Fine-root biomass and soil properties in a semideciduous and a lower montane rain forest in Panama

The distribution of root biomass and physical and chemical properties of the soils were studied in a semideciduous and in a lower montane rain forest in Panama. Roots and soil samples were taken by means of soil cores (25 cm deep) and divided into five, 5-cm deep sections. Soils were wet-sieved to retrieve the roots that were classified in four diameter classes: very fine roots (<1 mm), fine roots (1–2 mm), medium roots (2–5 mm) and coarse roots (5–50 mm). Soil samples were analyzed for organic carbon, total nitrogen, available phosphorus, exchangeable bases, cation exchange capacity, pH, aluminium and exchangeable acidity. Total root biomass measured with the soil corer (roots <50 mm in diameter) was not different between the forests (9.45 t ha^-1), while biomass of very fine roots was larger in the mountains (2.00 t ha^-1) than in the lowlands (1.44 t ha^-1). The soils in the semideciduous forest were low in available phosphorus, while in the mountains, soils had low pH, high exchangeable aluminium and exchangeable acidity, and low concentration of exchangeable bases. Phosphorus was in high concentration only in the first 5 cm of the soil. In both forests, there was an exponential reduction of root biomass with increasing depth, and most of the variation in the vertical distribution of roots less than 2 mm in diameter was explained by the concentration of nitrogen in the soils. The results of this study support the hypothesis that a large root biomass in montane forests is related to nutrients in low concentration and diluted in organic soils with high CEC and low bulk density, and that fine root biomass in tropical forests in inversely related to calcium availability but not a phosphorus as has been suggested for other forests.     

Changes in heated and autoclaved forest soils of S.E. Australia. I. Carbon and nitrogen

The effect of heating and autoclaving on extractable nitrogen, N mineralisation and C metabolism was studied by heating five forest soils in the laboratory, simulating the range of effects of heat due to bushfire. Top soil (0–5 cm) was heated to 60 °C, 120 °C and 250 °C for 30 minutes; unheated soil was taken as a control. Samples of the soil heated to 250 °C were also inoculated with fresh soil to accelerate the recovery of the microbial population. Soil autoclaving was carried out as another heat treatment (moist heat). Soils were analysed immediately after heating and 3 times during seven months of incubation to assess immediate and longer-term effects of heating.Extractable N (organic and mineral forms) increased after heating to 120 °C, but decreased with further heating to 250 °C suggesting the volatilisation of N. N associated with microbial biomass diminished with heating and was barely detectable after the 250 °C treatment. Microbial biomass was an important source of soluble N in heated soils, and only partly recovered during subsequent long incubation. The amount of N mineralised during incubation depended on both soil and temperature. Nitrification did not occur when soils were heated to 250 °C (with or without inoculum), or after autoclaving, demonstrating the high sensitivity of nitrifiers to heat. At the beginning of soil incubation, respiration was enhanced in heated soils (250 °C, 250 °C inoculated) and autoclaved soils, but after 30 days of incubation respiration decreased to values either similar to or lower than those in control. This respiration pattern indicated that a fraction of labile C was released by heating, which was quickly mineralised within 30 days of incubation. These results demonstrate some effects of soil heating on C and N dynamics in forest soils.     

Efficacy of Talaromyces flavus Alone or in Combination with other Antagonists in Controlling Verticillium dahliae in Growth Chamber Experiments

Talaromyces flat-US reduced viability of microsclerotia of Verticitlium dahliae on senescent potato stems collected from the field when applied as ascospores in carboxy-methylcellulose or in talcum powder. Incorporating an alginate wheat-bran preparation of T. fiavus in soil at a rate of 0.5% (w/w) was followed by a decrease of > 90% of the population of V. dahliae in soil at both 15 and 25 C. Population densities of V. dahliae were negatively correlated (r = -0.50; P = 0.001) with those of T. flavus. However, the population of V. dahliae was also reduced in soil with alginate wheat-bran alone. When incorporated in soil in alginate wheat-bran and simultaneously coated on seeds in ta.lcum powder. T. flavus reduced colonization of roots and infection of eggplants by K. dahliae. Although to a lesser extent than with the antagonist, alginate wheat-bran without T. flavus also reduced infection by the pathogen. Treatment with combinations of T. flavus with other biocontrol agents, viz. Bacillus subtilis, Fusarium oxysporum or Gliocladium roseum , containing half of the inoculum of the single application of each antagonist, gave similar control of root colonization and stem infection by V. dahliae as application of the single antagonists. Population densities on the root of each antagonist were not or only slightly affected by the presence of the co-inoculated antagonist suggesting that the combinations were compatible.     

Does soil acidity reduce subsoil rooting in Norway spruce (Picea abies)?

Increasing evidence suggests that forest soils in central and northern Europe as well as in North America have been significantly acidified by acid deposition during the last decades. The present investigation was undertaken to examine the effect of soil acidity on rooting patterns of 40-year-old Norway spruce trees by comparing fine and coarse roots among four stands which differed in soil acidity and Mg (and Ca) nutrition. The coarse root systems of four to five 40-year-old Norway spruce trees per stand were manually excavated. The sum of cross sectional area (CSA) at 60 cm soil depth and below of all vertical coarse roots, as a measure of vertical rooting intensity, was strongly reduced with increasing subsoil acidity of the stands. This pattern was confirmed when 5 additional acidic sites were included in the analysis. Fine root biomass in the mineral soil estimated by repeated soil coring was strongly reduced in the heavily acidified stands, but increased in the humic layer. Using ingrowth cores and a screen technique, we showed that the higher root biomass in the humic layer of the more acidic stands was a result of higher root production. Thus, reduced fine root biomass and coarse root CSA in deeper soil layers coincided with increased root growth in the humic layer. Root mineral analysis showed Ca/Al ratios decreased with decreasing base saturation in the deeper mineral soil (20–40 cm). In the top mineral soil, only minor differences were observed among stands. In general, low Ca/Al ratios coincided with low fine root biomass. Calcium/aluminum ratios determined in cortical cell walls using X-ray microanalysis showed a similar pattern as Ca/Al ratios based on analysis of whole fine roots, although the amplitude of changes among the stands was much greater. Aluminum concentrations and Ca/Al ratios in cortical cell walls were at levels found to inhibit root growth of spruce seedlings in laboratory experiments. The data support the idea that Al (or Ca/Al ratios) and acid deposition-induced Mg (and possibly Ca) deficiency are important factors influencing root growth and distribution in acidic forest soils. Changes in carbon partitioning within the root system may contribute to a reduction in deep root growth.     

Suppression of damping-off in maize seedlings by Pseudomonas corrugata

Two strains of Pseudomonas corrugata, (1 and 7), isolated from subtropical and temperate soils in Sikkim Himalaya, respectively, were subjected to Petri-dish as well as plant-based bioassay to examine their potential for disease suppression against three major pathogens of maize. A mixture of Pythium ultimum, P. arrhenomanes and Fusarium graminearum was introduced in the soil; maize seed inoculated with one of the two strains of Pseudomonas corrugata (1 or 7) were sown in pots containing such soil. The bacterial inoculation resulted in significant disease suppression as well as growth promotion of seedlings. The bacterial strains were also evaluated for their intrinsic antibiotic resistance against a range of concentrations of ten antibiotics. While the bacteria were found to be sensitive to gentamycin and rifampicin, they exhibited resistance against ampicillin, carbenicillin and penicillin, even at high concentrations.     

Effect of arbuscular mycorrhizae on soil microbial populations and associated plant performance of the salt marsh grass Spartina patens

The effect of arbuscular mycorrhizae (AM) on soil microbial populations and on growth performance of the high salt marsh plant Spartina patens was investigated in a AM suppression study on field-collected soil cores with S. patens. The application of benomyl resulted in a significant reduction of AM colonization on roots of S. patens, but did not completely suppress AM. Non-treated cores had significantly greater colonization (26 ± 6%) than either benomyl- (12 ± 7%) or benomyl-phosphorus-treated (7 ± 3%) cores at a depth of 2.5 cm. Colonization differences between cores declined with depth (5.0 and 7.5 cm), however, so that at 7.5 cm there was no difference between treatments. This decline was attributed to a reduction in oxygen availability with depth as evidenced by decreasing redox potential. Basic environmental conditions generally resembled those found at the field site. There were no environmental differences between treatments at the depths examined. Cell numbers and specific biomass of DAPI-stained organisms as well as members of the Domain Bacteria were significantly higher when AM colonization was suppressed, while those of the Domains Eucarya and Archaea were not significantly influenced. The increase in both microbial and bacterial population size and biomass in the presence of lower levels of AM colonization is most likely due to increases in carbon exudation to soil and rhizosphere populations that accompany AM suppression. PCR-RFLP analysis of nifH amplicons in bulk soil and rhizosphere at varying depths through the soil cores showed differences in banding patterns between rhizosphere and soil material in the presence of AM. The lack of such strong differences in the benomyl-treated cores suggests that AM colonization more strongly affects the nitrogen-fixing population than do physicochemical conditions (e.g. redox potential) alone. Plant growth performance assessed by analyzing root and leaf biomass, as well as excitation transfer efficiency of open photosynthesis system II (PS II) reaction centers (Fv/Fm) was not significantly influenced by AM. Significant differences were found between treatments for C/N ratios and nitrogen content in leaf tissue, indicating that suppression of AM increased plant nitrogen acquisition.     

Characterization and localization of prodiginines from Streptomyces lividans suppressing Verticillium dahliae in the absence or presence of Arabidopsis thaliana

The ascomycete Verticillium dahliae causes worldwide vascular wilt of many field and horticultural plants. The melanized resting structures of this fungus, so-called microsclerotia, survive for many years in soils and continuously re-infect plants. Due to the absence of known fungicides, Verticillium wilt causes immense crop losses. We discovered that the Gram-positive, spore-forming soil bacterium Streptomyces lividans expresses members of the prodiginine family during co-cultivation with V. dahliae. Using HPLC and LC-MS analysis of cultures containing S. lividans alone or grown together with V. dahliae, we found that undecylprodigiosin [394.4 M+H](+) is highly abundant, and streptorubin B [392.4 M+H](+) is present in smaller amounts. Within co-cultures, the quantity of undecylprodigiosin increased considerably and pigment concentrated at and within fungal hyphae. The addition of purified undecylprodigiosin to growing V. dahliae hyphae strongly reduced microsclerotia formation. Undecylprodigiosin was also produced when S. lividans grew on the roots of developing Arabidopsis thaliana plants. Furthermore, the presence of the undecylprodigiosin producer led to an efficient reduction of V. dahliae hyphae and microsclerotia on plant-roots. Based on these novel findings and previous knowledge, we deduce that the prodiginine investigated leads to multiple cellular effects, which ultimately impair specific pathways for signal transduction and apoptosis of the fungal plant pathogen.     

Land use and organic carbon content of some subtropical soils

Summary The assumption that the organic matter content of tropical forest soils is oxidized to atmospheric carbon dioxide when these soils are converted to agricultural use was tested using results of soil surveys in Puerto Rico (1940's, 1960's, and 1980's). Results showed that under intensive agricultural use, soil carbon in the top 18 cm of soil was about 30–37 Mg/ha, regardless of climatic conditions. Reduced intensity of agricultural use resulted in an increase of soil carbon in the order of 0.3–0.5 Mg.ha⁻¹. yr⁻¹ over a 40-yr period. Rates of soil carbon accumulation were inversely related to the sand content of soils. The relation between rates of soil carbon accumulation and climate or soil texture were better defined at higher soil carbon content. Soils under pasture accumulated soil carbon and often contained similar or greater amounts than adjacent mature forest soils (60–150 Mg/ha in the top 25 or 50 cm). Soils in moist climates exhibited greater variations in soil carbon content with changes in land use (both in terms of loss and recovery) than did soils in dry climates. However, in all life zones studied, the recovery of soil carbon after abandonment of agriculture was faster than generally assumed. Low carbon-to-nitrogen ratios suggested that intensively used soils may be stable in their nutrient retention capacity. The observed resiliency of these soils suggested that their role as atmospheric carbon sources has been overestimated, while their potential role as atmospheric carbon sinks has been underestimated.     

Impact of plant species and site on rhizosphere-associated fungi antagonistic to Verticillium dahliae kleb

Fungi with antagonistic activity toward plant pathogens play an essential role in plant growth and health. To analyze the effects of the plant species and the site on the abundance and composition of fungi with antagonistic activity toward Verticillium dahliae, fungi were isolated from oilseed rape and strawberry rhizosphere and bulk soil from three different locations in Germany over two growing seasons. A total of 4,320 microfungi screened for in vitro antagonism toward Verticillium resulted in 911 active isolates. This high proportion of fungi antagonistic toward the pathogen V. dahliae was found for bulk and rhizosphere soil at all sites. A plant- and site-dependent specificity of the composition of antagonistic morphotypes and their genotypic diversity was found. The strawberry rhizosphere was characterized by preferential occurrence of Penicillium and Paecilomyces isolates and low numbers of morphotypes (n = 31) and species (n = 13), while Monographella isolates were most frequently obtained from the rhizosphere of oilseed rape, for which higher numbers of morphotypes (n = 41) and species (n = 17) were found. Trichoderma strains displayed high diversity in all soils, but a high degree of plant specificity was shown by BOX-PCR fingerprints. The diversity of rhizosphere-associated antagonists was lower than that of antagonists in bulk soil, suggesting that some fungi were specifically enriched in each rhizosphere. A broad spectrum of new Verticillium antagonists was identified, and the implications of the data for biocontrol applications are discussed.     

Hydrologic Regime Controls Soil Phosphorus Fluxes in Restoration and Undisturbed Wetlands

Many wetland restoration projects occur on former agricultural soils that have a history of disturbance and fertilization, making them prone to phosphorus (P) release upon flooding. To study the relationship between P release and hydrologic regime, we collected soil cores from three restoration wetlands and three undisturbed wetlands around Upper Klamath Lake in southern Oregon, U.S.A. Soil cores were subjected to one of three hydrologic regimes—flooded, moist, and dry—for 7.5 weeks, and P fluxes were measured upon reflooding. Soils from restoration wetlands released P upon reflooding regardless of the hydrologic regime, with the greatest releases coming from soils that had been flooded or dried. Undisturbed wetland soils released P only after drying. Patterns in P release can be explained by a combination of physical and biological processes, including the release of iron‐bound P due to anoxia in the flooded treatment and the mineralization of organic P under aerobic conditions in the dry treatment. Higher rates of soil P release from restoration wetland soils, particularly under flooded conditions, were associated with higher total P concentrations compared with undisturbed wetland soils. We conclude that maintaining moist soil is the means to minimize P release from recently flooded wetland soils. Alternatively, prolonged flooding provides a means of liberating excess labile P from former agricultural soils while minimizing continued organic P mineralization and soil subsidence.     

Campylobacter jejuni inactivation in New Zealand soils

AIM: The study was undertaken to determine the inactivation rate of Campylobacter jejuni in New Zealand soils. METHODS AND RESULTS: Farm dairy effluent (FDE) inoculated at c. 10(5) ml(-1) with C. jejuni was applied to intact soil cores at a rate of 2 l m(-2). Four soils were used: Hamilton (granular); Taupo (pumice); Horotiu and Waihou (allophanic). After FDE application cores were incubated at 10 degrees C for up to 32 days. For all four soils all the FDE remained within the cores and at least 99% of C. jejuni were retained in the top 5 cm. Campylobacter jejuni had declined to the limit of detection (two C. jejuni 100 g(-1)) by 25 days in Hamilton and Taupo soils and by 32 days in Waihou soil. In contrast, in Horotiu soil the decline was only three orders of magnitude after 32 days. Simulated heavy rainfall was applied 4 and 11 days after FDE application and only about 1% of the applied C. jejuni were recovered in leachates. CONCLUSIONS: This study demonstrated that at least 99% of applied C. jejuni were retained in the top 5 cm of four soils where they survived for at least 25 days at 10 degrees C. SIGNIFICANCE AND IMPACT OF THE STUDY: Soil retention of C. jejuni is efficient at FDE application rates that prevent drainage losses. The low infectious dose of C. jejuni and its ability to survive up to 25 days have implications for stock management on dairy farms.     

Successful strategy for the selection of new strawberry-associated rhizobacteria antagonistic to Verticillium wilt

In order to isolate and characterize new strawberry-associated bacteria antagonistic to the soil-borne pathogenic fungus Verticillium dahliae Kleb., rhizobacterial populations from two different strawberry species, Greenish Strawberry (Fragaria viridis) and Garden Strawberry (F. x ananassa) obtained after plating onto King's B and glycerol-arginine agar, were screened for in vitro antagonism toward V. dahliae. The proportion of isolates with antifungal activity determined in in vitro assay against V. dahliae was higher for the Garden Strawberry than for the Greenish Strawberry. From 300 isolates, 20 isolates with strong antifungal activity were selected characterized by physiological profiling and molecular fingerprinting methods. Diversity among the isolates was characterized with molecular fingerprints using amplified ribosomal DNA restriction analysis (ARDRA) and the more discriminating BOX-PCR fingerprint method. The physiological profiles were well correlated with molecular fingerprinting pattern analysis. Significant reduction of Verticillium wilt by bacterial dipping bath treatment was shown in the greenhouse and in fields naturally infested by V. dahliae. The relative increase of yield ranged from 117% (Streptomyces albidoflavus S1) to 344% (Pseudomonas fluorescens P10) in greenhouse trials, and 113% (Streptomyces albidoflavus S1) to 247% (Pseudomonas fluorescens P6) in field trials. Evaluation resulted in the selection of three effective biocontrol agents (Pseudomonas fluorescens P6, P10, and Streptomyces diastatochromogenes S9) antagonistic to the Verticillium wilt pathogen.     

Isolation and characterization of hydrogen-oxidizing bacteria induced following exposure of soil to hydrogen gas and their impact on plant growth

In many legumes, the nitrogen fixing root nodules produce H2 gas that diffuses into soil. It has been demonstrated that such exposure of soil to H2 can promote plant growth. To assess whether this may be due to H2-oxidizing microorganisms, bacteria were isolated from soil treated with H2 under laboratory conditions and from soils collected adjacent to H2 producing soybean nodules. Nineteen isolates of H2-oxidizing bacteria were obtained and all exhibited a half-saturation coefficient (Ks) for H2 of about 1 ml l(-1). The isolates were identified as Variovorax paradoxus, Flavobacterium johnsoniae and Burkholderia spp. using conventional microbiological tests and 16S rRNA gene sequence analysis. Seventeen of the isolates enhanced (57-254%) root elongation of spring wheat seedlings. Using an Arabidopsis thaliana bioassay, plant biomass was increased by 11-27% when inoculated by one of four isolates of V. paradoxus or one isolate of Burkholderia that were selected for evaluation. The isolates of V. paradoxus found in both H2-treated soil and in soil adjacent to soybean nodules had the greatest impact on plant growth. The results are consistent with the hypothesis that H2-oxidizing bacteria in soils have plant growth promoting properties.     

Bioremediation of experimental petroleum spills on mineral soils in the Vestfold Hills,Antarctica

The effect of nutrient and water enhancement on the biodegradation of petroleum was tested in Antarctic mineral soils. Nitrogen, phosphorus and potassium were applied in solution, with or without gum xanthan or plastic covers, to sites artificially contaminated with distillate. The effectiveness of these procedures was assessed by measuring changes in total petroleum hydrocarbons; heptadecane/pristane and octadecane/phytane ratios; in concentrations of major hydrocarbon components and in microbial numbers and activity.Significantly lower hydrocarbon concentrations were recorded after one year in soils treated with fertilizer solutions, but only in the surface 3 cm. These soils also showed lowered heptadecane/pristane and octadecane/ phytane ratios and had the highest levels of microbial activity relative to other plots. Soils treated with gum xanthan. or covered with plastic had the highest residual hydrocarbon levels. Both treatments inhibited evaporative loss of hydrocarbon, and there were indications that gum xanthan was utilized by the microbiota as an alternative carbon source to distillate. Higher temperatures were recordecd under the plastic but no stimulation of biodegradation was detected.Estimated numbers of metabolically active bacteria were in the range 10⁷ to 10⁸ g^–1 dry weight of soil, with an estimated biomass of 0.03 to 0.26 mg g^–1 soil. Estimated numbers of amoebae were in the range 10⁶ to 10⁷ g^–1 soil (biomass of 2 to 4 mgg^–1). The highest populations were recorded in fertilized, contaminated soils, the only soils where petroleum degradation was demonstrated.     

The soil block test: Potential for improving our understanding of the role of soil source on performance

The soil block test is widely used in North America for evaluating the decay resistance of various wood-based materials. One drawback of this test is that soils from different sources may result in variable wood weight losses. Developing more definitive screening criteria for soils would help select soils that would be most appropriate for use in these procedures. Soils from seven different sources were characterized for soil texture, pH, water holding capacity, C:N ratio, bulk density and then used in soil block tests against two white rot and two brown rot fungi. While there were substantial differences in soil characteristics, none of the parameters were correlated with wood weight loss. The results illustrate the difficulty in predicting fungal behavior in laboratory tests based upon soil characteristics.     

The Influence of pH on Biodeterioration of a Tropical Timber Exposed to Mixed Cultures of Biocontrol and Wood-Rot Fungi

A laboratory investigation of the decay control potentials of Trichoderma viride and Penicillium sp. on the deterioration of obeche wood (Triplochiton scleroxylon). buffered at various pH. by wood-rot fungi ( Gloeophyllum sp. and Gloeophyllum sepiarium ), was carried out. Biomass determinations in carboxylmethyl cellulose broth at various pH showed that the biocontrol fungal strains exployed grew better as the pH approached neutral while the reverse was true for the wood-rot fungi. Deterioration of wood (buffered at various pH) simultaneously inoculated with the biocontrol and wood-rot fungi was more markedly reduced towards neutral pH than at lower pH values. Decay begun in wood initially infested with rot fungi before inoculation with biocontrol fungi was virtually halted at neutral pH. which was not the case in lower pH (2 and 3) buffered wood simultanecously inoculated with biocontrol and wood-rot fungi. A killing effect was indicated when the rot fungi failed to appear on potato–dextrose agar from interior sections of the wood blocks. Manipulation of pH may prove important in biological control of wood decay.     

Evaluation of potential biocontrol rhizobacteria from different host plants of Verticillium dahliae Kleb

AIMS: A screening approach was developed to assess the potential of rhizobacterial strains to control Verticillium wilt caused by Verticillium dahliae Kleb. METHODS AND RESULTS: Sixty randomly chosen antagonistic bacterial strains originally isolated from rhizosphere of three different host plants of V. dahliae--strawberry, potato and oilseed rape--were evaluated for biocontrol and plant growth promotion by analysing in vitro antagonism towards V. dahliae and other plant pathogenic fungi, production of fungal cell wall-degrading enzymes and plant growth-promoting effects on strawberry seedlings. To test the plant growth-promoting effect, a microplate assay with strawberry seedlings was developed. Although the rhizobacterial strains were isolated from different plants they showed effects on the growth of strawberry seedlings. According to the in vitro biocontrol and plant growth-promoting activity, the three best candidates Pseudomonas putida B E2 (strawberry rhizosphere), Ps. chlororaphis K15 (potato rhizosphere) and Serratia plymuthica R12 (oilseed rape rhizosphere) were selected for greenhouse experiments to verify the in vitro screening results. Under greenhouse conditions the isolates selected according to this strategy were as effective, or more effective than commercial biocontrol agents and may therefore possibly be valuable as antagonists of V. dahliae. CONCLUSIONS: In this study, the screening strategy resulted in a selection of three interesting biocontrol candidates against Verticillium: Ps. putida B E2 (strawberry rhizosphere), Ps. chlororaphis K15 (potato rhizosphere) and Ser. plymuthica R12 (oilseed rape rhizosphere). SIGNIFICANCE AND IMPACT OF THE STUDY: A new combination of in vitro screening methods including a microplate assay with strawberry seedlings to test the plant growth promoting effect which allow to more efficiently select potential biological control agents was developed successfully.     

Initial decay of woody fragments in soil is influenced by size, vertical position, nitrogen availability and soil origin

Fast-growing bacteria and fungi are expected to cause the initial stage of decomposition of woody fragments in and on soils, i.e. the respiration of sugars, organic acids, pectin and easily accessible cellulose and hemi-cellulose. However, little is known about the factors regulating initial wood decomposition. We examined the effect of wood fragment size, vertical position, nitrogen addition and soil origin on initial wood decay and on the relative importance of fungi and bacteria therein. Two fractions of birch wood were used in microcosm experiments, namely wood blocks (dimensions: 3 × 0.5 × 0.5 cm) and sawdust (dimensions: 0.5–2 mm). The woody fragments were enclosed in nylon bags and placed on top of- or buried in an abandoned arable soil and in a heathland soil. After 15, 25 and 40 weeks of incubation, fungal biomass was quantified (as ergosterol and chitin content) and bacterial numbers were determined. The results indicated that initial wood decay was mostly caused by fungi; bacteria were only contributing in sawdust in/on abandoned arable soil. Larger fragment size, burial of fragments and nitrogen addition positively influenced fungal biomass and activity. Fungal biomass and decay activities were much lower in woody fragments incubated in/on heathland soil than in those incubated in/on abandoned arable soil, indicating that soil origin is also an important factor determining initial wood decay.     

Pseudomonas community structure and antagonistic potential in the rhizosphere: insights gained by combining phylogenetic and functional gene-based analyses

The Pseudomonas community structure and antagonistic potential in the rhizospheres of strawberry and oilseed rape (host plants of the fungal phytopathogen Verticillium dahliae) were assessed. The use of a new PCR-DGGE system, designed to target Pseudomonas-specific gacA gene fragments in environmental DNA, circumvented common biases of 16S rRNA gene-based DGGE analyses and proved to be a reliable tool to unravel the diversity of uncultured Pseudomonas in bulk and rhizosphere soils. Pseudomonas-specific gacA fingerprints of total-community (TC) rhizosphere DNA were surprisingly diverse, plant-specific and differed markedly from those of the corresponding bulk soils. By combining multiple culture-dependent and independent surveys, a group of Pseudomonas isolates antagonistic towards V. dahliae was shown to be genotypically conserved, to carry the phlD biosynthetic locus (involved in the biosynthesis of 2,4-diacetylphloroglucinol - 2,4-DAPG), and to correspond to a dominant and highly frequent Pseudomonas population in the rhizosphere of field-grown strawberries planted at three sites in Germany which have different land use histories. This population belongs to the Pseudomonas fluorescens phylogenetic lineage and showed closest relatedness to P. fluorescens strain F113 (97% gacA gene sequence identity in 492-bp sequences), a biocontrol agent and 2,4-DAPG producer. Partial gacA gene sequences derived from isolates, clones of the strawberry rhizosphere and DGGE bands retrieved in this study represent previously undescribed Pseudomonas gacA gene clusters as revealed by phylogenetic analysis.