Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition

The relative importance of specific plant properties versus soil characteristics in shaping the bacterial community structure of the rhizosphere is a topic of considerable debate. Here, we report the results of a study on the bacterial composition of the rhizosphere of the wild plant Carex arenaria (sand sedge) growing at 10 natural sites in The Netherlands. The soil properties of the sandy soils at these sites were highly disparate, most notably in pH, chloride and organic matter content. Rhizosphere and bulk soil bacterial communities were examined by culture-independent means, namely, 16S rDNA-directed PCR-DGGE profiling. Large differences were observed between the bacterial communities of the different sites for both bulk and rhizosphere soil. Cluster analysis of bacterial profiles revealed that the rhizosphere community of each site was generally more closely related to the bulk soil community of that site rather than to rhizosphere communities of other sites. Hence, bacterial community structure within the rhizosphere of C. arenaria appeared to be determined to a large extent by the bulk soil community composition. This conclusion was supported by a reciprocal planting experiment, where C. arenaria shoots of different sites yielded highly similar rhizosphere communities when planted in the same soil.     

黑土区大豆基因型的根际细菌群落结构时空动态变化

The dynamics of rhizosphere microbial communities is important for plant health and productivity, and can be influenced by soil type, plant species or genotype, and plant growth stage. A pot experiment was carried out to examine the dynamics of microbial communities in the rhizosphere of two soybean genotypes grown in a black soil in Northeast China with a long history of soybean cultivation. The two soybean genotypes, Beifeng 11 and Hai 9731, differing in productivity were grown in a mixture of black soil and siliceous sand. The bacterial communities were compared at three zone locations including rhizoplane, rhizosphere, and bulk soil at the third node (V3), early flowering (R1), and early pod (R3) stages using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rDNA. The results of principal component analyses (PCA) showed that the bacterial community structure changed with growth stage. Spatially, the bacterial communities in the rhizoplane and rhizosphere were significantly different from those in the bulk soil. Nevertheless, the bacterial communities in the rhizoplane were distinct from those in the rhizosphere at the V3 stage, while no obvious differences were found at the R1 and R3 stages. For the two genotypes, the bacterial community structure was similar at the V3 stage, but differed at the R1 and R3 stages. In other words, some bacterial populations became dominant and some others recessive at the two later stages, which contributed to the variation of the bacterial community between the two genotypes. These results suggest that soybean plants can modify the rhizosphere bacterial communities in the black soil, and there existed genotype-specific bacterial populations in the rhizosphere, which may be related to soybean productivity.     

Microbial function in adjacent subtropical forest and agricultural soil

Soil microbial communities and their activities are altered by land use change; however impacts and extent of these alterations are often unclear. We investigated the functional responses of soil microbes in agricultural soil under sugarcane and corresponding native soil under Eucalyptus forest to additions of contrasting plant litter derived from soybean, sugarcane and Eucalyptus in a microcosm system, using a suite of complimentary techniques including enzyme assays and community level physiological profiles (CLPP). Initially agricultural soil had 50% less microbial biomass and lower enzyme activities than forest soil, but significantly higher nitrification rates. In response to litter addition, microbial biomass increased up to 11-fold in agricultural soil, but only 1.8-fold in forest soil, suggesting a prevalence of rapidly proliferating ‘r’ and slower growing ‘K’ strategists in the respective soils. Litter-driven change in microbial biomass and activities were short lived, largely returning to pre-litter addition levels by day 150. Decomposition rates of sugarcane and soybean litter as estimated via CO₂ production were lower in agricultural than in forest soil, but decomposition of more recalcitrant Eucalyptus litter was similar in both soils, contradicting the notion that microbial communities specialise in decomposing litter of the dominant local plant species. Enzyme activities and community level physiological profiles (CLPP) were closely correlated to microbial biomass and overall CO₂ production in the agricultural soil but not the forest soil, suggesting contrasting relationships between microbial population dynamics and activity in the two soils. Activities of enzymes that break down complex biopolymers, such as protease, cellulase and phenol oxidase were similar or higher in the agricultural soil, which suggests that the production of extracellular biopolymer-degrading enzymes was not a factor limiting litter decomposition. Enzyme and CLPP analyses produced contrasting profiles of microbial activity in the two soils; however the combination of both analyses offers additional insights into the changes in microbial function and community dynamics that occur after conversion of forest to agricultural land.     

Exotic plant influences soil nematode communities through litter input

The impact of exotic plant invasions on soil communities and nutrient cycling processes has received an increasing attention in recent years. To test whether the exotic plant invasions affect nematode communities through altering litter quality, we compared mass loss and nematode colonization during the stem litter decomposition of invasive Spartina alterniflora and native Phragmites australis in salt marshes of the Yangtze River estuary, China. Plastic drinking straws were synchronously used as controls. The addition of plant residues was found stimulating the growth of nematodes, particularly bacterial feeders on day 16 after burial. A top-down control of bacterivous nematodes by carnivores existed in nematode succession during the litter decomposition. With higher nitrogen content and lower C:N ratio, stem litter of the invasive S. alterniflora decayed faster and supported more abundant nematodes than the native P. australis. The greater nematode abundance in S. alterniflora was mainly due to two dominant genera of bacterial nematodes, namely Diplolaimelloides and Diplolaimella. Lower values of maturity index and structure index in S. alterniflora than in P. australis litter indicate that a more degraded food web condition resulted from the faster litter decay. A considerable difference in nematode community structures between two litter types only occurred in a certain period of the decomposition (from 8 to 32 days after burial), suggesting that the changes in faunal community structure are time dependent. In summary, this study confirmed the hypothesis that the invasion of S. alterniflora stimulates the growth of bacterial nematodes by producing higher quality of litter than the native P. australis. The results obtained here suggest that the invasion of exotic plant is likely to alter ecosystem functions indirectly through exerting its effect on soil decomposer communities such as nematodes.     

Soil microbial communities: Influence of geographic location and hydrocarbon pollutants

The importance and relevance of the geographical origin of the soil sample and the hydrocarbons in determining the functional or species diversity within different bacterial communities was evaluated using the community level physiological profiles (CLPP) and Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). Hydrocarbon contaminated and uncontaminated soils from different geographical locations were used in the study. In addition, the influence or relevance of the geographical location of the sample was further evaluated by artificially contaminating soils from different geographical locations with different petroleum products. The hydrocarbons rather than the geographical origin of the sample appear to be more important in determining functional or species diversity within the bacterial communities. Cluster analysis of the different community profiles using both functional and molecular responses revealed that the samples from different locations were as different as samples from the same location but from contaminated versus uncontaminated soils. The results of the soils from different locations artificially contaminated by different hydrocarbons also reached the same conclusion. The samples from different soils were as different as samples from the same soil contaminated by different petroleum products. In addition, the removal rate of the different hydrocarbons in the artificially contaminated soil was different. The results suggest that the pollutants rather than the geographical origin of the sample might be more important in determining the functional or species diversity within bacterial communities.     

应用新引物DGGE分析土壤中硝酸盐还原细菌群落

The narG gene is frequently used as a molecular marker for bacterial nitrate-reducing community analysis. In this study, a new set of primers targeting the narG gene was designed and applied to semi-nested polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) assay. The potential of the new primers was verified on DNA directly extracted from soils from five different experimental sites distributed in Central and Southern Italy. Specificity of the primers was determined by excision, amplification, and sequencing of bands resolved by DGGE. A phylogenetic analysis showed the correlation between the sequences retrieved from the soils studied and the narG sequences from β and γ-Proteobacteria. These primers expanded the existing molecular tools for ecological study on the size and diversity of nitrate-reducing bacterial community in soil.     

Changes in microbial communities in an apple orchard and its adjacent bush soil in response to season,land-use,and violet root rot infestation

Soil microbial communities in an apple orchard and its adjacent boundary bush with or without infestation by violet root rot were investigated for 2 years. Effects of season (spring, summer, and fall), land-use (apple orchard and boundary bush), and violet root rot (infested and healthy) on soil microbial populations, microbial activity, and microbial community structures were determined using physiological, cytochemical, and molecular (PCR-DGGE) approaches. Seasonal fluctuations were significant (P<0.05) in viable bacteria and fungal populations, bacterial FAME, fluorescein diacetate (FDA) hydrolysis, and diversity (H′) and evenness (J′) of community-level physiological profile (CLPP) in both years. However, seasonal differences of soil microbial guilds that utilize carbon substrate groups observed in the first year were not reproduced in the second year. The land-use factor differentiated the apple orchard from the boundary bush where viable bacterial population, bacterial FAME and FDA hydrolysis were significantly greater in both years. Infestation status of violet root rot, on the other hand, significantly increased bacterial FAME and FDA hydrolysis in both years. In addition, neither the land-use nor the disease infestation factor significantly influenced the utilization patterns of individual substrate guilds for the 2 years. In both years, saturated fatty acids were significantly more abundant in the orchard than in the bush soil, and monosaturated fatty acids vice versa. Principal component analyses for CLPP, FAME, and denaturing gradient gel electrophoresis (DGGE) consistently exhibited that, although the violet root rot influenced the soil microbial community structures both in the apple orchard and the boundary bush, overall magnitude of the difference in communities between the violet root rot infested and non-infested sites in the bush were greater than in the orchard, irrespective of the season. These results suggested that the seasonal and the land-use factors affected soil microbial community both quantitatively and qualitatively, whereas the impact of the violet root rot on the soil microbial community was mainly qualitative and more pronounced in the adjacent bush than in the orchard.     

Structure and function of microbial communities in the rhizosphere of Scots pine after tree-felling

We evaluated changes occurring in the rhizosphere microbial communities of Scots pine (Pinus sylvestris L.) due to tree-felling and decrease of the photosynthetic C flow into the soil under field conditions over one growing season. Samples were taken from tree rhizospheres, freshly felled stump rhizospheres and bulk soil. We used culture dependent (CFU counts, community level physiological profiles, CLPPs) and independent methods (fluorogenic MUF-substrates, PLFA pattern and PCR-DGGE) to monitor the microbial communities in soil samples. The numbers of cultivable bacteria and amounts of phosphatase activity in the rhizosphere of trees were significantly higher compared with those in the bulk soil. The organic C consuming community measured by CLPP was stimulated directly after the tree-felling in stump rhizospheres; utilization of the disintegration components of cellulose, hemicellulose and chitin increased. Furthermore, bacterial and fungal biomass as well as chitin decomposers (CFU) increased in the stump rhizosphere. After 11 weeks of tree-felling the stump rhizosphere soluble PO₄-P and NH₄-N as well as amounts of total C and N began to resemble the concentrations measured in the bulk soil. However, the stump rhizosphere community structure detected by PLFA and PCR-DGGE still resembled that of the tree rhizosphere.     

Cereal/legume rotation effects on rhizosphere bacterial community structure in west african soils

The increased use of cereal/legume crop rotation has been advocated as a strategy to increase cereal yields of subsistence farmers in West Africa, and is believed to promote changes in the rhizosphere that enhance early plant growth. In this study we investigated the microbial diversity of the rhizoplane from seedlings grown in two soils previously planted to cereal or legume from experimental plots in Gaya, Niger, and Kaboli, Togo. Soils from these legume rotation and continuous cereal plots were placed into containers and sown in a growth chamber with maize (Zea mays L.), millet (Pennisetum glaucum L.), sorghum (Sorghum bicolor L. Moench.), cowpea (Vigna unguiculata L.) or groundnut (Arachis hypogaea L.). At 7 and 14 days after sowing, 16S rDNA profiles of the eubacterial and ammonia-oxidizing communities from the rhizoplane and bulk soil were generated using denaturing gradient gel electrophoresis (DGGE). Community profiles were subjected to peak fitting analyses to quantify the DNA band position and intensities, after which these data were compared using correspondence and principal components analysis. The data showed that cropping system had a highly significant effect on community structure (p <0.005), irrespective of plant species or sampling time. Continuous cereal-soil grown plants had highly similar rhizoplane communities across crop species and sites, whereas communities from the rotation soil showed greater variability and clustered with respect to plant species. Analyses of the ammonia-oxidizing communities provided no evidence of any effects of plant species or management history on ammonia oxidizers in soil from Kaboli, but there were large shifts with respect to this group of bacteria in soils from Gaya. The results of these analyses show that crop rotation can cause significant shifts in rhizosphere bacterial communities.     

重金属复合污染农田土壤DNA的快速提取及其PCR-DGGE分析

国内首次运用FastPrep○R 核酸快速提取系统提取了重金属复合污染农田土壤的DNA ,并对其进行了聚合酶链反应—变性梯度凝胶电泳 (PCR DGGE)分析。结果表明 ,FastPrep○R核酸提取仪与相应的FastD NASPINKitforSoil试剂盒联用时 ,能有效地分离到纯度较高的重金属污染农田土壤的DNA。PCR DGGE电泳图谱表明 ,PCR产物经DGGE检测后得到的电泳条带清晰且分离效果好 ,可以明显反映出重金属复合污染导致了农田土壤微生物在基因上的损伤 ,影响到农田土壤生态系统的细菌丰富度 ,改变了土壤环境的优势菌群 ,从而使农田土壤微生物群落结构多样性发生变化。可见 ,FastPrep○R核酸提取系统同样适用于重金属污染农田土壤环境中微生物基因组DNA的快速分离和纯化 ,得到的DNA可直接用于PCR DGGE分析。     

Long-term plant growth legacies overwhelm short-term plant growth effects on soil microbial community structure

Plant-soil feedbacks are gaining attention for their ability to determine plant community development. Plant-soil feedback models and research assume that plant-soil interactions occur within days to weeks, yet, little is known about how quickly and to what extent plants change soil community composition. We grew a dominant native plant (Pseudoroegneria spicata) and a dominant non-native plant (Centaurea diffusa) separately in both native- and non-native-cultivated field soils to test if these species could overcome soil legacies and create new soil communities in the short-term. Soil community composition before and after plant growth was assessed in bulk and rhizosphere soils using phospholipid fatty acid analyses. Nematode abundance and mycorrhizal colonization were also measured following plant growth. Field-collected, native-cultivated soils showed greater bacterial, Gram (−), fungal, and arbuscular mycorrhizal PLFA abundance and greater PLFA diversity than field-collected, non-native-cultivated soils. Both plant species grew larger in native- than non-native-cultivated soils, but neither plant affected microbial composition in the bulk or rhizosphere soils after two months. Plants also failed to change nematode abundance or mycorrhizal colonization. Plants, therefore, appear able to create microbial legacies that affect subsequent plant growth, but contrary to common assumptions, the species in this study are likely to require years to create these legacies. Our results are consistent with other studies that demonstrate long-term legacies in soil microbial communities and suggest that the development of plant-soil feedbacks should be viewed in this longer-term context.     

Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils

A number of studies have reported species specific selection of microbial communities in the rhizosphere by plants. It is hypothesised that plants influence microbial community structure in the rhizosphere through rhizodeposition. We examined to what extent the structure of bacterial and fungal communities in the rhizosphere of grasses is determined by the plant species and different soil types. Three grass species were planted in soil from one site, to identify plant-specific influences on rhizosphere microbial communities. To quantify the soil-specific effects on rhizosphere microbial community structure, we planted one grass species (Lolium perenne L.) into soils from three contrasting sites. Rhizosphere, non-rhizosphere (bulk) and control (non-planted) soil samples were collected at regular intervals, to examine the temporal changes in soil microbial communities. Rhizosphere soil samples were collected from both root bases and root tips, to investigate root associated spatial influences. Both fungal and bacterial communities were analysed by terminal restriction fragment length polymorphism (TRFLP). Both bacterial and fungal communities were influenced by the plant growth but there was no evidence for plant species selection of the soil microbial communities in the rhizosphere of the different grass species. For both fungal and bacterial communities, the major determinant of community structure in rhizospheres was soil type. This observation was confirmed by cloning and sequencing analysis of bacterial communities. In control soils, bacterial composition was dominated by Firmicutes and Actinobacteria but in the rhizosphere samples, the majority of bacteria belonged to Proteobacteria and Acidobacteria. Bacterial community compositions of rhizosphere soils from different plants were similar, indicating only a weak influence of plant species on rhizosphere microbial community structure.     

Microbial communities in forest floors under four tree species in coastal British Columbia

We compare forest floor microbial communities in pure plots of four tree species (Thuja plicata, Tsuga heterophylla, Pseudotsuga menziesii, and Picea sitchensis) replicated at three sites on Vancouver Island. Microbial communities were characterised through community level physiological profiles (CLPP), and profiling of phospholipid fatty acids (PLFA).Microbial communities from cedar forest floors had higher potential C utilisation than the other species. The F layer of the forest floor under cedar contained significantly higher bacterial biomass (PLFA) than the F layer under the other three tree species. There were differences in microbial communities among the three sites: Upper Klanawa had the highest bacterial biomass and potential C utilisation; this site also had the highest N availability in the forest floors. Forest floor H layers under hemlock and Douglas-fir contained greater biomass of Gram positive, Gram negative bacteria and actinomycetes than F layers based on PLFA, and H layers under spruce contained greater biomass of Gram negative bacteria than F layers. There were no significant differences in bacterial biomass between forest floor layers under cedar. Fungal biomass displayed opposite trends to bacteria and actinomycetes, being lowest in cedar forest floors, and highest in the F layer and at the site with lowest N availability. There were also differences in community composition among species and sites, with cedar forest floors having a much lower fungal:bacterial ratio than spruce, hemlock and Douglas-fir. The least fertile Sarita Lake site had a much greater fungal:bacterial ratio than the more fertile San Juan and Upper Klanawa sites. Forest floor layer had the greatest effect on microbial community structure and potential function, followed by site, and tree species. The similarity in trends among measures of N availability and microbial communities is further evidence that these techniques provide information on microbial communities that is relevant to N cycling processes in the forest floor.     

Local variation in belowground multitrophic interactions

A growing number of studies point at the involvement of root herbivores in influencing plant performance, community composition and succession. However, little is known about the factors that control root herbivore abundance and the role of local variation in the effectiveness of these factors. Here, we performed a full factorial experiment with plants, root-feeding nematodes and rhizosphere microbial communities from two dune sites, to test the hypothesis that the outcome of belowground multitrophic interactions depends on local differences between the interacting organisms. The organisms included the marram grass Ammophila arenaria, the cyst nematode Heterodera arenaria, microbial plant pathogens and natural enemies of the nematodes from two coastal foredune systems, one in The Netherlands and one in Wales. The two plant populations differed at the molecular and phenotypic level, and the microbial communities from the two dune sites differed in the composition of the dominant soil fungi but not of the dominant bacteria. Plants were negatively affected by the rhizosphere microorganisms from one of the sites. Nevertheless, nematode performance was not affected by the origin of both the host plants and the microbial communities. The reproductive output of the cyst nematode depended on the presence of microorganisms, as well as on inter-population variability in the response of the nematode to these natural enemies. In the absence of microorganisms, the two nematode populations differed in the number and size of the produced cysts, although maternal effects cannot be excluded. Inter-population differences in the host plant were a secondary factor in the nematode-microorganisms interactions, and did not influence bottom-up control of the cyst nematodes. Our results did not reveal strong signals of coevolution in belowground multitrophic interactions of plants, cyst nematodes and soil microbial communities. We conclude that the interactions between the studied organisms do not necessarily depend on their local vs. non-local origin. Nevertheless, we were able to show that local variation in soil organism community composition can be an important factor in determining the outcome of interactions in belowground multitrophic systems.     

Response of soil microbial communities to compost amendments

Soil organic matter is considered as a major component of soil quality because it contributes directly or indirectly to many physical, chemical and biological properties. Thus, soil amendment with composts is an agricultural practice commonly used to improve soil quality and also to manage organic wastes. We evaluated in laboratory scale experiments the response of the soilborne microflora to the newly created soil environments resulting from the addition of three different composts in two different agricultural soils under controlled conditions. At a global level, total microbial densities were determined by classical plate count methods and global microbial activities were assessed by measuring basal respiration and substrate induced respiration (SIR). Soil suppressiveness to Rhizoctonia solani diseases was measured through bioassays performed in greenhouses. At a community level, the modifications of the metabolic and molecular structures of bacterial and fungal communities were assessed. Bacterial community level physiological profiles (CLPP) were determined using Biolog™ GN microtiter plates. Bacterial and fungal community structures were investigated using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting. Data sets were analyzed using analysis of variance and ordination methods of multivariate data. The impact of organic amendments on soil characteristics differed with the nature of the composts and the soil types. French and English spent mushroom composts altered all the biological parameters evaluated in the clayey soil and/or in the sandy silty clay soil, while green waste compost did not modify either bacterial and fungal densities, SIR values nor soil suppressiveness in any of the soils. The changes in bacterial T-RFLP fingerprints caused by compost amendments were not related to the changes in CLPP, suggesting the functional redundancy of soil microorganisms. Assessing the density, the activity and the structure of the soil microflora allowed us not only to detect the impact of compost amendment on soil microorganisms, but also to evaluate its effect at a functional level through the variation of soil disease suppressiveness. Differences in disease suppressiveness were related to differences in chemical composition, in availability of nutrients at short term and in microbial composition due to both incorporation and stimulation of microorganisms by the compost amendments.     

Nitrogen availability decreases prokaryotic diversity in sandy soils

In this study, the interrelation between nitrogen availability and prokaryotic diversity are studied using a well-characterised system from a long-term field experiment on a loamy sandy soil. The prokaryotic potential functional diversity and community composition were assessed using community-level physiological profiling (CLPP), and their phylogenetic diversity was analysed using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) in combination with sequencing analysis. Highest prokaryotic potential functional diversity was measured in the control soil receiving no N fertilisation, indicating an efficient as well as versatile utilisation of the substrates in this soil. Both substrate utilisation richness and substrate utilisation evenness, the two constituents of the functional diversity, were decreased with increasing N supply. Furthermore, distinct prokaryotic community compositions were generated in N-enriched soils compared to unfertilised control soils. These differences suggest a dominance of populations adapted to utilising readily available substrates. We demonstrated that the shift in prokaryotic functional diversity was connected to a shift in the phylogenetic structure of the bacterial and archaeal communities. Taken together, our data clearly show that, for the sandy soil system, prokaryotic diversity and N availability were interrelated.     

Functional and molecular responses of soil microbial communities under differing soil management practices

The effects of soil management on some microbiological properties and soil bacterial community structure were evaluated. Two field sites with the same soil type, located on the same geographic area adjacent to one other, have received different soil management practices and cultivation. One site has been subjected for 20 years to intensive horticulture under conventional tillage and irrigation with low quality salt-rich water; the second field site has been uncultivated for a long period and was turned to organic farming practices over the last 5 years and is currently cultivated with fruit orchard. Total bacterial counts, microbial ATP, microbial community metabolic (BIOLOG^®) profiles, and DNA fingerprinting by PCR-DGGE were determined. Two-way ANOVA revealed that total bacterial counts were not significantly (P>0.3) affected by the two different management practices; ATP content was consistently and significantly (P<0.001) lower in salt-water irrigated soil than in organic soil at the three sampling times. The cluster analysis of community level physiological profiles indicated that microbial communities were much more uniform in organic soil than in irrigated one, suggesting that salt-water irrigation could have affected the size of the microbial population, its metabolic activities, as well as its composition. Molecular patterns fitted the BIOLOG^® profile diversity. In particular, at any sampling time, PCR-DGGE patterns of bacterial DNA, extracted by an indirect method, significantly discriminated irrigated from organic soil samples. The PCR-DGGE patterns of total soil DNA, extracted by a direct method, showed a moderate to significant variation among irrigated and organic soil samples. Biochemical, microbiological and molecular data contributed to evidence a significantly different response of indigenous microflora to soil management by using saline water or organic farming.     

Daily dynamics of bacterial numbers, CO2 emissions from soil and relationships between their wavelike fluctuations and succession of the microbial community

The daily dynamics of the number of copiotrophic and oligotrophic bacteria (in colony-forming units) and CO₂ emissions from cultivated soils after short- and long-term disturbances were studied for 25–27 days in a microfield experiment. The relationship of the wavelike fluctuations of the bacterial number and CO₂ emission with the succession of the soil microbial community was determined by the polymerase chain reaction method—denaturing gradient gel electrophoresis (PCR-DGGE). Short-term disturbances involved the application of organic or mineral fertilizers, pesticides, and plant residues to the soils of different plots. The long-term effect was a result of using biological and intensive farming systems for three years. The short-term disturbances resulted in increased peaks of the bacterial number, the significance of which was confirmed by harmonics analysis. The daily dynamics of the structure of the soil microbial community, which was studied for 27 days by the DGGE method, also had an oscillatory pattern. Statistical processing of the data (principal components analysis, harmonics and cross-correlation analyses) has revealed significant fluctuations in the structure of microbial communities coinciding with those of the bacterial populations. The structure of the microbial community changed within each peak of the dynamics of the bacterial number (but not from peak to peak), pointing to the cyclical character of the short-term succession. The long-term effects resulted in a less intense response of the microbiota—a lower rate of CO₂ emission from the soil cultivated according to the organic farming system.     

Shifts in soil bacterial communities associated with the potato rhizosphere in response to aromatic sulfonate amendments

Desulfonation is an important process in the sulfur cycle, through which organic sulfur compounds are mineralized, releasing S. Desulfonating bacteria are known to respond to inorganic S soil amendments. However, the extent to which these communities shift as a response to the addition of organic sulfur in the soil remains elusive. Here, we investigated how amendments of soil with inorganic or organic sulfur compounds influence the bacterial communities associated with potato, in a microcosm experiment. The soil was amended with two doses of linear alkylbenzene sulfonate (LAS), here used as a model aromatic sulfonate compound, or with sulfate. Degradation of LAS was observed already at the young plant stage, as in all treatments 10- to 50-fold reductions of the initial (background) LAS concentrations were noted. Quantitative PCR analyses showed no significant effects of treatment on the bacterial abundances, which tended to increase from the young plant to the flowering stages of plant development. The bacterial community structures, determined via PCR-DGGE, were strongly affected by the presence of plants. This rhizosphere effect became more apparent at the flowering stages. Both the bacterial and β-proteobacterial community structures were affected by the presence of LAS, but dose-related effects were not observed. LAS also caused significant changes in the community structures, as compared to those in inorganic sulfate amended soil. Sulfate did not influence the bacterial community structures and only affected the β-proteobacterial ones at the flowering stage. Surprisingly, the presence of LAS did not exert any significant effect on the abundance of the Variovorax asfA gene, although clone libraries revealed a dominance of Variovorax types in the rhizosphere, especially in the high-level LAS treatment. Our results suggest that rhizosphere communities are key players in LAS degradation in soils, and that desulfonator Variovorax spp. plays a minor role in the mineralization of aromatic sulfonates in soil cropped with potato.     

A PCR-DGGE method for detecting arbuscular mycorrhizal fungi in cultivated soils

Arbuscular mycorrhizal (AM) fungi (AMF) are important components of agro-ecosystems and are especially significant for productive low-input agriculture. Molecular techniques are used to investigate fungal community composition in uncultivated, disturbed, or contaminated soils, but this approach to community analysis of AMF in agricultural soils has not been reported. In this study, a polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) procedure for the detection of fungal 18S ribosomal RNA gene was developed with reference cultures of seven isolates (representing five AMF species). These reference cultures were chosen because isolates of their species were putatively identified in a previous survey of farm field soils in the province of Saskatchewan, Canada. A reference PCR-DGGE profile was generated using DNA extracted and amplified from the spores of these cultures. The effectiveness of the procedure was tested by its application to soil samples from 38 farms. Prominent bands from the PCR-DGGE profiles of these samples were excised for sequence analysis. The total number of species recovered was low in comparison to other AMF community surveys of temperate climate locations. The majority of the sequences recovered were Glomus species. Scutellospora calospora, a previously undetected AM fungus in Saskatchewan was found. Though not without its drawbacks, this approach to community composition analysis of AMF was faster than conventional trap cultivation methods.