Modelling field-data of preferential flow in paddy soil induced by earthworm burrows.

Dye tracer studies revealed that earthworm burrows in the compacted plough pan of a Chinese paddy rice field can serve as preferential flow paths. It is, however, unclear whether the observed bypass of the compacted soil horizon might be explained by differences in hydraulic properties between the plough pan, the worm burrows with a surrounding denser drilosphere and the un-compacted subsoil, or by lower-permeable macropore walls. The objective is to separately analyse effects of the individual flow domains and to identify possible limiting factors (bottlenecks) in the flow system for better soil drainage management. Hydraulic properties are inversely estimated from in situ measurements of pressure heads and evaporation by using HYDRUS_1D code. Field data of 2D pressure head progression after dye tracer infiltration in the vicinity of worm burrows are simulated using HYDRUS_2D. The axisymmetric 2D flow model considers a highly permeable cylindrical macropore region in the centre of the flow domain, assuming Darcy's law is valid. The match between simulated and measured pressure head fields improved after including a lower-permeable drilosphere pore domain. Scenario simulations show that the inflow into the 'bypass-flow' domain are reduced by the homogenized topsoil (i.e., after puddling) and limited if the macropore domain is relatively shallow. The results suggest that basic structural features may in this concept be considered as one possibility to describe observed preferential flow patterns. The separate consideration of soil structural effects may help developing and improving management strategies for manipulation of preferential flow in soils of paddy fields.

The activator of the Rhodospirillum rubrum PHB depolymerase is a polypeptide that is extremely resistant to high temperature (121 degrees C) and other physical or chemical stresses.

Hydrolysis of native (amorphous) polyhydroxybutyrate (nPHB) granules isolated from different sources by soluble PHB depolymerase of Rhodospirillum rubrum in vitro requires the presence of a heat-stable compound (activator). The activator was purified and was resistant against various physical and chemical stresses such as heat (up to 130 degrees C), pH 1-12, dryness, oxidation by H2O2, reducing and denaturing compounds (2-mercaptoethanol, 5 M guanidinium-HCl) and many solvents including phenol/chloroform. The activator coding gene was identified by N-terminal sequencing of the purified protein, and the deduced protein showed significant homology to magnetosome-associated protein (Mms16) of magnetotactic bacteria. Analysis of the activation process in vitro showed that the activator acts on nPHB granules but not on the depolymerase. The effect of the activator could be mimicked by pretreatment of nPHB granules with trypsin or other proteases but protease activity of the purified activator was not detected. Evidence is shown that different mechanisms were responsible for activation of nPHB by trypsin and activator, respectively. PHB granule-associated protein (PhaP) of Ralstonia eutropha nPHB granules were cleaved by trypsin but no cleavage occurred after activator treatment. Hydrolysis of artificial protein-free PHB granules coated with negatively charged detergents (sodium dodecyl sulfate (SDS), cholate but not cetyltrimethyl-ammonium bromide (CTAB)) did not require activation and confirmed that surface layer proteins of nPHB granules are the targets of the activator rather than lipids. All experimental data are in agreement with the assumption that trypsin and the activator enable the PHB depolymerase to find and to bind to the polymer surface: trypsin by removing a portion of proteins from the polymer surface, the activator by modifying the surface structure in a not yet understood manner presumably by interaction with phasins of the proteinous surface layer of nPHB.