Bulk Soil (bulk + soil)

Distribution by Scientific Domains
Distribution within Life Sciences

Selected Abstracts

Microbial succession of nitrate-reducing bacteria in the rhizosphere of Poa alpina across a glacier foreland in the Central Alps

K. Deiglmayr
Summary Changes in community structure and activity of the dissimilatory nitrate-reducing community were investigated across a glacier foreland in the Central Alps to gain insight into the successional pattern of this functional group and the driving environmental factors. Bulk soil and rhizosphere soil of Poa alpina was sampled in five replicates in August during the flowering stage and in September after the first snowfalls along a gradient from 25 to 129 years after deglaciation and at a reference site outside the glacier foreland (> 2000 years deglaciated). In a laboratory-based assay, nitrate reductase activity was determined colorimetrically after 24 h of anaerobic incubation. In selected rhizosphere soil samples, the community structure of nitrate-reducing microorganisms was analysed by restriction fragment length polymorphism (RFLP) analysis using degenerate primers for the narG gene encoding the active site of the membrane-bound nitrate reductase. Clone libraries of the early (25 years) and late (129 years) succession were constructed and representative clones sequenced. The activity of the nitrate-reducing community increased significantly with age mainly due to higher carbon and nitrate availability in the late succession. The community structure, however, only showed a small shift over the 100 years of soil formation with pH explaining a major part (19%) of the observed variance. Clone library analysis of the early and late succession pointed to a trend of declining diversity with progressing age. Presumably, the pressure of competition on the nitrate reducers was relatively low in the early successional stage due to minor densities of microorganisms compared with the late stage; hence, a higher diversity could persist in this sparse environment. These results suggest that the nitrate reductase activity is regulated by environmental factors other than those shaping the genetic structure of the nitrate-reducing community. [source]

Universal and species-specific bacterial ,fungiphiles' in the mycospheres of different basidiomycetous fungi

J. A. Warmink
Summary In previous work, several bacterial groups that show a response to fruiting bodies (the mycosphere) of the ectomycorrhizal fungus Laccaria proxima were identified. We here extend this work to a broader range of fungal fruiting bodies sampled at two occasions. PCR-DGGE analyses showed clear effects of the mycosphere of diverse fungi on the total bacterial and Pseudomonas communities in comparison with those in the corresponding bulk soil. The diversities of the Pseudomonas communities increased dramatically in most of the mycospheres tested, which contrasted with a decrease of the diversity of the total bacterial communities in these habitats. The data also indicated the existence of universal (i.e. Pseudomonas poae, P. lini, P. umsongensis, P. corrugata, P. antarctica and Rahnella aquatilis) as well as specific (i.e. P. viridiflava and candidatus Xiphinematobacter americani) fungiphiles, defined as bacteria adapted to the mycospheres of, respectively, three or more or just one fungal species. The selection of such fungiphiles was shown to be strongly related to their capacities to use particular carbonaceous compounds, as evidenced using principal components analyses of BIOLOG-based substrate utilization tests. The differentiating compounds, i.e. l -arabinose, l -leucine, m-inositol, m-arabitol, d -mannitol and d -trehalose, were tentatively linked to compounds known to occur in mycosphere exudates. [source]

Cultivation-independent analysis of Pseudomonas species in soil and in the rhizosphere of field-grown Verticillium dahliae host plants

Rodrigo Costa
Summary Despite their importance for rhizosphere functioning, rhizobacterial Pseudomonas spp. have been mainly studied in a cultivation-based manner. In this study a cultivation-independent method was used to determine to what extent the factors plant species, sampling site and year-to-year variation influence Pseudomonas community structure in bulk soil and in the rhizosphere of two Verticillium dahliae host plants, oilseed rape and strawberry. Community DNA was extracted from bulk and rhizosphere soil samples of flowering plants collected at three different sites in Germany in two consecutive years. Pseudomonas community structure and diversity were assessed using a polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) system to fingerprint Pseudomonas -specific 16S rRNA gene fragments amplified from community DNA. Dominant and differentiating DGGE bands were excised from the gels, cloned and sequenced. The factors sampling site, plant species and year-to-year variation were shown to significantly influence the community structure of Pseudomonas in rhizosphere soils. The composition of Pseudomonas 16S rRNA gene fragments in the rhizosphere differed from that in the adjacent bulk soil and the rhizosphere effect tended to be plant-specific. The clone sequences of most dominant bands analysed belonged to the Pseudomonas fluorescens lineage and showed closest similarity to culturable Pseudomonas known for displaying antifungal properties. This report provides a better understanding of how different factors drive Pseudomonas community structure and diversity in bulk and rhizosphere soils. [source]

Citrate-mediated increase in the uptake of weathered 2,2-bis(p -chlorophenyl)1,1-dichloroethylene residues by plants

Jason C. White
Abstract Experiments were conducted to determine the ability of citrate to enhance the plant uptake of weathered 2,2-bis(p -chlorophenyl) 1,1-dichloroethylene (p,p,-DDE) from soil. Plots containing three rows of clover, mustard, hairy vetch, or rye grass were constructed in soils containing p,p,-DDE. On 11 occasions, the rows of each crop received water or sodium citrate (0.005 or 0.05 M). For each crop, there were significant reductions in p,p,-DDE concentration in the soil fractions (near root and rhizosphere) closely associated with the plant versus bulk soil. The roots of each crop accumulated 2 to 5 times more of the weathered contaminant (dry wt) than present in the bulk soil. Citrate (0.05 M) increased the concentration of p,p,-DDE in the roots of clover, mustard, and hairy vetch by 39% compared with vegetation that received water. In batch desorption studies, the release of weathered p,p,-DDE was significantly greater in the presence of 0.05 M citrate than in water. Citrate increased the extracted aqueous concentrations of five metal ions (Al, Fe, Ca, K, Mn) from soil by five- to 23-fold over distilled water. We hypothesize that citrate physically disrupts the soil through chelation of structural metal ions and release of bound humic material, facilitating p,p,-DDE availability and uptake by plants. [source]

A model incorporating the diffuse double layer to predict the electrical conductivity of bulk soil

M. A. Mojid
Summary A model has been developed to predict the electrical conductivity of bulk soil. The total soil-water content is divided into free water and water in the diffuse double layer (DDL) around clay particles. These two fractions of soil water conduct electrical current through the soil and are assumed to act in parallel with the soil solid. The volume of water in the DDL is evaluated from the surface area of the clay and the thickness of the DDL. The surface area of the clay is estimated from its cation exchange capacity (CEC) and surface charge density. A transmission coefficient correcting for the effect of the tortuous flow path of current through the soil, and a proportionality constant relating the electrical conductivity of water in the DDL to that of free water, are included in the model. The transmission coefficient is a function of the contents of water and clay and has been modelled in terms of these factors. The values of the proportionality constant and those relating to the transmission coefficient were optimized for five different soils. The electrical conductivities of the five soils estimated by the model compare well with the measured values, which, however, deviate systematically from predictions by the three-component model of Rhoades et al. [source]

Fate of microbial residues in sandy soils of the South African Highveld as influenced by prolonged arable cropping

W. Amelung
Summary Long-term cultivation of former grassland soils results in a significant decline of both living and dead microbial biomass. We evaluated the effect of duration of cropping on the preservation of fungal and bacterial residues in the coarse-textured soils of the South African Highveld. Composite samples were taken from the top 20 cm of soils (Plinthustalfs) that have been cropped for periods varying from 0 to 98 years in each of three different agro-ecosystems in the Free State Province. Amino sugars were determined as markers for the microbial residues in bulk soil and its particle-size fractions. Long-term cultivation reduced N in the soil by 55% and the contents of amino sugars by 60%. Loss rates of amino sugars followed bi-exponential functions, suggesting that they comprised both labile and stable fractions. With increased duration of cropping the amino sugars attached to silt dissipated faster than those associated with the clay. This dissipation was in part because silt was preferentially lost through erosion, while clay particles (and their associated microbial residues) remained. Erosion was not solely responsible for the reduction in amino sugar concentrations, however. Bacterial amino sugars were lost in preference to fungal ones as a result of cultivation, and this effect was evident in both silt- and clay-sized separates. This shift from fungal to bacterial residues was most pronounced within the first 20 years after converting the native grassland to arable cropland, but continued after 98 years of cultivation. [source]

Loss of phosphorus from soil in semi-arid northern Tanzania as a result of cropping: evidence from sequential extraction and 31P-NMR spectroscopy

D. Solomon
Summary In semi-arid northern Tanzania, the native woodland is being rapidly cleared and replaced by low input agriculture. This has resulted in pronounced environmental degradation, and in particular loss of phosphorus (P) from the soil. We have used sequential extraction and 31P-NMR to investigate the effects of land use changes, i.e. native woodland, degraded woodland, cultivation for 3 and 15 years and homestead fields where manure was applied, on the amount and structural composition of P in this soil. Clearing and continuous cultivation reduced both organic and inorganic P in the soil. The difference in the amount of organic P from the bulk soil of the fields cultivated for 3 and 15 years was not statistically significant (P <,0.05), suggesting that most of the depletion in organic P occurred during the first 3 years of cultivation. By contrast, in the homesteads, there was much organic and inorganic P in the soil. The 31P-NMR revealed that cultivation resulted in a 53% depletion of orthophosphate diester P, whereas only a 30% and 39% reduction of orthophosphate monoester P was found in the bulk soil after 3 and 15 years of cultivation, respectively. These results concur with the suggestion that diester P constitutes more easily mineralizable forms of organic P in soil than does monoester P. Our 31P-NMR also showed that 70% of the inorganic orthophosphate P was depleted from the coarse and fine sand separates as a result of cultivation. The influence of clearing and subsequent cropping on the amount and forms of P was more pronounced in the coarse and fine sand than in the silt and clay, stressing the importance of particle size and chemical properties such as organic matter and oxides in the availability of P in this soil. Our results show that the current low input agricultural practice is not sustainable, and that practices must be developed to combat the ongoing degradation of the soil. A combined use of available organic materials such as animal manure with the judicious use of inorganic fertilizers can replenish the soil's fertility. [source]

Growth of Frankia strains in leaf litter-amended soil and the rhizosphere of a nonactinorhizal plant

Babur S. Mirza
Abstract The ability of Frankia strains to grow in the rhizosphere of a nonactinorhizal plant, Betula pendula, in surrounding bulk soil and in soil amended with leaf litter was analyzed 6 weeks after inoculation of pure cultures by in situ hybridization. Growth responses were related to taxonomic position as determined by comparative sequence analysis of nifH gene fragments and of an actinomycetes-specific insertion in Domain III of the 23S rRNA gene. Phylogenetic analyses confirmed the basic classification of Frankia strains by host infection groups, and allowed a further differentiation of Frankia clusters within the Alnus host infection group. Except for Casuarina -infective Frankia strains, all other strains of the Alnus and the Elaeagnus host infection groups displayed growth in the rhizosphere of B. pendula, and none of them grew in the surrounding bulk soil that was characterized by a very low organic matter content. Only a small number of strains that all belonged to a distinct phylogenetic cluster within the Alnus host infection group grew in soil amended with ground leaf litter from B. pendula. These results demonstrate that saprotrophic growth of frankiae is a common trait for most members of the genus, and the supporting factors for growth (i.e. carbon utilization capabilities) varied with the host infection group and the phylogenetic affiliation of the strains. [source]

Ecology and characterization of polyhydroxyalkanoate-producing microorganisms on and in plants

Ilona Gasser
Abstract Polyhydroxyalkanoates are energy reserve polymers produced by bacteria to survive periods of starvation in natural habitats. Little is known about the ecology of polyhydroxyalkanoate-producing bacteria. To analyse the occurrence of this specific group on/in seven different plant species, a combined strategy containing culture-dependent and -independent methods was applied. Using microbial fingerprint techniques (single-strand conformation polymorphism analysis with specific primers for phaC gene encoding the key enzyme of the polyhydroxyalkanoate synthesis), a high number of bands were especially found for the rhizosphere. Furthermore, cluster analysis revealed plant species-specific communities. Isolation of bacteria, recognition of brightly refractile cytoplasmatic inclusions, lipophilic stainings and a PCR strategy targeted on the phaC gene were used as a culture-dependent strategy for the detection of polyhydroxyalkanoate-producing bacteria. Results again represent a high degree of plant specificity: the rhizosphere of sugar beet contained the highest number of positive strains. This was confirmed by quantitative PCR: the relative copy number of phaC was statistically and significantly enhanced in all rhizospheres in comparison with bulk soil. New polyhydroxyalkanoate-producing bacterial species were detected: for example, Burkholderia terricola, Lysobacter gummosus, Pseudomonas extremaustralis, Pseudomonas brassicacearum and Pseudomonas orientalis. Our results confirm the hypothesis that the rhizosphere is an interesting hidden reservoir for polyhydroxyalkanoate producers. [source]

Bacterial quorum sensing and nitrogen cycling in rhizosphere soil

Kristen M. DeAngelis
Abstract Plant photosynthate fuels carbon-limited microbial growth and activity, resulting in increased rhizosphere nitrogen (N) mineralization. Most soil organic nitrogen is macromolecular (chitin, protein, nucleotides); enzymatic depolymerization is likely rate limiting for plant nitrogen accumulation. Analyzing Avena (wild oat) planted in microcosms containing sieved field soil, we observed increased rhizosphere chitinase and protease-specific activities, bacterial cell densities, and dissolved organic nitrogen (DON) compared with bulk soil. Low-molecular-weight (MW) DON (<3000 Da) was undetectable in bulk soil but comprised 15% of rhizosphere DON. Extracellular enzyme production in many bacteria requires quorum sensing (QS), cell-density-dependent group behavior. Because proteobacteria are considered major rhizosphere colonizers, we assayed the proteobacterial QS signals N -acyl-homoserine lactones (AHLs), which were significantly increased in the rhizosphere. To investigate the linkage between soil signaling and nitrogen cycling, we characterized 533 bacterial isolates from Avena rhizosphere: 24% had chitinase or protease activity and AHL production; disruption of QS in seven of eight isolates disrupted enzyme activity. Many Alphaproteobacteria were newly found with QS-controlled extracellular enzyme activity. Enhanced specific activities of nitrogen-cycling enzymes accompanied by bacterial density-dependent behaviors in rhizosphere soil gives rise to the hypothesis that QS could be a control point in the complex process of rhizosphere nitrogen mineralization. [source]

Use of a novel nonantibiotic triple marker gene cassette to monitor high survival of Pseudomonas fluorescens SBW25 on winter wheat in the field

Lotta Jäderlund
Abstract Pseudomonas fluorescens SBW25 was tagged with a triple marker gene cassette containing gfp, encoding green fluorescent protein; luxAB, encoding luciferase; and telABkilA, encoding tellurite resistance, and the tagged strain was monitored in the first Swedish field release of a genetically modified microorganism (GMM). The cells were inoculated onto winter wheat seeds and the GMM cells (SBW25,tgl) were monitored in the field from September 2005 to May 2006 using plating, luminometry and microscopic analyses. Cell numbers were high on all sampling occasions and metabolically active cells were detected on all plant parts. Field results were similar to those obtained in a parallel phytotron study, although the amount of SBW25,tgl detected on shoots was significantly higher in the phytotron than in the field. After winter, cell counts were 100-fold higher on the roots and root-associated soil compared with prewinter measurements, although the cells had a lower relative metabolic activity. The wheat seeds were naturally infested with Microdochium nivale, but no treatment resulted in reduction of disease symptoms. No SWB25,tgl cells were ever found in bulk soil or uninoculated plants. The Swedish field trial results complement and contrast with prior field studies performed with the same parent organism in the United Kingdom under different soil, plant and climatic conditions. [source]

Structure and diversity of Gram-negative sulfate-reducing bacteria on rice roots

Daniel Scheid
Abstract Specific PCR assays were used to amplify the 16S rRNA genes of the Desulfobacteriaceae and the Desulfovibrionaceae from extracted environmental DNA from rice roots. 16S rDNA-based community patterns of the Desulfobacteriaceae were generated via terminal restriction fragment length polymorphism analysis from rice roots and compared with bulk soil. The molecular fingerprints showed no significant difference between rice roots and bulk soil, but changes during the vegetation period. 16S rDNA clone libraries and sequencing showed that the predominant terminal restriction fragments represented distinct phylogenetic groups. The 16S rDNA clone sequences of the Desulfobacteriaceae fell in the phylogenetic radiation of Desulfonema and Desulfosarcina or grouped within the Desulforhabdus,Syntrophobacter assemblage. Three of the latter sequences were closely affiliated with the MPN isolate EZ-2C2 from rice roots. All Desulfovibrionaceae 16S rDNA clone sequences, with one exception, were affiliated with the MPN isolate F1-7b from rice roots. The clustering of the clone sequences and the close phylogenetic affiliation with isolates from MPN enrichments from the same habitat in two cases indicated that these sequence clusters may represent predominant Gram-negative sulfate reducers on rice roots. Quantification of the bacterial abundances was accomplished by rRNA dot blot hybridization. In total the Gram-negative sulfate reducers accounted for approximately 2,3% of the total rRNA content. The relative rRNA abundance of the Desulfobacteriaceae was, at 1.4%, higher than that of the Desulfovibrionaceae (0.5%). [source]

Indirect effects of soil moisture reverse soil C sequestration responses of a spring wheat agroecosystem to elevated CO2

Abstract Increased plant productivity under elevated atmospheric CO2 concentrations might increase soil carbon (C) inputs and storage, which would constitute an important negative feedback on the ongoing atmospheric CO2 rise. However, elevated CO2 often also leads to increased soil moisture, which could accelerate the decomposition of soil organic matter, thus counteracting the positive effects via C cycling. We investigated soil C sequestration responses to 5 years of elevated CO2 treatment in a temperate spring wheat agroecosystem. The application of 13C-depleted CO2 to the elevated CO2 plots enabled us to partition soil C into recently fixed C (Cnew) and pre-experimental C (Cold) by 13C/12C mass balance. Gross C inputs to soils associated with Cnew accumulation and the decomposition of Cold were then simulated using the Rothamsted C model ,RothC.' We also ran simulations with a modified RothC version that was driven directly by measured soil moisture and temperature data instead of the original water balance equation that required potential evaporation and precipitation as input. The model accurately reproduced the measured Cnew in bulk soil and microbial biomass C. Assuming equal soil moisture in both ambient and elevated CO2, simulation results indicated that elevated CO2 soils accumulated an extra ,40,50 g C m,2 relative to ambient CO2 soils over the 5 year treatment period. However, when accounting for the increased soil moisture under elevated CO2 that we observed, a faster decomposition of Cold resulted; this extra C loss under elevated CO2 resulted in a negative net effect on total soil C of ,30 g C m,2 relative to ambient conditions. The present study therefore demonstrates that positive effects of elevated CO2 on soil C due to extra soil C inputs can be more than compensated by negative effects of elevated CO2 via the hydrological cycle. [source]

Sequestration and turnover of plant- and microbially derived sugars in a temperate grassland soil during 7 years exposed to elevated atmospheric pCO2

Abstract Temperate grasslands contribute about 20% to the global terrestrial carbon (C) budget with sugars contributing 10,50% to this soil C pool. Whether the observed increase of the atmospheric CO2 concentration (pCO2) leads to additional C sequestration into these ecosystems or enhanced mineralization of soil organic matter (SOM) is still unclear. Therefore, the aim of the presented study was to investigate the impact of elevated atmospheric pCO2 on C sequestration and turnover of plant- (arabinose and xylose) and microbially derived (fucose, rhamnose, galactose, mannose) sugars in soil, representing a labile SOM pool. The study was carried out at the Swiss Free Air Carbon Dioxide Enrichment (FACE) experiment near Zurich. For 7 years, Lolium perenne swards were exposed to ambient and elevated pCO2 (36 and 60 Pa, respectively). The additional CO2 in the FACE plots was depleted in 13C compared with ambient plots, so that ,new' (<7 years) C inputs could be determined by means of compound-specific stable isotope analysis (13C : 12C). Samples were fractionated into clay, silt, fine sand and coarse sand, which yielded relatively stable and labile SOM pools with different turnover rates. Total sugar sequestration into bulk soil after 7 years of exposure to elevated pCO2 was about 28% compared with the control plots. In both ambient and elevated plots, total sugar concentrations in particle size fractions increased in the order sandbulk soil samples after 7 years under elevated pCO2. In the ambient plots, sugars were enriched in 13C by up to 10, when compared with bulk soil samples from the same plots. The enrichment of 13C in plant-derived sugars was up to 13.4, when compared with parent plant material. After 7 years, the ,13C values of individual sugars decreased under elevated (13C-depleted) CO2 in bulk soil and particle size fractions, varying between ,13.7, and ,37.8, under elevated pCO2. In coarse and fine sand, silt and clay fractions newly produced sugars made up 106%, 63%, 60% and 45%, respectively, of the total sugars present after 7 years. Mean residence time (MRT) of the sugars were calculated according to two models revealing a few decades, mean values increasing in the order coarse sand[source]

Compound-specific stable-isotope (,13C) analysis in soil science

Bruno Glaser
Abstract This review provides current state of the art of compound-specific stable-isotope-ratio mass spectrometry (,13C) and gives an overview on innovative applications in soil science. After a short introduction on the background of stable C isotopes and their ecological significance, different techniques for compound-specific stable-isotope analysis are compared. Analogous to the ,13C analysis in bulk samples, by means of elemental analyzer,isotope-ratio mass spectrometry, physical fractions such as particle-size fractions, soil microbial biomass, and water-soluble organic C can be analyzed. The main focus of this review is, however, to discuss the isotope composition of chemical fractions (so-called molecular markers) indicating plant- (pentoses, long-chain n-alkanes, lignin phenols) and microbial-derived residues (phospholipid fatty acids, hexoses, amino sugars, and short-chain n-alkanes) as well as other interesting soil constituents such as "black carbon" and polycyclic aromatic hydrocarbons. For this purpose, innovative techniques such as pyrolysis,gas chromatography,combustion,isotope-ratio mass spectrometry, gas chromatography,combustion,isotope-ratio mass spectrometry, or liquid chromatography,combustion,isotope-ratio mass spectrometry were compared. These techniques can be used in general for two purposes, (1) to quantify sequestration and turnover of specific organic compounds in the environment and (2) to trace the origin of organic substances. Turnover times of physical (sand < silt < clay) and chemical fractions (lignin < phospholipid fatty acids < amino sugars , sugars) are generally shorter compared to bulk soil and increase in the order given in brackets. Tracing the origin of organic compounds such as polycyclic aromatic hydrocarbons is difficult when more than two sources are involved and isotope difference of different sources is small. Therefore, this application is preferentially used when natural (e.g., C3-to-C4 plant conversion) or artificial (positive or negative) 13C labeling is used. Substanzspezifische Stabilisotopenanalyse (,13C) in der Bodenforschung Dieser Artikel fasst den Stand der Forschung bezüglich der substanzspezifischen Stabilisotopenanalyse (,13C) zusammen. Innovative Anwendungen und ein Ausblick für künftige Forschungsaktivitäten werden anhand von Fallbeispielen gegeben. Zunächst wird die ökologische Bedeutung von stabilen C-Isotopen kurz erläutert. Daran schließt sich ein methodischer Teil an, in welchem die verschiedenen Techniken gegenüber gestellt werden. Analog zu ,13C-Messungen der Feinerde mittels Elementaranalysator-Isotopenverhältnis-Massenspektrometrie können physikalisch isolierte Fraktionen (z.,B. Korngrößenfraktionen, mikrobielle Biomasse, DOC) analysiert werden. Der Schwerpunkt dieses Übersichtsartikels liegt jedoch in der Diskussion der C-Isotopensignatur chemischer Fraktionen (sog. Biomarker), welche Rückschlüsse auf Herkunft und Dynamik pflanzlicher (Pentosen, langkettige n-Alkane, Ligninphenole) und mikrobieller Rückstände (Phospholipidfettsäuren, Hexosen, Aminozucker und kurzkettige n-Alkane) sowie anderer interessanter Substanzen im Boden erlaubt wie z.,B. ,Black Carbon" und polyzyklische aromatische Kohlenwasserstoffe. Zu diesem Zweck kommen innovative Techniken zum Einsatz wie z.,B. Pyrolyse-Gaschromatographie-Isotopenverhältnismassenspektrometrie, Gaschromatographie-Verbrennungs-Isotopenverhältnismassenspektrometrie und Flüssigkeitschromatographie-Oxidations-Isotopenverhältnismassenspektrometrie. Innovative ökologische Anwendungen werden erläutert, welche sich prinzipiell in zwei Kategorien einteilen lassen: (1) Quantifizierung der Sequestrierung und des Umsatzes dieser Verbindungen in der Umwelt; (2) Untersuchung der Herkunft spezifischer organischer Substanzen. Umsatzzeiten physikalischer (Sand < Schluff < Ton) und chemischer Fraktionen (Lignin < Phospholipidfettsäuren < Aminozucker , Zucker) sind generall kleiner als jene der gesamten organischen Substanz in der Feinerde und nehmen in der in Klammern angegebenen Reihenfolge zu. Die Untersuchung der Herkunft organischer Substanzen (z.,B. polyzyklischer aromatischer Kohlenwasserstoffe) ist problematisch, weil die Unterschiede der Isotopensignatur verschiedener Quellen gering sind und meist mehr als zwei Quellen zur Isotopensignatur des untersuchten Biomarkers beitragen. Deswegen sollte die Untersuchung der Herkunft organischer Substanzen auf Tracer-Experimente beschränkt werden, wie z.,B. nach natürlicher (C3-C4-Pflanzenwechsel) bzw. künstlicher (13C-An- oder -Abreicherung) Markierung. [source]

Redox potential of bulk soil and soil solution concentration of nitrate, manganese, iron, and sulfate in two Gleysols

Tim Mansfeldt
Abstract While the reduction of nitrate-N, Mn(III,IV), Fe(III), and sulfate-S in soil has been studied intensively in the laboratory, field research has received only limited attention. This study investigated the relationship between redox potential (EH) measured in bulk soil and concentrations of nitrate, Mn2+, Fe2+, and sulfate in the soil solution of two Gleysols differing in drainage status from the Marsh area of Schleswig-Holstein, Northern Germany. The soils are silty-sandy and developed from calcareous marine sediments. Redox potentials were monitored weekly with permanently installed Pt electrodes, and soil solution was obtained biweekly by ceramic suction cups from 10, 30, 60, and 150,cm depth over one year. Median EH at 10, 30, 60, and 150,cm depths was 470, 410, 410, and 20 mV in the drained soil and 500, 480, 30, and ,170 mV in the undrained soil, respectively. A decrease in EH below critical values was accompanied in the soil solutions (pH 7.4 to 7.8) by disappearance of nitrate below 0 to 200 mV, appearance of Mn2+ below 350 mV, and Fe2+ below 0 to 50 mV. Both metals disappeared from soil solution after aeration. In the sulfide-bearing environment of the 150,cm depth of the undrained soil, however, the sulfate concentrations were highest at such EH values at which sulfate should be unstable. This discrepancy was reflected in the fact that at this depth bulk soil EH was about 400 mV lower than soil solution EH (250 mV). When investigating the dynamics of nitrate, Mn, and Fe in soils, bulk soil EH provides semi-quantitative information in terms of critical EH ranges. However, in sulfidic soil environments the interpretation of EH measured in bulk soil is uncertain. Redoxpotenzial des Bodens und Bodenlösungskonzentrationen von Nitrat, Mangan, Eisen und Sulfat in zwei Kalkmarschen Während die Reduktion von Nitrat-N, Mn(III,IV), Fe(III) und Sulfat-S in Böden intensiv im Labor untersucht worden ist, haben Felduntersuchungen sich damit kaum beschäftigt. In dieser Arbeit wurde die Beziehung zwischen dem Redoxpotenzial (EH) der Bodenmatrix und den Bodenlösungskonzentrationen von Nitrat, Mn2+, Fe2+ und Sulfat in zwei unterschiedlich drainierten Kalkmarschen Schleswig-Holsteins untersucht. Die Böden sind schluffig-sandig und haben sich aus kalkhaltigen marinen Sedimenten entwickelt. Über ein Jahr wurden in 10, 30, 60 und 150,cm Tiefe die EH wöchentlich mit permanent installierten Pt-Elektroden gemessen und die Bodenlösung zweiwöchentlich mittels keramischer Saugkerzen gewonnen. Der Medianwert des EH betrug in 10, 30, 60 und 150,cm Tiefe 470, 410, 410 und 20 mV im drainierten Boden und 500, 480, 30 und ,170 mV im nicht drainiertem Boden. Ein Abfall im EH unter kritische Werte war in der Bodenlösung (pH 7,4 bis 7,8) von einem Verschwinden des Nitrats unterhalb 0 bis 200 mV und einem Auftreten des Mn2+ unterhalb 350 mV und des Fe2+ unterhalb 0 bis 50 mV begleitet. Beide Metalle verschwanden nach Belüftung aus der Bodenlösung. Im sulfidhaltigen Milieu in 150,cm Tiefe des nicht drainierten Bodens waren die Konzentrationen des Sulfats jedoch bei solchen EH -Werten am höchsten, bei denen das Sulfat instabil sein sollte. Diese Unstimmigkeit spiegelt sich darin wieder, dass das EH in dieser Bodentiefe um ungefähr 400 mV niedriger war als das EH der Bodenlösung (250 mV). Wenn die Dynamik von Nitrat, Mn und Fe in Böden untersucht wird, stellt das in der Bodenmatrix gemessene EH semiquantitative Informationen im Sinne kritischer EH -Bereiche zur Verfügung. Im sulfidhaltigen Bodenmilieu ist die Interpretation des in der Bodenmatrix gemessenen EH jedoch unsicher. [source]

atz gene expressions during atrazine degradation in the soil drilosphere

Abstract One of the various ecosystemic services sustained by soil is pollutant degradation mediated by adapted soil bacteria. The pathways of atrazine biodegradation have been elucidated but in situ expression of the genes involved in atrazine degradation has yet to be demonstrated in soil. Expression of the atzA and atzD genes involved in atrazine dechlorination and s -triazine ring cleavage, respectively, was investigated during in situ degradation of atrazine in the soil drilosphere and bulked samples from two agricultural soils that differed in their ability to mineralize atrazine. Interestingly, expression of the atzA gene, although present in both soils, was not detected. Atrazine mineralization was greatest in Epoisses soil, where a larger pool of atzD mRNA was consistently measured 7 days after atrazine treatment, compared with Vezin soil (146 vs. 49 mRNA per 10616S rRNA, respectively). Expression of the atzD gene varied along the degradation time course and was profoundly modified in soil bioturbated by earthworms. The atzD mRNA pool was the highest in the soil drilosphere (casts and burrow-linings) and it was significantly different in burrow-linings compared with bulk soil (e.g. 363 vs. 146 mRNA per 10616S rRNA, 7 days after atrazine treatment in Epoisses soil). Thus, consistent differences in atrazine mineralization were demonstrated between the soil drilosphere and bulk soil. However, the impact of bioturbation on atrazine mineralization depended on soil type. Mineralization was enhanced in casts, compared with bulk soil, from Epoisses soil but in burrow-linings from Vezin soil. This study is the first to report the effects of soil bioturbation by earthworms on s -triazine ring cleavage and its spatial variability in soil. [source]

Field studies on the environmental fate of the Cry1Ab Bt-toxin produced by transgenic maize (MON810) and its effect on bacterial communities in the maize rhizosphere

Abstract Field studies were done to assess how much of the transgenic, insecticidal protein, Cry1Ab, encoded by a truncated cry1Ab gene from Bacillus thuringiensis (Bt), was released from Bt-maize MON810 into soil and whether bacterial communities inhabiting the rhizosphere of MON810 maize were different from those of the rhizosphere of nontransgenic maize cultivars. Bacterial community structure was investigated by SSCP (single-strand conformation polymorphism) of PCR-amplified 16S rRNA genes from community DNA. Using an improved extraction and detection protocol based on a commercially available ELISA, it was possible to detect Cry1Ab protein extracted from soils to a threshold concentration of 0.07 ng/g soil. From 100 ng of purified Cry1Ab protein added per gram of soil, only an average of 37% was extractable. At both field sites investigated, the amount of Cry1Ab protein in bulk soil of MON810 field plots was always lower than in the rhizosphere, the latter ranging from 0.1 to 10 ng/g soil. Immunoreactive Cry1Ab protein was also detected at 0.21 ng/g bulk soil 7 months after harvesting, i.e. in April of the following year. At this time, however, higher values were found in residues of leaves (21 ng/g) and of roots (183 ng/g), the latter corresponding to 12% of the Cry1Ab protein present in intact roots. A sampling 2 months later indicated further degradation of the protein. Despite the detection of Cry1Ab protein in the rhizosphere of MON810 maize, the bacterial community structure was less affected by the Cry1Ab protein than by other environmental factors, i.e. the age of the plants or field heterogeneities. The persistence of Cry1Ab protein emphasizes the importance of considering post-harvest effects on nontarget organisms. [source]

A coupled model of stomatal conductance, photosynthesis and transpiration

ABSTRACT A model that couples stomatal conductance, photosynthesis, leaf energy balance and transport of water through the soil,plant,atmosphere continuum is presented. Stomatal conductance in the model depends on light, temperature and intercellular CO2 concentration via photosynthesis and on leaf water potential, which in turn is a function of soil water potential, the rate of water flow through the soil and plant, and on xylem hydraulic resistance. Water transport from soil to roots is simulated through solution of Richards' equation. The model captures the observed hysteresis in diurnal variations in stomatal conductance, assimilation rate and transpiration for plant canopies. Hysteresis arises because atmospheric demand for water from the leaves typically peaks in mid-afternoon and because of uneven distribution of soil matric potentials with distance from the roots. Potentials at the root surfaces are lower than in the bulk soil, and once soil water supply starts to limit transpiration, root potentials are substantially less negative in the morning than in the afternoon. This leads to higher stomatal conductances, CO2 assimilation and transpiration in the morning compared to later in the day. Stomatal conductance is sensitive to soil and plant hydraulic properties and to root length density only after approximately 10 d of soil drying, when supply of water by the soil to the roots becomes limiting. High atmospheric demand causes transpiration rates, LE, to decline at a slightly higher soil water content, ,s, than at low atmospheric demand, but all curves of LE versus ,s fall on the same line when soil water supply limits transpiration. Stomatal conductance cannot be modelled in isolation, but must be fully coupled with models of photosynthesis/respiration and the transport of water from soil, through roots, stems and leaves to the atmosphere. [source]

Viruses in soils: morphological diversity and abundance in the rhizosphere

M.M. Swanson
Abstract Soil viruses are potentially of great importance as they may influence the ecology and evolution of soil biological communities through both an ability to transfer genes from host to host and as a potential cause of microbial mortality. Despite this importance, the area of soil virology is understudied. Here, we report the isolation and preliminary characterisation of viruses from soils in the Dundee area of Scotland. Different virus morphotypes including tailed, polyhedral (spherical), rod shaped, filamentous and bacilliform particles were detected in the soil samples. An apparent predominance of small spherical and filamentous bacteriophages was observed, whereas tailed bacteriophages were significantly less abundant. In this report, we also present observations and characterisation of viruses from different soil functional domains surrounding wheat roots: rhizosheath, rhizosphere and bulk soil. In spite of the differences in abundance of bacterial communities in these domains, no significant variations in viral population structure in terms of morphology and abundance were found. Typically, there were approximately 1.1,1.2 × 109 virions g,1 dry weight, implicating remarkable differences in virus-to-bacteria ratios in domains close to roots, rhizosphere and rhizosheath (approximately 0.27) and in bulk soil (approximately 4.68). [source]

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

Rodrigo Costa
Summary 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. [source]

The role of mineral and organic components in phenanthrene and dibenzofuran sorption by soil

R. Celis
Summary Improved predictions of sorption of hydrophobic organic compounds (HOCs) in soil require a better knowledge of the relative contribution of inorganic and organic soil constituents to the sorption process. In this paper, sorption of a three-ring polycyclic aromatic hydrocarbon (phenanthrene) and a three-ring heterocyclic,aromatic compound (dibenzofuran) by six agricultural soils, their clay-size fractions, and a series of single, binary, and ternary model sorbents was evaluated to elucidate the relative role of soil mineral and organic components in the retention of these two model HOCs. The sorption coefficients for phenanthrene and dibenzofuran on purified soil organic materials (Kd = 821,9080 litre kg,1) were two orders of magnitude greater than those measured on mineral model sorbents (Kd = 0,114 litre kg,1). This, along with the strong correlation between sorption and the organic C content of the soil clay fractions (r = 0.99, P < 0.01), indicated a primary role of soil organic matter in the retention of both compounds. However, weak relationships between phenanthrene and dibenzofuran sorption coefficients and the organic C content of the bulk soils and variability of Koc values among soils, clay fractions, and model sorbents (1340,21020 litre kg,1 C for phenanthrene and 1685,7620 litre kg,1 C for dibenzofuran) showed that sorption was not predictable exclusively from the organic C content of the materials. Organic matter heterogeneity and domain blockage arising from organic matter,clay interactions and associated pH shifts were identified as the most likely causes of the different organic C-normalized sorption capacities of the soils. A direct contribution from minerals to the sorption of phenanthrene and dibenzofuran by the soils studied was likely to be small. Our results suggested that suitable descriptors for the extent of organic matter,mineral interactions would help to improve current Koc -based sorption predictions and subsequently the assessment of risk associated with the presence of HOCs in soil. [source]

Carbon and nitrogen isotope composition of bulk soils, particle-size fractions and organic material after treatment with hydrofluoric acid

M. W. I. Schmidt
Summary Soils and sediments contain only small amounts of organic matter, and large concentrations of paramagnetic metals can give poor solid-state nuclear magnetic resonance (NMR) spectra of organic matter. Pretreatment of samples with hydrofluoric acid (HF) dissolves significant proportions of the mineral matrix and extracts paramagnetic elements. We investigated the effects of 10% HF treatment on the stable isotope content of carbon (C) and nitrogen (N) of organic matter from soils, composts and shales. Additionally we inferred molecular and isotopic characteristics of lost materials from calculations of isotope mass balances. Treatment with HF enriched C and N in mineral samples substantially (factors 2.5,42.4), except for Podzol B horizons (1.1,1.7) and organic material (1.0,1.3). After treatment most of the C (59.7,91.7%) and N (53.7,86.6%) was recovered, although changing C/N ratios often indicated a preferential loss of N-rich material. Isotope ratios of C and N in the remaining material became more negative when net alterations exceeded 0.3,. The isotope ratios of the lost material contained more 13C (1,2,) and 15N (1,4,) than the initial organic matter. Acid hydrolysis typically removes proteins, amino acids and polysaccharides, all of which are enriched in 13C, and in the case of proteins and amino acids, enriched in 15N as well. We conclude that HF treatment released fresh, soluble, probably microbial, biomass in addition to carbohydrates. Net changes of the bulk chemical composition of organic matter were small for most soils, size fractions and plant material, but not for samples containing little organic matter, or those rich in easily soluble organic matter associated with iron oxides, such as Podzol B horizons. [source]