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

(A) Amount of 14C-amino acids remaining in soil sample after various periods of incubation. A mix of eleven labeled amino acids added and 14CO2 released also measured. From Jones et al. (2004) with permission. (B) Amount of 14C-glucose remaining in soil solution after various periods and for various concentrations in final solution. From Hill et al. (2008) with permission.
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Figure 3: (A) Amount of 14C-amino acids remaining in soil sample after various periods of incubation. A mix of eleven labeled amino acids added and 14CO2 released also measured. From Jones et al. (2004) with permission. (B) Amount of 14C-glucose remaining in soil solution after various periods and for various concentrations in final solution. From Hill et al. (2008) with permission.

Mentions: The methodology devised to examine the turnover of LMW compounds in soil is quite different from the dilution analysis that works in the plankton community. The necessity for the different methodology is shown in Figure 3A. In soil there are large numbers of low-activity microbes poised to respond quickly to added substrates. Because of this, uptake is immediate and complete for all of the added substrates, both amino acids and sugars; respiration of substrates to 14CO2 also begins immediately which, incidentally, is proof that microbes are involved and not inorganic processes. Figure 3B shows that the rate of uptake into microbes is not affected by the concentration of the added substrate, at least at concentrations below 1 mM. Isotope dilution with different quantities of added glucose or amino acid does not work when all the substrate is immediately taken up. A modification that does work is to add additional water, to use homogenization, and centrifugation to extract bacteria from the soil matrix before adding the labeled leucine, and to measure incorporation of leucine into cellular protein (Bååth, 1994, 1998; Rousk and Bååth, 2011).


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)

(A) Amount of 14C-amino acids remaining in soil sample after various periods of incubation. A mix of eleven labeled amino acids added and 14CO2 released also measured. From Jones et al. (2004) with permission. (B) Amount of 14C-glucose remaining in soil solution after various periods and for various concentrations in final solution. From Hill et al. (2008) with permission.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: (A) Amount of 14C-amino acids remaining in soil sample after various periods of incubation. A mix of eleven labeled amino acids added and 14CO2 released also measured. From Jones et al. (2004) with permission. (B) Amount of 14C-glucose remaining in soil solution after various periods and for various concentrations in final solution. From Hill et al. (2008) with permission.
Mentions: The methodology devised to examine the turnover of LMW compounds in soil is quite different from the dilution analysis that works in the plankton community. The necessity for the different methodology is shown in Figure 3A. In soil there are large numbers of low-activity microbes poised to respond quickly to added substrates. Because of this, uptake is immediate and complete for all of the added substrates, both amino acids and sugars; respiration of substrates to 14CO2 also begins immediately which, incidentally, is proof that microbes are involved and not inorganic processes. Figure 3B shows that the rate of uptake into microbes is not affected by the concentration of the added substrate, at least at concentrations below 1 mM. Isotope dilution with different quantities of added glucose or amino acid does not work when all the substrate is immediately taken up. A modification that does work is to add additional water, to use homogenization, and centrifugation to extract bacteria from the soil matrix before adding the labeled leucine, and to measure incorporation of leucine into cellular protein (Bååth, 1994, 1998; Rousk and Bååth, 2011).

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