Oxygen uptake and denitrification in soil aggregates

A mathematical model of oxygen uptake by bacteria in agricultural soils is presented with the goal of predicting anaerobic regions in which denitrification occurs. In an environment with a plentiful supply of oxygen, microorganisms consume oxygen through normal respiration. When the local oxygen concentration falls below a threshold level, denitrification may take place leading to the release of nitrous oxide, a potent agent for global warming. A two-dimensional model is presented in which one or more circular soil aggregates are located at a distance below the ground-level at which the prevailing oxygen concentration is prescribed. The level of denitrification is estimated by computing the area of any anaerobic cores which may develop in the interior of the aggregates. The oxygen distribution throughout the model soil is calculated first for an aggregated soil for which the ratio of the oxygen diffusivities between an aggregate and its surround is small via an asymptotic analysis. Second, the case of a non-aggregated soil featuring one or more microbial hotspots, for which the diffusion ratio is arbitrary, is examined numerically using the boundary-element method. Calculations with multiple aggregates demonstrate a sheltering effect whereby some aggregates receive less oxygen than their neighbours. In the case of an infinite regular triangular network representing an aggregated soil, it is shown that there is an optimal inter-aggregate spacing which minimises the total anaerobic core area

Pseudomonad Swarming Motility Is Restricted to a Narrow Range of High Matric Water Potentials

Using a novel experimental system that allows control of the matric potential of an agar slab, we explored the hydration conditions under which swarming motility is possible. If there is recognition that this physical parameter is a key determinant of swarming, it is usually neither controlled nor measured rigorously but only manipulated through proxies, namely, the agar concentration and the drying time of “soft” agar plates (swarming plates). We contend that this not only obscures the biophysical mechanisms underlying swarming but also impedes a full assessment of its clinical and environmental significances. Our results indicate that swarming motility is restricted to a narrow range of high matric water potentials in the three pseudomonads tested (Pseudomonas sp. DSS73, Pseudomonas syringae B728a, and Pseudomonas aeruginosa PA14). The threshold below which no swarming was observed was about −0.45 kPa for the first and about −0.1 kPa for the latter two. Above the threshold, the expansion rate of DSS73 swarms increased exponentially with the matric potential. Mutants deficient in surfactant production were totally or partially unable to expand rapidly on the surface of the agar slab. Our results thus suggest that swarming motility in pseudomonads is restricted to (micro)sites where ambient humidity is very high (relative humidity of >99.99%). The spatiotemporal occurrence of such sites is limited in many types of terrestrial environments

Exposure to solute stress affects genome-wide expression but not the polycyclic aromatic hydrocarbon-degrading activity of Sphingomonas sp. strain LH128 in biofilms.

Members of the genus Sphingomonas are important catalysts for removal of polycyclic aromatic hydrocarbons (PAHs) in soil, but their activity can be affected by various stress factors. This study examines the physiological and genome-wide transcription response of the phenanthrene-degrading Sphingomonas sp. strain LH128 in biofilms to solute stress (invoked by 450 mM NaCl solution), either as an acute (4-h) or a chronic (3-day) exposure. The degree of membrane fatty acid saturation was increased as a response to chronic stress. Oxygen consumption in the biofilms and phenanthrene mineralization activities of biofilm cells were, however, not significantly affected after imposing either acute or chronic stress. This finding was in agreement with the transcriptomic data, since genes involved in PAH degradation were not differentially expressed in stressed conditions compared to nonstressed conditions. The transcriptomic data suggest that LH128 adapts to NaCl stress by (i) increasing the expression of genes coping with osmolytic and ionic stress such as biosynthesis of compatible solutes and regulation of ion homeostasis, (ii) increasing the expression of genes involved in general stress response, (iii) changing the expression of general and specific regulatory functions, and (iv) decreasing the expression of protein synthesis such as proteins involved in motility. Differences in gene expression between cells under acute and chronic stress suggest that LH128 goes through changes in genome-wide expression to fully adapt to NaCl stress, without significantly changing phenanthrene degrading activity

Development of disease symptoms and fungal pathogens on shoot bases in continuous winter wheat, and effects of fungicides

Field plots in three consecutive crops of winter wheat were sampled at approximately 2-week intervals from April to July in 1989, 1990 and 1991. Culm and stem bases were examined for symptoms of eyespot, sharp eyespot and brown foot rot. The W-type and R-type of Pseudocercosporella herpotrichoides, P. anguioides, Fusarium culmorum, F. avenaceum and Microdochium nivale grown from this plant material on agar were identified. Eyespot was most severe in 1991, when plant development was least rapid following cool weather in late winter and the summer was relatively cool and wet. Sharp eyespot was most severe in 1990, which had a warm summer with moderate rainfall. The other warm summer, 1989, was drier and these conditions favoured late development of brown foot rot, associated mainly with F. culmorum which was scarce at other times. Sharp eyespot sometimes increased where prochloraz, which decreased eyespot, was applied. Distinct symptoms of more than one disease occurred less frequently on the same stem than expected from the individual total occurrences, but co-occurrences of different fungi were often more frequent than expected. In July 1990, Fusarium spp. co-occurred with R-type, but not W-type, P. herpotrichoides more frequently than expected, and in July 1990 and 1991 M. nivale and both W-type and R-type co-occurred more frequently than expected. Fusarium spp. and M. nivale were more frequent, especially in the earlier samples, on nodes than on internodes, whilst P. herpotrichoides normally infected at the internodes. The results suggest that stems weakened or altered by a primary colonizer are often a suitable substrate for a secondary colonizer, often a Fusarium sp., which may begin infection at a distance from the original lesion and often not cause distinct symptoms itself