patterns emerged through the effects of an invasive fish species on lake plant communities.
2. Specifically, we tested whether invasion of Minnesota (U.S.A.) lakes by Cyprinus carpio (common carp), an omnivorous, benthivorous fish known to reduce abundance and richness of aquatic plants, differentially affected native versus non-native plant species. We applied statistical models to a large, long-term monitoring dataset (206 macrophyte taxa recorded in 913 lakes over a 20-year time period) to test whether carp altered community composition, to identify which macrophyte species were most sensitive to carp and determine whether species characteristics predicted carp sensitivity, and to characterise consequences of carp invasion on lake-level vegetation attributes.
3. We found that carp exerted strong selective pressure on community composition. Native macrophytes, those with a more aquatic growth form, and those considered less tolerant of disturbance (i.e. higher coefficients of conservatism) were more sensitive to carp. Conversely, no introduced macrophytes exhibited sensitivity to carp and all had higher probabilities of occurrence as carp abundance increased. The net effect of carp invasion was a shift toward less species-rich plant communities characterised by more non-native and disturbance-tolerant species.
4. These results have several implications for conservation and management. First, they reinforce the need to prevent further spread of carp outside of their native range. Where carp have already established, their control should be incorporated into efforts to restore aquatic vegetation; this may be an essential step for recovering particular plant species of high conservation importance. Furthermore, reducing carp abundance could have ancillary benefits of reducing dominance by invasive plant species. Lastly, where carp cannot be eliminated, managers should target native macrophytes that are relatively tolerant of carp in shoreline plantings and other revegetation efforts.

     

Multi‐trophic impacts of an invasive aquatic plant

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Inhibitory effects of Eucalyptus globulus on understorey plant growth and species richness are greater in non‐native regions

Aim

We studied the novel weapons hypothesis in the context of the broadly distributed tree species Eucalyptus globulus. We evaluated the hypothesis that this Australian species would produce stronger inhibitory effects on species from its non‐native range than on species from its native range.

Location

We worked in four countries where this species is exotic (U.S.A., Chile, India, Portugal) and one country where it is native (Australia).

Time period

2009–2012.

Major taxa studied

Plants.

Methods

We compared species composition, richness and height of plant communities in 20 paired plots underneath E. globulus individuals and open areas in two sites within its native range and each non‐native region. We also compared effects of litter leachates of E. globulus on root growth of seedlings in species from Australia, Chile, the U.S.A. and India.

Results

In all sites and countries, the plant community under E. globulus canopies had lower species richness than did the plant community in open areas. However, the reduction was much greater in the non‐native ranges: species richness declined by an average of 51% in the eight non‐native sites versus 8% in the two native Australian sites. The root growth of 15 out of 21 species from the non‐native range were highly suppressed by E. globulus litter leachates, whereas the effect of litter leachate varied from facilitation to suppression for six species native to Australia. The mean reduction in root growth for Australian plants was significantly lower than for plants from the U.S.A., Chile and India.

Main conclusions

Our results show biogeographical differences in the impact of an exotic species on understorey plant communities. Consistent with the novel weapons hypothesis, our findings suggest that different adaptations of species from the native and non‐native ranges to biochemical compounds produced by an exotic species may play a role in these biogeographical differences.     

Seed dispersal by rivers in tropical dry forests: An overlooked process in tropical central Mexico

Aims

Rivers are important corridors for the movement, migration and dispersal of aquatic organisms, including seeds from riparian plants. Although tropical dry forests (TDF) are among the most extensive and floristically rich ecosystems of tropical habitats, and the most globally endangered ecosystem, less attention has been given to riparian corridors within this ecosystem. Although most TDFs manifest peak seed dispersal during dry seasons, we hypothesized that riparian corridors may show a dispersal peak during the rainy season, due to an anticipated ‘sweep or drag effect’, resulting from river overflow and bank erosion. Our main aims were to investigate whether there were any differences in the seed communities transported by the river to sites in rainy as opposed to dry seasons, and to evaluate any possible relationship between the riparian seed community and river flow.

Location

Amacuzac River, drainage of the Balsas basin, State of Morelos, Mexico.

Methods

To evaluate the above assumption, we associated Amacuzac River flow with the number of species and seeds dispersed by water. We also characterized and evaluated differences between seed communities transported by the river during the rainy and dry seasons, and between four different sites located along the river. We used univariate and ordination NMDS techniques to evaluate patterns between seasons at the community level.

Results

Forty‐five plant species were identified from 909 seeds collected from the river. The composition of riparian seed communities was markedly different between seasons but not between sites. Seed abundances were significantly higher in the rainy than in the dry season and varied between sites. Seed species diversity in the river (H’ = 1.6–1.9) showed no significant differences between seasons or sites, but species assemblages and dominance varied according to season. Ordination techniques and subsequent fitting analyses showed that seed species composition was positively associated with river flow.

Conclusions

Seed dispersal patterns generated by rivers are significant mechanisms for structuring the composition and distribution of the riparian plant community in Mexican TDF. Varying species assemblages and seed abundance dispersed by the river throughout the year is a relevant and until now unknown consequence that may affect the dynamics and composition of riparian plant communities in this region. This study initiative will promote new avenues of research regarding plant establishment and succession.     

Rapid local adaptation mediates zooplankton community assembly in experimental mesocosms

Adaptive evolution can occur over similar timescales as ecological processes such as community assembly, but its particular effects on community assembly and structure and their magnitude are poorly understood. In experimental evolution trials, Daphnia magna were exposed to varying environments (presence and absence of fish and artificial macrophytes) for 2 months. Then, in a common gardening experiment, we compared zooplankton community composition when either experimentally adapted or D. magna from the original population were present. Local adaptation of D. magna significantly altered zooplankton community composition, leading to a suppression of abundances for some zooplankton taxa and facilitation for others. The effect size of D. magna adaptation was similar to that of adding fish or macrophytes to mesocosms, two important drivers of zooplankton community structure. Our results suggest that substantial amounts of variation in community composition in natural systems may be unexplained if evolutionary dynamics are ignored.     

Community collocation of four submerged macrophytes on two kinds of sediments in Lake Taihu, China

To explore a method for rapid restoration and artificial regulation of submerged macrophytes in large-scale restoration of eutrophic lakes, the succession and the biodiversity changes of four communities composed of four native, common submerged macrophytes, Hydrilla verticillata, Potamogeton malaianus, Vallisneria spiralis and Najas marina, on two kinds of sediments were investigated. Under low light intensity (reduced by 99%), the plant biomass changed with seasonal changes, plant competition, and environmental stress. The competitive capability for light differed in the four species due to different shoot height and tiller number. After 405 days of transplantation, H. verticillata became dominant in all communities. The biomass of H. verticillata, with strong ability to endure low water light environment, accounted for more than 90% of the total community biomass, and P. malaianus had only weak growth, while V. spiralis and N. marina almost disappeared. Based on livability and biomass of submerged macrophytes on two sediment types, brown clay sediment appeared to be more favorable for the settlement of the plants, while fertile sludge sediment was suitable for vegetative growth. In conclusion, the improvement of habitats and the selection of appropriate plant species are of the greatest importance for ecological restoration of the aquatic ecosystem.     

Responses of four submerged macrophytes to freshwater snail density (Radix swinhoei) under clear‐water conditions: A mesocosm study

Macrophytes play a key role in stabilizing clear‐water conditions in shallow freshwater ecosystems. Their populations are maintained by a balance between plant grazing and plant growth. As a freshwater snail commonly found in shallow lakes, Radix swinhoei can affect the growth of submerged macrophytes by removing epiphyton from the surface of aquatic plants and by grazing directly on macrophyte organs. Thus, we conducted a long‐term (11‐month) experiment to explore the effects of snail density on macrophytes with distinctive structures in an outdoor clear‐water mesocosm system (with relatively low total nitrogen (TN, 0.66 ± 0.27 mg/L) and total phosphorus (TP, 36 ± 20 μg/L) and a phytoplankton chlorophyll a (Chla) range of 14.8 ± 4.9 μg/L) based on two different snail densities (low and high) and four macrophyte species treatments (Myriophyllum spicatum, Potamogeton wrightii, P. crispus, and P. oxyphyllus). In the high‐density treatment, snail biomass and abundance (36.5 ± 16.5 g/m² and 169 ± 92 ind/m², respectively) were approximately twice that observed in the low‐density treatment, resulting in lower total and aboveground biomass and ramet number in the macrophytes. In addition, plant height and plant volume inhabited (PVI) showed species‐specific responses to snail densities, that is, the height of P. oxyphyllus and PVI of M. spicatum were both higher under low‐density treatment. Thus, compared with low‐density treatment, the inhibitory effects of long‐term high snail density on macrophytes by direct feeding may be greater than the positive effects resulting from epiphyton clearance when under clear‐water conditions with low epiphyton biomass. Thus, under clear‐water conditions, the growth and community composition of submerged macrophytes could be potentially modified by the manual addition of invertebrates (i.e., snails) to lakes if the inhibitory effects from predatory fish are minor.     

Strong Indirect Effects of a Submersed Aquatic Macrophyte, Vallisneria americana, on Bacterioplankton Densities in a Mesotrophic Lake

Phytoplankton and allochthonous matter are important sources of dissolved organic carbon (DOC) for planktonic bacteria in aquatic ecosystems. But in small temperate lakes, aquatic macrophytes may also be an important source of DOC, as well as a source or sink for inorganic nutrients. We conducted micro- and mesocosm studies to investigate the possible effects of an actively growing macrophyte, Vallisneria americana, on bacterial growth and water chemistry in mesotrophic Calder Lake. A first microcosm (1 L) study conducted under high ambient NH ₄ ⁺ levels (NH ₄ ⁺ 10 µM) demonstrated that macrophytes had a positive effect on bacterial densities through release of DOC and P. A second microcosm experiment, conducted under NH ₄ ⁺ -depleted conditions (NH ₄ ⁺ < 10 µM), examined interactive effects of macrophytes and their sediments on bacterial growth and water chemistry. Non-rooted macrophytes had negative effects on bacterial numbers, while rooted macrophytes had no significant effects, despite significant increases in DOC and P. A 70-L mesocosm experiment manipulated macrophytes, as well as N and P supply under surplus NH ₄ ⁺ conditions (NH ₄ ⁺ 10 µM), and measured effects on bacterial growth, Chl a concentrations, and water chemistry. Bacterial growth and Chl a concentrations declined with macrophyte additions, while bacterial densities increased with P addition (with or without N). Results suggest that the submersed macrophyte Vallisneria exerts a strong but indirect effect on bacteria by modifying nutrient conditions and/or suppressing phytoplankton. Effects of living macrophytes differed with ambient nutrient conditions: under NH ₄ ⁺ -surplus conditions, submersed macrophytes stimulated bacterioplankton through release of DOC or P, but in NH ₄ ⁺ -depleted conditions, the influence of Vallisneria was negative or neutral. Effects of living macrophytes on planktonic bacteria were apparently mediated by the macrophytes use and/or release of nutrients, as well as through possible effects on phytoplankton production.     

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

Background

To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease. The digestive tract includes diverse habitats and hosts the human body's greatest bacterial density. We describe the bacterial community composition of ten digestive tract sites from more than 200 normal adults enrolled in the Human Microbiome Project, and metagenomically determined metabolic potentials of four representative sites.

Results

The microbiota of these diverse habitats formed four groups based on similar community compositions: buccal mucosa, keratinized gingiva, hard palate; saliva, tongue, tonsils, throat; sub- and supra-gingival plaques; and stool. Phyla initially identified from environmental samples were detected throughout this population, primarily TM7, SR1, and Synergistetes. Genera with pathogenic members were well-represented among this disease-free cohort. Tooth-associated communities were distinct, but not entirely dissimilar, from other oral surfaces. The Porphyromonadaceae, Veillonellaceae and Lachnospiraceae families were common to all sites, but the distributions of their genera varied significantly. Most metabolic processes were distributed widely throughout the digestive tract microbiota, with variations in metagenomic abundance between body habitats. These included shifts in sugar transporter types between the supragingival plaque, other oral surfaces, and stool; hydrogen and hydrogen sulfide production were also differentially distributed.

Conclusions

The microbiomes of ten digestive tract sites separated into four types based on composition. A core set of metabolic pathways was present across these diverse digestive tract habitats. These data provide a critical baseline for future studies investigating local and systemic diseases affecting human health.     

Longitudinal analysis of the vaginal microflora in pregnancy suggests that L. crispatus promotes the stability of the normal vaginal microflora and that L. gasseri and/or L. iners are more conducive to the occurrence of abnormal vaginal microflora

Background  

Despite their antimicrobial potential, vaginal lactobacilli often fail to retain dominance, resulting in overgrowth of the vagina by other bacteria, as observed with bacterial vaginosis. It remains elusive however to what extent interindividual differences in vaginal Lactobacillus community composition determine the stability of this microflora. In a prospective cohort of pregnant women we studied the stability of the normal vaginal microflora (assessed on Gram stain) as a function of the presence of the vaginal Lactobacillus index species (determined through culture and molecular analysis with tRFLP).     

Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape

Background

The advent of molecular techniques in microbial ecology has aroused interest in gaining an understanding about the spatial distribution of regional pools of soil microbes and the main drivers responsible of these spatial patterns. Here, we assessed the distribution of crenarcheal, bacterial and fungal communities in an alpine landscape displaying high turnover in plant species over short distances. Our aim is to determine the relative contribution of plant species composition, environmental conditions, and geographic isolation on microbial community distribution.

Methodology/Principal Findings

Eleven types of habitats that best represent the landscape heterogeneity were investigated. Crenarchaeal, bacterial and fungal communities were described by means of Single Strand Conformation Polymorphism. Relationships between microbial beta diversity patterns were examined by using Bray-Curtis dissimilarities and Principal Coordinate Analyses. Distance-based redundancy analyses and variation partitioning were used to estimate the relative contributions of different drivers on microbial beta diversity. Microbial communities tended to be habitat-specific and did not display significant spatial autocorrelation. Microbial beta diversity correlated with soil pH. Fungal beta-diversity was mainly related to soil organic matter. Though the effect of plant species composition was significant for all microbial groups, it was much stronger for Fungi. In contrast, geographic distances did not have any effect on microbial beta diversity.

Conclusions/Significance

Microbial communities exhibit non-random spatial patterns of diversity in alpine landscapes. Crenarcheal, bacterial and fungal community turnover is high and associated with plant species composition through different set of soil variables, but is not caused by geographical isolation.