Effects of agronomical measures on the microbial diversity of soils as related to the suppression of soil-borne plant pathogens

The diversity of soil microbial communities can be key to the capacity of soils tosuppress soil-borne plant diseases. As agricultural practice, as well as directedagronomical measures, are known to be able to affect soil microbial diversity, it isplausible that the soil microflora can be geared towards a greater suppressivity ofsoil-borne diseases as a result of the selection of suitable soil management regimes.In the context of a programme aimed at investigating the microbial diversity of soilsunder different agricultural regimes, including permanent grassland versus arableland under agricultural rotation, we assessed how soil microbial diversity is affectedin relation to the suppression of the soil-borne potato pathogen Rhizoctoniasolani AG3. The diversity in the microbial communities over about a growingseason was described by using cultivation-based – plating on different media – and cultivation-independent – soil DNA-based PCR followed by denaturing gradient gel electrophoresis (DGGE) community fingerprinting – methods. The results showed great diversity in the soil microbiota at both the culturable and cultivation-independent detection levels. Using cultivation methods, various differences between treatments with respect to sizes of bacterial and fungal populations were detected, with highest population sizes generally found in rhizospheres. In addition, the evenness of eco-physiologically differing bacterial types was higher in grassland than in arable land under rotation. At the cultivation-independent level, clear differences in the diversities of several microbial groups between permanent grassland and arable land under rotation were apparent. Bio-assays that assessed the growth of R. solani AG3 hyphae through soil indicated a greater growth suppression in grassland than in arable land soils. Similarly, an experiment performed in the glasshouse showed clear differences in both microbial diversities and suppressiveness of R. solani growth in soil, depending on the presence of either maizeor oats as the crop. The significance of these findings for designing soil managementstrategies is discussed.     

The prokaryotic diversity of biological soil crusts in the Sonoran Desert (Organ Pipe Cactus National Monument, AZ)

We studied prokaryotic community structure and composition in biological soil crusts (BSCs) from the Sonoran Desert, and their variability over space and time, using statistically analyzed, PCR-based molecular surveys of environmental 16S rRNA genes. Four sites, tens of km apart, were sampled, 3 times over a 1 year period, collecting 10 duplicate samples every 50 m in each site. Denaturing gradient gel electrophoresis (DGGE) revealed communities much less diverse than those of typical soil assemblages, displaying dominance of some bacterial types. No differences in crust microbial diversity or composition were detected between crusts under plant canopies and those in plant interspaces, indicating a likely crust independence from higher plant resources. However, statistically significant variability with space and time could be detected, and samples within a site were more similar than samples between sites. Both temporal and spatial variability in community composition involved non-dominant members of the community. Extensive sequencing and phylogenetic analysis revealed a large array of bacterial types, many novel. The most common included members of Cyanobacteria, Proteobacteria, Actinobacteria and Acidobacteria. Bacteriodetes, Chloroflexi and Gemmatimonadetes were not seen in high numbers, but were present in all sites, and Deinococci were also detected. Archaea were present, but as minor components. Sonoran BSC communities were distinct in rough compositional character from those in bulk arid soils or agricultural soils, and contained reoccurring, uncultured microbes.     

Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China

The long-term application of excessive chemical fertilizers has resulted in the degeneration of soil quality parameters such as soil microbial biomass, communities, and nutrient content, which in turn affects crop health, productivity, and soil sustainable productivity. The objective of this study was to develop a rapid and efficient solution for rehabilitating degraded cropland soils by precisely quantifying soil quality parameters through the application of manure compost and bacteria fertilizers or its combination during maize growth. We investigated dynamic impacts on soil microbial count, biomass, basal respiration, community structure diversity, and enzyme activity using six different treatments [no fertilizer (CK), N fertilizer (N), N fertilizer + bacterial fertilizer (NB), manure compost (M), manure compost + bacterial fertilizer (MB), and bacterial fertilizer (B)] in the plowed layer (0–20 cm) of potted soil during various maize growth stages in a temperate cropland of eastern China. Denaturing gradient electrophoresis (DGGE) fingerprinting analysis showed that the structure and composition of bacterial and fungi communities in the six fertilizer treatments varied at different levels. The Shannon index of bacterial and fungi communities displayed the highest value in the MB treatments and the lowest in the N treatment at the maize mature stage. Changes in soil microorganism community structure and diversity after different fertilizer treatments resulted in different microbial properties. Adding manure compost significantly increased the amount of cultivable microorganisms and microbial biomass, thus enhancing soil respiration and enzyme activities (p<0.01), whereas N treatment showed the opposite results (p<0.01). However, B and NB treatments minimally increased the amount of cultivable microorganisms and microbial biomass, with no obvious influence on community structure and soil enzymes. Our findings indicate that the application of manure compost plus bacterial fertilizers can immediately improve the microbial community structure and diversity of degraded cropland soils.     

Species Composition of Bacterial Communities Influences Attraction of Mosquitoes to Experimental Plant Infusions

In the container habitats of immature mosquitoes, catabolism of plant matter and other organic detritus by microbial organisms produces metabolites that mediate the oviposition behavior of Aedes aegypti and Aedes albopictus. Public health agencies commonly use oviposition traps containing plant infusions for monitoring populations of these mosquito species, which are global vectors of dengue viruses. In laboratory experiments, gravid females exhibited significantly diminished responses to experimental infusions made with sterilized white oak leaves, showing that attractive odorants were produced through microbial metabolic activity. We evaluated effects of infusion concentration and fermentation time on attraction of gravid females to infusions made from senescent bamboo or white oak leaves. We used plate counts of heterotrophic bacteria, total counts of 4′,6-diamidino-2-phenylindole-stained bacterial cells, and 16S ribosomal DNA (rDNA) polymerase chain reaction–denaturing gradient gel electrophoresis (DGGE) to show that changes in the relative abundance of bacteria and the species composition of bacterial communities influenced attraction of gravid A. aegypti and A. albopictus mosquitoes to infusions. DGGE profiles showed that bacterial species composition in infusions changed over time. Principal components analysis indicated that oviposition responses to plant infusions were in general most affected by bacterial diversity and abundance. Analysis of bacterial 16S rDNA sequences derived from DGGE bands revealed that Proteobacteria (Alpha-, Beta-, Delta-, and Gamma-) were the predominant bacteria detected in both types of plant infusions. Gravid A. aegypti were significantly attracted to a mix of 14 bacterial species cultured from bamboo leaf infusion. The oviposition response of gravid mosquitoes to plant infusions is strongly influenced by abundance and diversity of bacterial species, which in turn is affected by plant species, leaf biomass, and fermentation time.     

不同施肥制度土壤微生物量碳氮变化及细菌群落16S rDNA V3 片段PCR产物的DGGE分析

应用化学分析和变性梯度凝胶电泳（DGGE）技术分离PCR扩增的16S rDNA的方法,研究了不同施肥制度对土壤微生物量碳、氮变化及微生物多样性的影响。结果表明,连续15a长期试验下,土壤微生物量碳（SMB-C）和微生物量氮（SMB-N）的含量大小均为长期撂荒（CK0）土壤高于农田土壤,而在农田土壤中,长期施肥的处理（NPK、NPKM、NPKSt和NPKF）高于长期不施肥处理（CK）,不同的种植制度中,长期复种轮作（NPKF）高于长期复种连作（NPK）;各处理的SMB-C/SOC（土壤有机碳）和SMB-N/TN（全氮）的比值的变化趋势与SMB-C和SMB-N变化一致;从PCR-DGGE分析,长期氮磷钾化肥配施有机肥（NPKM）处理的微生物量碳、氮的含量最高,微生物丰度最高,细菌物种最多,其次为长期撂荒（CK0）,CK处理细菌物种最少。UPGMC聚类分析表明NPK和NPKF处理细菌的群落结构相似,CK和CK0处理细菌的群落结构相似,而NPKM和NPKSt处理细菌的群落结构相似。     

Numerical Analysis of Grassland Bacterial Community Structure under Different Land Management Regimens by Using 16S Ribosomal DNA Sequence Data and Denaturing Gradient Gel Electrophoresis Banding Patterns

Bacterial diversity in unimproved and improved grassland soils was assessed by PCR amplification of bacterial 16S ribosomal DNA (rDNA) from directly extracted soil DNA, followed by sequencing of ~45 16S rDNA clones from each of three unimproved and three improved grassland samples (A. E. McCaig, L. A. Glover, and J. I. Prosser, Appl. Environ. Microbiol. 65:1721–1730, 1999) or by denaturing gradient gel electrophoresis (DGGE) of total amplification products. Semi-improved grassland soils were analyzed only by DGGE. No differences between communities were detected by calculation of diversity indices and similarity coefficients for clone data (possibly due to poor coverage). Differences were not observed between the diversities of individual unimproved and improved grassland DGGE profiles, although considerable spatial variation was observed among triplicate samples. Semi-improved grassland samples, however, were less diverse than the other grassland samples and had much lower within-group variation. DGGE banding profiles obtained from triplicate samples pooled prior to analysis indicated that there was less evenness in improved soils, suggesting that selection for specific bacterial groups occurred. Analysis of DGGE profiles by canonical variate analysis but not by principal-coordinate analysis, using unweighted data (considering only the presence and absence of bands) and weighted data (considering the relative intensity of each band), demonstrated that there were clear differences between grasslands, and the results were not affected by weighting of data. This study demonstrated that quantitative analysis of data obtained by community profiling methods, such as DGGE, can reveal differences between complex microbial communities.     

Comparison of soil microbial communities from two distinct karst areas in Hungary

Karst areas belong to the most exposed terrestrial ecosystems, therefore their study have a priority task in Hungary, as well. The aim of this study was to compare the structure, activity and diversity of soil microbial communities from two distinct Hungarian karst areas (Aggtelek NP and Tapolca-basin). Soil samples were taken three times from 6 distinct sites, from different depths. Soil microbial biomass C (MBC), microbial biomass N (MBN), basal respiration (BRESP) and substrate induced respiration (SIR) were measured. The phylogenetic diversity of bacterial communities was compared by Denaturing Gradient Gel Electrophoresis (DGGE). The highest MBC, MBN, BRESP and SIR values were measured in the rendzina soil from Aggtelek. On the basis of biomass and respiration measurements, microbial communities differentiated mainly according to soil depths whereas DGGE profiles of bacterial communities resulted in groups mainly according to sampling sites.     

The Effect of Resource Islands on Abundance and Diversity of Bacteria in Arid Soils

Bacteria and nutrients were determined in upper soil samples collected underneath and between canopies of the dominant perennial in each of three sites along a steep precipitation gradient ranging from the Negev desert in the south of Israel to a Mediterranean forest in the north. Bacterial abundance, monitored by phospholipid fatty acid analysis, was significantly higher under the shrub canopy (compared to barren soils) in the arid and semi-arid sites but not in the Mediterranean soils. Bacterial community composition, determined using terminal restriction fragment length polymorphism and clone libraries, differed according to the sample’s origin. Closer examination revealed that in the arid and semi-arid sites, α-Proteobacteria are more abundant under the shrub canopy, while barren soils are characterized by a higher abundance of Actinobacteria. The bacterial communities in the Mediterranean soils were similar in both patch types. These results correspond to the hypothesis of “resource islands”, suggesting that shrub canopies provide a resource haven in low-resource landscapes. Yet, a survey of the physicochemical parameters of inter- and under-shrub soils could not attribute the changes in bacterial diversity to soil moisture, organic matter, or essential macronutrients. We suggest that in the nutrient-poor soils of the arid and semi-arid sites, bacteria occupying the soil under the shrub canopy may have longer growth periods under favorable conditions, resulting in their increased biomass and altered community composition.     

Effects of water fluctuations on microbial mass and activity in soil

When previously dried soil was remoistened, a series of microbial events occurred. The bacterial plate count population increased rapidly, with a doubling time of 4–5 h. The length of fungal hyphae and microscopic counts of bacteria increased more slowly. The microscopically counted bacterial population was estimated to have a doubling time of about 90 h. The respiratory burst occurring after 2–3 days coincided with the maximal growth rate of the bacterial plate count population. From the respiratory data, plate count bacteria were estimated to have a cell mass of 0.4 pg dry weight, whereas the mass of microscopically counted bacteria was only 10% of this. Changes in bacterial DNA content corresponded to changes in the microscopic count, whereas changes in soil catalase activity mainly corresponded to changes in the fungal biomass, which was dominant.It is suggested that bacterial plate counts and microscopic counts represent two distinct populations of bacteria, which for practical purposes may be termed zymogenous and autochthonous, respectively.     

Evaluation of Bacterial Diversity in Soil Microcosms at Different Moisture Contents

The succession analysis of bacterial diversity in the A horizons (rich in organic matter) of three contrasting types of soil—burozem, soddy gley soil, and chernozem—showed that the bacterial diversity of soil microcosms in humid regions can be adequately evaluated only if soil samples are incubated at different soil moisture contents. A complete account of actinobacteria and proteobacteria requires the levels of soil moisture corresponding to the maximum capillary–sorption moisture and capillary moisture, respectively. The bacterial diversity, whose value was maximum on the 40th day of succession, was higher in soddy gley soil than in burozem. The taxonomic structures of the bacterial communities of these two types of soil were different. After wetting chernozem samples from arid regions, the soil bacterial community changed insignificantly with time and drastically differed from that of soils from humid regions. The difference in the bacterial diversity of soils was the most distinct when it was evaluated by measuring the proportion between proteobacteria and actinobacteria.     

Effects of wetland degradation on bacterial community in the Zoige Wetland of Qinghai-Tibetan Plateau (China)

Wetland degradation makes significant impacts on soil, and bacterial communities in soil are likely to respond to these impacts. The purpose of this study was to investigate the impacts of soil property, soil type and soil depth on bacterial community in different stages of soil degradation in the Zoige Wetland. Microbial biomass carbon was estimated from chloroform fumigation-extraction. Bacterial communities were evaluated by cluster and principal component analysis of DGGE banding patterns and sequencing of partial 16S rDNA PCR amplicons. Experimental results showed that microbial biomass carbon decreased with the soil types (Peat soil > Swamp soil > Meadow soil > Sandy soil) and declined with soil depths (0–20 > 20–40 > 40–60 cm). Bacterial community was affected by soil type more primarily than by soil depth. In addition, the microbial biomass carbon was strongly correlated with soil water content, soil organic carbon and total nitrogen. Sequence analysis of DGGE bands indicated that bacterial phyla of α-Proteobacteria, γ-Proteobacteria, Bacteroidetes, Flavobacterium and Unidentified bacterium predominantly existed in the soil. All these results suggest that specific changes in soil property, soil type and soil depth affected soil bacterial community both quantitatively and qualitatively.     

Characterization of Humus Microbial Communities in Adjacent Forest Types That Differ in Nitrogen Availability

To address the link between soil microbial community composition and soil processes, we investigated the microbial communities in forest floors of two forest types that differ substantially in nitrogen availability. Cedar-hemlock (CH) and hemlock-amabilis fir (HA) forests are both common on northern Vancouver Island, B.C., occurring adjacently across the landscape. CH forest floors have low nitrogen availability and HA high nitrogen availability. Total microbial biomass was assessed using chloroform fumigation-extraction and community composition was assessed using several cultivation-independent approaches: denaturing gradient gel electrophoresis (DGGE) of the bacterial communities, ribosomal intergenic spacer analysis (RISA) of the bacterial and fungal communities, and phospholipid fatty acid (PLFA) profiles of the whole microbial community. We did not detect differences in the bacterial communities of each forest type using DGGE and RISA, but differences in the fungal communities were detected using RISA. PLFA analysis detected subtle differences in overall composition of the microbial community between the forest types, as well as in particular groups of organisms. Fungal PLFAs were more abundant in the nitrogen-poor CH forests. Bacteria were proportionally more abundant in HA forests than CH in the lower humus layer, and Gram-positive bacteria were proportionally more abundant in HA forests irrespective of layer. Bacterial and fungal communities were distinct in the F, upper humus, and lower humus layers of the forest floor and total biomass decreased in deeper layers. These results indicate that there are distinct patterns in forest floor microbial community composition at the landscape scale, which may be important for understanding nutrient availability to forest vegetation.     

Biodiversity acts as insurance of productivity of bacterial communities under abiotic perturbations

Anthropogenic disturbances are detrimental to the functioning and stability of natural ecosystems. Critical ecosystem processes driven by microbial communities are subjected to these disturbances. Here, we examine the stabilizing role of bacterial diversity on community biomass in the presence of abiotic perturbations such as addition of heavy metals, NaCl and warming. Bacterial communities with a diversity gradient of 1–12 species were subjected to the different treatments, and community biomass (OD₆₀₀) was measured after 24 h. We found that initial species richness and phylogenetic structure impact the biomass of communities. Under abiotic perturbations, the presence of tolerant species in community largely contributed in community biomass production. Bacterial diversity stabilized the biomass across the treatments, and differential response of bacterial species to different perturbations was the key reason behind these effects. The results suggest that biodiversity is crucial for maintaining the stability of ecosystem functioning and acts as ecological insurance under abiotic perturbations. Biodiversity in natural ecosystems may also uphold the ecosystem functioning under anthropogenic disturbance.     

Bacterial Communities Associated with <Emphasis Type="Italic">Chenopodium album</Emphasis> and <Emphasis Type="Italic">Stellaria media</Emphasis> Seeds from Arable Soils

The bacterial community compositions in Chenopodium album and Stellaria media seeds recovered from soil (soil weed seedbank), from bulk soil, and from seeds harvested from plants grown in the same soils were compared. It was hypothesized that bacterial communities in soil weed seedbanks are distinct from the ones present in bulk soils. For that purpose, bacterial polymerase chain reaction denaturing gradient gel electrophoresis (PCR–DGGE) fingerprints, made from DNA extracts of different soils and seed fractions, were analyzed by principal component analysis. Bacterial fingerprints from C. album and S. media seeds differed from each other and from soil. Further, it revealed that bacterial fingerprints from soil-recovered and plant-harvested seeds from the same species clustered together. Hence, it was concluded that microbial communities associated with seeds in soil mostly originated from the mother plant and not from soil. In addition, the results indicated that the presence of a weed seedbank in arable soils can increase soil microbial diversity. Thus, a change in species composition or size of the soil weed seedbank, for instance, as a result of a change in crop management, could affect soil microbial diversity. The consequence of increased diversity is yet unknown, but by virtue of identification of dominant bands in PCR–DGGE fingerprints as Lysobacter oryzae (among four other species), it became clear that bacteria potentially antagonizing phytopathogens dominate in C. album seeds in soil. The role of these potential antagonists on weed and crop plant growth was discussed.     

The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi‐arid soils

Biogeochemical processes and ecosystemic functions are mostly driven by soil microbial communities. However, most methods focus on evaluating the total microbial community and fail to discriminate its active fraction which is linked to soil functionality. Precisely, the activity of the microbial community is strongly limited by the availability of organic carbon (C) in soils under arid and semi‐arid climate. Here, we provide a complementary genomic and metaproteomic approach to investigate the relationships between the diversity of the total community, the active diversity and ecosystem functionality across a dissolved organic carbon (DOC) gradient in southeast Spain. DOC correlated with the ecosystem multifunctionality index composed by soil respiration, enzyme activities (urease, alkaline phosphatase and β‐glucosidase) and microbial biomass (phospholipid fatty acids, PLFA). This study highlights that the active diversity (determined by metaprotoemics) but not the diversity of the whole microbial community (evaluated by amplicon gene sequencing) is related to the availability of organic C and it is also connected to the ecosystem multifunctionality index. We reveal that DOC shapes the activities of bacterial and fungal populations in Mediterranean semi‐arid soils and determines the compartmentalization of functional niches. For instance, Rhizobales thrived at high‐DOC sites probably fuelled by metabolism of one‐C compounds. Moreover, the analysis of proteins involved in the transport and metabolism of carbohydrates revealed that Ascomycota and Basidiomycota occupied different nutritional niches. The functional mechanisms for niche specialization were not constant across the DOC gradient.     

Unexpectedly High Bacterial Diversity in Arctic Tundra Relative to Boreal Forest Soils, Revealed by Serial Analysis of Ribosomal Sequence Tags

Arctic tundra and boreal forest soils have globally relevant functions that affect atmospheric chemistry and climate, yet the bacterial composition and diversity of these soils have received little study. Serial analysis of ribosomal sequence tags (SARST) and denaturing gradient gel electrophoresis (DGGE) were used to compare composite soil samples taken from boreal and arctic biomes. This study comprises an extensive comparison of geographically distant soil bacterial communities, involving the analysis of 12,850 ribosomal sequence tags from six composite soil samples. Bacterial diversity estimates were greater for undisturbed arctic tundra soil samples than for boreal forest soil samples, with the highest diversity associated with a sample from an extreme northern location (82^oN). The lowest diversity estimate was obtained from an arctic soil sample that was disturbed by compaction and sampled from a greater depth. Since samples from the two biomes did not form distinct clusters on the basis of SARST data and DGGE fingerprints, factors other than latitude likely influenced the phylogenetic compositions of these communities. The high number of ribosomal sequences analyzed enabled the identification of possible cosmopolitan and endemic bacterial distributions in particular soils.     

Microbial diversity of topographical gradient profiles in Fushan forest soils of Taiwan

To evaluate the microbial diversity of Fushan forest soils, the variation of soil properties, microbial populations, and soil DNA with soil depth in three sites of different altitude were analyzed. Microbial population, moisture content, total organic carbon (C_org), and total nitrogen (N_tot) decreased with increasing soil depth. The valley site had the lowest microbial populations among the three tested sites due to the low organic matter content. Bacterial population was the highest among the microbial populations. The ratios of cellulolytic microbes to the total bacteria in organic layers were high, implying their roles in the carbon cycle. The microbial biomass carbon (C_mic) and nitrogen (N_mic) contents ranged from 130.5 to 564.1 μg g⁻¹ and from 16.7 to 95.4 μg g⁻¹, respectively. The valley had the lowest C_mic and N_mic. The organic layer had the highest C_mic and N_mic and decreased with soil depth. Analysis using denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR) amplicons of 16S rDNA showed that the bacterial diversity of the three sites were very similar to each other in the major bands, and the variation was in the minor bands. However, the patterns in PCR-DGGE profile through gradient horizons were different, indicating the prevalence of specific microbes at different horizons. These results suggest that the microbial diversity in the deeper horizons is not simply the diluted analogs of the surface soils and that some microbes dominate only in the deeper horizons. Topography influenced the quantity and diversity of microbial populations.     

A culture-independent study of free-living fungi in biological soil crusts of the Colorado Plateau: their diversity and relative contribution to microbial biomass

Molecular methodologies were used to investigate free-living fungal communities associated with biological soil crusts (BSCs), along km-scale transects on the Colorado Plateau (USA). Two cyanobacteria-dominated crust types that did not contain significant lichen cover were examined. Fungal community diversity and composition were assessed with PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting and sequencing, and fungi-specific quantitative PCR was used to measure fungal population densities as compared with those of bacteria. Our results clearly indicate that free-living fungi, while ubiquitous in BSCs, are less diverse and contribute far less biomass than their bacterial counterparts. Biological soil crust fungal community structure differed from that of uncrusted soils in their surroundings. Phylogenetic analyses placed the majority of BSC fungi within the Ascomycota , confirmed the importance of dematiaceous fungi, and pointed to members of the genera Alternaria and Acremonium as the most common free-living fungi in these crusts. Phylotypes potentially representing novel taxa were recovered, as were several belonging to the Basidiomycota that would not have been readily recognized by culture-dependant means.     

Bacterial Communities Involved in Soil Formation and Plant Establishment Triggered by Pyrite Bioweathering on Arctic Moraines

In arctic glacier moraines, bioweathering primed by microbial iron oxidizers creates fertility gradients that accelerate soil development and plant establishment. With the aim of investigating the change of bacterial diversity in a pyrite-weathered gradient, we analyzed the composition of the bacterial communities involved in the process by sequencing 16S rRNA gene libraries from different biological soil crusts (BSC). Bacterial communities in three BSC of different morphology, located within 1 m distance downstream a pyritic conglomerate rock, were significantly diverse. The glacier moraine surrounding the weathered site showed wide phylogenetic diversity and high evenness with 15 represented bacterial classes, dominated by Alphaproteobacteria and pioneer Cyanobacteria colonizers. The bioweathered area showed the lowest diversity indexes and only nine bacterial families, largely dominated by Acidobacteriaceae and Acetobacteraceae typical of acidic environments, in accordance with the low pH of the BSC. In the weathered BSC, iron-oxidizing bacteria were cultivated, with counts decreasing along with the increase of distance from the rock, and nutrient release from the rock was revealed by environmental scanning electron microscopy-energy dispersive X-ray analyses. The vegetated area showed the presence of Actinomycetales, Verrucomicrobiales, Gemmatimonadales, Burkholderiales, and Rhizobiales, denoting a bacterial community typical of developed soils and indicating that the lithoid substrate of the bare moraine was here subjected to an accelerated colonization, driven by iron-oxidizing activity.     

Numerical analysis of grassland bacterial community structure under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns

Bacterial diversity in unimproved and improved grassland soils was assessed by PCR amplification of bacterial 16S ribosomal DNA (rDNA) from directly extracted soil DNA, followed by sequencing of ~45 16S rDNA clones from each of three unimproved and three improved grassland samples (A. E. McCaig, L. A. Glover, and J. I. Prosser, Appl. Environ. Microbiol. 65:1721-1730, 1999) or by denaturing gradient gel electrophoresis (DGGE) of total amplification products. Semi-improved grassland soils were analyzed only by DGGE. No differences between communities were detected by calculation of diversity indices and similarity coefficients for clone data (possibly due to poor coverage). Differences were not observed between the diversities of individual unimproved and improved grassland DGGE profiles, although considerable spatial variation was observed among triplicate samples. Semi-improved grassland samples, however, were less diverse than the other grassland samples and had much lower within-group variation. DGGE banding profiles obtained from triplicate samples pooled prior to analysis indicated that there was less evenness in improved soils, suggesting that selection for specific bacterial groups occurred. Analysis of DGGE profiles by canonical variate analysis but not by principal-coordinate analysis, using unweighted data (considering only the presence and absence of bands) and weighted data (considering the relative intensity of each band), demonstrated that there were clear differences between grasslands, and the results were not affected by weighting of data. This study demonstrated that quantitative analysis of data obtained by community profiling methods, such as DGGE, can reveal differences between complex microbial communities.