R. R. Yarwood

Coupled Microbial and Transport Processes in Soils

This paper reviews methods for modeling coupled microbial and transport processes in variably saturated porous media. Of special interest in this work are interactions between active microbial growth and other transport processes such as gas diffusion and interphase exchange of O2 and other constituents that partition between the aqueous and gas phases. The role of gas–liquid interfaces on microbial transport is also discussed, and various possible kinetic and equilibrium formulations for bacterial cell attachment and detachment are reviewed. The primary objective of this paper is to highlight areas in which additional research may be needed—both experimental and numerical—to elucidate mechanisms associated with the complex interactions that take place between microbial processes and flow and transport processes in soils. In addition to their general ecological significance, these interactions have global-scale implications for C cycling in the environment and the related issue of climate change.

Considerations for modeling bacterial-induced changes in hydraulic properties of variably saturated porous media

Bacterial-induced changes in the hydraulic properties of porous media are important in a variety of disciplines. Most of the previous research on this topic has focused on liquid-saturated porous media systems that are representative of aquifer sediments. Unsaturated or variably saturated systems such as soils require additional considerations that have not been fully addressed in the literature. This paper reviews some of the earlier studies on bacterial-induced changes in the hydraulic properties of saturated porous media, and discusses characteristics of unsaturated or variably saturated porous media that may be important to consider when modeling such phenomena in these systems. New data are presented from experiments conducted in sand-packed columns with initially steady unsaturated flow conditions that show significant biomass-induced changes in pressure heads and water contents and permeability reduction during growth of a Pseudomonas fluorescens bacterium.

Soil Microbe Active Community Composition and Capability of Responding to Litter Addition after 12 Years of No Inputs

ABSTRACT One explanation given for the high microbial diversity found in soils is that they contain a large inactive biomass that is able to persist in soils for long periods of time. This persistent microbial fraction may help to buffer the functionality of the soil community during times of low nutrients by providing a reservoir of specialized functions that can be reactivated when conditions improve. A study was designed to test the hypothesis: in soils lacking fresh root or detrital inputs, microbial community composition may persist relatively unchanged. Upon addition of new inputs, this community will be stimulated to grow and break down litter similarly to control soils. Soils from two of the Detrital Input and Removal Treatments (DIRT) at the H. J. Andrews Experimental Forest, the no-input and control treatment plots, were used in a microcosm experiment where Douglas-fir needles were added to soils. After 3 and 151 days of incubation, soil microbial DNA and RNA was extracted and characterized using quantitative PCR (qPCR) and 454 pyrosequencing. The abundance of 16S and 28S gene copies and RNA copies did not vary with soil type or amendment; however, treatment differences were observed in the abundance of archaeal ammonia-oxidizing amoA gene abundance. Analysis of ∼110,000 bacterial sequences showed a significant change in the active (RNA-based) community between day 3 and day 151, but microbial composition was similar between soil types. These results show that even after 12 years of plant litter exclusion, the legacy of community composition was well buffered against a dramatic disturbance.