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Few studies have been conducted on adaptations of microbial communities to low and fluctuating temperatures using environmentally relevant conditions. In this study, six Himalayan and two temperate soils were selected as candidates for low-temperature/freeze-thaw (FT)-adapted and susceptible soils, respectively. Redundancy analysis with forward selection was used to create a model of environmental parameters explaining variability in the initial microbial abundance and 4 °C activities. The best predictor was soil carbon, explaining more than 74% of data variability ( P=0.002), despite significant differences in the soil characteristics and environmental history. We tested the hypothesis that the reproduced Himalayan FT fluctuations select physiologically similar communities in distinct soils. Microcosms were experimentally subjected to two separate 50 and 60 FT cycle (FTC) experiments. A significant decrease in abundance, 4 °C basal respiration and drastic rearrangements in community-level physiological profiles (CLPP) were observed in microcosms with temperate soils until 40 FTC. CLPP remained distinct from those of the Himalayan soils. Minor changes were observed in the Himalayan soils, confirming that microbial populations with physiological traits consistent with the noncontinuous permafrost conditions reside in the Himalayan soils, whereas the surviving temperate soil microorganisms actively adjusted to novel environmental conditions. [ABSTRACT FROM AUTHOR]

The microbial population in soil contaminated with abattoir effluent was investigated using the spread plate method. The results revealed a high mean count of 3.70±0.01×106 cfu/g and 1.40±0.04×104 cfu/g for bacteria and fungi respectively. The counts were higher than that of the control soil sample with 2.40±0.02×104 cfu/g and 1.10±0.02×103 cfu/g for the bacteria and fungi respectively. Among the bacteria isolated, Escherichia coli had the highest frequency of occurrence of 21.0 %, followed by Bacillus subtilis and Staphylococcus aureus with 17.0 % each and Bacillus anthracis with 13.0 %. The lowest frequency of occurrence of 4 % was observed in Bacillus polymyxa and Staphylococcus epidermidis respectively. In terms of fungal isolates, Aspergillus niger had the highest frequency of occurrence of 27 %, followed by Fusarium sporotrichioides (22 %) while Absidia sp and Mucor pusillus with 6 % each. Results of the physicochemical analysis showed that the contaminated soil samples had mean pH of 7.36, mean temperature of 33 °C, Cation Exchange Capacity (CEC) of 18.53 % and nitrogen concentration of 0.23 mg/g. [ABSTRACT FROM AUTHOR]

Degradation of benzene, toluene, and ethylbenzene (BTE) by microbial populations indigenous to the soil and populations proliferated from the indigenous using biogenic substrates were compared. The reaction system consisted of aerobic microcosms representing an unsaturated soil. Microcosms supplemented with glucose and citrate, when compared to the unsupplemented microcosms, showed increases in bacterial counts, but the overall degradation rates for B, T, or E were reduced in spite of shorter lag times. Both biogenic substrate supplements were non-beneficial for BTE degradation due largely to the preferential and healthy growth of the indigenous populations on the biogenic substrates, and thus the urgency of developing a favorable amount of BTE degraders was reduced. [ABSTRACT FROM AUTHOR]

Abstract: Electrokinetic remediation has been successfully used to remove organic contaminants and heavy metals within soil. The electrokinetic process changes basic soil properties, but little is known about the impact of this remediation technology on indigenous soil microbial activities. This study reports on the effects of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil. The main removal mechanism of diesel was electroosmosis and most of the bacteria were transported by electroosmosis. After 25days of electrokinetic remediation (0.63mAcm−2), soil pH developed from pH 3.5 near the anode to pH 10.8 near the cathode. The soil pH change by electrokinetics reduced microbial cell number and microbial diversity. Especially the number of culturable bacteria decreased significantly and only Bacillus and strains in Bacillales were found as culturable bacteria. The use of EDTA as an electrolyte seemed to have detrimental effects on the soil microbial activity, particularly in the soil near the cathode. On the other hand, the soil dehydrogenase activity was enhanced close to the anode and the analysis of microbial community structure showed the increase of several microbial populations after electrokinetics. It is thought that the main causes of changes in microbial activities were soil pH and direct electric current. The results described here suggest that the application of electrokinetics can be a promising soil remediation technology if soil parameters, electric current, and electrolyte are suitably controlled based on the understanding of interaction between electrokinetics, contaminants, and indigenous microbial community. [Copyright &y& Elsevier]

Abstract: Habitat based protection gives soil microbial communities the ability to withstand unfavourable environmental periods. Soils differ in their ability to support and maintain microbial functions through their variation in physical and chemical properties. This paper explores the use of biocidal treatments to assess the ability of soils to protect N2-fixing communities from adverse conditions. The acetylene reduction assay was used to measure nitrogenase activity by free-living bacteria in soil exposed to additional C, and biocidal treatments (steam or CHCl3). N2-fixing microbial communities in soils with higher clay contents (∼50%) withstood fumigation treatment, demonstrated through acetylene reduction activity and a nifH PCR response, whereas those in sandy soils failed to survive. Based on this study and other research on soil aggregates, it was concluded that microbial survival in different soils was related to the ability of aggregates to provide protection against biocidal exposure within the soil matrix. This has consequences for the amount and duration N2-fixing activities in soils exposed to adverse environmental conditions. [Copyright &y& Elsevier]

Abstract: Water availability is a primary limiting factor facing agricultural systems in most semi-arid regions across the world. This study is part of a larger long-term project to develop and evaluate integrated crop and livestock systems in order to reduce dependence on underground water sources by optimizing cotton (Gossypium hirsutum) production in the Texas High Plains of U.S. Selected microbial, chemical and biochemical properties were studied (between 7 and 10 years) in a clay loam soil (fine, mixed, thermic Torrertic Paleustolls) under continuous cotton compared to an integrated cropping-livestock system that included cotton, forage, and Angus-cross-stocker beef steers (initial body weight 249kg). For the integrated system, steers grazed in sequence a perennial warm-season grass ‘WW-B. Dahl’ old world bluestem (Bothriochloa bladhii) paddock, and then rye (Secale cereale L.) and wheat (Triticum aestivum L.) grown in two paddocks (stages) of a rotation with cotton. Our previous studies after 5 years showed greater microbial biomass C (MBC) in perennial pasture (193mgkg−1 soil) and the rotation when sampled under rye or cotton (average of 237mgkg−1 soil) compared to continuous cotton (124mgkg−1 soil) at 0–5cm. After 7 years, MBC became significantly higher in the rotation independent of the crop compared to continuous cotton in this study. At the end of 10 years, total C was higher in both the rotation and pasture of the integrated cropping-livestock system (average across grazing treatments: 17.3gkg−1 soil) compared to continuous cotton (11.4gCkg−1 soil). Soil MBC and several enzyme activities were higher under non-grazed areas compared to grazed areas within the integrated cropping-livestock system in some samplings. Microbial community structure of pasture soil showed higher FAME indicators for G− (i.e., a17:0 and cy19:0) and actinomycetes (i.e., 10Me17:0) under grazed areas compared to non-grazed areas. Microbial community structure of pasture soil showed higher fungal populations compared to continuous cotton. The rotation showed intermediate sum of bacterial FAME indicators among systems (continuous cotton>rotation>pasture) and a tendency for numerically slightly higher fungi:bacterial ratios compared to continuous cotton. This study demonstrated increases in microbial biomass and enzyme activities of C-, N-, P- and S-cycling within an integrated cropping-livestock system that may represent positive changes in soil functioning compared to continuous cotton. [Copyright &y& Elsevier]

Abstract: Re-vegetation of eroded soil restores organic carbon concentrations and improves the physical stability of the soil, which may then extend the range of microhabitats and influence soil microbial activity and functional stability through its effects on soil bacterial community structure. The objectives of this study were (i) to evaluate the restorative effect of re-vegetation on soil physical stability, microbial activity and bacterial community structure; (ii) to examine the effects of soil physical microhabitats on bacterial community structure and diversity and on soil microbial functional stability. Soil samples were collected from an 18-year-old eroded bare soil restored with either Cinnamomum camphora (“Eroded Cc”) or Lespedeza bicolour (“Eroded Lb”). An uneroded soil planted with Pinus massoniana (“Uneroded Pm”) and an eroded bare soil served as references. The effect of microhabitats was assessed by physical destruction with a wet shaking treatment. Soil bacterial community structure and diversity were measured using a terminal restriction fragment length polymorphism (T-RFLP) approach, while soil microbiological stability (resistance and resilience) was determined by measuring short-term (28 days) decomposition rate of added barley (Hordeum vulgare) powder following copper and heat perturbations. The results demonstrated that re-vegetation treatment affected the recovery of physical and biological stability, microbial decomposition and the bacterial community structure. Although the restored soils overshot the Uneroded Pm sample in physical stability, they had lower microbial decomposition and less resilience to copper and heat perturbations than the Uneroded Pm samples. Soil physical destruction by shaking had the same effect on soil physical stability, but different effects on soil microbial functional stability. There were significant effects of vegetation treatment and perturbation type, and interactive effects among vegetation treatment, shaking and perturbation type on bacterial community structure. The destruction of aggregate structure increased resilience of the Eroded Lb sample and also altered its bacterial community structure. Both copper and heat perturbations resulted in significantly different community structure from the unperturbed controls, with a larger effect of copper than heat perturbation. Bacterial diversity (Shannon index) increased following the perturbations, with a more profound effect in the Uneroded Pm sample than in the restored soils. The interactive effects of vegetation treatment and shaking on microbial community and stability suggest that soil aggregation may contribute to the generation of bacterial community structure and mediation of biological stability via the protection afforded by soil organic carbon. Differential effects of re-vegetation treatment suggest that the long-term effects are mediated through changes in the quality and quantity of C inputs to soil. [Copyright &y& Elsevier]

Abstract: Soil and rhizosphere microbial communities in agroecosystems may be affected by soil, climate, plant species, and management. The management and environmental factors controlling microbial biomass and community structure were identified in a three-year field experiment. The experiment consisted of a tomato production agroecosystem with the following nine treatments: bare soil, black polyethylene mulch, white polyethylene mulch, vetch cover crop, vetch roots only, vetch shoots only, rye cover crop, rye roots only, and rye shoots only. The following hypotheses were tested: (1) Temperature and moisture differences between polyethylene-covered and cover-cropped treatments are partly responsible for treatment effects on soil microbial community composition, and (2) Different species of cover crops have unique root and shoot effects on soil microbial community composition. Microbial biomass and community composition were measured by phospholipid fatty acid analysis. Microbial biomass was increased by all cover crop treatments, including root only and shoot only. Cover cropping increased the absolute amount of all microbial groups, but Gram-positive bacteria decreased in proportion under cover crops. We attribute this decrease to increased readily available carbon under cover-cropped treatments, which favored other groups over Gram-positive bacteria. Higher soil temperatures under certain treatments also increased the proportion of Gram-positive bacteria. Vetch shoots increased the amount and proportion of Gram-negative bacteria, fungi, and arbuscular mycorrhizal fungi in the rhizosphere of tomato plants. The imposed treatments were much more significant than soil temperature, moisture, pH, and texture in controlling microbial biomass and community structure. [Copyright &y& Elsevier]

Abstract: We designed an oligonucleotide microarray using probe sequences based upon a phylogenetic analysis of 16S rRNA genes recovered from members of the bacterial division Acidobacteria. A total of 42,194 oligonucleotide probes targeting members of the Acidobacteria division at multiple phylogenetic levels were included on a high-density microarray. Positive control hybridizations revealed a linear relationship between hybridization signal and template concentration, and a substantial decrease in non-specific hybridization was achieved through the addition of 2.5 M betaine to the hybridization buffer. A mean hybridization signal value was calculated for each Acidobacteria lineage, with the resultant lineage-specific hybridization data revealing strong predictive value for the positive control hybridizations. The Acidobacteria phylochip was then used to evaluate Acidobacteria rRNA genes from a Wisconsin soil and within a soil clay fraction. The Acidobacteria hybridization profile revealed the predominance of Acidobacteria subdivisions four and six, and also suggested a decrease in the abundance of subdivision six relative to subdivision four in the soil clay fraction. The change in relative abundance of these subdivisions in a soil clay fraction was supported by data from quantitative PCR. These results support the utility of a phylogenetic microarray in revealing changes in microbial population-level distributions in a complex soil microbial assemblage. [Copyright &y& Elsevier]

Abstract: Copper (Cu) is accumulating in agricultural soils worldwide creating concern for adverse impacts on soil microbial communities and associated ecosystem services. In order to evaluate the structural and functional resilience of soil microbial communities to increasing Cu levels, we compared a Cu-adapted and a corresponding non-adapted soil microbial community for their abilities to resist experimental Cu pollution. Laboratory soil microcosms were set-up with either High-Cu soil from Cu-amended field plots (63 g Cu m−2) or with Low-Cu control soil from the same five-year field experiment. Laboratory treatments consisted of Cu amendments in the presence or absence of pig manure. Microbial activities (soil respiration, substrate-induced respiration, [3H]leucine incorporation), bacterial community structure (terminal restriction fragment length polymorphism, T-RFLP), community-level physiological profiles, and pollution-induced bacterial community tolerance (PICT detected using the [3H]leucine incorporation technique) were monitored for 12 weeks. The High-Cu and Low-Cu soil microbial communities initially exhibited almost identical structure and function and could only be distinguished from each other by their differential Cu tolerance. Experimental Cu pollution inhibited microbial activities, affected bacterial community structure, and induced further bacterial community tolerance to Cu. However, Low-Cu and High-Cu soil microbial communities showed essentially identical responses. Manure amendment did not protect against Cu toxicity and slightly increased Cu bioavailability as measured by a Cu-specific whole-cell bacterial biosensor. Our results indicate convergence of bacterial community structure and function in the High-Cu and Low-Cu soils during the five-year field experiment. We conclude that soil bacterial communities can exhibit structural and functional resilience to a five-year Cu exposure by virtue of their ability to develop Cu tolerance without affecting overall community structure. The observed increased Cu tolerance may involve phenotypic adaptation or selection at the micro-diversity level, for example an increased proportion of Cu-resistant strains within each bacterial species, which go undetected by T-RFLP community fingerprinting. Finally, our results indicate that Cu-dissolved organic matter complexes contribute to microbial toxicity in manure-amended soils implying that free Cu may comprise a poor predictor of metal toxicity. [Copyright &y& Elsevier]

Abstract: Storage of samples is often an unavoidable step in environmental data collection, since available analytical capacity seldom permits immediate processing of large sample sets needed for representative data. In microbiological soil studies, sample pretreatments may have a strong influence on measurement results, and thus careful consideration is required in the selection of storage conditions. The aim of this study was to investigate the suitability of prolonged (up to 16weeks) frozen or air-dried storage for divergent soil materials. The samples selected to this study were mineral soil (clay loam) from an agricultural field, humus from a pine forest and compost from a municipal sewage sludge composting field. The measured microbiological parameters included functional profiling with ten different hydrolysing enzyme activities determined by artificial fluorogenic substrates, and structural profiling with bacterial 16S rDNA community fingerprints by amplicon length heterogeneity analysis (LH-PCR). Storage of samples affected the observed fluorescence intensity of the enzyme assay''s fluorophor standards dissolved in soil suspension. The impact was highly dependent on the soil matrix and storage method, making it important to use separate standardisation for each combination of matrix type, storage method and time. Freezing proved to be a better storage method than air-drying for all the matrices and enzyme activities studied. The effect of freezing on the enzyme activities was small (<20%) in clay loam and forest humus and moderate (generally 20–30%) in compost. The most dramatic decreases (>50%) in activity were observed in compost after air-drying. The bacterial LH-PCR community fingerprints were unaffected by frozen storage in all matrices. The effect of storage treatments was tested using a new statistical method based on showing similarity rather than difference of results. [Copyright &y& Elsevier]

Abstract: Long-term diversity-disturbance responses of soil bacterial communities to copper were determined from field-soils (Spalding; South Australia) exposed to Cu in doses ranging from 0 through to 4012mgCukg−1 soil. Nearly 6 years after application of Cu, the structure of the total bacterial community showed change over the Cu gradient (PCR-DGGE profiling). 16S rRNA clone libraries, generated from unexposed and exposed (1003mgCu addedkg−1 soil) treatments, had significantly different taxa composition. In particular, Acidobacteria were abundant in unexposed soil but were nearly absent from the Cu-exposed sample (P<0.05), which was dominated by Firmicute bacteria (P<0.05). Analysis of community profiles of Acidobacteria, Bacillus, Pseudomonas and Sphingomonas showed significant changes in structural composition with increasing soil Cu. The diversity (Simpsons index) of the Acidobacteria community was more sensitive to increasing concentrations of CaCl-extractable soil Cu (CuExt) than other groups, with decline in diversity occurring at 0.13CuExt mgkg−1 soil. In contrast, diversity in the Bacillus community increased until 10.4CuExt mgkg−1 soil, showing that this group was 2 orders of magnitude more resistant to Cu than Acidobacteria. Sphingomonas was the most resistant to Cu; however, this group along with Pseudomonas represented only a small percentage of total soil bacteria. Changes in bacterial community structure, but not diversity, were concomitant with a decrease in catabolic function (BioLog). Reduction in function followed a dose-response pattern with CuExt levels (R 2=0.86). The EC50 for functional loss was 0.21CuExt mgkg−1 soil, which coincided with loss of Acidobacteria diversity. The microbial responses were confirmed as being due to Cu and not shifts in soil pH (from use of CuSO4) as parallel Zn-based field plots (ZnSO4) were dissimilar. Changes in the diversity of most bacterial groups with soil Cu followed a unimodal response – i.e. diversity initially increased with Cu addition until a critical value was reached, whereupon it sharply decreased. These responses are indicative of the intermediate-disturbance-hypothesis, a macroecological theory that has not been widely tested in environmental microbial ecosystems. [Copyright &y& Elsevier]

Abstract: 2,4-Dichlorophenoxyacetic acid butyl ester (2,4-D butyl ester) is extensively applied for weed control in cultivation fields in China, but its effect on soil microbial community remains obscure. This study investigated the microbial response to 2,4-D butyl ester application at different concentrations (CK, 10, 100 and 1000 μg g−1) in the soils with two fertility levels, using soil dilution plate method and phospholipid fatty acid (PLFA) analysis. Culturable microorganisms were affected by the herbicide in both soils, particularly at the higher concentration. After treating soil with 100 μg g−1 herbicide, culturable bacteria and actinomycetes were significantly higher, compared to other treatments. Treatment of soil with 1000 μg g−1 2,4-D butyl ester caused a decline in culturable microbial counts, with the exception of fungal numbers, which increased over the incubation time. PLFA profiles showed that fatty acids for Gram-negative (GN) bacteria, Gram-positive (GP) bacteria, total bacteria and total fungi, as well as total PLFAs, varied with herbicide concentration for both soil samples. As herbicide concentration increased, the GN/GP ratio decreased dramatically in the two soils. The higher stress level was in the treatments with high concentrations of herbicide (1000 μg g−1) for both soils. Principal component analysis of PLFAs showed that the addition of 2,4-D butyl ester significantly shifted the microbial community structure in the two soils. These results showed that the herbicide 2,4-D butyl ester might have substantial effects on microbial population and microbial community structure in agricultural soils. In particular, the effects of 2,4-D butyl ester were greater in soil with low organic matter and fertility level than in soil with high organic matter and fertility level. [Copyright &y& Elsevier]

Abstract: The effect of copper on the abundance, diversity and resistance of viable heterotrophic and copper resistant bacterial populations (CuR) was evaluated in soils differing only by their amount and type of organic matter. These soils have been obtained using a vineyard soil that had been subjected to three different organic matter managements (Not Amended (NA) or amended with Straw (S) or Conifer Compost (CC)) in a long term field experiment. Soil microcosms were artificially contaminated with copper (250 mg Cu kg−1 of soil) and incubated for 35 days. Throughout the incubation, a differential copper impact on viable heterotrophic and CuR bacterial enumeration was demonstrated according to the soil organic status with a magnitude which followed the order: NA > CC ≥ S. Diversity of CuR bacteria revealed no significant difference between the uncontaminated soils, as determined by 16S rRNA sequencing. However, copper spiking induced an enrichment of particular populations depending on soil, with Methylobacterium, Ralstonia and Staphylococcus like species becoming dominant in NA, S and CC soils, respectively. Evaluation of the copA gene distribution and diversity, through PCR detection and sequencing, revealed that few CuR bacteria (from 7 to 13%) possessed this genetic determinant before the addition of metal. Copper contamination induced an increase in the dissemination of homologous copA genes only in Ralstonia like species indigenous to S soils. From a functional point of view, copper minimum inhibitory concentration for each CuR strain was measured. It did not highlight variable copper resistance efficiency between strains belonging to different taxonomic groups, harboring or not the copA gene, and originating from different soils contaminated or not by copper. [Copyright &y& Elsevier]

Abstract: Tillage may influence the microbial populations involved in soil aggregation. We evaluated the effects of no till (NT) and conventional tillage (CT, tillage depth about 7 cm) continuous spring wheat system on culturable heterotrophic bacterial communities predominant in microaggregates (0.25–0.05 mm) and on soil-aggregating basidiomycete fungi in aggregate-size classes (4.75–2.00, 2.00–0.25, and 0.25–0.05 mm) at 0–20 cm depth of a Williams loam (fine-loamy, mixed, Typic Argiustolls) in dryland Montana, USA. Enzyme-linked immunosorbent assay used to quantify antigenic response to basidiomycete cell walls, was higher in NT than in CT in 4.75–2.00 mm size class in 2007 and higher in all classes and years at 0–5 cm depth, but was not different between tillage, years, and classes at 5–20 cm. The culturable bacteria from microaggregates were subjected to a soil sedimentation assay to determine their soil binding capability. The proportion of isolates which can function as soil aggregators was higher in NT than in CT at 0–5 cm but was not different at 5–20 cm. Our results provide a first insight into the beneficial effects of dryland NT compared to CT in reducing soil disturbance and residue incorporation and enriching the proportion of microorganisms responsible for aggregation, especially at the soil surface. [Copyright &y& Elsevier]

Abstract: Eucalyptus is one of the fastest growing woody plants in the world, but few studies have reported the soil microbial community composition in Eucalyptus ecosystems. This study investigated the soil microbial communities in plantations of 3-, 7-, 10- and 13-year-old Eucalyptus in subtropical China based on phospholipid fatty acids (PLFA) analysis. The variation in soil microbial biomass and community compositions were influenced by sampling site and season and the interaction of both, which were consistent with the variation in soil total nitrogen (TN), soil organic carbon (SOC) and soil moisture. The number and abundances of PLFAs, and the amount of soil TN and SOC were higher in plantation of 13-year-old Eucalyptus than those in other younger plantations, suggesting that the soil properties and the soil microbial community composition is not negatively affected by the planting of Eucalyptus. The ratio of monounsaturated-to-branched fatty acids, the proportional abundance (mol%) of bacterial PLFA and fungal PLFA varied significantly with Eucalyptus plantations of different age, suggesting that the individual PLFA signatures might be sensitive indicators of soil properties associated with forest plantations. [Copyright &y& Elsevier]

Heavy metal pollution of soil is a significant environmental problem with a negative potential impact on human health and agriculture. Rhizosphere, as an important interface of soil and plants, plays a significant role in phytoremediation of contaminated soil by heavy metals, in which, microbial populations are known to affect heavy metal mobility and availability to the plant through release of chelating agents, acidification, phosphate solubilization and redox changes, and therefore, have potential to enhance phytoremediation processes. Phytoremediation strategies with appropriate heavy metal-adapted rhizobacteria or mycorrhizas have received more and more attention. In addition, some plants possess a range of potential mechanisms that may be involved in the detoxification of heavy metals, and they manage to survive under metal stresses. High tolerance to heavy metal toxicity could rely either on reduced uptake or increased plant internal sequestration, which is manifested by an interaction between a genotype and its environment.A coordinated network of molecular processes provides plants with multiple metal-detoxifying mechanisms and repair capabilities. The growing application of molecular genetic technologies has led to an increased understanding of mechanisms of heavy metal tolerance/accumulation in plants and, subsequently, many transgenic plants with increased heavy metal resistance, as well as increased uptake of heavy metals, have been developed for the purpose of phytoremediation. This article reviews advantages, possible mechanisms, current status and future direction of phytoremediation for heavy-metal–contaminated soils. [ABSTRACT FROM AUTHOR]

Summary: The effects of organic manure, mineral fertilizer (NPK), and P-deficiency fertilization (NK) on the individual biomass of young wheat plants, arbuscular mycorrhizal (AM) colonization in wheat root systems, population sizes of soil organic phosphorus mineralizing bacteria (OPMB) and inorganic phosphate solubilizing bacteria (IPSB) as well as soil P-mineralization and -solubilization potential were investigated in a long-term (18-year) fertilizer experiment. The experiment included five treatments: organic manure, an equal mixture of organic manure and mineral fertilizer, fertilizer NPK, fertilizer NK, and the control (without fertilization). Plant biomass, population sizes of soil OPMB and IPSB were greatly increased (P<0.05) by the application of organic manure and slightly increased by the balanced application of mineral fertilizer, while undiminished AM colonization in wheat root system was only observed in the case of the NK treatment. Compared to balanced fertilization, P-deficiency fertilization resulted in a significant increase (P<0.05) of OPMB-specific mineralization potential (soil P-mineralization potential per OPMB cell) and highest IPSB-specific solubilization potential (soil P-solubilization potential per IPSB cell), suggesting that OPMB and IPSB are likely more metabolically active in P-deficiency fertilized soils after long-term fertilizer management, and mycorrhizal plants are more dependent on AM in P-poor soils than in P-fertilized soils. Our results also showed the different effects of mineral fertilizer versus organic manure on soil P-mineralization and -solubilization potentials, as well as specific potentials of OPMB and IPSB in arable soils. [Copyright &y& Elsevier]

Summary: Social interactions among microbes that engage in cooperative behaviors are well studied in laboratory contexts , but little is known about the scales at which initially cooperative microbes diversify into socially conflicting genotypes in nature. The predatory soil bacterium Myxococcus xanthus responds to starvation by cooperatively forming multicellular fruiting bodies in which a portion of the population differentiates into stress-resistant spores . Natural M. xanthus populations are spatially structured , and genetically divergent isolates from distant origins exhibit striking developmental antagonisms that decrease spore production in chimeric fruiting bodies . Here we show that genetically similar isolates of M. xanthus from a centimeter-scale population also exhibit strong and pervasive antagonisms when mixed in development. Negative responses to chimerism were less intense on average among local strains than among global isolates, although no significant correlation was found between genetic distance at multilocus sequence typing (MLST) loci and the degree of social asymmetry between competitors. A test for self/nonself discrimination during vegetative swarming revealed a great diversity of distinct self-recognition types even among identical MLST genotypes. Such nonself exclusion may serve to direct the benefits of cooperation to close kin within diverse populations in which the probability of social conflict among neighbors is high. [Copyright &y& Elsevier]

A specificity of Brassicaceous plants is the production of sulphur secondary metabolites called glucosinolates that can be hydrolysed into glucose and biocidal products. Among them, isothiocyanates are toxic to a wide range of microorganisms and particularly soil-borne pathogens. The aim of this study was to investigate the role of glucosinolates and their breakdown products as a factor of selection on rhizosphere microbial community associated with living Brassicaceae. We used a DNA-stable isotope probing approach to focus on the active microbial populations involved in root exudates degradation in rhizosphere. A transgenic Arabidopsis thaliana line producing an exogenous glucosinolate and the associated wild-type plant associated were grown under an enriched 13CO2 atmosphere in natural soil. DNA from the rhizospheric soil was separated by density gradient centrifugation. Bacterial (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Acidobacteria), Archaea and fungal community structures were analysed by DGGE fingerprints of amplified 16S and 18S rRNA gene sequences. Specific populations were characterized by sequencing DGGE fragments. Roots of the transgenic plant line presented an altered profile of glucosinolates and other minor additional modifications. These modifications significantly influenced microbial community on roots and active populations in the rhizosphere. Alphaproteobacteria, particularly Rhizobiaceae, and fungal communities were mainly impacted by these Brassicaceous metabolites, in both structure and composition. Our results showed that even a minor modification in plant root could have important repercussions for soil microbial communities. [ABSTRACT FROM AUTHOR]

The biodegradation of nonextractable residues (NER) of pesticides in soil is still poorly understood. The aim of this study was to evaluate the influence of NER ageing and fresh soil addition on the microbial communities responsible for their mineralisation. Soil containing either 15 or 90-day-old NER of 13C-2,4-D (NER15 and NER90, respectively) was incubated for 90 days with or without fresh soil. The addition of fresh soil had no effect on the mineralisation of NER90 or of SOM, but increased the extent and rate of NER15 mineralisation. The analyses of 13C-enriched FAME (fatty acids methyl esters) profiles showed that the fresh soil amendment only influenced the amount and structure of microbial populations responsible for the biodegradation of NER15. By coupling biological and chemical analyses, we gained some insight into the nature and the biodegradability of pesticide NER. [Copyright &y& Elsevier]

Calcium cyanamide (CaCN2) has been one of the potential candidates as soil disinfectant since the restriction of methyl bromide in soil fumigation due to its ecological risk. However, little information is available on effects of CaCN2 on soil microbial community. In this study, the soil microbial communities and the fate of pathogen Fusarium oxysporum (Schlechtend, Fr) f. sp. cucumberinum (Owen) Snyder and Hansen (F.O. f. sp. cucumberinum) in response to CaCN2 treatment was evaluated. F.O. f. sp. cucumberinum population in soil treated with CaCN2 at rates of 80 and 200gm−2 was suppressed by 88.7 and 92.2% after 15d of CaCN2 application. Bacterial, fungal, and actinomycete populations were also greatly decreased after 3d of CaCN2 application, but they recovered to the control level by 15d. The variation in functional diversity of soil microbes characterized by principal component analysis, diversity and evenness indices based on Biolog data followed a similar trend. Meanwhile, the band number from the DGGE of soil 16S rDNA fragments increased from 9 for the non-CaCN2-treated soil to 10 or 12 after different rates of CaCN2 application at 15d, indicating the increase of abundant rDNA types in the community. The results suggest that CaCN2 application had only a short-term and transitory impact on the indigenous soil microbial community in contrast to the long-term suppression of the F.O. f. sp. cucumberinum population. It is feasible to reduce Fusarium wilt without significant impact on microbial community by application of CaCN2 at reasonable doses. [Copyright &y& Elsevier]

There is a need for research projects to provide scientific arguments favouring a greater implementation of tree-based intercropping (TBI) systems in Canada’s rural landscape. We tested the hypothesis that TBI increases the beta-diversity and stability of soil microbial communities compared to conventional monocropping (CM) systems. Soil from TBI research plots in St-Rémi (Québec) and Guelph (Ontario) were intensively sampled along 56-point grid patterns and compared to soil sampled in a similar manner in adjacent CM systems. Phospholipid fatty acids (PLFAs) were extracted from each sample, purified and methylated, and subsequently analyzed by gas chromatography. The spatial heterogeneity (i.e., microbial beta-diversity) of whole PLFA profiles from each field were analyzed using multivariate statistical procedures (PCA and PERMDISP), and those of individual PLFAs were analyzed using Levene’s and Moses’ tests. Microbial beta-diversity, based on a measure of dispersion among PLFA profiles within each sampling grid, was significantly higher in the TBI than in the CM system at the St-Rémi site only. Multivariate multiple regression analyses failed to reveal any significant relationship between soil physico-chemical variables and shifts in soil PLFA profiles. We compared the concentrations of broad microbial groups in both cropping systems using Tukey’s test and found a higher incidence of arbuscular mycorrhizal fungi (AMF) in TBI systems at both sites, and a greater ratio of gram positive-to-gram negative bacteria in the TBI system at the St-Rémi site only. In order to determine microbial stability, we monitored changes in microbial biomass of bulked soil samples from the sampling grids after these had been exposed to varying concentrations of a heavy metal (Cu) contaminant. Data were then fitted to decreasing exponential functions and model parameters were used to derive an index of microbial stability. Higher microbial stability was found in the TBI than in the CM system at the St-Rémi site only. Because our hypotheses regarding soil microbial beta-diversity and stability were confirmed at only one of two sites, our conclusions warrant prudence and discretion. Future research should explore the possible role of tree roots in maintaining AMF and other beneficial soil organisms for alley crops. [Copyright &y& Elsevier]

Abstract: We studied, under two different plant compositions, the short-term effects of glyphosate on rhizosphere soil microbial communities through the utilization of cultivation-dependent and -independent techniques. A short-term pot study was carried out using factorial treatments that included two different compositions of forage plant species (triticale versus a mixture of triticale and pea) and two concentrations of glyphosate (50 and 500mgactiveingredientkg−1 soil, as a commercial formulation, Roundup Plus) arranged in a completely randomized design experiment with four replicates. Control plants (no glyphosate added) were clipped in an attempt to compare two methods of weed control (manual=clipping; chemical=herbicide treatment). Rhizosphere soil was sampled 15 and 30 days after glyphosate treatment and the following soil components were determined: potentially mineralizable nitrogen, ammonium content, community-level physiological profiles using Biolog Ecoplates™, DNA microbial biomass and genotype diversity by means of PCR-DGGE. Fifteen days after herbicide treatment, a glyphosate-induced stimulation of the activity and functional diversity of the cultivable portion of the heterotrophic soil microbial community was observed, most likely due to glyphosate acting as an available source of C, N and P. On the other hand, 30 days after herbicide treatment, both the activity and diversity of the rhizosphere soil microbial communities showed an inconsistent response to glyphosate addition. Apart from its intended effect on plants, glyphosate had non-target effects on the rhizosphere soil microbial community which were, interestingly, more enhanced in triticale than in “triticale+pea” pots. Biolog™ was more sensitive than PCR-DGGE to detect changes in soil microbial communities induced by glyphosate and plant composition. [Copyright &y& Elsevier]

Abstract: Invasive plant species have been shown to alter the microbial community composition of the soils they invade and it is suggested that this below-ground perturbation of potential pathogens, decomposers or symbionts may feedback positively to allow invasive success. Whether these perturbations are mediated through specific components of root exudation are not understood. We focussed on 8-hydroxyquinoline, a putative allelochemical of Centaurea diffusa (diffuse knapweed) and used an artificial root system to differentiate the effects of 8-hydroxyquinoline against a background of total rhizodeposition as mimicked through supply of a synthetic exudate solution. In soil proximal (0–10cm) to the artificial root, synthetic exudates had a highly significant (P <0.001) influence on dehydrogenase, fluorescein diacetate hydrolysis and urease activity. In addition, 8-hydroxyquinoline was significant (p =0.003) as a main effect on dehydrogenase activity and interacted with synthetic exudates to affect urease activity (p =0.09). Hierarchical cluster analysis of 16S rDNA-based DGGE band patterns also identified a primary affect of synthetic exudates and a secondary affect of 8-hydroxyquinoline on bacterial community structure. Thus, we show that the artificial rhizosphere produced by the synthetic exudates was the predominant effect, but, that the influence of the 8-hydroxyquinoline signal on the activity and structure of soil microbial communities could also be detected. [Copyright &y& Elsevier]

Abstract: Increased vegetative growth and soil carbon (C) storage under elevated carbon dioxide concentration ([CO2]) has been demonstrated in a number of experiments. However, the ability of ecosystems, either above- or belowground, to maintain increased C storage relies on the response of soil processes, such as those that control nitrogen (N) mineralization, to climatic change. These soil processes are mediated by microbial communities whose activity and structure may also respond to increasing atmospheric [CO2]. We took advantage of a long-term (ca 10y) CO2 enrichment experiment in a sweetgum plantation located in the southeastern United States to test the hypothesis that observed increases in root production in elevated relative to ambient CO2 plots would alter microbial community structure, increase microbial activity, and increase soil nutrient cycling. We found that elevated [CO2] had no detectable effect on microbial community structure using 16S rRNA gene clone libraries, on microbial activity measured with extracellular enzyme activity, or on potential soil N mineralization and nitrification rates. These results support findings at other forested Free Air [CO2] Enrichment (FACE) sites. [Copyright &y& Elsevier]

Abstract: The molecular diversity of bacterial chitinases in the bulk soils of arable land was investigated using culture-independent methods. The results demonstrate that bacterial chitinases in arable soils are highly diverse and comprise unique groups when their sequences were compared to those in public databases. The diversity of bacterial chitinases in arable soil was further evaluated using conventional phylogenetic analysis, the UniFrac analysis of the phylogenetic data, and the multidimensional scaling (MDS) analysis of T-RFLP profiles to elucidate the relationship between the diversity of bacterial chitinases and soil characteristics. These analyses indicate that environmental factors such as soil type and pH are responsible for shaping the composition of bacterial chitinases. [Copyright &y& Elsevier]

Abstract: CO2 capture and sto rage in deep saline aquifers or depleted gas and oil reservoirs offer is one option for reducing greenhouse gas emissions. Our study aims at investigating the environmental impact of CO2 leakage from deep reservoirs into near-surface terrestrial environmen ts. To understand the effect of unlikely, but potential CO2 release on such an ecosystem, detailed knowledge on the abundance and diversity of plants and microorganisms is essential. Therefore, an ecosystem study has been conducted within the Network of Excellence “ CO2GeoNet” on a natural CO2 vent at the Laacher See, Germany. The investigation of environmentally important microbial communities in the soil samples show ed significant differe nces between the CO2-rich (>90% of soil gas), the medium CO2 (20%), and the control site with background CO2 concentrations. The ecosystem appears to have adapted to the different conditions through species substitution or adaptation, showing a shift towards anaerobic and acidophilic species under elevated CO2 con centrations. At the end, this study should identify possible candidates in the botanical and microbial kingdoms, whose presence or absence provide easily detectable indicators for the leakage of CO2 fro m deep reservoirs into near-surface terrestrial ecosystems. [Copyright &y& Elsevier]

The impact of pioneer plant species Tussilago farfara on structural, functional, and growth characterization of microbial community colonizing the spoil colliery substrate was studied in a laboratory microcosm experiment. Microcosms consisting of spoil substrate (0.7 dm3 of tertiary alkaline clay sediment from Sokolov brown-coal mine area) from a pioneer site (without vegetation, 5 years after heaping) were cultivated in a greenhouse with one plant of this species. Plant roots substantially increased microbial diversity and biomass after one season (7 months) of cultivation. Roots influenced the microbial community and had nearly twice the size, higher growth, and metabolic potential in comparison to the control. The development of microbial specialists improves the plant nutrient status. Bacterial nitrogen (N)2 fixators (Bradyrhizobium japonicum, Rhizobium radiobacter) and arbuscular mycorrhizal fungi were confirmed in the rhizosphere of Tussilago farfara. [ABSTRACT FROM AUTHOR]

Adoption of glyphosate-resistant canola (Brassica napus L.) has increased glyphosate applications to this crop, and concerns have been raised about unintended consequences of these multiple applications. A field trial was conducted to evaluate the effects of pre-seed and in-crop glyphosate and alternative herbicides on soil microbial community functional structure, diversity and biomass. Pre-seed treatments were 2,4-D, glyphosate and 2,4-D +glyphosate, and in-crop treatments were glyphosate applied once, glyphosate applied twice, ethalfluralin, ethalfluralin+sethoxydim+ethametsulfuron+clopyralid, and sethoxydim+ethametsulfuron. Rhizosphere and bulk soil was collected at flowering stage of canola and analyzed for bacterial community-level substrate utilization patterns and microbial biomass C (MBC). Where differences were significant, pre-seed application of both 2,4-D and glyphosate altered the functional structure and reduced the functional diversity of soil bacteria, but increased MBC. These effects were not necessarily concurrent. The reduction in functional diversity was due to reduction in evenness, which means that the soil where both pre-seed herbicides had been applied was dominated by only few functional groups. In 1 year, two in-crop applications of glyphosate also reduced the functional diversity of soil bacteria when applied after pre-seed 2,4-D, as did in-crop sethoxydim+ethametsulfuron following pre-seed glyphosate. Even though significant differences between herbicides were fewer than non-significant differences, i.e., there were no changes in soil microbial community structure, diversity or biomass in response to glyphosate or alternative herbicides applied to glyphosate-resistant canola in most cases, the observed changes in soil microbial communities could affect soil food webs and biological processes. [Copyright &y& Elsevier]

Abstract: Stable Isotope Probing (SIP) is a powerful tool for analysing the fate of pesticides in soil. Together with FAME (Fatty Acid Methyl Esters), it can help identify biodegradation pathways and recycling into the microbial biomass. The fate of ring-labelled 13C-2,4-dichlorophenoxyacetic acid or 2,4-D (C2,4-D) was determined in soil during a 6-month incubation. The distribution of 13C among the microbial biomass, the CO2 respired, the water, methanol and dichloromethane soluble fractions, and the residual non-extracted bulk soil was measured. Molecular analyses were carried out on the lipid and the non-extractable fractions. After 8 days, about half of the initial amount of C2,4-D was mineralised; the other half remained in soil as non-extractable residues (NER). C2,4-D continued to be mineralised, suggesting that NER were still bioavailable. Analysis of C2,4-D-enriched FAME contained in the lipid fraction suggested that a succession of microbial populations was involved in 2,4-D biodegradation. This is possibly due to the change of 2,4-D availability. The C2,4-D yield coefficient and degrader diversity evolved during the incubation, providing corroboratory evidence that different physiological groups were active during the incubation. The 13C-labelled microbial community was always less diverse than the total community, even at the end of the incubation, suggesting that the cross-feeding community is also a specific part of the total community. This work shows that molecular analysis of 13C-labelled pesticides is a useful tool for understanding both chemical and biological aspects of their fate in soil. [Copyright &y& Elsevier]

Abstract: Rhizodeposit-carbon provides a major energy source for microbial growth in the rhizosphere of grassland soils. However, little is known about the microbial communities that mediate the rhizosphere carbon dynamics, especially how their activity is influenced by changes in soil management. We combined a 13CO2 pulse-labeling experiment with phospholipid fatty acid (PLFA) analysis in differently managed Belgian grasslands to identify the active rhizodeposit-C assimilating microbial communities in these grasslands and to evaluate their response to management practices. Experimental treatments consisted of three mineral N fertilization levels (0, 225 and 450kgNha−1 y−1) and two mowing frequencies (3 and 5 times y−1). Phospholipid fatty acids were extracted from surface (0–5cm) bulk (BU) and root-adhering (RA) soil samples prior to and 24h after pulse-labeling and were analyzed by gas chromatography–combustion-isotope ratio mass spectrometry (GC–c-IRMS). Soil habitats significantly differed in microbial community structure (as revealed by multivariate analysis of mol% biomarker PLFAs) as well as in gram-positive bacterial rhizodeposit-C uptake (as revealed by greater 13C-PLFA enrichment following pulse-labeling in RA compared to BU soil in the 450N/5M treatment). Mowing frequency did not significantly alter the relative abundance (mol%) or activity (13C enrichment) of microbial communities. In the non-fertilized treatment, the greatest 13C enrichment was seen in all fungal biomarker PLFAs (C16:1ω5, C18:1ω9, C18:2ω6,9 and C18:3ω3,6,9), which demonstrates a prominent contribution of fungi in the processing of new photosynthate-C in non-fertilized grassland soils. In all treatments, the lowest 13C enrichment was found in gram-positive bacterial and actinomycetes biomarker PLFAs. Fungal biomarker PLFAs had significantly lower 13C enrichment in the fertilized compared to non-fertilized treatments in BU soil (C16:1ω5, C18:1ω9) as well as RA soil (all fungal biomarkers). While these observations clearly indicated a negative effect of N fertilization on fungal assimilation of plant-derived C, the effect of N fertilization on fungal abundance could only be detected for the arbuscular mycorrhizal fungal (AMF) PLFA (C16:1ω5). On the other hand, increases in the relative abundance of gram-positive bacterial PLFAs with N fertilization were found without concomitant increases in 13C enrichment following pulse-labeling. We conclude that in situ 13C pulse-labeling of PLFAs is an effective tool to detect functional changes of those microbial communities that are dominantly involved in the immediate processing of new rhizosphere-C. [Copyright &y& Elsevier]

Bacterial succession in soil was studied for two variants of initiation (moistening and moistening with addition of glucose). To determine the numbers of viable gram-negative bacteria, the modified nalidixic acid method was applied. The numbers of gram-negative bacteria revealed by this method were 2 to 3.5 times higher than those determined by the traditional method. In a developing community, the highest total bacterial numbers were observed on day 7; afterwards their numbers decreased and stabilized at a level exceeding four-to fivefold the initial one. In both experimental variants, the highest numbers of viable gram-negative bacteria were revealed on day 15 (75–85% of the total bacterial numbers). Morphology of these bacteria suggests their classification as cytophagas (chitinophagas) utilizing chitin from the dead fungal mycelium. [ABSTRACT FROM AUTHOR]

Abstract: In an effort to generate more information on the use of biosolids in the turf industry, a study was conducted to compare the effectiveness of biosolids with recommended organic sources in enhancing soil microbial populations and N availability in putting green sand rootzones. The treatments included four types of rootzones as follows: sand (control), sand mixed with Dakota reed-sedge peat (10%, v/v), sand mixed with yard-waste compost (10%, v/v), and sand mixed with biosolids (10%, v/v), which were established at the North Shore Country Club golf course, Glenview, IL, USA in 1997. All plots received the same fertilizers mainly in organic forms at 100kgNha−1 year−1. Creeping bentgrass (Agrostis palustris) turf was established, and was managed as a practice putting green. Soil microbial biomass in the rootzone (0–30cm) was higher either under compost (fall 2004 and summer 2005) or biosolids (summer 2003) than other treatments. Rootzone ammonium oxidizer populations were higher with biosolids (5400g−1 soil) than peat (1200g−1 soil) and compost (500g−1 soil) amendment and in control (400g−1 soil) in summer 2003. The nitrite oxidizer populations were higher with biosolids (24000g−1 soil) than compost (8300g−1 soil) and peat (4700g−1 soil) amendment and in control (3700g−1 soil) in summer 2005. Soil potentially mineralizable N, also being lowest in control, was higher in the biosolids-amended than compost- and peat-amended rootzones. In most seasons, the nitrate concentrations in biosolids rootzone (3.16–19.3mgkg−1) were higher than in compost (2.79–17.7mgkg−1), peat (1.83–14.4mgkg−1), and control rootzone (0.81–15.2mgkg−1). The study indicates that while compost could restore soil microbial biomass better than peat, biosolids could maintain greater N supply than peat and compost. [Copyright &y& Elsevier]

Exposure to pollution exerts strong selective pressure on microbial communities, which may affect their potential to adapt to current or future environmental challenges. In this microcosm study, we used DNA fingerprinting based on 16S rRNA genes to document the impact of high concentrations of benzene on two bacterial communities from a benzene-contaminated aquifer situated below a petrochemical plant (SIReN, UK). The two groundwaters harboured distinct aerobic benzene-degrading communities able to metabolize benzene to below detection levels (1 μg L−1). A benzene concentration of 100 mg L−1 caused a major shift from Betaproteobacteria to Actinobacteria, in particular Arthrobacter spp. A similar shift from Betaproteobacteria to Arthrobacter spp. and Rhodococcus erythropolis was observed in minimal medium (MM) inoculated with a third groundwater. These Gram-positive-dominated communities were able to grow on benzene at concentrations up to 600 mg L−1 in groundwater and up to 1000 mg L−1 in MM, concentrations that cause significant solvent stress to cellular systems. Therefore, Gram-positive bacteria were better competitors than Gram-negative organisms under experimental conditions of high benzene loads, which suggests that solvent-tolerant Gram-positive bacteria can play a role in the natural attenuation of benzene or the remediation of contaminated sites. [ABSTRACT FROM AUTHOR]

The long-term impacts of Cu- and Zn-rich sewage sludge additions on the structure of the microbial community in a field under pasture were investigated using a combination of multiplex-terminal restriction fragment length polymorphism (M-TRFLP) and T-RFLP profiling approaches. Changes in the community structure of bacteria, fungi, archaea and actinobacteria were observed in soils that had previously received Cu- (50–200 mg kg−1 soil) and Zn- (150–450 mg kg−1 soil) rich sewage sludge additions. Changes in the structure of all microbial groups measured were observed at Cu and Zn rates below the current EU guidelines (135 mg kg−1 Cu and 300 mg kg−1 Zn). The response of the fungal community, and to a lesser extent the bacterial and archaeal community, to Cu was dose dependent. The fungal community also showed a dose-dependent response to Zn, which was not observed in the other microbial groups assessed. Redundancy analysis demonstrated that individual terminal restriction fragments responded to both Cu and Zn and these may have potential as genetic markers of long-term metal effects in soil. [ABSTRACT FROM AUTHOR]

The impact and frequency of forest harvesting could significantly affect soil microbial community (SMC) structure and functioning. The ability of soil microorganisms to perform biogeochemical processes is critical for sustaining forest productivity and has a direct impact on decomposition dynamics and carbon storage potential. The Wind River Canopy Crane Research Forest in SW, WA, provided a unique opportunity to study a forest chronosequence and the residual effects of harvesting on the SMC in comparison to old-growth forests. The objective of this study was to determine the effect of clear-cutting and stand age on temporal dynamics of SMC and physiological stress markers using phospholipid fatty acid (PLFA) profiling. Soil microbial PLFA profiles were determined seven times over 22 months (Nov. 02 to Sep. 04) in old-growth coniferous forest stands (300–500 years) and 8 (CC8)- or 25 (CC25)-year-old replanted clear-cuts. PLFA patterns of the SMC shifted because of clear-cutting, but seasonal temporal changes had greater shifts than differences among stand age. The microbial biomass (total PLFA) and bacterial, fungal, and selected other PLFAs were significantly reduced in CC8 but not in CC25 sites relative to the old-growth sites. An increase in stress indicators [PLFA ratios of saturated/monsaturated and (cy17:0 + cy19:0)/(16:1ω7 + 18:1ω7)] in late summer was related to water stress. Although the canopy and litter input are quite different for a 25-year clear-cut compared to virgin old-growth forest, we conclude that the composition of the microbial communities, 25 years after clear-cutting, has recovered sufficiently to be much more similar to old-growth forests than a recent clear-cut at this Pacific Northwest forest site. The study shows the potential of PLFA analysis for profiling microbial communities and their stress status under field conditions, but wide temporal shifts emphasize the need for sampling over seasons to fully interpret ecosystem management impacts on microbial populations. [ABSTRACT FROM AUTHOR]

Traditionally, the identification and characterization of microbial communities in contaminated soil and water has previously been limited to those microorganisms that are culturable. The application of molecular techniques to study microbial populations at contaminated sites without the need for culturing has led to the discovery of unique and previously unrecognized microorganisms as well as complex microbial diversity in contaminated soil and water which shows an exciting opportunity for bioremediation strategies. Nucleic acid extraction from contaminated sites and their subsequent amplification by polymerase chain reaction (PCR) has proved extremely useful in assessing the changes in microbial community structure by several microbial community profiling techniques. This review examines the current application of molecular techniques for the characterization of microbial communities in contaminated soil and water. Techniques that identify and quantify microbial population and catabolic genes involved in biodegradation are examined. In addition, methods that directly link microbial phylogeny to its ecological function at contaminated sites as well as high throughput methods for complex microbial community studies are discussed. [Copyright &y& Elsevier]

Arbuscular mycorrhizal fungi (AMF) are potentially important in nutrient cycling in agricultural soils and particularly in soils managed for organic production; little is known, however, about the interrelationships between AMF and other members of soil microbial communities. Ammonia oxidizing bacteria (AOB) are a trophic group of bacteria having an enormous impact on nitrogen availability in soils and are expected to be influenced by the presence of AMF. In a field study, we utilized a unique genetic system comprised of a mycorrhiza defective tomato mutant (named rmc) and its mycorrhiza wild-type progenitor (named 76RMYC+). We examined the effect of AMF by comparing AOB community composition and populations in soil containing roots of the two tomato genotypes in an organically managed soil. Responses of AOB to soil N and P amendments were also studied in the same experiment. Phylogenetic analysis of cloned AOB sequences, derived from excised denaturing gradient gel electrophoresis (DGGE) bands, revealed that the organic farm soil supported a diverse yet stable AOB community, which was neither influenced by mycorrhizal colonization of roots nor by N and P addition to the soil. Real-time TaqMan polymerase chain reaction (PCR) was used to quantify AOB population sizes and showed no difference between any of the treatments. An alternative real-time PCR protocol for quantification of AOB utilizing SYBR green yielded similar results as the TaqMan real-time PCR method, although with slightly lower resolution. This alternative method is advantageous in not requiring the detailed background information about AOB community composition required for adaptation of the TaqMan system for a new soil. [ABSTRACT FROM AUTHOR]

Background, Aims and Scope. Soil microbial community diversity has been suggested as a way of assessing the 'health or 'quality of soils. While molecular (genetic) or biochemical (phenotypic) measurements of microbial diversity have their place, functional diversity is popular in that it relates to the activity of the soil microflora, particularly in the carbon cycle. Community Level Physiological Profiles (CLPPs) are usually assessed by carbon substrate utilization. The aim here is to review the various methods available for CLPP assessment. Main Features. The original method for CLPP determination was based upon the Biolog plate with its range of 95 carbon substrates and many studies have been employing this over the past 15 years. However, a number of criticisms have been leveled at the method, principally that it relies upon the growth of an extracted microbial population, which may not represent the true functioning of the whole soil. A multiple carbon-source, substrate induced respiration method (multi-SIR) was developed that did measure the response of the whole soil community without the need for growth but it did not have the convenience of the microtitre plate format. MicroResp™ was designed to overcome the deficiencies in both methods and we have applied it to a range of media including mineral and organic soils, sediments and litter. In addition we have adapted the method to the testing of a wide range of carbon substrates such as hydrocarbons, terpenes and pesticides. Results. The MicroResp™ technique covers the middle road of relevance and convenience, being a 'whole soil method in a flexible microtitre plate format. It also has the advantage that it can be adapted for the use of radiolabelled (14C) substrates, which increases the specificity and sensitivity of the assay. A few direct comparisons between MicroResp™ have been made. We have found that its discriminatory ability compares favourably with Biolog while other users have reported it to be superior to the multiple SIR approach. A number of laboratories around the world are now utilizing MicroResp™ and reporting good sensitivity to changes to the microbial community due to such varied factors as age of forest rehabilitation, heavy metal treatment, hydrocarbon exposure, salinity, peatland vegetation, cropping system and tree clone type. Discussion. A comparison of the available methods reveals that each has its advantages and drawbacks. The choice of method may depend upon the particular hypotheses or questions. Conclusions. MicroResp™ offers a convenient, rapid and sensitive method for the determination of Community Level Physiological Profiles. Its application in a number of case studies has demonstrated its utility and advantages over other methods though its full potential for characterizing soil activity is yet to be realized. Perspectives. Increasing awareness of the environmental pressures on soils and the need to monitor soil health has resulted in a range of potential indicators. Microbial functional diversity is one such indicator that seeks to characterize a core soil attribute. The availability of rapid methods for its assessment will aid our understanding of such pressures on basic soil functioning. [ABSTRACT FROM AUTHOR]

Using TAMIII multi-channel thermocalorimetry combined with direct microorganism counting (bacteria, actinomycetes and fungi) under laboratory conditions, we determined the microbial population count, resistance and activity toward cadmium (Cd) toxicity in soil. The thermokinetic parameters, which can represent soil microbial activity, were calculated from power-time curves of soil microbial activity obtained by microcalorimetric measurement. Simultaneous application of the two methods showed that growth rate constant (k), peak-heat output power (Pmax) and the number of living microorganisms decreased with increasing concentration of Cd. Anncrease in Cd concentration resulted in the decrease of the peakheat output power and increase in the time of the peak of power. However, the relationships between the thermokinetic parameters (k and Pmax) and the number of microorganism were not linear, but the trend was similar. Our research also suggests that microcalorimetry is a very sensitive, simple and useful technique for in vitro investigation of the effects of toxic heavy metals on soil microbial activity. [ABSTRACT FROM AUTHOR]

The introduction of new approaches for characterizing microbial communities and imaging soil environments has benefited soil microbiology by providing new ways of detecting and locating microorganisms. Consequently, soil microbiology is poised to progress from simply cataloguing microbial complexity to becoming a systems science. A systems approach will enable the structures of microbial communities to be characterized and will inform how microbial communities affect soil function. Systems approaches require accurate analyses of the spatio–temporal properties of the different microenvironments present in soil. In this Review we advocate the need for the convergence of the experimental and theoretical approaches that are used to characterize and model the development of microbial communities in soils. [ABSTRACT FROM AUTHOR]

The article presents a study that investigates the effect of phosphinothricin based herbicide on soil microorganisms. The research was conducted to culturable aerobic bacteria, actimocetes and fungi by monitoring its soil microbial populations and activities for 40 days using dehydrogenase activity and microcosm experiments. The study reveals that insufficient bioavailability of chemicals in soil may lead to low biological degradation of substances and susceptibility to pesticide residues. It also asserts that widespread use of glufosinate provides harmful effects on soil microorganisms as well as other activities because of the toxicity it inhibits.

The objective of this investigation was to determine the incidence of Trichoderma viride in the populations of microorganisms of the soil and in the development of the implants, it was used as pattern the Robust variety and as implants the genotype Island 6-13. Four treatments were used and a totally randomized design, in a reddish Brown soil Ferzialitico, the mixtures 5:1 and 3:1(v:v) were rehearsed, being observed in the counts of fungus, bacterium and actinomicetos that the biggest results were obtained in the mixture3:1and the treatment T-4 since it maintained in the whole experiment the biggest populations in the soil, like it is appreciated the best results are obtained when they are carried of Trichoderma. [ABSTRACT FROM AUTHOR]

Changes in the diversity and structure of soil microbial communities may offer a key to understanding the impact of environmental factors on soil quality in agriculturally managed systems. Twenty-five years of biodynamic, bio-organic, or conventional management in the DOK long-term experiment in Switzerland significantly altered soil bacterial community structures, as assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. To evaluate these results, the relation between bacterial diversity and bacterial community structures and their discrimination potential were investigated by sequence and T-RFLP analyses of 1,904 bacterial 16S rRNA gene clones derived from the DOK soils. Standard anonymous diversity indices such as Shannon, Chaol, and ACE or rarefaction analysis did not allow detection of management-dependent influences on the soil bacterial community. Bacterial community structures determined by sequence and T-RFLP analyses of the three gene libraries substantiated changes previously observed by soil bacterial community level T-RFLP profiling. This supported the value of high-throughput monitoring tools such as T-RFLP analysis for assessment of differences in soil microbial communities. The gene library approach also allowed identification of potential management-specific indicator taxa, which were derived from nine different bacterial phyla. These results clearly demonstrate the advantages of community structure analyses over those based on anonymous diversity indices when analyzing complex soil microbial communities. [ABSTRACT FROM AUTHOR]

The key role of telluric microorganisms in pesticide degradation is well recognized but the possible relationships between the biodiversity of soil microbial communities and their functions still remain poorly documented. If microorganisms influence the fate of pesticides, pesticide application may reciprocally affect soil microorganisms. The objective of our work was to estimate the impact of 2,4-D application on the genetic structure of bacterial communities and the 2,4-D-degrading genetic potential in relation to 2,4-D mineralization. Experiments combined isotope measurements with molecular analyses. The impact of 2,4-D on soil bacterial populations was followed with ribosomal intergenic spacer analysis. The 2,4-D degrading genetic potential was estimated by real-time PCR targeted on tfdA sequences coding an enzyme specifically involved in 2,4-D mineralization. The genetic structure of bacterial communities was significantly modified in response to 2,4-D application, but only during the intense phase of 2,4-D biodegradation. This effect disappeared 7 days after the treatment. The 2,4-D degrading genetic potential increased rapidly following 2,4-D application. There was a concomitant increase between the tfdA copy number and the 14C microbial biomass. The maximum of tfdA sequences corresponded to the maximum rate of 2,4-D mineralization. In this soil, 2,4-D degrading microbial communities seem preferentially to use the tfd pathway to degrade 2,4-D. [ABSTRACT FROM AUTHOR]

Microbial displacement in the soil is an important process for bioremediation and dispersal of wastewater pathogens. We evaluated cell movement in surface and subsurface red-yellow podzolic soil driven by advection and microbial motility and also survival of a microbial population at high pressure as is prevalent in deep soil layers. Pseudomonas fluorescens Br 12, resistant to rifampycin and kanamycin, was used as a model organism traceable in non-sterile soil. Our results showed that more than 40% of the P. fluorescens population survived under high pressure, and that microbial motility was not a major factor for its displacement in the soil. Cells were adsorbed in similar amounts to surface and subsurface soils, but more viable cells were present in the leachate of surface than in subsurface soils. The nature of this unexpected cell binding to the subsurface soil was studied by EPR, Mossbauer, NMR, and infrared techniques, suggesting iron had a weak interaction with microbes in soil. P. fluorescens movement in soil resulted mainly from convection forces rather than microbial motility. The transport of this bacterium along the transept toward groundwater encountered restricted viability, although it survived under high pressure conditions simulating those in deep soil layers. [ABSTRACT FROM AUTHOR]

Methyl bromide is highly effective in reducing soil pathogens. Although its use was to be phased out completely in the United States by Jan. 1, 2005, due to environmental concerns, a 1-year critical-use exemption will allow tree fruit growers to use the fumigant through the end of the year. To explore possible replacements for methyl bromide, we compared the effects of pre- and postplant treatments and amendments on soil microbial communities and tree vigor in a replanted peach orchard. Both soil sterilization treatments and organic carbon amendments changed the composition of microbial communities in the soil. High microbial biomass is generally considered beneficial to agricultural soils; we found that it was usually highest in soils that received the organic carbon amendment and lowest in those with soil sterilization. However, tree vigor was highest with the sterilization treatments. The effects of a microbial inoculants/organic carbon combination on microbial communities and plant vigor were no different from simply adding organic carbon. [ABSTRACT FROM AUTHOR]

The guts of soil-feeding macroinvertebrates contain a complex microbial community that is involved in the transformation of ingested soil organic matter. In a companion paper (T. Lemke, U. Stingl, M. Egert, M. W. Friedrich, and A. Brune, Appl. Environ. Microbiol. 69:6650-6658, 2003), we show that the gut of our model organism, the humivorous larva of the cetoniid beetle Pachnoda ephippiata, is characterized by strong midgut alkalinity, high concentrations of microbial fermentation products, and the presence of a diverse, yet unstudied microbial community. Here, we report on the community structure of bacteria and archaea in the midgut, hindgut, and food soil of P. ephippiata larvae, determined with cultivation-independent techniques. Clone libraries and terminal restriction fragment length polymorphism analysis of 16S rRNA genes revealed that the intestines of P. ephippiata larvae contain a complex gut microbiota that differs markedly between midgut and hindgut and that is clearly distinct from the microbiota in the food soil. The bacterial community is dominated by phylogenetic groups with a fermentative metabolism (Lactobacillales, Clostridiales, Bacillales, and CytophagaFlavobacterium-Bacteroides [CFB] phylum), which is corroborated by high lactate and acetate concentrations in the midgut and hindgut and by the large numbers of lactogenic and acetogenic bacteria in both gut compartments reported in the companion paper. Based on 16S rRNA gene frequencies, Actinobacteria dominate the alkaline midgut, while the hindgut is dominated by members of the CFB phylum. The archaeal community, however, is less diverse. 16S rRNA genes affiliated with mesophilic Crenarchaeota, probably stemming from the ingested soil, were most frequent in the midgut, whereas Methanobacteriaceae-related 16S rRNA genes were most frequent in the hindgut. These findings agree with the reported restriction of methanogenesis to the hindgut of Pachnoda larvae. [ABSTRACT FROM AUTHOR]