Microbial utilization

Clearly, the concentration of exudates and rhizodeposits depends on soil nutritional status and on plant species this may affect the microbial utilization and subsequent turnover of rhizodeposits in soil. 

E. Bremer and P. J. Kuikman, Microbial utilization of C(U) glucose in. soil is affected by the amount and timing of gluco.se additions. Soil Biol. Biochein. 26 511 (1994). 

Yamada H, Asano Y, Hino T, et al. 1979. Microbial utilization of acrylonitrile. J Ferment Technol 57 8-14. 

Calvillo YM, Alexander M (1996) Mechanism of microbial utilization of biphenyl sorbed to polyacrylic beads. Appl Microbiol Biotechnol 45 383-390... 

Bazylinski, D. A., Wirsen, C. O. Jannasch, H. W. (1989)- Microbial utilization of naturally occurring hydrocarbons at the Guaymas Basin hydrothermal vent site. Applied and Environmental Microbiology, 55, 2832-6. 

E. M. Prosen, D. Radlein, J. Piskorz, D. S. Scott, and R. L. Legge, Microbial utilization of levoglucosan in wood pyrolysate as a carbon and energy source, Biotechnol. Bioeng., 42 (1993) 538-541. 

Munster, U., and R. J. Chrost. 1990. Origin, composition, and microbial utilization of dissolved organic matter. In Aquatic Microbial Ecology (J. Overbeck and R. J. Chrost, Eds.), pp. 8-46. Springer-Verlag, Berlin. 

The strength of the bioassay approach is that it directly estimates the fraction of natural DOC that can be used by a natural microbial assemblage under defined conditions. However, there are numerous manipulations of water samples during bioassay incubations, and the effects of these manipulations on the measured parameters are not well known. For example, containment of water samples can rapidly alter microbial population structure. Nutrients, rather than carbon, can be limiting for microbial utilization of DOM. Moreover, there are no standard protocols for bioassay experiments. Different indicators of DOM utilization are measured by different investigators, and many of the measured parameters rely on conversion factors that are also quite variable. The extent of DOM utilization also depends upon the duration and temperature of the bioassay experiment. Despite these shortcomings, the bioassay experiment remains the best approach for estimating the bioavailability of DOM. 

Even though substrate quality (i.e., chemical composition) is widely believed to be an important factor influencing microbial utilization of DOM, there are relatively few studies relating the composition and bioavailability of DOM. Sensitive assays for the measurement of the relative activities of various extracellular enzymes can provide an indication of the chemical composition of the bioreactive components of DOM (Sinsabaugh and Findlay, 1995 Findlay et al., 1998). The enzymatic potential of bacterial populations appears to respond fairly rapidly to seasonal changes in DOM composition in the Hudson River system. These observations clearly indicate that the chemical composition of DOM influences the microbial processing of DOM. 

The retention of DOM in microbial biofilms involves several processes (A) sorption of a DOM molecule to the biofilm, (B) diffusion into the biofilm, (C) cleavage by extracellular enzymes (in the case of high-molecular-weight organic matter), and (D) uptake and microbial utilization of the DOM molecule. 

Benner, R., and J. Vaun McArthur. 1988. Effects of temperature on microbial utilization of lignocellulose detritus in a chemically impacted stream. Microbiol Ecology 16 323—330. 

Reversible sorption of phenolic acids by soils may provide some protection to phenolic acids from microbial degradation. In the absence of microbes, reversible sorption 35 days after addition of 0.5-3 mu mol/g of ferulic acid or p-coumaric acid was 8-14% in Cecil A(p) horizon and 31-38% in Cecil B-t horizon soil materials. The reversibly sorbed/solution ratios (r/s) for ferulic acid or p-coumaric acid ranged from 0.12 to 0.25 in A(p) and 0.65 to 0.85 in B-t horizon soil materials. When microbes were introduced, the r/s ratio for both the A(p) and B-t horizon soil materials increased over time up to 5 and 2, respectively, thereby indicating a more rapid utilization of solution phenolic acids over reversibly sorbed phenolic acids. The increase in r/s ratio and the overall microbial utilization of ferulic acid and/or p-coumaric acid were much more rapid in A(p) than in B-t horizon soil materials. Reversible sorption, however, provided protection of phenolic acids from microbial utilization for only very short periods of time. Differential soil fixation, microbial production of benzoic acids (e.g., vanillic acid and p-hydroxybenzoic acid) from cinnamic acids (e.g., ferulic acid and p-coumaric acid, respectively), and the subsequent differential utilization of cinnamic and benzoic acids by soil microbes indicated that these processes can substantially influence the magnitude and duration of the phytoxicity of individual phenolic acids (Blum, 1998). 

Blum, U. Effects of microbial utilization of phenolic acids and their phenolic acid breakdown products on allelopathic interactions. J Chem Ecol 1998 24 685-708. 

In test tubes (i.e., closed system unpublished data) containing 1 g air-dried autoclaved Cecil Ap - horizon soil (pH 5.0), 82 pg p-coumaric acid, Hoagland s solution (all solutions adjusted to pH 5.0), and soil extract for inoculum (total of 1.5 ml) the average linear transformation rates for p-coumaric acid over 48 hr, once microbial utilization was evident, were 3.6 x 10"4 + 1.7 x 10"4 picomole/CFU of p-coumaric acid utilizing bacteria/h, about 130 times slower than what was observed for the mean utilization in the steady-state continuous flow system. The CFU of p-coumaric acid utilizing bacteria/g soil in the test tube system averaged 1.46 x 108 over the 48 h interval. Initial CFU of p-coumaric acid utilizing bacterial populations/g soil 24 hr after addition of inoculum were 105+15. Utilization of p-coumaric acid by microbes in the test tubes was determined by 0.25 M EDTA (pH 7.0) extractions at 6 h intervals and HPLC analyses.2 CFU for bacteria that utilized p-coumaric acid as a sole carbon source were also determined at 6 h intervals by... 

Blum et al.9 isolated bacterial colonies from Cecil A-horizon soils treated with individual phenolic acids, either p-coumaric acid or vanillic acid, and then tested these isolated bacterial colonies for their ability to utilize only p-coumaric acid, only vanillic acid, or both phenolic acids. They found that the majority of isolates (>72%) could utilize both phenolic acids while a much smaller fraction (<28%) could only use the phenolic acid with which the soil had been treated. Since soils contain a variety of phenolic acids, as well as other organic molecules, Blum et al.9 subsequently determined changes in phenolic acid utilizing bacterial populations after Cecil A-horizon soils were enriched with an equal molar mixture composed of 7 phenolic acids plus or minus glucose. Since the addition of glucose did not modify the increase of phenolic acid utilizing bacteria (approximately 1000% for the 0.25 pmol/g soil phenolic acid treatment), Blum et al.9 concluded that the reduced microbial utilization of phenolic acids observed in the presence of glucose... 

We observed that for freshly contaminated soil, the compound readily desorbed into the aqueous phase and was available for microbial consumption whereas for soils containing mostly the non-labile material, the contaminant availability was limited by the mass transfer into the aqueous phase. The fraction of contaminant, which is irreversibly bound to soil is typically present in micropores or chemically bound to soil humic matter and thus is not accessible for microbial utilization. These observations are in agreement with those reported for other chemicals in the literature. It is believed that the longer the contaminant age within the soil the lower the fraction of the contaminant that will be bioavailable. The observations have significant implications to the current remedy and the possibility of natural attenuation at the site. 

A study conducted in deep waters of the North Atlantic found no preferential microbial utilization of L- or D-amino acids during uptake experiments (Perez et al., 2003) yet, the presence of D-amino acids may retard the hydrolysis rate of peptides. But D/L-amino acid ratios in DOM and HWMDOM rarely exceed 1 even in the deep ocean (some surface ocean samples analyzed by Perez et al. (2003) did show values >1 for d/l-aspartic acid). The ratio could approach or exceed 1 if peptides containing D-amino acids (e.g., peptidoglycan, which contains only a few amino acids) were preferentially preserved with depth. Instead, near constant d/l ratios... 

Pearson, A., Kraunz, K. S., Sessions, A. L., Dekas, A. E., Leavitt, W. D., and Edwards, K. J. (2008). Quantifying microbial utilization of marsh sediments by using the C-13 petroleum hydrocarbons in salt content of bacterial rRNA . Appl. Environ. Microbiol. 74, 1157—1166. 

One culture-dependent method that is now being widely utilized in analysis of community-level physiological profiles (Garland and Mills, 1991 Zak et al., 1994) is available commercially as the BIOLOG system. This system is based on the microbial utilization (detected by the reduction of a tetrazolium dye) of a suite of 95 different carbon sources that can be categorized... 

Bacterial sulfate reduction appeeirs to proceed to considerable depths in marine sediments but rates computed from changes in interstitial water sulfate concentrations, with suitable corrections for diffusion and sedimentation, are generally orders of magnitude below those in surface muds (Goldhaber and Kaplan, 1975). Again, this probably reflects a depletion of utilizable organic matter in the deeper layers by microbial utilization and conversion to more intractable humates and kerogens. 

Seawater DOM has numerous sources and sinks and a range of potential reactions. Sources of the sub-micron components include exudation from phytoplankton, microbial degradation of bioparticles, animal wastes (excretion), viral infection of bacteria, sloppy feeding by zooplankton and other animals, and input of dissolved molecules from rivers and surface sediments. Removal mechanisms include photodegradation, sorption to sinking particles, and microbial utilization. Tritiated thymidine and leucine uptake experiments indicate that up to half of the carbon formed by photosynthesis is shunted via dissolved organic molecule intermediates into bacteria. 

The seasonal timing of the DOM loading also affects the effectiveness of UV photolysis and microbial utilization. Obviously, runoff loading events in cold, low light periods of the year will lead to less effective degradation and utilization of the organic compounds by biota of the ecosystem. These altered rates of UV-mediated metabolism will in turn affect rates of nutrient regeneration and subsequent productivity at many biotic levels. 

Temporal variation in DOC quality provides clues to explain the spatial variation. The decline of DOC-specific absorption in stratified surface waters [22, 23] and lake versus feeder stream [90] are attributed to cumulative photo-bleaching of the DOC pool. While photobleached DOC is in some cases subject to enhanced microbial utilization [105], the old and previously bleached DOC of saline prairie lakes is metabolized very slowly [90]. It is self-evident that photobleached DOC will not be dominant in the DOC pool while the rate of influx of non-bleached DOC is high. If hydraulic residence time is short then even low rates of DOC influx or production will be adequate to prevent accumulation of photobleached DOC. 

Both vernolate and EPTC had half-lives of 3 days in EPTC-history soil compared to 17 and 13 days, respectively, in non-history soil (Figure 4). A single carbon increase in the S-alkyl group (vernolate) did not appear to significantly influence microbial utilization. 

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