Late-successional biological soil crusts in a biodiversity hotspot: an example of congruency in species richness

Understanding the biodiversity of functionally important communities in Earth’s ecosystems is vital in the apportionment of limited ecosystem management funds and efforts. In southern California shrublands, which lie in a global biodiversity hotspot, biological soil crusts (BSCs) confer critical ecosystem services; however, their biodiversity remains unknown. In this study, six sites (n = 4 each, 25 m²) were established along a mediterranean shrubland environmental gradient in southern California. Here, the biodiversity of all BSC-forming lichens and bryophytes was evaluated, related to environmental traits along the gradient, and compared to species richness among North American ecosystems supporting BSCs (data from previous studies). In total, 59 BSC-forming lichens and bryophytes were observed, including the very rare Sarcogyne crustacea, a rare moss, and five endemic lichen species. Over half (61%) of the species observed were found at a single site. Along the gradient, species evenness of late-successional BSC was related to dew point and elevation, and both evenness and richness were related to distance to coast. Using an ordination analysis, five distinct late-successional BSC communities were identified: Riversidian, Spike moss, Casperian, Alisian, and Lagunian. Twenty-five lichens and 19 bryophytes are newly reported for North American BSC-forming organisms, now comprising ~1/2 of the North American total. BSCs in North American hot and cold deserts were approximately 4.0 and 2.4 times less species rich than BSCs found in southern California shrublands, respectively. Given the anthropogenic impacts on quality and distribution of California mediterranean shrublands, our results show that these sites represent important refugia of BSC species in this globally important region.     

Niche partitioning of bacterial communities in biological crusts and soils under grasses,shrubs and trees in the Kalahari

The Kalahari of southern Africa is characterised by sparse vegetation interspersed with microbe-dominated biological soil crusts (BSC) which deliver a range of ecosystem services including soil stabilisation and carbon fixation. We characterised the bacterial communities of BSCs (0–1 cm depth) and the subsurface soil (1–2 cm depth) in an area typical of lightly grazed Kalahari rangelands, composed of grasses, shrubs, and trees. Our data add substantially to the limited amount of existing knowledge concerning BSC microbial community structure, by providing the first bacterial community analyses of both BSCs and subsurface soils of the Kalahari region based on a high throughput 16S ribosomal RNA gene sequencing approach. BSC bacterial communities were distinct with respect to vegetation type and soil depth, and varied in relation to soil carbon, nitrogen, and surface temperature. Cyanobacteria were predominant in the grass interspaces at the soil surface (0–1 cm) but rare in subsurface soils (1–2 cm depth) and under the shrubs and trees. Bacteroidetes were significantly more abundant in surface soils of all areas even in the absence of a consolidated crust, whilst subsurface soils yielded more sequences affiliated to Acidobacteria, Actinobacteria, Chloroflexi, and Firmicutes. The common detection of vertical stratification, even in disturbed sites, suggests a strong potential for BSC recovery after physical disruption, however severe depletion of Cyanobacteria near trees and shrubs may limit the potential for natural BSC regeneration in heavily shrub-encroached areas.     

A Three-Scale Analysis of Bacterial Communities Involved in Rocks Colonization and Soil Formation in High Mountain Environments

Alpha and beta diversities of the bacterial communities growing on rock surfaces, proto-soils, riparian sediments, lichen thalli, and water springs biofilms in a glacier foreland were studied. We used three molecular based techniques to allow a deeper investigation at different taxonomic resolutions: denaturing gradient gel electrophoresis, length heterogeneity-PCR, and automated ribosomal intergenic spacer analysis. Bacterial communities were mainly composed of Acidobacteria, Proteobacteria, and Cyanobacteria with distinct variations among sites. Proteobacteria were more represented in sediments, biofilms, and lichens; Acidobacteria were mostly found in proto-soils; and Cyanobacteria on rocks. Firmicutes and Bacteroidetes were mainly found in biofilms. UniFrac P values confirmed a significant difference among different matrices. Significant differences (P < 0.001) in beta diversity were observed among the different matrices at the genus–species level, except for lichens and rocks which shared a more similar community structure, while at deep taxonomic resolution two distinct bacterial communities between lichens and rocks were found.     

Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land,Antarctica

Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment.     

Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils

Background

Soil bacteria are important drivers for nearly all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil. In contrast to the importance of soil bacteria for ecosystem functioning, we understand little how different management types affect the soil bacterial community composition.

Methodology/Principal Findings

We used pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to identify changes in bacterial diversity and community structure in nine forest and nine grassland soils from the Schwäbische Alb that covered six different management types. The dataset comprised 598,962 sequences that were affiliated to the domain Bacteria. The number of classified sequences per sample ranged from 23,515 to 39,259. Bacterial diversity was more phylum rich in grassland soils than in forest soils. The dominant taxonomic groups across all samples (>1% of all sequences) were Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Firmicutes. Significant variations in relative abundances of bacterial phyla and proteobacterial classes, including Actinobacteria, Firmicutes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes and Alphaproteobacteria, between the land use types forest and grassland were observed. At the genus level, significant differences were also recorded for the dominant genera Phenylobacter, Bacillus, Kribbella, Streptomyces, Agromyces, and Defluviicoccus. In addition, soil bacterial community structure showed significant differences between beech and spruce forest soils. The relative abundances of bacterial groups at different taxonomic levels correlated with soil pH, but little or no relationships to management type and other soil properties were found.

Conclusions/Significance

Soil bacterial community composition and diversity of the six analyzed management types showed significant differences between the land use types grassland and forest. Furthermore, bacterial community structure was largely driven by tree species and soil pH.     

Community Assembly of Biological Soil Crusts of Different Successional Stages in a Temperate Sand Ecosystem, as Assessed by Direct Determination and Enrichment Techniques

In temperate regions, biological soil crusts (BSCs: complex communities of cyanobacteria, eukaryotic algae, bryophytes, and lichens) are not well investigated regarding community structure and diversity. Furthermore, studies on succession are rare. For that reason, the community assembly of crusts representing two successional stages (initial, 5 years old; and stable, >20 years old) were analyzed in an inland sand ecosystem in Germany in a plot-based approach (2 × 18 plots, each 20 × 20 cm). Two different methods were used to record the cyanobacteria and eukaryotic algae in these communities comprehensively: determination directly out of the soil and enrichment culture techniques. Additionally, lichens, bryophytes, and phanerogams were determined. We examine four hypotheses: (1) A combination of direct determination and enrichment culture technique is necessary to detect cyanobacteria and eukaryotic algae comprehensively. In total, 45 species of cyanobacteria and eukaryotic algae were detected in the study area with both techniques, including 26 eukaryotic algae and 19 cyanobacteria species. With both determination techniques, 22 identical taxa were detected (11 eukaryotic algae and 11 cyanobacteria). Thirteen taxa were only found by direct determination, and ten taxa were only found in enrichment cultures. Hence, the hypothesis is supported. Additionally, five lichen species (three genera), five bryophyte species (five genera), and 24 vascular plant species occurred. (2) There is a clear difference between the floristic structure of initial and stable crusts. The different successional stages are clearly separated by detrended correspondence analysis, showing a distinct structure of the community assembly in each stage. In the initial crusts, Klebsormidium flaccidum, Klebsormidium cf. klebsii, and Stichococcus bacillaris were important indicator species, whereas the stable crusts are especially characterized by Tortella inclinata. (3) The biodiversity of BSC taxa and vascular plant species increases from initial to stable BSCs. There are significantly higher genera and species numbers of cyanobacteria and eukaryotic algae in initial BSCs. Stable BSCs are characterized by significantly higher species numbers of bryophytes and vascular plant species. The results show that, in the investigated temperate region, the often-assumed increase of biodiversity in the course of succession is clearly taxa-dependent. Both successional stages of BSCs are diversity “hot spots” with about 29 species of all taxa per 20 × 20 cm plot. (4) Nitrogen and chlorophyll a concentrations increase in the course of succession. The chlorophyll a content of the crusts (cyanobacteria, eukaryotic algae, bryophyte protonemata) is highly variable across the studied samples, with no significant differences between initial and stable BSCs; nor were ecologically significant differences in soil nutrient contents observed. According to our results, we cannot confirm this hypothesis; the age difference between our two stages is probably not big enough to show such an increase. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Diurnal variations of chlorophyll fluorescence and CO2 exchange of biological soil crusts in different successional stages in the Gurbantunggut Desert of northwestern China

Biological soil crusts (BSCs) formed by different combinations of photosynthetic algae, cyanobacteria, lichens and mosses are well-developed in the Gurbantunggut Desert of northwestern China. To investigate the different responses of BSCs to environmental factors, the diurnal variations of chlorophyll fluorescence and CO₂ exchange of BSCs in different successional stages were measured following artificial rehydration in the field. Results showed that the maximum potential quantum efficiency of PSII (F _v/F _m), the actual PSII efficiency (Φ_PSII) and the relative rate of electron transport as well as net photosynthesis of the different successional BSCs varied similarly and changed markedly with diurnal fluctuations in light and temperature. Further analyses indicated that CO₂ exchange and photosynthetic pigment content of chlorophyll (Chl) a, Chl b and carotenoids increased with the developmental level of BSCs, from cyanobacterial crust to lichen crust to moss crust. The differences in responses of BSCs to environmental factors and photosynthetic pigment content may be partially attributed to differences in species composition and morphological characteristics of the various BSCs. Overall, moss crust is better adapted to a wide range of irradiance and higher temperatures than lichen and cyanobacterial crusts. Therefore, BSCs in a later successional stage are expected to play a more important role in desertification control than those of the earlier stages.     

Response and resilience of soil biocrust bacterial communities to chronic physical disturbance in arid shrublands

The impact of 10 years of annual foot trampling on soil biocrusts was examined in replicated field experiments at three cold desert sites of the Colorado Plateau, USA. Trampling detrimentally impacted lichens and mosses, and the keystone cyanobacterium, Microcoleus vaginatus, resulting in increased soil erosion and reduced C and N concentrations in surface soils. Trampled biocrusts contained approximately half as much extractable DNA and 20–52% less chlorophyll a when compared with intact biocrusts at each site. Two of the three sites also showed a decline in scytonemin-containing, diazotrophic cyanobacteria in trampled biocrusts. 16S rRNA gene sequence and terminal restriction fragment length polymorphism (T-RFLP) analyses of soil bacteria from untrampled and trampled biocrusts demonstrated a reduced proportion (23–65% reduction) of M. vaginatus and other Cyanobacteria in trampled plots. In parallel, other soil bacterial species that are natural residents of biocrusts, specifically members of the Actinobacteria, Chloroflexi and Bacteroidetes, became more readily detected in trampled than in untrampled biocrusts. Replicate 16S rRNA T-RFLP profiles from trampled biocrusts at all three sites contained significantly more fragments (n=17) than those of untrampled biocrusts (n⩽6) and exhibited much higher variability among field replicates, indicating transition to an unstable disturbed state. Despite the dramatic negative impacts of trampling on biocrust physical structure and composition, M. vaginatus could still be detected in surface soils after 10 years of annual trampling, suggesting the potential for biocrust re-formation over time. Physical damage of biocrusts, in concert with changing temperature and precipitation patterns, has potential to alter performance of dryland ecosystems for decades.     

Impact of grazing intensity on seasonal variations in soil organic carbon and soil CO2 efflux in two semiarid grasslands in southern Botswana

Biological soil crusts (BSCs) are an important source of organic carbon, and affect a range of ecosystem functions in arid and semiarid environments. Yet the impact of grazing disturbance on crust properties and soil CO₂ efflux remain poorly studied, particularly in African ecosystems. The effects of burial under wind-blown sand, disaggregation and removal of BSCs on seasonal variations in soil CO₂ efflux, soil organic carbon, chlorophyll a and scytonemin were investigated at two sites in the Kalahari of southern Botswana. Field experiments were employed to isolate CO₂ efflux originating from BSCs in order to estimate the C exchange within the crust. Organic carbon was not evenly distributed through the soil profile but concentrated in the BSC. Soil CO₂ efflux was higher in Kalahari Sand than in calcrete soils, but rates varied significantly with seasonal changes in moisture and temperature. BSCs at both sites were a small net sink of C to the soil. Soil CO₂ efflux was significantly higher in sand soils where the BSC was removed, and on calcrete where the BSC was buried under sand. The BSC removal and burial under sand also significantly reduced chlorophyll a, organic carbon and scytonemin. Disaggregation of the soil crust, however, led to increases in chlorophyll a and organic carbon. The data confirm the importance of BSCs for C cycling in drylands and indicate intensive grazing, which destroys BSCs through trampling and burial, will adversely affect C sequestration and storage. Managed grazing, where soil surfaces are only lightly disturbed, would help maintain a positive carbon balance in African drylands.     

Biological soil crusts increase the resistance of soil nitrogen dynamics to changes in temperatures in a semi-arid ecosystem

Aims

Biological soil crusts (BSCs), composed of mosses, lichens, liverworts and cyanobacteria, are a key component of arid and semi-arid ecosystems worldwide, and play key roles modulating several aspects of the nitrogen (N) cycle, such as N fixation and mineralization. While the performance of its constituent organisms largely depends on moisture and rainfall conditions, the influence of these environmental factors on N transformations under BSC soils has not been evaluated before.

Methods

The study was done using soils collected from areas devoid of vascular plants with and without lichen-dominated BSCs from a semi-arid Stipa tenacissima grassland. Soil samples were incubated under different temperature (T) and soil water content (SWC) conditions, and changes in microbial biomass-N, dissolved organic nitrogen (DON), amino acids, ammonium, nitrate and both inorganic N were monitored. To evaluate how BSCs modulate the resistance of the soil to changes in T and SWC, we estimated the Orwin and Wardle Resistance index.

Results

The different variables studied were more affected by changes in T than by variations in SWC at both BSC-dominated and bare ground soils. However, under BSCs, a change in the dominance of N processes from a net nitrification to a net ammonification was observed at the highest SWC, regardless of T.

Conclusions

Our results suggest that the N cycle is more resistant to changes in T in BSC-dominated than in bare ground areas. They also indicate that BSCs could play a key role in minimizing the likely impacts of climate change on the dynamics of N in semi-arid environments, given the prevalence and cover of these organisms worldwide.     

Plant Interactions with Changes in Coverage of Biological Soil Crusts and Water Regime in Mu Us Sandland,China

Plant interactions greatly affect plant community structure. Dryland ecosystems are characterized by low amounts of unpredictable precipitation as well as by often having biological soil crusts (BSCs) on the soil surface. In dryland plant communities, plants interact mostly as they compete for water resources, and the direction and intensity of plant interaction varies as a function of the temporal fluctuation in water availability. Since BSCs influence water redistribution to some extent, a greenhouse experiment was conducted to test the hypothesis that the intensity and direction of plant interactions in a dryland plant community can be modified by BSCs. In the experiment, 14 combinations of four plant species (Artemisia ordosica, Artemisia sphaerocephala, Chloris virgata and Setaria viridis) were subjected to three levels of coverage of BSCs and three levels of water supply. The results show that: 1) BSCs affected plant interaction intensity for the four plant species: a 100% coverage of BSCs significantly reduced the intensity of competition between neighboring plants, while it was highest with a 50% coverage of BSCs in combination with the target species of A. sphaerocephala and C. virgata; 2) effects of the coverage of BSCs on plant interactions were modified by water regime when the target species were C. virgata and S. viridis; 3) plant interactions were species-specific. In conclusion, the percent coverage of BSCs affected plant interactions, and the effects were species-specific and could be modified by water regimes. Further studies should focus on effects of the coverage of BSCs on plant-soil hydrological processes.     

Vertical profiles of microbial communities in perfluoroalkyl substance-contaminated soils

Poly- and perfluoroalkyl compounds (PFASs) are ubiquitous in the environment, but their influences on microbial community remain poorly known. The present study investigated the depth-related changes of archaeal and bacterial communities in PFAS-contaminated soils. The abundance and structure of microbial community were characterized using quantitative PCR and high-throughput sequencing, respectively. Microbial abundance changed considerably with soil depth. The richness and diversity of both bacterial and archaeal communities increased with soil depth. At each depth, bacterial community was more abundant and had higher richness and diversity than archaeal community. The structure of either bacterial or archaeal community displayed distinct vertical variations. Moreover, a higher content of perfluorooctane sulfonate (PFOS) could have a negative impact on bacterial richness and diversity. The rise of soil organic carbon content could increase bacterial abundance but lower the richness and diversity of both bacterial and archaeal communities. In addition, Proteobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, and Acidobacteria were the major bacterial groups, while Thaumarchaeota, Euryarchaeota, and unclassified Archaea dominated in soil archaeal communities. PFASs could influence soil microbial community.     

Yeast population of the Kindo Peninsula lichens

Yeast abundance and species diversity in the lichens collected at the Kindo Peninsula (Karelia) were studied. A total of 14 lichen species analyzed belonged to the genera Bryoria, Cladonia, Hypogymnia, Icmadophila, Nephroma, Peltigera, and Ramalina. Abundance of cultured yeasts in lichens was intermediate between soil and phyllosphere. The average yeast number on lichens was ~2.5 × 10³ CFU/g, while it exceeded 8 × 10³ CFU/g on plants and reached only 1 × 10³ CFU/g in soil. Yeast population of different parts of Cladonia lichens was found to vary significantly in abundance, species diversity, and community structure. The highest yeast abundance and diversity were revealed in the growth zone. Fifteen yeast species were isolated from lichens, including 6 basidiomycetous and 9 ascomycetous ones. Unlike soils and plants, yeast population of lichens consisted mainly of ascomycetous species, with predominance of Candida sphagnicola and anamorphous yeasts of the genus Dothiora. These results show that yeasts from different taxonomic and ecological groups are a necessary component of lichens; conditions favoring the preservation and development of specific yeast communities differing from the typical soil and phyllosphere yeast complexes are formed in the lichens of northern taiga forests.     

Improved appreciation of the functioning and importance of biological soil crusts in Europe: the Soil Crust International Project (SCIN)

Here we report details of the European research initiative “Soil Crust International” (SCIN) focusing on the biodiversity of biological soil crusts (BSC, composed of bacteria, algae, lichens, and bryophytes) and on functional aspects in their specific environment. Known as the so-called “colored soil lichen community” (Bunte Erdflechtengesellschaft), these BSCs occur all over Europe, extending into subtropical and arid regions. Our goal is to study the uniqueness of these BSCs on the regional scale and investigate how this community can cope with large macroclimatic differences. One of the major aims of this project is to develop biodiversity conservation and sustainable management strategies for European BSCs. To achieve this, we established a latitudinal transect from the Great Alvar of Öland, Sweden in the north over Gössenheim, Central Germany and Hochtor in the Hohe Tauern National Park, Austria down to the badlands of Tabernas, Spain in the south. The transect stretches over 20° latitude and 2,300 m in altitude, including natural (Hochtor, Tabernas) and semi-natural sites that require maintenance such as by grazing activities (Öland, Gössenheim). At all four sites BSC coverage exceeded 30 % of the referring landscape, with the alpine site (Hochtor) reaching the highest cyanobacterial cover and the two semi-natural sites (Öland, Gössenheim) the highest bryophyte cover. Although BSCs of the four European sites share a common set of bacteria, algae (including cyanobacteria) lichens and bryophytes, first results indicate not only climate specific additions of species, but also genetic/phenotypic uniqueness of species between the four sites. While macroclimatic conditions are rather different, microclimatic conditions and partly soil properties seem fairly homogeneous between the four sites, with the exception of water availability. Continuous activity monitoring of photosystem II revealed the BSCs of the Spanish site as the least active in terms of photosynthetic active periods.     

Bacterial Community Responses to Soils along a Latitudinal and Vegetation Gradient on the Loess Plateau,China

Soil bacterial communities play an important role in nutrient recycling and storage in terrestrial ecosystems. Loess soils are one of the most important soil resources for maintaining the stability of vegetation ecosystems and are mainly distributed in northwest China. Estimating the distributions and affecting factors of soil bacterial communities associated with various types of vegetation will inform our understanding of the effect of vegetation restoration and climate change on these processes. In this study, we collected soil samples from 15 sites from north to south on the Loess Plateau of China that represent different ecosystem types and analyzed the distributions of soil bacterial communities by high-throughput 454 pyrosequencing. The results showed that the 142444 sequences were grouped into 36816 operational taxonomic units (OTUs) based on 97% similarity. The results of the analysis showed that the dominant taxonomic phyla observed in all samples were Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria and Planctomycetes. Actinobacteria and Proteobacteria were the two most abundant groups in all samples. The relative abundance of Actinobacteria increased from 14.73% to 40.22% as the ecosystem changed from forest to sandy, while the relative abundance of Proteobacteria decreased from 35.35% to 21.40%. Actinobacteria and Proteobacteria had significant correlations with mean annual precipitation (MAP), pH, and soil moisture and nutrients. MAP was significantly correlated with soil chemical and physical properties. The relative abundance of Actinobacteria, Proteobacteria and Planctomycetes correlated significantly with MAP, suggesting that MAP was a key factor that affected the soil bacterial community composition. However, along with the MAP gradient, Chloroflexi, Bacteroidetes and Cyanobacteria had narrow ranges that did not significantly vary with the soil and environmental factors. Overall, we conclude that the edaphic properties and/or vegetation types are driving bacterial community composition. MAP was a key factor that affects the composition of the soil bacteria on the Loess Plateau of China.     

Changes in the bacterial populations of the highly alkaline saline soil of the former lake Texcoco (Mexico) following flooding

Flooding an extreme alkaline-saline soil decreased alkalinity and salinity, which will change the bacterial populations. Bacterial 16S rDNA libraries were generated of three soils with different electrolytic conductivity (EC), i.e. soil with EC 1.7 dS m⁻¹ and pH 7.80 (LOW soil), with EC 56 dS m⁻¹ and pH 10.11 (MEDIUM soil) and with EC 159 dS m⁻¹ and pH 10.02 (HIGH soil), using universal bacterial oligonucleotide primers, and 463 clone 16S rDNA sequences were analyzed phylogenetically. Library proportions and clone identification of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Firmicutes and Cloroflexi showed that the bacterial communities were different. Species and genera of the Rhizobiales, Rhodobacterales and Xanthomonadales orders of the α- and γ-subdivision of Proteobacteria were found at the three sites. Species and genera of the Rhodospirillales, Sphingobacteriales, Clostridiales, Oscillatoriales and Caldilineales were found only in the HIGH soil, Sphingomonadales, Burkholderiales and Pseudomonadales in the MEDIUM soil, Myxococcales in the LOW soil, and Actinomycetales in the MEDIUM and LOW soils. It was found that the largest diversity at the order and species level was found in the MEDIUM soil as bacteria of both the HIGH and LOW soils were found in it.     

Bacterial,Archaeal and Fungal Succession in the Forefield of a Receding Glacier

Glacier forefield chronosequences, initially composed of barren substrate after glacier retreat, are ideal locations to study primary microbial colonization and succession in a natural environment. We characterized the structure and composition of bacterial, archaeal and fungal communities in exposed rock substrates along the Damma glacier forefield in central Switzerland. Soil samples were taken along the forefield from sites ranging from fine granite sand devoid of vegetation near the glacier terminus to well-developed soils covered with vegetation. The microbial communities were studied with genetic profiling (T-RFLP) and sequencing of clone libraries. According to the T-RFLP profiles, bacteria showed a high Shannon diversity index (H) (ranging from 2.3 to 3.4) with no trend along the forefield. The major bacterial lineages were Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Cyanobacteria. An interesting finding was that Euryarchaeota were predominantly colonizing young soils and Crenarchaeota mainly mature soils. Fungi shifted from an Ascomycota-dominated community in young soils to a more Basidiomycota-dominated community in old soils. Redundancy analysis indicated that base saturation, pH, soil C and N contents and plant coverage, all related to soil age, correlated with the microbial succession along the forefield.     

Progressive and retrogressive ecosystem development coincide with soil bacterial community change in a dune system under lowland temperate rainforest in New Zealand

Background

It is established that plant communities show patterns of change linked to progressive and retrogressive stages of ecosystem development. It is not known, however, whether bacterial communities also show similar patterns of change associated with long-term ecosystem development.

Methods

We studied soil bacterial communities along a 6,500 year dune chronosequence under lowland temperate rain forest at Haast, New Zealand. Pyrosequencing of 16S rRNA genes was used to observe structural change in bacterial communities during the process of pedogenesis and ecosystem development.

Results

Bacterial communities showed patterns of change during pedogenesis, with the largest change during the first several hundred years after dune stabilization. The most abundant bacterial taxa were Alphaproteobacteria, Actinobacteria and Acidobacteria. These include taxa most closely related to nitrogen-fixing bacteria, and suggest heterotrophic nitrogen input may be important throughout the chronosequence. Changes in bacterial community structure were related to changes in several soil properties, including total phosphorus, C:N ratio, and pH. The Bacteroidetes, Actinobacteria, Cyanobacteria, Firmicutes, and Betaproteobacteria all showed a general decline in abundance as pedogenesis proceeded, while Acidobacteria, Alphaproteobacteria, and Plantctomycetes tended to increase as soils aged.

Conclusions

There were trends in the dynamics of bacterial community composition and structure in soil during ecosystem development. Bacterial communities changed in ways that appear to be consistent with a model of ecosystem progression and retrogression, perhaps indicating fundamental processes underpin patterns of below and above-ground community change during ecosystem development.     

Shifting Species Interaction in Soil Microbial Community and Its Influence on Ecosystem Functions Modulating

The supportive and negative evidence for the stress gradient hypothesis (SGH) led to an ongoing debate among ecologists and called for new empirical and theoretical work. In this study, we took various biological soil crust (BSCs) samples along a spatial gradient with four environmental stress levels to examine the fitness of SGH in microbial interactions and evaluate its influence on biodiversity–function relationships in BSCs. A new assessment method of species interactions within hard-cultured invisible soil community was employed, directly based on denaturing gradient gel electrophoresis fingerprint images. The results showed that biotic interactions in soil phototroph community dramatically shifted from facilitation to dominant competition with the improvement of microhabitats. It offered new evidence, which presented a different perspective on the hypothesis that the relative importance of facilitation and competition varies inversely along the gradient of abiotic stress. The path analysis indicated that influence of biotic interactions (r?=?0.19, p?<?0.05) on ecosystem functions is lower than other community properties (r?=?0.62, p?<?0.001), including soil moisture, crust coverage, and biodiversity. Furthermore, the correlation between species interactions and community properties was non-significant with low negative influence (r?=??0.27, p?>?0.05). We demonstrate that the inversion of biotic interaction as a response to the gradient of abiotic stresses existed not only in the visible plant community but also in the soil microbial community.     

Genotypic and Phenotypic Diversity of Cyanobacteria in Biological Soil Crusts of the Succulent Karoo and Nama Karoo of Southern Africa

Biological soil crusts (BSCs) are communities of cryptogamic organisms, occurring in arid and semiarid regions all over the world. Based on both morphological identification and genetic analyses, we established a first cyanobacterial inventory using the biphasic approach for BSCs within two major biomes of southern Africa. The samples were collected at two different sites in the Succulent Karoo and one in the Nama Karoo. After cultivation and morphological identification, the 16S rRNA gene was sequenced from the cyanobacterial cultures. From the soil samples, the DNA was extracted, and the 16S rRNA gene sequenced. All the sequences of the clone libraries from soil and cultures were compared with those of the public databases. Forty-five different species were morphologically identified in the samples of the Succulent Karoo (observatories of Soebatsfontein and Goedehoop). Based on the genetic analyses, 60 operational taxonomic units (OTUs) were identified for the Succulent Karoo and 43 for the Nama Karoo (based on 95 % sequence similarity). The cloned sequences corresponded well with the morphologically described taxa in cultures and sequences in the public databases. Besides known species of typical crust-forming cyanobacterial genera (Microcoleus, Phormidium, Tolypothrix and Scytonema), we found sequences of so far undescribed species of the genera Leptolyngbya, Pseudanabaena, Phormidium, Oscillatoria, Schizothrix and Microcoleus. Most OTUs were restricted to distinct sites. Grazed soils showed lower taxa numbers than undisturbed soils, implying the presence of early successional crust types and reduced soil surface protection. Our combined approach of morphological identification and genetic analyses allowed both a taxa inventory and the analysis of species occurring under specific habitat conditions.