Limits...
Microbes in nature are limited by carbon and energy: the starving-survival lifestyle in soil and consequences for estimating microbial rates.

Hobbie JE, Hobbie EA - Front Microbiol (2013)

Bottom Line: As a result, dilution assays with the addition of labeled substrates cannot be used.As a result of disturbance as well as of natural root release, concentrations of individual amino acids of ~10 μM are measured.This contrasts with concentrations of a few nanomolar found in aquatic systems and raises questions about possible differences in the bacterial strategy between aquatic and soil ecosystems.

View Article: PubMed Central - PubMed

Affiliation: The Ecosystems Center, Marine Biological Laboratory Woods Hole, MA, USA.

ABSTRACT
Understanding microbial transformations in soils is important for predicting future carbon sequestration and nutrient cycling. This review questions some methods of assessing one key microbial process, the uptake of labile organic compounds. First, soil microbes have a starving-survival life style of dormancy, arrested activity, and low activity. Yet they are very abundant and remain poised to completely take up all substrates that become available. As a result, dilution assays with the addition of labeled substrates cannot be used. When labeled substrates are transformed into (14)CO2, the first part of the biphasic release follows metabolic rules and is not affected by the environment. As a consequence, when identical amounts of isotopically substrates are added to soils from different climate zones, the same percentage of the substrate is respired and the same half-life of the respired (14)CO2 from the labeled substrate is estimated. Second, when soils are sampled by a variety of methods from taking 10 cm diameter cores to millimeter-scale dialysis chambers, amino acids (and other organic compounds) appear to be released by the severing of fine roots and mycorrhizal networks as well as from pressing or centrifuging treatments. As a result of disturbance as well as of natural root release, concentrations of individual amino acids of ~10 μM are measured. This contrasts with concentrations of a few nanomolar found in aquatic systems and raises questions about possible differences in the bacterial strategy between aquatic and soil ecosystems. The small size of the hyphae (2-10 μm diameter) and of the fine roots (0.2-2 mm diameter), make it very difficult to sample any volume of soil without introducing artifacts. Third, when micromolar amounts of labeled amino acids are added to soil, some of the isotope enters plant roots. This may be an artifact of the high micromolar concentrations applied.

No MeSH data available.


Related in: MedlinePlus

Leucine uptake kinetics in Atlantic Ocean.(A) Incorporation into bacteria of 3H-leucine at 6 nM concentrations. (B) The relationships between added amino acid concentrations and their corresponding turnover times. The error bars show single standard errors. The Y-axis intercept of the regression line is an estimate of turnover time at maximum bioavailable ambient concentration of amino acids. From Zubkov et al. (2008) with permission.
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Figure 2: Leucine uptake kinetics in Atlantic Ocean.(A) Incorporation into bacteria of 3H-leucine at 6 nM concentrations. (B) The relationships between added amino acid concentrations and their corresponding turnover times. The error bars show single standard errors. The Y-axis intercept of the regression line is an estimate of turnover time at maximum bioavailable ambient concentration of amino acids. From Zubkov et al. (2008) with permission.

Mentions: In planktonic systems, the turnover of organic compounds is defined as the substrate concentration (S) divided by the uptake velocity (v). This may be measured by a short-term incubation of the sample with an array of different concentrations of a labeled substrate. The incubation must take place while uptake of the bacterioplankton is directly proportional to time (as shown in Figure 2A). The uptake velocity is sometimes increased by including the carbon respired during the experiment. When the concentration of substrate added (A) is close to the concentration S, the uptake follows Michaelis–Menten kinetics and the experiment can be analyzed as a dilution bioassay (Figure 2B). When the uptake velocity, v, is measured at various concentrations of A, each result can be plotted as a turnover time for that amount (A) of added substrate plus an unknown natural level of substrate (S). The extrapolation to zero added substrate (the Y intercept) is then the turnover at the natural level of substrate (Wright and Hobbie, 1966). In ultraoligotrophic ocean waters picomolar (pM) concentrations of leucine were added for uptake studies (Zubkov et al., 2008). The kinetic analysis of water from the Atlantic Ocean incubated for 30 min (Figure 2) shows that leucine was present in very low concentrations (0.1–0.2 nM and that the turnover time, the intercept on the Y axis, was around 5 h. See also Hobbie and Hobbie (2012) for a detailed explanation of the derivation of the equations.


Microbes in nature are limited by carbon and energy: the starving-survival lifestyle in soil and consequences for estimating microbial rates.

Hobbie JE, Hobbie EA - Front Microbiol (2013)

Leucine uptake kinetics in Atlantic Ocean.(A) Incorporation into bacteria of 3H-leucine at 6 nM concentrations. (B) The relationships between added amino acid concentrations and their corresponding turnover times. The error bars show single standard errors. The Y-axis intercept of the regression line is an estimate of turnover time at maximum bioavailable ambient concentration of amino acids. From Zubkov et al. (2008) with permission.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3824246&req=5

Figure 2: Leucine uptake kinetics in Atlantic Ocean.(A) Incorporation into bacteria of 3H-leucine at 6 nM concentrations. (B) The relationships between added amino acid concentrations and their corresponding turnover times. The error bars show single standard errors. The Y-axis intercept of the regression line is an estimate of turnover time at maximum bioavailable ambient concentration of amino acids. From Zubkov et al. (2008) with permission.
Mentions: In planktonic systems, the turnover of organic compounds is defined as the substrate concentration (S) divided by the uptake velocity (v). This may be measured by a short-term incubation of the sample with an array of different concentrations of a labeled substrate. The incubation must take place while uptake of the bacterioplankton is directly proportional to time (as shown in Figure 2A). The uptake velocity is sometimes increased by including the carbon respired during the experiment. When the concentration of substrate added (A) is close to the concentration S, the uptake follows Michaelis–Menten kinetics and the experiment can be analyzed as a dilution bioassay (Figure 2B). When the uptake velocity, v, is measured at various concentrations of A, each result can be plotted as a turnover time for that amount (A) of added substrate plus an unknown natural level of substrate (S). The extrapolation to zero added substrate (the Y intercept) is then the turnover at the natural level of substrate (Wright and Hobbie, 1966). In ultraoligotrophic ocean waters picomolar (pM) concentrations of leucine were added for uptake studies (Zubkov et al., 2008). The kinetic analysis of water from the Atlantic Ocean incubated for 30 min (Figure 2) shows that leucine was present in very low concentrations (0.1–0.2 nM and that the turnover time, the intercept on the Y axis, was around 5 h. See also Hobbie and Hobbie (2012) for a detailed explanation of the derivation of the equations.

Bottom Line: As a result, dilution assays with the addition of labeled substrates cannot be used.As a result of disturbance as well as of natural root release, concentrations of individual amino acids of ~10 μM are measured.This contrasts with concentrations of a few nanomolar found in aquatic systems and raises questions about possible differences in the bacterial strategy between aquatic and soil ecosystems.

View Article: PubMed Central - PubMed

Affiliation: The Ecosystems Center, Marine Biological Laboratory Woods Hole, MA, USA.

ABSTRACT
Understanding microbial transformations in soils is important for predicting future carbon sequestration and nutrient cycling. This review questions some methods of assessing one key microbial process, the uptake of labile organic compounds. First, soil microbes have a starving-survival life style of dormancy, arrested activity, and low activity. Yet they are very abundant and remain poised to completely take up all substrates that become available. As a result, dilution assays with the addition of labeled substrates cannot be used. When labeled substrates are transformed into (14)CO2, the first part of the biphasic release follows metabolic rules and is not affected by the environment. As a consequence, when identical amounts of isotopically substrates are added to soils from different climate zones, the same percentage of the substrate is respired and the same half-life of the respired (14)CO2 from the labeled substrate is estimated. Second, when soils are sampled by a variety of methods from taking 10 cm diameter cores to millimeter-scale dialysis chambers, amino acids (and other organic compounds) appear to be released by the severing of fine roots and mycorrhizal networks as well as from pressing or centrifuging treatments. As a result of disturbance as well as of natural root release, concentrations of individual amino acids of ~10 μM are measured. This contrasts with concentrations of a few nanomolar found in aquatic systems and raises questions about possible differences in the bacterial strategy between aquatic and soil ecosystems. The small size of the hyphae (2-10 μm diameter) and of the fine roots (0.2-2 mm diameter), make it very difficult to sample any volume of soil without introducing artifacts. Third, when micromolar amounts of labeled amino acids are added to soil, some of the isotope enters plant roots. This may be an artifact of the high micromolar concentrations applied.

No MeSH data available.


Related in: MedlinePlus