D. Grinev

Microbial diversity affects self-organization of the soil–microbe system with consequences for function

Soils are complex ecosystems and the pore-scale physical structure regulates key processes that support terrestrial life. These include maintaining an appropriate mixture of air and water in soil, nutrient cycling and carbon sequestration. There is evidence that this structure is not random, although the organizing mechanism is not known. Using X-ray microtomography and controlled microcosms, we provide evidence that organization of pore-scale structure arises spontaneously out of the interaction between microbial activity, particle aggregation and resource flows in soil. A simple computational model shows that these interactions give rise to self-organization involving both physical particles and microbes that gives soil unique material properties. The consequence of self-organization for the functioning of soil is determined using lattice Boltzmann simulation of fluid flow through the observed structures, and predicts that the resultant micro-structural changes can significantly increase hydraulic conductivity. Manipulation of the diversity of the microbial community reveals a link between the measured change in micro-porosity and the ratio of fungal to bacterial biomass. We suggest that this behaviour may play an important role in the way that soil responds to management and climatic change, but that this capacity for self-organization has limits.

Fungal colonization in soils with different management histories: modeling growth in three-dimensional pore volumes

Despite the importance of fungi in soil functioning they have received comparatively little attention, and our understanding of fungal interactions and communities is lacking. This study aims to combine a physiologically based model of fungal growth with digitized images of internal pore volume of samples of undisturbed soil from contrasting management practices to determine the effect of physical structure on fungal growth dynamics. We quantified pore geometries of the undisturbed-soil samples from two contrasting agricultural practices, conventionally plowed (chisel plow) (CT) and no till (NT), and from native-species vegetation land use on land that was taken out of production in 1989 (NS). Then we modeled invasion of a fungal species within the soil samples and evaluated the role of soil structure on the progress of fungal colonization of the soil pore space. The size of the studied pores was > or =110 microm. The dynamics of fungal invasion was quantified through parameters of a mathematical model fitted to the fungal invasion curves. Results indicated that NT had substantially lower porosity and connectivity than CT and NS soils. For example, the largest connected pore volume occupied 79% and 88% of pore space in CT and NS treatments, respectively, while it only occupied 45% in NT. Likewise, the proportion of pore space available to fungal colonization was much greater in NS and CT than in NT treatment, and the dynamics of the fungal invasion differed among the treatments. The relative rate of fungal invasion at the onset of simulation was higher in NT samples, while the invasion followed a more sigmoidal pattern with relatively slow invasion rates at the initial time steps in NS and CT samples. Simulations allowed us to elucidate the contribution of physical structure to the rates and magnitudes of fungal invasion processes. It appeared that fragmented pore space disadvantaged fungal invasion in soils under long-term no-till, while large connected pores in soils under native vegetation or in tilled agriculture promoted the invasion.

Simultaneous Preservation of Soil Structural Properties and Phospholipid Proflles: A Comparison ofThree Drying Techniques

Abstract There is a need to simultaneously preserve evidence of interactions between the biological community and soil structural properties of a soil in as near an intact (natural) state as possible. Three dehydration techniques were implemented and assessed for their ability to minimise disruption of both biological and physical properties of the same arable soil sample. Dehydration techniques applied until samples were at constant weight were i) air-drying at 20 °C (AD); ii) −80 °C freeze for 24 h, followed by freeze-drying (−80FD); and iii) liquid nitrogen snap freeze, followed by freeze-drying (LNFD) and were compared to a moist control. Physical structure was determined and quantifled in three dimensions using X-ray computed tomography and microbial phenotypic community composition was assessed using phospholipid fatty acid (PLFA) proflling. This study conflrms that any form of dehydration, when preparing soil for simultaneous biological and physical analysis, will alter the soil physical properties, and cause some change in apparent community structure. Freeze-drying (both the LNFD and −80FD treatments) was found to minimise disruption (when compared to the moist control soil) to both the soil physical properties and the community structure and is a preferable technique to air-drying which markedly alters the size and character of the pore network, as well as the phenotypic proflle. The LNFD was the preferred treatment over the −80FD treatment as samples show low variability between replicates and a fast turn-around time between samples. Therefore snap freezing in liquid nitrogen, followed by freeze drying is the most appropriate form of dehydration when two sets of data, both physical and biological, need to be preserved simultaneously from a soil core.

Biologica invasion in soil: Complex network analysis

A network model for soil pore space is developed and applied to the analysis of biological invasion of microorganisms in soil. The model was parameterized for two soil samples with different compaction (loosely and densely packed) from images derived from an X-ray micro-tomography system. The data were then processed using 3-D imaging techniques, to construct the networks of pore structures with in the soil samples. The network structure is characterized by the measurement of features that are relevant for biological colonization through soil. These include the distribution of channel lengths, node coordination numbers, location and size of channel bottlenecks, and the topology of the largest connected cluster. The pore-space networks are then used to investigate the spread of a microorganism through soil, in which the transmissibility between pores is defined as a function of the channel characteristics. The same spreading process is investigated in artificially constructed homogeneous networks with the same average properties as the original ones. The comparison shows that the extent of invasion is lower in the original networks than in the homogeneous ones: this proves that inherent heterogeneity and correlations contribute to the resilience of the system to biological invasion.