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

Uptake of 14C-glycine at five concentrations from rhizosphere by maize plants. Plant values are means ± SEM (n = 5). From Jones et al. (2005b) with permission.
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Figure 6: Uptake of 14C-glycine at five concentrations from rhizosphere by maize plants. Plant values are means ± SEM (n = 5). From Jones et al. (2005b) with permission.

Mentions: The evidence presented about the fate of LMW compounds in aquatic systems shows that sugars and amino acids commonly pass through cell membranes and enter eukaryotes both via diffusion and by transport systems. What is the evidence for effect of concentrations of LMW compounds on uptake into plant roots? The only published study we know of is that for glycine uptake in maize plants (Jones et al., 2005b; Figure 6). Uptake was very low until the glycine concentration exceeded 10 μM. In a similar study, Campbell (2010) grew cucumber plants on sterile sand and Hoagland’s solution and tested the uptake of 14C-leucine into roots at 0.1, 1, 10, 100, and 150 μM. Incorporation was very low until leucine concentrations of 100 and 150 μM were reached. Significant uptake was also measured for uptake of labeled amino acids into tomato roots at concentrations of 10–20 μM (Ge et al., 2009). It is likely that labeled amino acids will enter the roots of many species of plants when uptake is measured at tens and hundreds of micromolar concentrations of substrate.


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)

Uptake of 14C-glycine at five concentrations from rhizosphere by maize plants. Plant values are means ± SEM (n = 5). From Jones et al. (2005b) with permission.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Uptake of 14C-glycine at five concentrations from rhizosphere by maize plants. Plant values are means ± SEM (n = 5). From Jones et al. (2005b) with permission.
Mentions: The evidence presented about the fate of LMW compounds in aquatic systems shows that sugars and amino acids commonly pass through cell membranes and enter eukaryotes both via diffusion and by transport systems. What is the evidence for effect of concentrations of LMW compounds on uptake into plant roots? The only published study we know of is that for glycine uptake in maize plants (Jones et al., 2005b; Figure 6). Uptake was very low until the glycine concentration exceeded 10 μM. In a similar study, Campbell (2010) grew cucumber plants on sterile sand and Hoagland’s solution and tested the uptake of 14C-leucine into roots at 0.1, 1, 10, 100, and 150 μM. Incorporation was very low until leucine concentrations of 100 and 150 μM were reached. Significant uptake was also measured for uptake of labeled amino acids into tomato roots at concentrations of 10–20 μM (Ge et al., 2009). It is likely that labeled amino acids will enter the roots of many species of plants when uptake is measured at tens and hundreds of micromolar concentrations of substrate.

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