Evidence of non-DDD pathway in the anaerobic degradation of DDT in tropical soil

DDT transformation to DDD in soil is the most commonly reported pathway under anaerobic conditions. A few instances of DDT conversion to products other than DDD/DDE have been reported under aerobic conditions and hardly any under anaerobic conditions. In particular, few reports exist on the anaerobic degradation of DDT in African tropical soils, despite DDT contamination arising from obsolete pesticide stockpiles in the continent as well as new contamination from DDT use for mosquito and tsetse fly control. Moreover, the development of possible remediation strategies for contaminated sites demands adequate understanding of different soil processes and their effect on DDT persistence, hence necessitating the study. The aim of this work was to study the effect of simulated anaerobic conditions and slow-release carbon sources (compost) on the dissipation of DDT in two tropical clay soils (paddy soil and field soil) amenable to periodic flooding. The results showed faster DDT dissipation in the field soil but higher metabolite formation in the paddy soil. To explain this paradox, the levels of dissolved organic carbon and carbon mineralization (CH₄ and CO₂) were correlated with p,p-DDT and p,p-DDD concentrations. It was concluded that DDT underwent reductive degradation (DDD pathway) in the paddy soil and both reductive (DDD pathway) and oxidative degradation (non-DDD pathway) in the field soil.

Large variation in glyphosate mineralization in 21 different agricultural soils explained by soil properties

Glyphosate and its main metabolite aminomethylphosphonic acid (AMPA) have frequently been detected in surface water and groundwaters. Since adequate glyphosate mineralization in soil may reduce its losses to environment, improved understanding of site specific factors underlying pesticide mineralization in soils is needed. The aim of this study was to investigate the relationship between soil properties and glyphosate mineralization. To establish a sound basis for resilient correlations, the study was conducted with a large number of 21 agricultural soils, differing in a variety of soil parameters, such as soil texture, soil organic matter content, pH, exchangeable ions etc. The mineralization experiments were carried out with ¹⁴C labelled glyphosate at a soil water tension of -15 kPa and at a soil density of 1.3 g cm^-3 at 20 ± 1 °C for an incubation period of 32 days. The results showed that the mineralization of glyphosate in different agricultural soils varied to a great extent, from 7 to 70% of the amount initially applied. Glyphosate mineralization started immediately after application, the highest mineralization rates were observed within the first 4 days in most of the 21 soils. Multiple regression analysis revealed exchangeable acidity (H⁺ and Al³⁺), exchangeable Ca²⁺ ions and ammonium lactate extractable K to be the key soil parameters governing glyphosate mineralization in the examined soils. A highly significant negative correlation between mineralized glyphosate and NaOH-extractable residues (NaOH-ER) in soils strongly suggests that NaOH-ER could be used as a simple and reliable parameter for evaluating the glyphosate mineralization capacity. The NaOH-ER were composed of glyphosate, unknown ¹⁴C-residues, and AMPA (12%-65%, 3%-34%, 0%-11% of applied ¹⁴C, respectively). Our results highlighted the influential role of soil exchangeable acidity, which should therefore be considered in pesticide risk assessments and management to limit efficiently the environmental transfers of glyphosate.

Bacteria utilizing plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil

Root exudates shape microbial communities at the plant-soil interface. Here we compared bacterial communities that utilize plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a greenhouse using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant-derived carbon, ¹³ C-CO₂ labelling of plants was performed for two weeks at the EC50 stage, followed by isopycnic density gradient centrifugation of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing. Our findings suggest substantially different bacterial key players and interaction mechanisms between plants and bacteria utilizing plant-derived carbon in the rhizosphere of subsoils and topsoil. Among the three soil depths, clear differences were found in ¹³ C enrichment pattern across abundant operational taxonomic units (OTUs). Whereas, OTUs linked to Proteobacteria were enriched in ¹³ C mainly in the topsoil, in both subsoil layers OTUs related to Cohnella, Paenibacillus, Flavobacterium showed a clear ¹³ C signal, indicating an important, so far overseen role of Firmicutes and Bacteriodetes in the subsoil rhizosphere.

Enhanced degradation of isoproturon in an agricultural soil by a Sphingomonas sp. strain and a microbial consortium

Isoproturon (IPU) degradation in an agricultural soil inoculated with an isolated IPU-degrader strain (Sphingomonas sp. strain AK1, IS) or a microbial consortium (MC) harboring this strain, with or without carrier material, were investigated in soil microcosm experiments during 46 days. Effect of the carrier material and inoculation size on IPU-degradation efficacy of the inoculants were studied. Mineralization, extractable residues and non-extractable residues of ¹⁴C-labeled IPU were analyzed. The low IPU mineralization in untreated soil (7.0%) was enhanced to different extents by inoculation of IS (17.4%-46.0%) or MC (58.9%-67.5%). Concentrations of IPU residues in soils amended with MC (0.002-0.095 μg g dry soil^-1) were significantly lower than in soils amended with IS (0.02-0.67 μg g dry soil^-1) and approximately 10 times lower than in the uninoculated soil (0.06-0.80 μg g dry soil^-1). Less extractable residues and non-extractable residues were detected in soil with higher IPU mineralization. Inoculation size (as indicated by the volume of liquid cultures or by the number of carrier particles) determined the IPU-removal efficacy of IS in soil, but this effect was less pronounced for MC. The low sorption of IPU to soil and the decreasing IPU-mineralizing rates suggested incapability of IS to establish the IPU-mineralizing function in the soil. The thorough removal of IPU and persistent IPU-mineralizing activity of soil inoculated with MC indicated a high persistence of IPU-metabolic trait. Our results showed that microbial consortia might be more efficient than single degrader strains to enhance clean-up of organic chemicals in soil.

Targeting allergenic fungi in agricultural environments aids the identification of major sources and potential risks for human health

Fungi are, after pollen, the second most important producers of outdoor airborne allergens. To identify sources of airborne fungal allergens, a workflow for qPCR quantification from environmental samples was developed, thoroughly tested, and finally applied. We concentrated on determining the levels of allergenic fungi belonging to Alternaria, Cladosporium, Fusarium, and Trichoderma in plant and soil samples from agricultural fields in which cereals were grown. Our aims were to identify the major sources of allergenic fungi and factors potentially influencing their occurrence. Plant materials were the main source of the tested fungi at and after harvest. Amounts of A. alternata and C. cladosporioides varied significantly in fields under different management conditions, but absolute levels were very high in all cases. This finding suggests that high numbers of allergenic fungi may be an inevitable side effect of farming in several crops. Applied in large-scale studies, the concept described here may help to explain the high number of sensitization to airborne fungal allergens.

Persistence and dioxin-like toxicity of carbazole and chlorocarbazoles in soil

Halogenated carbazoles have recently been detected in soil and water samples, but their environmental effects and fate are unknown. Eighty-four soil samples obtained from a site with no recorded history of pollution were used to assess the persistence and dioxin-like toxicity of carbazole and chlorocarbazoles in soil under controlled conditions for 15 months. Soil samples were divided into two temperature conditions, 15 and 20 °C, both under fluctuating soil moisture conditions comprising 19 and 44 drying-rewetting cycles, respectively. This was characterized by natural water loss by evaporation and rewetting to -15 kPa. Accelerated solvent extraction (ASE) and cleanup were performed after incubation. Identification and quantification were done using high-resolution gas chromatogram/mass spectrometer (HRGC/MS), while dioxin-like toxicity was determined by ethoxyresorufin-O-deethylase (EROD) induction in H4IIA rat hepatoma cells assay and multidimensional quantitative structure-activity relationships (mQSAR) modelling. Carbazole, 3-chlorocarbazole and 3,6-dichlorocarbazole were detected including trichlorocarbazole not previously reported in soils. Carbazole and 3-chlorocarbazole showed significant dissipation at 15 °C but not at 20 °C incubating conditions indicating that low temperature could be suitable for dissipation of carbazole and chlorocarbazoles. 3,6-Dichlorocarbazole was resistant at both conditions. Trichlorocarbazole however exhibited a tendency to increase in concentration with time. 3-Chlorocarbazole, 3,6-dibromocarbazole and selected soil extracts exhibited EROD activity. Dioxin-like toxicity did not decrease significantly with time, whereas the sum chlorocarbazole toxic equivalence concentrations (∑TEQ) did not contribute significantly to the soil assay dioxin-like toxicity equivalent concentrations (TCDD-EQ). Carbazole and chlorocarbazoles are persistent with the latter also toxic in natural conditions.

Abundance and diversity of ammonia-oxidizing prokaryotes in the root-rhizosphere complex of Miscanthus × giganteus grown in heavy metal-contaminated soils

Mine wastes have been considered as a source of heavy metal (HM) contamination in the environment and negatively impact many important ecosystem services provided by soils. Plants like Miscanthus, which tolerate high HM concentrations in soil, are often used for phytoremediation and provide the possibility to use these soils at least for the production of energy crops. However, it is not clear if plant growth at these sites is limited by the availability of nutrients, mainly nitrogen, as microbes in soil might be affected by the contaminant. Therefore, in this study, we investigated in a greenhouse experiment the response of ammonia-oxidizing microbes in the root-rhizosphere complex of Miscanthus × giganteus grown in soils with different levels of long-term arsenic (As) and lead (Pb) contamination. Quantitative PCR of the ammonia monooxigenease gene (amoA) was performed to assess the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) at two different points of plant growth. Furthermore, bulk soil samples before planting were analyzed. In addition, terminal restriction fragment length polymorphism (T-RFLP) analysis was used to investigate the diversity of archaeal amoA amplicons. Whereas high concentrations of As and Pb in soil (83 and 15 g/kg, respectively) resulted independent from plant growth in a clear reduction of AOA and AOB compared to the control soils with lower HM contents, in soils with contamination levels of 10 g/kg As and 0.2 g/kg Pb, only AOB were negatively affected in bulk soil samples. Diversity analysis of archaeal amoA genes revealed clear differences in T-RFLP patterns in response to the degree of HM contamination. Therefore, our results could clearly prove the different response patterns of AOA and AOB in HM-contaminated soils and the development of archaeal amoA phylotypes which are more tolerant towards HMs in soil samples from the areas that were impacted the most by mining waste, which could contribute to functional redundancy of ammonia-oxidizing microbes in soils and stability of nitrification pattern.

Polymorphism in morels: isozyme electrophoretic analysis

The aim of this study was to assess whether isozyme polymorphism in different members of the Morchellaceae could be used to improve the systematics in this fungal group and to characterize intraspecific crossings between monosporal strains in Morchella esculenta. For this purpose, isozyme electrophoretic analysis of the following enzymes was performed: glutamine synthetase, NAD-glutamate dehydrogenase, NADP-glutamate dehydrogenase, aspartate aminotransferase, malate dehydrogenase, NAD-glyceraldehyde phosphate dehydrogenase, glucose phosphate isomerase, and superoxide dismutase. The analyses allowed discrimination at the inter- or intra-specific levels and could help to establish a method of identification for strains in the Morchellaceae. To a certain extent they appeared to be suitable to analyze interactions of monosporal strains of Morchella esculenta in pairing experiments. The polymorphism shown in this study was consistent with the phylogenetic relationships between the investigated strains only at the genus level.Key words: isozyme analysis, electrophoresis, Morchella sp., polymorphism.

Incorporation of carbon from decomposing litter of two pioneer plant species into microbial communities of the detritusphere

Initial ecosystems are characterized by a low availability of nutrients and a low soil organic matter content. Interactions of plants and microorganisms in such environments, particularly in relation to litter decomposition, are very important for further ecosystem development. In a litter decomposition study using an initial substrate from a former mining area, we applied the litter of two contrasting pioneer plant species (legume vs. pasture plants), Lotus corniculatus and Calamagrostis epigejos, which are commonly observed in the study area. Litter decomposition was investigated and carbon (C) translocation from litter into soil microorganisms was described by following (13) C from labelled plant litter materials into the fraction of phospholipid fatty acids. Labile C compounds of both plant litter types were easily degraded during the first 4 weeks of litter decomposition. In contrast to climax ecosystems, where the importance of fungi for litter degradation has been shown in many studies, in our experiment, data clearly indicate an outcompetition of fungi by Gram-positive bacteria as soon as available nitrogen is limited in the detritusphere.

Effects of genetically modified starch metabolism in potato plants on photosynthate fluxes into the rhizosphere and on microbial degraders of root exudates

A high percentage of photosynthetically assimilated carbon is released into soil via root exudates, which are acknowledged as the most important factor for the development of microbial rhizosphere communities. As quality and quantity of root exudates are dependent on plant genotype, the genetic engineering of plants might also influence carbon partitioning within the plant and thus microbial rhizosphere community structure. In this study, the carbon allocation patterns within the plant-rhizosphere system of a genetically modified amylopectin-accumulating potato line (Solanum tuberosum L.) were linked to microbial degraders of root exudates under greenhouse conditions, using (13)C-CO(2) pulse-chase labelling in combination with phospholipid fatty acid (PLFA) analysis. In addition, GM plants were compared with the parental cultivar as well as a second potato cultivar obtained by classical breeding. Rhizosphere samples were obtained during young leaf developmental and flowering stages. (13)C allocation in aboveground plant biomass, water-extractable organic carbon, microbial biomass carbon and PLFA as well as the microbial community structure in the rhizosphere varied significantly between the natural potato cultivars. However, no differences between the GM line and its parental cultivar were observed. Besides the considerable impact of plant cultivar, the plant developmental stage affected carbon partitioning via the plant into the rhizosphere and, subsequently, microbial communities involved in the transformation of root exudates.

Impact of soil water regime on degradation and plant uptake behaviour of the herbicide isoproturon in different soil types

The environmental fate of the worldwide used herbicide isoproturon was studied in four different, undisturbed lysimeters in the temperate zone of Middle Europe. To exclude climatic effects due to location, soils were collected at different regions in southern Germany and analyzed at a lysimeter station under identical environmental conditions. (14)C-isoproturon mineralization varied between 2.59% and 57.95% in the different soils. Barley plants grown on these lysimeters accumulated (14)C-pesticide residues from soil in partially high amounts and emitted (14)CO(2) in an extent between 2.01% and 13.65% of the applied (14)C-pesticide. Plant uptake and (14)CO(2) emissions from plants were inversely linked to the mineralization of the pesticide in the various soils: High isoproturon mineralization in soil resulted in low plant uptake whereas low isoproturon mineralization in soil resulted in high uptake of isoproturon residues in crop plants and high (14)CO(2) emission from plant surfaces. The soil water regime was identified as an essential factor that regulates degradation and plant uptake of isoproturon whereby the intensity of the impact of this factor is strongly dependent on the soil type.

Abundance of microbes involved in nitrogen transformation in the rhizosphere of Leucanthemopsis alpina (L.) Heywood grown in soils from different sites of the Damma glacier forefield

Glacier forefields are an ideal playground to investigate the role of development stages of soils on the formation of plant-microbe interactions as within the last decades, many alpine glaciers retreated, whereby releasing and exposing parent material for soil development. Especially the status of macronutrients like nitrogen differs between soils of different development stages in these environments and may influence plant growth significantly. Thus, in this study, we reconstructed major parts of the nitrogen cycle in the rhizosphere soil/root system of Leucanthemopsis alpina (L.) HEYWOOD: as well as the corresponding bulk soil by quantifying functional genes of nitrogen fixation (nifH), nitrogen mineralisation (chiA, aprA), nitrification (amoA AOB, amoA AOA) and denitrification (nirS, nirK and nosZ) in a 10-year and a 120-year ice-free soil of the Damma glacier forefield. We linked the results to the ammonium and nitrate concentrations of the soils as well as to the nitrogen and carbon status of the plants. The experiment was performed in a greenhouse simulating the climatic conditions of the glacier forefield. Samples were taken after 7 and 13 weeks of plant growth. Highest nifH gene abundance in connection with lowest nitrogen content of L. alpina was observed in the 10-year soil after 7 weeks of plant growth, demonstrating the important role of associative nitrogen fixation for plant development in this soil. In contrast, in the 120-year soil copy numbers of genes involved in denitrification, mainly nosZ were increased after 13 weeks of plant growth, indicating an overall increased microbial activity status as well as higher concentrations of nitrate in this soil.

Degradation capacity of a 1,2,4-trichlorobenzene mineralizing microbial community for traces of organochlorine pesticides

A soil-borne microbial community isolated from a contaminated site was previously shown to mineralize 1,2,4-trichlorobenzene (1,2,4-TCB) under aerobic conditions. The key degrader in this community was identified as Bordetella sp. F2. The objective of the study was to test the capacity of the microbial community to degrade a complex mixture of 27 organochlorine compounds and pesticides (OCPs) commonly detected in the environment. The hypothesis was that the microbes would utilize the OCPs as carbon sources at the low concentrations of these compounds, found in natural waters and soil solution. The study was carried out in liquid culture and the changes in concentration of the OCPs were monitored using GC-MS. Data analysis was done using a multivariate analysis method similar to Principal Response Curve (PRC) analysis. Contrary to expectations, the data analysis showed a general trend where higher concentrations were observed in the microbially treated samples relative to the controls. The observed trend was attributed to decreased volatilization due to sorption of the chemicals by microbes since most of the compounds in the cocktail had high Kow values. Nevertheless, when using adequate statistical methods for analysing the very complex data set, correlation of Kow and K(H) values with the loadings of the PRCs showed that three chlorinated mono-aromatics - pentachlorobenzene, pentachloroanisole and octachloroanisole - were amenable to degradation. This provided indications that the community could hold promise for the degradation of higher-chlorinated mono-aromatic OCPs.

Comparison of barley succession and take-all disease as environmental factors shaping the rhizobacterial community during take-all decline

The root disease take-all, caused by Gaeumannomyces graminis var. tritici, can be managed by monoculture-induced take-all decline (TAD). This natural biocontrol mechanism typically occurs after a take-all outbreak and is believed to arise from an enrichment of antagonistic populations in the rhizosphere. However, it is not known whether these changes are induced by the monoculture or by ecological rhizosphere conditions due to a disease outbreak and subsequent attenuation. This question was addressed by comparing the rhizosphere microflora of barley, either inoculated with the pathogen or noninoculated, in a microcosm experiment in five consecutive vegetation cycles. TAD occurred in soil inoculated with the pathogen but not in noninoculated soil. Bacterial community analysis using terminal restriction fragment length polymorphism of 16S rRNA showed pronounced population shifts in the successive vegetation cycles, but pathogen inoculation had little effect. To elucidate rhizobacterial dynamics during TAD development, a 16S rRNA-based taxonomic microarray was used. Actinobacteria were the prevailing indicators in the first vegetation cycle, whereas the third cycle-affected most severely by take-all-was characterized by Proteobacteria, Bacteroidetes, Chloroflexi, Planctomycetes, and Acidobacteria. Indicator taxa for the last cycle (TAD) belonged exclusively to Proteobacteria, including several genera with known biocontrol traits. Our results suggest that TAD involves monoculture-induced enrichment of plant-beneficial taxa.

Batch experiments versus soil pore water extraction--what makes the difference in isoproturon (bio-)availability?

Two approaches to determine pesticide (bio-)availability in soils (i) batch experiments with "extraction with an excess of water" (EEW) and (ii) the recently introduced "soil pore water (PW) extraction" of pesticide incubated soil samples have been compared with regard to the sorption behavior of the model compound isoproturon in soils. A significant correlation between TOC and adsorbed pesticide amount was found when using the EEW approach. In contrast, there was no correlation between TOC and adsorbed isoproturon when using the in situ PW extraction method. Furthermore, sorption was higher at all concentrations in the EEW method when comparing the distribution coefficients (K(d)) for both methods. Over all, sorption in incubated soil samples at an identical water tension (-15 kPa) and soil density (1.3 g cm(-3)) appears to be controlled by a complex combination of sorption driving soil parameters. Isoproturon bioavailability was found to be governed in different soils by binding strength and availability of sorption sites as well as water content, whereas the dominance of either one of these factors seems to depend on the individual composition and characteristics of the respective soil sample. Using multiple linear regression analysis we obtained furthermore indications that the soil pore structure is affected by the EEW method due to disaggregation, resulting in a higher availability of pesticide sorption sites than in undisturbed soil samples. Therefore, it can be concluded that isoproturon sorption is overestimated when using the EEW method, which should be taken into account when using data from this approach or similar batch techniques for risk assessment analysis.

Evaluation of two methods for quantification of hsp70 mRNA from the waterborne pathogen Cryptosporidium parvum by reverse transcription real-time PCR in environmental samples

We optimized and evaluated two mRNA extraction methods to quantify induced hsp70 mRNA from viable and injured Cryptosporidium parvum oocysts by reverse transcription quantitative real-time PCR (RT-qPCR) in raw and treated manure. Methods based on guanidinium isothiocyanate/phenol/chloroform (GITC-PC) purification and direct mRNA extraction with magnetic oligo(dT)25-coated beads were evaluated for applicability and sensitivity. Both methods proved to be suitable for processing manure samples. With washed manure samples and oocyst disruption by bead beating for 165 s in time intervals with cumulative pooling of the lysate fractions, optimum RT-qPCR results were achieved. On average, 2.6 times more hsp70 mRNA was detected with the oligo(dT)25 method in comparison to the GITC-PC based method using fresh oocysts, whereas less mRNA was detected in aged oocysts. For fresh oocysts, analytical and method detection limits for the oligo(dT)25 based method were 1.7 cDNA copies/qPCR reaction and 5150 oocysts/mL manure, and for the GITC-PC based method 17 cDNA copies/qPCR reaction and 4950 oocysts/mL, respectively. In 12 months old oocysts with reduced viability, mRNA was occasionally detected only by the GITC-PC based method. Failure of or reduced detection with the oligo(dT)25 based method was apparently a result of weakened oocyst walls leading to quicker release of mRNA and therefore mRNA shredding by bead beating in the relatively long stretch between the capture sequence and the RT-qPCR target sites.

In situ mass distribution quotient (iMDQ) - a new factor to compare bioavailability of chemicals in soils?

Aim of this work was the development of a new non-biological factor to determine microbial in situ bioavailability of chemicals in soils. Pesticide residues were extracted from ten highly different agricultural soils that had been incubated with the (14)C-herbicide isoproturon (IPU) under comparable soil conditions (water tension - 15 kPa; soil density 1.3 g cm(-3)). Two different pesticide extraction approaches were compared: (i) (14)C-pesticide residues were measured in the pore water (PW) which was extracted from soil by centrifugation; (ii) (14)C-pesticide residues were extracted from soil samples with an excess of water (EEW). We introduce the pesticide's in situ mass distribution quotient (iMDQ) as a measure for pesticide bioavailability, which is calculated as a quotient of adsorbed and dissolved chemical amounts for both approaches (iMDQ(PW), iMDQ(EEW)). Pesticide mineralization in soils served as a reference for real microbial availability. A highly significant correlation between iMDQ(PW) and mineralization showed that PW extraction is adequate to assess IPU bioavailability. In contrast, no correlation exists between IPU mineralization and its extractability from soil with EEW. Therefore, it can be concluded that soil equilibration at comparable conditions and subsequent PW extraction is vital for a isoproturon bioavailability ranking of soils.

Changes of diversity pattern of proteolytic bacteria over time and space in an agricultural soil

The genetic heterogeneity of neutral metalloprotease (npr) gene fragments from soil proteolytic bacteria was investigated at a cultivated field site with four different soil types and at three different depths in April, July, and October. Terminal restriction fragment length polymorphism (T-RFLP) analyses of polymerase chain reaction-amplified npr gene fragments were applied to study the dynamic of the npr gene pool with regard to environmental conditions. The aim of this study was to relate differences in npr community structure and richness to the vertical, site, and seasonal variations naturally occurring at the field site under investigation. T-RFLP analysis revealed a noticeable seasonal variability in the community structure of npr-containing bacteria. The data suggest that the composition of the npr proteolytic bacterial population in July differed from those at the other dates. Additionally, the diversity of npr genes decreased with increasing soil depth revealing the highest values in upper layers. The reasons behind the observed patterns in the community structure might be mainly seasonal and vertical variation of the quantity and heterogeneity of available substrates as well as spatial isolation caused by a varying water amount and the connectivity of soil particles among the soil profile. Sequencing and phylogenetical analysis of 120 npr clones from the top soils collected in July revealed that most of the clones exhibit only poor homology to npr genes of isolates previously obtained from various environments, indicating the presence of until now uncharacterized npr coding proteolytic bacteria at the study site.

Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils

Crucial steps in geochemical cycles are in many cases performed by more than one group of microorganisms, but the significance of this functional redundancy with respect to ecosystem functioning is poorly understood. Ammonia-oxidizing archaea (AOA) and their bacterial counterparts (AOB) are a perfect system to address this question: although performing the same transformation step, they belong to well-separated phylogenetic groups. Using pig manure amended with different concentrations of sulfadiazine (SDZ), an antibiotic that is frequently used in veterinary medicine, it was possible to affect AOB and AOA to different degrees. Addition of manure stimulated growth of AOB in both soils and, interestingly, also growth of AOA was considerably stimulated in one of the soils. The antibiotic treatments decreased the manure effect notably on AOB, whereas AOA were affected to a lower extent. Model calculations concerning the respective proportions of AOA and AOB in ammonia oxidation indicate a substantial contribution of AOA in one of the soils that further increased under the influence of SDZ, hence indicating functional redundancy between AOA and AOB.

In vitro antagonism of an actinobacterial Kitasatospora isolate against the plant pathogen Phytophthora citricola as elucidated with ultrahigh resolution mass spectrometry

Many soil microorganisms antagonistic to soil borne plant pathogens are well known for their ability to control diseases in situ. A variety of substances, like lytic enzymes, siderophores and antibiotics, produced by these organisms have the potential to protect roots against pathogens. Understanding the ecology and a functional assessment of antagonistic microbial communities in soil requires in-depth knowledge of the mechanisms involved in these interactions, a challenging task in complex systems if low-resolution methods are applied. We propose an information-rich strategy of general relevance, composed of adequate preconcentration in conjunction with ultrahigh resolution ion cyclotron resonance Fourier transform mass spectrometry (ICR-FT/MS) and nuclear magnetic resonance (NMR) spectroscopy to identify any bioactive substances in complex systems. This approach is demonstrated on the specific example of substance identification considered responsible for in vitro antagonism of an actinobacterial antagonist isolated from European beech (Fagus sylvatica) rhizosphere soil against the oomycetous root rot pathogen Phytophthora citricola. The isolate belonging to the genus Kitasatospora exhibited strong antibiosis against the oomycete in vitro. The bioactive substance was observed to exhibit a molar mass of 281.1699 g/mol in positive electrospray ionization mass spectra, and the high mass accuracy of the ICR-FT/MS measurements allowed a precise assignment of a molecular formula that was found identical to the macrolide polyketide cycloheximide C(15)H(23)NO(4)+H(+); its identity was then unequivocally confirmed by the information-rich atomic signature of proton NMR spectroscopy. In conclusion, the combination of the near orthogonal methods (pre)fractionation, ultrahigh-resolution ICR-FT mass spectrometry (yielding molecular and MS(n) fragment signatures) and nuclear magnetic resonance spectroscopy (providing atomic signatures) has been found capable of identifying a biocontrol active compound of Kitasatospora active against Phytophthora citricola expediently, quickly, and accurately. This straightforward approach is of general applicability to elucidate biocontrol mechanisms in any complex system with improved efficiency.

Effects of cattle husbandry on abundance and activity of methanogenic archaea in upland soils

In the present study, we tested the hypothesis that animal treading associated with a high input of organic matter would favour methanogenesis in soils used as overwintering pasture. Hence, methane emissions and methanogen populations were examined at sections with different degree of cattle impact in a Farm in South Bohemia, Czech Republic. In spring, methane emission positively corresponded to the gradient of animal impact. Applying phospholipid etherlipid analysis, the highest archaeal biomass was found in section severe impact (SI), followed by moderate impact (MI) and no impact. The same trend was observed for the methanogens as showed by real-time quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes. The detection of monounsaturated isoprenoid side chain hydrocarbons (i20:1) indicated the presence of acetoclastic methanogens in the cattle-impacted sites. This result was corroborated by the phylogenetic analysis of mcrA gene sequences obtained from section SI, which showed that 33% of the analysed clones belonged to the genus Methanosarcina. The majority of the sequenced clones (41%) showed close affiliations with uncultured rumen archaeons. This leads to the assumption that a substantial part of the methanogenic community in plot SI derived from the grazing cattle itself. Compared to the spring sampling, in autumn, a significant reduction in archaeal biomass and number of copies of mcrA genes was observed mainly for section MI. It can be concluded that after 5 months without cattle impact, the severely impact section maintained its methane production potential, whereas the methane production potential under moderate impact returned to background values.

Influence of ozone on litter quality and its subsequent effects on the initial structure of colonizing microbial communities

Ozone is considered as the main factor in air pollution related to a decline of forest in North America and Europe. In the present study, the effect of changed litter quality, due to ozone stress to trees, on the microbial communities colonizing the subsequent litter was investigated. Litter bag technique using beech and spruce litter from ozone-stressed and control trees, was combined with 16S and 18S rRNA-based fingerprinting methods and cloning to characterize phylogenetic diversity. Litter bags were incubated for 2 and 8 weeks in a beech-spruce mixed forest. Differences between the structure of microbial communities colonizing control and ozone-exposed litter were evident by fingerprints of 16S and 18S rRNA RT-PCR products. RT-PCR products, from litter degraded for 8 weeks, were cloned to identify the bacterial and fungal groups. Clones similar to members of Actinobacteria dominated the bacterial libraries, whereas effects of changed litter quality were mainly observed for the Proteobacteria. Fungal libraries were dominated by clones similar to Ascomycota members. Reduced proportion of clones similar to Basidiomycota and Zygomycota in library from ozone-stressed spruce trees and Chytridiomycota from ozone-stressed beech trees was observed when compared to their control counterparts. As hypothesized, changed litter quality due to elevated O3 did influence the structure of litter-colonizing microbial communities. However, these differences were not as pronounced as those between the two plant species.

Application of microbial hot spots enhances pesticide degradation in soils

Through transfer of an active, isoproturon degrading microbial community, pesticide mineralization could be successfully enhanced in various soils under laboratory and outdoor conditions. The microbes, extracted from a soil having high native ability to mineralize this chemical, were established on expanded clay particles and distributed to various soils in the form of microbial "hot spots". Both, diffusion controlled isoproturon mass flow towards these "hot spots" (6microg d(-1)) as well as microbial ability to mineralize the herbicide (approximately 5microg d(-1)) were identified as the main processes enabling a multiple augmentation of the native isoproturon mineralization even in soils with heavy metal contamination. Soil pH-value appears to exert an important effect on the sustainability of this process.

[Identification of 1,2,4-trichlorobenzene-mineralizing bacteria and their function analysis]

Two strains, E3 and F2, capable to mineralize 1,2,4-trichlorobenzene (1,2,4-TCB) were isolated from a chlorinated benzenes contaminated soil using (14)C-1, 2,4-TCB as carbon source. They were identified by their 16S rDNA coding genes and fluoresence in situ hybridization (FISH) analysis as members of the genus Bordetella. A similarity of 100% were observed between strains E3 and F2 with their 16S rDNA sequences. They had the highest homology of 100% with Bordetella sp. QJ2-5 and the closest relation to described species, Bordetella petrii (GDH030510) with a similary of 99.4%. Strains E3 and F2 could degrade about 90% of 1,2,4-TCB and mineralize 58% and 46% of 1,2,4-TCB to CO2 within 30 days in mineral liquid cultures, respectively. Biomass was formed during the mineralization process.

Traditional cattle manure application determines abundance, diversity and activity of methanogenic Archaea in arable European soil

Based on lipid analyses, 16S rRNA/rRNA gene single-strand conformation polymorphism fingerprints and methane flux measurements, influences of the fertilization regime on abundance and diversity of archaeal communities were investigated in soil samples from the long-term (103 years) field trial in Bad Lauchstädt, Germany. The investigated plots followed a gradient of increasing fertilization beginning at no fertilization and ending at the 'cattle manure' itself. The archaeal phospholipid etherlipid (PLEL) concentration was used as an indicator for archaeal biomass and increased with the gradient of increasing fertilization, whereby the concentrations determined for organically fertilized soils were well above previously reported values. Methane emission, although at a low level, were occasionally only observed in organically fertilized soils, whereas the other treatments showed significant methane uptake. Euryarchaeotal organisms were abundant in all investigated samples but 16S rRNA analysis also demonstrated the presence of Crenarchaeota in fertilized soils. Lowest molecular archaeal diversity was found in highest fertilized treatments. Archaea phylogenetically most closely related to cultured methanogens were abundant in these fertilized soils, whereas Archaea with low relatedness to cultured microorganisms dominated in non-fertilized soils. Relatives of Methanoculleus spp. were found almost exclusively in organically fertilized soils or cattle manure. Methanosarcina-related microorganisms were detected in all soils as well as in the cattle manure, but soils with highest organic application rate were specifically dominated by a close phylogenetic relative of Methanosarcina thermophila. Our findings suggest that regular application of cattle manure increased archaeal biomass, but reduced archaeal diversity and selected for methanogenic Methanoculleus and Methanosarcina strains, leading to the circumstance that high organic fertilized soils did not function as a methane sink at the investigated site anymore.

Isolation and characterization of 1,2,4-trichlorobenzene mineralizing Bordetella sp. and its bioremediation potential in soil

A soil which has been polluted with chlorinated benzenes for more than 25 years was used for isolation of adapted microorganisms able to mineralize 1,2,4-trichlorobenzene (1,2,4-TCB). A microbial community was enriched from this soil and acclimated in liquid culture under aerobic conditions using 1,2,4-TCB as a sole available carbon source. From this community, two strains were isolated and identified by comparative sequence analysis of their 16S-rRNA coding genes as members of the genus Bordetella with Bordetella sp. QJ2-5 as the highest homological strain and with Bordetella petrii as the closest related described species. The 16S-rDNA of the two isolated strains showed a similarity of 100%. These strains were able to mineralize 1,2,4-TCB within two weeks to approximately 50% in liquid culture experiments. One of these strains was reinoculated to an agricultural soil with low native 1,2,4-TCB degradation capacity to investigate its bioremediation potential. The reinoculated strain kept its biodegradation capability: (14)C-labeled 1,2,4-TCB applied to this inoculated soil was mineralized to about 40% within one month of incubation. This indicates a possible application of the isolated Bordetella sp. for bioremediation of 1,2,4-TCB contaminated sites.

Organochlorine pesticides in soils under different land usage in the Taihu Lake region, China

A field study was conducted in the Taihu Lake region, China in 2004 to reveal the organochlorine pesticide concentrations in soils after the ban of these substances in the year 1983. Thirteen organochlorine pesticides (OCPs) were analyzed in soils from paddy field, tree land and fallow land. Total organochlorine pesticide residues were higher in agricultural soils than in uncultivated fallow land soils. Among all the pesticides, sigmaDDX (DDD, DDE and DDT) had the highest concentration for all the soil samples, ranging from 3.10 ng/g to 166.55 ng/g with a mean value of 57.04 ng/g and followed by sigmaHCH, ranging from 0.73 ng/g to 60.97 ng/g with a mean value of 24.06 ng/g. Dieldrin, endrin, HCB and alpha-endosulfan were also found in soils with less than 15 ng/g. Ratios of p,p'-(DDD+DDE)/DDT in soils under three land usages were: paddy field > tree land > fallow land, indicating that land usage influenced the degradation of DDT in soils. Ratios of p,p'-(DDD+DDE)/DDT > 1, showing aged residues of DDTs in soils of the Taihu Lake region. The results were discussed with data from a former study that showed very low actual concentrations of HCH and DDT in soils in the Taihu Lake region, but according to the chemical half-lives and their concentrations in soils in 1980s, the concentration of DDT in soils seemed to be underestimated. In any case our data show that the ban on the use of HCH and DDT resulted in a tremendous reduction of these pesticide residues in soils, but there are still high amounts of pesticide residues in soils, which need more remediation processes.

A new cultivation independent approach to detect and monitor common Trichoderma species in soils

A set of primers was developed for the detection, identification and quantification of common Trichoderma species in soil samples. Based on a broad range master alignment primers were derived to amplify an approximate 540 bp fragment comprising the internal transcribed spacer region 1 (ITS 1), 5.8S rDNA and internal transcribed spacer region 2 (ITS 2) from all taxonomic Clades of the genus Trichoderma. The primer set was applied to test strains as well as community DNA isolated from arable and forest soil. For all tested isolates the corresponding internal transcribed spacer regions of Trichoderma spp. strains were amplified, but none of non-Trichoderma origin. PCR with community DNA from soil yielded products of the expected size. Analysis of a clone library established for an arable site showed that all amplified sequences originated exclusively from Trichoderma species mainly being representatives of the Clades Hamatum, Harzianum and Pachybasioides and comprising most of the species known for biocontrol ability. In a realtime PCR approach the primer set uTf/uTr also proved to be a suitable system to quantify DNA of Trichoderma spp. in soils.

A new method for the detection of alkane-monooxygenase homologous genes (alkB) in soils based on PCR-hybridization

An improved method was developed that allowed the specific detection of the gene alkB (coding for the rubredoxin dependent alkane monooxygenase) from bacteria without any obvious strain specific discrimination using a combination of PCR and hybridization. This approach enabled a fast culture-independent monitoring of environmental samples for the occurrence of alkB, and an estimation of the gene copy number and the genetic diversity. Both parameters provide useful informations for an assessment of the intrinsic biodegradation potential that is present at a site. The method was applied to soil samples from different uncontaminated sites. alkB was highly abundant and redundant in all soils tested. Potential biodegradation of n-alkanes was also demonstrated for these soils with substrate utilization assays. Cell numbers of hydrocarbon degraders estimated as MPN varied from 10(3) to 10(6)g(-1) soil (dry weight) for the different soils. Gene copy numbers estimated with MPN-PCR ranged within 1-40*10(4)ng(-1) soil DNA. Analysis of the diversity of the alkB sequences obtained from a grassland and an agricultural soil indicated that the alkane degrading microbial populations occurring at these sites were rather diverse. Compared on protein level, three major clusters were distinguishable for both soils that showed highest similarities to AlkB from the Gram-positives Nocardioides and Mycobacterium, and the Gram-negative Alcanivorax. The majority of the cloned AlkB sequences were homologous to proteins from the Gram-positive bacteria. However, significant differences from published sequences were observed; homologies varied from 50% to 90% (identity of amino acids).

Shifts in microbial community functions and nitrifying communities as a result of combined application of copper and mefenoxam

In this microcosm study, we focused on the effect of a combined application of copper and mefenoxam on the functional diversity of soil microbial communities. Treatments with combined and separate applications of copper and mefenoxam were sampled at 24 and 60 days and control soil was sampled at 0, 24 and 60 days. Structural and metabolic profiling of microorganisms were performed by arbitrarily primed (AP) and RNA arbitrarily primed-PCR (RAP-PCR). Cluster analysis resulted in separate grouping of AP and RAP-PCR profiles, with differences between control and treatments being more pronounced with respect to RAP-PCR profiles. amoA, a functional molecular marker for beta-subgroup ammonia-oxidizing bacteria, could only be detected at day 60 in treatments of mefenoxam, and mefenoxam+copper, with higher gene copies in the latter. There was also an increase in potential nitrification activity on application of mefenoxam and mefenoxam+copper. Comparison of amoA diversity was performed by denaturing gradient gel electrophoresis followed by construction of a clone library of amoA fragments amplified from the mefenoxam+copper-treated sample. Analysis of clones was performed by restriction digestion and subsequent sequencing. Patterns 1 and 5 were seen in 93% of the clones and clustered together with amoA sequences of Nitrosospira, indicating that Nitrosospira-like organisms are the major nitrifiers under mefenoxam treatments.

Microbial colonization of beech and spruce litter--influence of decomposition site and plant litter species on the diversity of microbial community

The present study was conducted to investigate the effect of decomposition site and plant litter species on the colonizing microbial communities. For this, litter bag technique using beech and spruce litter was combined with RNA-based fingerprinting and cloning. Litter bags were incubated for 2 and 8 weeks in the Ah horizon of beech and beech-spruce mixed forest sites. Although sugars and starch were rapidly lost, lignin content increased by more than 40% for beech and more than doubled for spruce litter at both soil sites at the end of the experiment. Denaturing gradient gel electrophoresis analysis of 16S and 18S rRNA RT-PCR products was used for screening of differences between bacterial and fungal communities colonizing the two litter types. Development of the microbial community over time was observed to be specific for each litter type and decomposition site. RT-PCR products from both litter types incubated in beech-spruce mixed forest site were also cloned to identify the bacterial and fungal colonizers. The 16S rRNA clone libraries of beech litter were dominated by gamma-proteobacterial members, whereas spruce libraries were mainly composed of alpha-, beta-, and gamma-proteobacterial members. Ascomycota members dominated the 18S rRNA clone libraries. Clones similar to Zygomycota were absent from spruce, whereas those similar to Basidiomycota and Glomeromycota were absent from beech libraries. Selective effects of litter quality were observed after 8 weeks. The study provides an insight into the bacterial and fungal communities colonizing beech and spruce litter, and the importance of litter quality and decomposition site as key factors in their development and succession.

Influence of freeze-thaw stress on the structure and function of microbial communities and denitrifying populations in soil

Microbial N2O release during the course of thawing of soil was investigated in model experiment focusing on denitrification, since freeze-thaw has been shown to cause significant physical and biological changes in soil, including a surge of N2O and CO2. The origin of these is still controversially discussed. The increase in denitrification after thawing may be attributed to the diffusion of organic substrates newly available to denitrifiers from disrupted soil aggregates, leading to an increase in microbial activity. Laboratory experiments with upper soil layer of a grassland were conducted in microcosms for real-time gas measurements during the entire phase of freeze and thaw. Shifts in microbial communities were evident on resolution of 16S and 18S rRNA genes and transcripts by denaturing gradient gel electrophoresis (DGGE). Microbial expression profiles were compared by RNA-arbitrarily primed PCR technique and subsequent resolution of amplified products on acrylamide gels. Differences in expression levels of periplasmic nitrate reductase gene (napA) and cytochrome cd1 nitrite reductase (nirS) were observed by most-probable-number-reverse transcription-PCR, with higher levels of expression occurring just after thawing began, followed by a decrease. napA and nirS DGGE profiles showed no change in banding patterns with fingerprints derived from DNA, whereas those derived from cDNA showed a clear succession of denitrifying bacteria, with the most complex pattern being observed at the end of the N2O surge. This study provides insight into the structural community changes and expression dynamics of denitrifiers as a result of freeze-thaw stress. Also, the results presented here support the belief that the gas fluxes observed during thawing is a result of freezing initiated high microbial activity.

Short term effects of ozone on the plant-rhizosphere-bulk soil system of young beech trees

Plant growth largely depends on microbial community structure and function in the rhizosphere. In turn, microbial communities in the rhizosphere rely on carbohydrates provided by the host plant. This paper presents the first study on ozone effects in the plant-rhizosphere-bulk soil system of 4-year-old beech trees using outdoor lysimeters as a research platform. The lysimeters were filled with homogenized soil from the corresponding horizons of a forest site, thus minimizing field heterogeneity. Four lysimeters were treated with ambient ozone (1 x O3) and four with double ambient ozone concentrations (2 x O3; restricted to 150 ppb). In contrast to senescence, which was almost unaffected by ozone treatment, both the photochemical quantum yield of photosystem II (PSII) and leaf gas exchange were reduced (11 - 45 %) under the elevated O3 regime. However, due to large variation between the plants, no statistically significant O3 effect was found. Even though the amount of primary metabolites, such as sugar and starch, was not influenced by elevated O3 concentrations, the reduced photosynthetic performance was reflected in leaf biochemistry in the form of a reduction in soluble phenolic metabolites. The rhizosphere microbial community also responded to the O3 treatment. Both community structure and function were affected, with a tendency towards a lower diversity and a significant reduction in the potential nutrient turnover. In contrast, litter degradation was unaffected by the fumigation, indicating that in situ microbial functionality of the bulk soil did not change.

Structural and functional diversity of microbial communities from a lake sediment contaminated with trenbolone, an endocrine-disrupting chemical

Effects of trenbolone (TBOH), a hormone used in cattle production, on the structure and function of microbial communities in a fresh water sediment from a lake in Southern Germany were studied in a microcosm experiment. The microbial community structure and the total gene pool of the sediment, assessed by 16S rRNA/rDNA and RAPD fingerprint analysis, respectively, were not significantly affected by TBOH. In contrast, the N-acetyl-glucosaminidase activity was almost 50% lower in TBOH treated samples (P<0.05). Also, the substrate utilization potential, measured using the BIOLOG system, was reduced after TBOH treatment. Interestingly, this potential did not recover at the end of the experiment, i.e. 19 days after the addition of the chemical. Repeated application of TBOH did not lead to an additional reduction in the substrate utilization potential. Overall results indicate that microbial community function was more sensitive to TBOH treatment than the community structure and the total gene pool.

Characterization of bacterial community structure in rhizosphere soil of grain legumes

Molecular techniques were used to characterize bacterial community structure, diversity (16S rDNA), and activity (16S rRNA) in rhizospheres of three grain legumes: faba beans (Vicia faba L., cv. Scirocco), peas (Pisum sativum L., cv. Duel) and white lupin (Lupinus albus L., cv. Amiga). All plants were grown in the same soil under controlled conditions in a greenhouse and sampled after fruiting. Amplified 16S rDNA and rRNA products (using universal bacterial primers) were resolved by denaturing gradient gel electrophoresis (DGGE). Distinct profiles were observed for the three legumes with most of the bands derived from RNA being a subset of those derived from DNA. Comparing the total bacterial profiles with actinomycete-specific ones (using actinomycete-specific primers) highlighted the dominance of this group in the three rhizospheres. 16S PCR and RT-PCR products were cloned to construct libraries and 100 clones from each library were sequenced. Actinomycetes and proteobacteria dominated the clone libraries with differences in the groups of proteobacteria. Absence of beta-subdivision members in pea and gamma-subdivision members of proteobacteria in faba bean rhizosphere was observed. Plant-dependent rhizosphere effects were evident from significant differences in the bacterial community structure of the legume rhizospheres under study. The study gives a detailed picture of both residing and "active" bacterial community in the three rhizospheres. The high abundance of actinomycetes in the rhizospheres of mature legumes indicates their possible role in soil enrichment after the legumes are plowed into the soil as biofertilizers.

Diversity of transcripts of nitrite reductase genes (nirK and nirS) in rhizospheres of grain legumes

Transcription of the nirK and nirS genes coding for dissimilatory bacterial nitrite reductases was analyzed by reverse transcription PCR (RT-PCR) of mRNA isolated from rhizosphere samples of three economically important grain legumes at maturity: Vicia faba, Lupinus albus, and Pisum sativum. The nirK gene and transcripts could be detected in all the rhizosphere samples. In contrast, nirS could not be detected. Sampling variations were analyzed by comparing denaturing gradient gel electrophoresis profiles derived from nirK RT-PCR products. High similarity was observed between the replicates, and so one representative product per legume was cloned. Clones with the correct insert size were screened by restriction fragment length polymorphism by using the restriction enzyme MspI. The clones could be distributed into 12 different patterns. Patterns 1, 3, 4, 5, and 7 were common in clone libraries of the three rhizosphere types under study. Patterns 2, 9, 10, and 11 were absent from Pisum rhizospheres, while patterns 6, 8, and 12 were absent from the Vicia library. Pattern 1, which was the most dominant in the Vicia and Lupinus libraries, constituted about 25% of all clones. The Lupinus library had clones representing all 12 patterns, indicating it to be the most diverse among the three. Clones representative of each pattern were sequenced. All patterns grouped together forming a distinct cluster, which was divergent from previously described nirK sequences in the database. The study revealed a hitherto unknown diversity of denitrifiers in legume rhizospheres. A plant-dependent rhizosphere effect on the transcripts of a gene was evident.

RNA fingerprinting of microbial community in the rhizosphere soil of grain legumes

Microbial structural and expression profiles of the rhizospheres of three legumes, faba beans, peas and white lupin, were compared by RNA-arbitrarily primed PCR technique. Two different primers, M13 reverse and 10-mer primers, were used in the amplification and products resolved on non-denaturing polyacrylamide gel. With both DNA and RNA profiles Lupinus and Pisum rhizospheres were more similar to each other than to Vicia rhizosphere. The RAP-PCR products were also dot blotted and probed for bacterial peptidase transcripts. Plant-dependent rhizosphere effect was evident by the marked absence of transcripts for bacterial neutral metallopeptidase in Lupinus rhizosphere. The results of dot blot were further confirmed by RT-PCR for the expression of bacterial neutral metallopeptidase in the three rhizospheres.

Stimulation of reductive dechlorination of hexachlorobenzene in soil by inducing the native microbial activity

The reductive dechlorination and behaviour of (14)C-hexachlorobenzene (HCB) was investigated in an arable soil. The activity of the native anaerobic microbial communities could be induced by saturating the soil with water. Under these conditions high rates of dechlorination were observed. After 20 weeks of incubation only 1% of the applied 14C-HCB could be detected in the fraction of extractable residues. Additional organic substances, like wheat straw and lucerne straw, however considerably delayed and reduced the dechlorination process in the soil. The decline of HCB was not only caused by dechlorination but also by the formation of non-extractable residues, whereby their amounts varied with time depending on the experimental conditions. Several dechlorination products were detected, indicating the following main HCB transformation pathway: HCB --> PCB --> 1,2,3,5-TeCB --> 1,3,5-TCB --> 1,3-DCB, with 1,3,5-TCB as main intermediate dechlorination product. The other TeCB-, TCB- and DCB-isomers were also detected in low amounts, showing the presence of more than one dechlorination pathway. Since the methane production rates were lowest when the dechlorination rates were highest, it can be assumed that methanogenic bacteria were not involved in the dechlorination process of HCB. The established 14C-mass balances show, that with increasing dechlorination and incubation times, the 14C-recoveries decreased.

Bacterial diversity in agricultural soils during litter decomposition

Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band. Furthermore, a mixture of strains yielded distinguishable bands. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. A field experiment performed with litter in nylon bags was used to evaluate the bacterial diversity during the decomposition of readily degradable rye and more refractory wheat material in comparable luvisols and cambisols in northern, central, and southern Germany. The amount of bacterial DNA in the fresh litter was small. The DNA content increased rapidly after the litter was added to the soil, particularly in the rapidly decomposing rye material. Concurrently, diversity indices, such as the Shannon-Weaver index, evenness, and equitability, which were calculated from the number and relative abundance (intensity) of the bacterial DNA bands amplified from genes coding for 16S rRNA, increased during the course of decomposition. This general trend was not significant for evenness and equitability at any time. The indices were higher for the more degradation-resistant wheat straw than for the more easily decomposed rye grass. Thus, the DNA band patterns indicated that there was increasing bacterial diversity as decomposition proceeded and substrate quality decreased. The bacterial diversity differed for the sites in northern, central, and southern Germany, where the same litter material was buried in the soil. This shows that in addition to litter type climate, vegetation, and indigenous microbes in the surrounding soil affected the development of the bacterial communities in the litter.

Biomineralisation of 1,2,4-trichlorobenzene in soils by an adapted microbial population

In laboratory experiments the mineralisation of 14C-labelled 1,2,4-trichlorobenzene (1,2,4-TCB) in soils was studied by direct measurement of the evolved 14CO2. The degradation capacity of the indigenous microbial population was investigated in an agricultural soil and in a soil from a contaminated site. Very low mineralisation of 1% within 23 days was measured in the agricultural soil. Whereas in the soil from the contaminated site the mineralisation occurred very fast and in high rates; up to 62% of the initially applied amount of 1,2,4-TCB were mineralised within 23 days. The transfer of the adapted microbial population into the agricultural soil significantly enhanced the mineralisation of 1,2,4-TCB in this soil, reflecting, that the transferred microbial population survived and maintained its degradation ability in the new microbial ecosystem. Additional nutrition sources ((NH4)2HPO4) increased the mineralisation rates in the first days significantly in the contaminated soil. In the soil from the contaminated site high amounts of non extractable 14C-residues were formed.

Variation of stabilised, microbial and biologically active carbon and nitrogen in soil under contrasting land use and agricultural management practices

Land use and agricultural practices modify both the amounts and properties of C and N in soil organic matter. In order to evaluate land use and management-dependent modifications of stable and labile C and N soil pools, (i). organic C and total N content, (ii). microbial (C(mic)) and N (N(mic)) content and (iii). C and N mineralisation rates, termed biologically active C and N, were estimated in arable, grassland and forest soils from northern and southern Germany. The C/N-ratios were calculated for the three levels (i)-(iii) and linked to the eco-physiological quotients of biotic-fixed C and N (C(mic)/C(org), N(mic)/N(t)) and biomass-specific C and N mineralisation rate (qCO(2), qN(min)). Correlations could mainly be determined between organic C, total N, C(mic), N(mic) and C mineralisation for the broader data set of the land use systems. Generally, the mineralisation activity rate at 22 degrees C was highly variable and ranged between 0.11 and 17.67 microg CO(2)-C g(-1) soil h(-1) and -0.12 and 3.81 microg (deltaNH(4)(+)+deltaNO(3)(-))-N g(-1) soil h(-1). Negative N data may be derived from both N immobilisation and N volatilisation during the experiments. The ratio between C and N mineralisation rate differed significantly between the soils ranging from 5 to 37, and was not correlated to the soil C/N ratio and C(mic)/N(mic) ratio. The C/N ratio in the 'biologically active' pool was significantly smaller in soils under conventional farming than those under organic farming systems. In a beech forest, it increased from the L, Of to the Ah horizon. The biologically active C and N pools refer to the current microbial eco-physiology and are related to the need for being C and N use efficient as indicated by metabolic qCO(2) and qN(min) quotients.

A TaqMan-PCR protocol for quantification and differentiation of the phytopathogenic Clavibacter michiganensis subspecies

Real-time TaqMan-PCR assays were developed for detection, differentiation and absolute quantification of the pathogenic subspecies of Clavibacter michiganensis (Cm) in one single PCR run. The designed primer pair, targeting intergenic sequences of the rRNA operon (ITS) common in all subspecies, was suitable for the amplification of the expected 223-nt DNA fragments of all subspecies. Closely related bacteria were completely discriminated, except of Rathayibacter iranicus, from which weak PCR product bands appeared on agarose gel after 35 PCR cycles. Sufficient specificity of PCR detection was reached by introduction of the additional subspecies specific probes used in TaqMan-PCR. Only Cm species were detected and there was clear differentiation among the subspecies C. michiganensis sepedonicus (Cms), C. michiganensis michiganensis (Cmm), C. michiganensis nebraskensis (Cmn), C. michiganensis insidiosus (Cmi) and C. michiganensis tessellarius (Cmt). The TaqMan assays were optimized to enable a simultaneous quantification of each subspecies. Validity is shown by comparison with cell counts.

Phospholipid etherlipid and phospholipid fatty acid fingerprints in selected euryarchaeotal monocultures for taxonomic profiling

Phospholipid etherlipid (PLEL) derived isoprenoids and phospholipid fatty acids (PLFA) were determined in eight Euryarchaeotal monocultures for taxonomic profiling. For the first time significant amounts of fatty acids in the PLFA of Euryarchaeota were determined. The PLFA proportion varied between 11.3 and 35.5% of the total phospholipid side chains except in Methanothermus fervidus where PLFA accounted for 89.0% of the total phospholipid side chains. Fractionation of fatty acids prior to gas chromatography mass spectrometry analysis revealed that non-ester-linked fatty acids dominated which accounted for 85.5-95.2% of total PLFA in all investigated archaeal strains. PLEL concentration and composition was estimated in accordance with previous studies with two exceptions. In the polar (phospho)lipid fraction of Methanopyrus kandleri side chains possibly derived from hydroxyarchaeol as well as acyclic and cyclic caldarchaeol were identified. In phospholipid extracts of Methanothermus fervidus the 'H-formed' caldarchaeol could not be detected. Overall, PLEL derived isoprenoids as well as PLFA enabled taxonomic differentiation of the selected microorganisms into phylogenetically related groups.