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Microbes on the cliff: alpine cushion plants structure bacterial and fungal communities
Frontiers in microbiology, 2013
Plants affect the spatial distribution of soil microorganisms, but the influence of the local abiotic context is poorly documented. We investigated the effect of a single plant species, the cushion plant Silene acaulis, on habitat conditions, and microbial community. We collected soil from inside (In) and outside (Out) of the cushions on calcareous and siliceous cliffs in the French Alps along an elevation gradient (2,000-3,000 masl). The composition of the microbial communities was assessed by Capillary-Electrophoresis Single Strand Conformation Polymorphism (CE-SSCP). Univariate and multivariate analyses were conducted to characterize the response of the microbial beta-diversity to soil parameters (total C, total N, soil water content, N − NH + 4 , N − NO − 3 , and pH). Cushions affected the microbial communities, modifying soil properties. The fungal and bacterial communities did not respond to the same abiotic factors. Outside the cushions, the bacterial communities were strongly influenced by bedrock. Inside the cushions, the bacterial communities from both types of bedrock were highly similar, due to the smaller pH differences than in open areas. By contrast, the fungal communities were equally variable inside and outside of the cushions. Outside the cushions, the fungal communities responded weakly to soil pH. Inside the cushions, the fungal communities varied strongly with bedrock and elevation as well as increases in soil nutrients and water content. Furthermore, the dissimilarities in the microbial communities between the In and Out habitats increased with increasing habitat modification and environmental stress. Our results indicate that cushions act as a selective force that counteracts the influence of the bedrock and the resource limitations on the bacterial and fungal communities by buffering soil pH and enhancing soil nutrients. Cushion plants structure microbial communities, and this effect increases in stressful, acidic and nutrient-limited environments.
Mini-review Structure and function of alpine and arctic soil microbial communities
2005
Cultivation-independent molecular phylogenetic techniques are now widely employed to examine environmental microbial diversity; however, the relationship between microbial community structure and ecosystem function is unclear. This review synthesizes cultivation-independent views of microbiological diversity with our current understanding of nutrient dynamics in alpine and arctic soils. Recently, we have begun to explore connections between microbial community structure and function in soils from the alpine Niwot Ridge LTER site in Colorado, USA, whose ecology has been extensively investigated for over 50 years. We examined the diversity of bacterial, eucaryal, and archaeal small subunit rRNA genes in tundra and talus soils across seasons in the alpine. This work has provided support for spatial and seasonal shifts in specific microbial groups, which correlate well with previously documented transitions in microbial processes. In addition, these preliminary results suggest that the physiologies of certain groups of organisms may scale up to the ecosystem level, providing the basis for testable hypotheses about the function of specific microbes in this system. These studies have also expanded on the known diversity of life, as these soils harbor bacterial and eucaryotic lineages that are distantly related to other known organisms. In contrast to the alpine, microbial diversity in the arctic has been little explored; only three published studies have used molecular techniques to examine these soils. Because of the importance of these systems, particularly to the global C cycle, and their vulnerability to current and impending climate change, the microbial diversity of these soils needs to be further investigated. 2005 Elsevier SAS. All rights reserved.
Structure and function of alpine and arctic soil microbial communities
Research in Microbiology, 2005
Cultivation-independent molecular phylogenetic techniques are now widely employed to examine environmental microbial diversity; however, the relationship between microbial community structure and ecosystem function is unclear. This review synthesizes cultivationindependent views of microbiological diversity with our current understanding of nutrient dynamics in alpine and arctic soils. Recently, we have begun to explore connections between microbial community structure and function in soils from the alpine Niwot Ridge LTER site in Colorado, USA, whose ecology has been extensively investigated for over 50 years. We examined the diversity of bacterial, eucaryal, and archaeal small subunit rRNA genes in tundra and talus soils across seasons in the alpine. This work has provided support for spatial and seasonal shifts in specific microbial groups, which correlate well with previously documented transitions in microbial processes. In addition, these preliminary results suggest that the physiologies of certain groups of organisms may scale up to the ecosystem level, providing the basis for testable hypotheses about the function of specific microbes in this system. These studies have also expanded on the known diversity of life, as these soils harbor bacterial and eucaryotic lineages that are distantly related to other known organisms. In contrast to the alpine, microbial diversity in the arctic has been little explored; only three published studies have used molecular techniques to examine these soils. Because of the importance of these systems, particularly to the global C cycle, and their vulnerability to current and impending climate change, the microbial diversity of these soils needs to be further investigated. 2005 Elsevier SAS. All rights reserved.
Frontiers in Microbiology, 2013
Plants and soil microorganisms interact to play a central role in ecosystem functioning. To determine the potential importance of biotic interactions in shaping the distributions of these organisms in a high-alpine subnival landscape, we examine co-occurrence patterns between plant species and bulk soil bacteria abundances. In this context, a co-occurrence relationship reflects a combination of several assembly processes: that both parties can disperse to the site, that they can survive the abiotic environmental conditions, and that interactions between the biota either facilitate survival or allow for coexistence. Across the entire landscape, 31% of the bacterial sequences in this dataset were significantly correlated to the abundance distribution of one or more plant species. These sequences fell into 14 clades, 6 of which are related to bacteria that are known to form symbioses with plants in other systems. Abundant plant species were more likely to have significant as well as stronger correlations with bacteria and these patterns were more prevalent in lower altitude sites. Conversely, correlations between plant species abundances and bacterial relative abundances were less frequent in sites near the snowline. Thus, plant-bacteria associations became more common as environmental conditions became less harsh and plants became more abundant. This pattern in co-occurrence strength and frequency across the subnival landscape suggests that plant-bacteria interactions are important for the success of life, both below-and above-ground, in an extreme environment.
Frontiers in Microbiology, 2012
Plants and soil microorganisms interact to play a central role in ecosystem functioning. To determine the potential importance of biotic interactions in shaping the distributions of these organisms in a high-alpine subnival landscape, we examine co-occurrence patterns between plant species and bulk soil bacteria abundances. In this context, a co-occurrence relationship reflects a combination of several assembly processes: that both parties can disperse to the site, that they can survive the abiotic environmental conditions, and that interactions between the biota either facilitate survival or allow for coexistence. Across the entire landscape, 31% of the bacterial sequences in this dataset were significantly correlated to the abundance distribution of one or more plant species. These sequences fell into 14 clades, 6 of which are related to bacteria that are known to form symbioses with plants in other systems. Abundant plant species were more likely to have significant as well as stronger correlations with bacteria and these patterns were more prevalent in lower altitude sites. Conversely, correlations between plant species abundances and bacterial relative abundances were less frequent in sites near the snowline. Thus, plant-bacteria associations became more common as environmental conditions became less harsh and plants became more abundant. This pattern in co-occurrence strength and frequency across the subnival landscape suggests that plant-bacteria interactions are important for the success of life, both below-and above-ground, in an extreme environment.
Vegetation-Associated Impacts on Arctic Tundra Bacterial and Microeukaryotic Communities
Applied and Environmental Microbiology, 2014
The Arctic is experiencing rapid vegetation changes, such as shrub and tree line expansion, due to climate warming, as well as increased wetland variability due to hydrological changes associated with permafrost thawing. These changes are of global concern because changes in vegetation may increase tundra soil biogeochemical processes that would significantly enhance atmospheric CO 2 concentrations. Predicting the latter will at least partly depend on knowing the structure, functional activities, and distributions of soil microbes among the vegetation types across Arctic landscapes. Here we investigated the bacterial and microeukaryotic community structures in soils from the four principal low Arctic tundra vegetation types: wet sedge, birch hummock, tall birch, and dry heath. Sequencing of rRNA gene fragments indicated that the wet sedge and tall birch communities differed significantly from each other and from those associated with the other two dominant vegetation types. Distinct microbial communities were associated with soil pH, ammonium concentration, carbon/nitrogen (C/N) ratio, and moisture content. In soils with similar moisture contents and pHs (excluding wet sedge), bacterial, fungal, and total eukaryotic communities were correlated with the ammonium concentration, dissolved organic nitrogen (DON) content, and C/N ratio. Operational taxonomic unit (OTU) richness, Faith's phylogenetic diversity, and the Shannon species-level index (H=) were generally lower in the tall birch soil than in soil from the other vegetation types, with pH being strongly correlated with bacterial richness and Faith's phylogenetic diversity. Together, these results suggest that Arctic soil feedback responses to climate change will be vegetation specific not just because of distinctive substrates and environmental characteristics but also, potentially, because of inherent differences in microbial community structure. P. 2015.
Plant succession and rhizosphere microbial communities in a recently deglaciated alpine terrain
Basic and Applied Ecology, 2005
This study describes how early and late successional plant species affect soil microorganisms in alpine ecosystems. We quantify the relative importance of plant species and soil properties as determinants of belowground microbial communities. Sixteen plant species were selected from six successional stages (4-14-20-43-75-135 years) within the foreland of the Rotmoosferner glacier, Austria, and at one (reference) site outside the foreland. The size, composition and function of the communities of microorganism in the bulk soil and the rhizosphere were characterized by ninhydrin-reactive nitrogen, phospholipid fatty acids and enzyme activities (b-glucosidase, b-xylosidase, N-acetyl-b-glucosaminidase, leucine aminopeptidase, acid phosphatase, sulphatase). The results show that the microbial data could be grouped according to early (up to 43 years) and late-colonizing plant species (75 or more years). In early succession, no plant species or soil age effect was detected on the microbial biomass, phospholipid fatty acids, or enzyme activity. The rhizosphere microbial community was similar to that in the bulk soil, which in turn was determined by the abiotic environmental conditions. In late succession, improved soil conditions probably mediated plant species effects on the belowground microbial community. The most pronounced rhizosphere effects were attributed to plant species of the 75and 135-year-old sites. The microbial colonization (size, composition, activity) of the bulk soil predominantly followed changes in vegetation cover, plant life forms and soil ARTICLE IN PRESS www.elsevier.de/baae (D. Tscherko). organic matter. In summary, the observed successional pattern of the above-and belowground communities provides an example of the facilitation models of primary succession.
Microbial diversity in alpine tundra soils correlates with snow cover dynamics
The ISME Journal, 2009
The temporal and spatial snow cover dynamics is the primary factor controlling the plant communities' composition and biogeochemical cycles in arctic and alpine tundra. However, the relationships between the distribution of snow and the diversity of soil microbial communities remain largely unexplored. Over a period of 2 years, we monitored soil microbial communities at three sites, including contiguous alpine meadows of late and early snowmelt locations (LSM and ESM, respectively). Bacterial and fungal communities were characterized by using molecular fingerprinting and cloning/sequencing of microbial ribosomal DNA extracted from the soil. Herein, we show that the spatial and temporal distribution of snow strongly correlates with microbial community composition. High seasonal contrast in ESM is associated with marked seasonal shifts for bacterial communities; whereas less contrasted seasons because of long-lasting snowpack in LSM is associated with increased fungal diversity. Finally, our results indicate that, similar to plant communities, microbial communities exhibit important shifts in composition at two extremes of the snow cover gradient. However, winter conditions lead to the convergence of microbial communities independently of snow cover presence. This study provides new insights into the distribution of microbial communities in alpine tundra in relation to snow cover dynamics, and may be helpful in predicting the future of microbial communities and biogeochemical cycles in arctic and alpine tundra in the context of a warmer climate.