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

Laboratory study of Michaelis–Menten kinetics from the incorporation of glucose at a variety of concentrations by a lake bacteria culture (low Km, low Vmax) and an algal culture (Chlamydomonas sp., high Km, high Vmax).Km of bacteria is 27 nM; Km of algae is 27,000 nM. Note that uptake of algae resembles diffusion. Modified from Wright and Hobbie (1966).
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Figure 5: Laboratory study of Michaelis–Menten kinetics from the incorporation of glucose at a variety of concentrations by a lake bacteria culture (low Km, low Vmax) and an algal culture (Chlamydomonas sp., high Km, high Vmax).Km of bacteria is 27 nM; Km of algae is 27,000 nM. Note that uptake of algae resembles diffusion. Modified from Wright and Hobbie (1966).

Mentions: In the literature, the present understanding is that LMW compounds are present in micromolar concentrations in the soil. What happens in experiments when these high concentrations of labeled amino acids or sugars are added and when plants or animals are present? Fundamental information on the topic comes from studies in aquatic systems and with aquatic organisms. For example, the kinetics of the uptake of glucose in freshwaters was investigated (Figure 5) with a bacterial culture (Km of 27 nM) and an algal culture of Chlamydomonas sp. (Km of 27 μM) over a range of low concentrations (Wright and Hobbie, 1966). The bacterial culture was freshly isolated; the algae grew either in the light or on high concentrations of glucose in the dark (Bennett and Hobbie, 1972). In the experiment in Figure 5, at low concentrations (<1 μM), the bacterial uptake rises to Vmax as the transport systems become saturated. Over the range 0.3 to 11 μM glucose (0.05–2 mg l-1) algal uptake increased linearly. This linear increase over the entire range of expected glucose concentrations indicates that a diffusion-like process is driving the uptake. Therefore, if the labeled glucose is added at only one relatively high concentration, which is typical of most soil measurements made, there is no recognition of the importance of concentration added and algal uptake is believed to outcompete bacterial uptake. However, the ecological question is not whether LMW compounds enter the cell but rather whether the contribution of sugars and amino acids is important to the energy and growth requirement of these cells? The value of studying uptake at a number of concentrations of the added substrate is obvious.


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)

Laboratory study of Michaelis–Menten kinetics from the incorporation of glucose at a variety of concentrations by a lake bacteria culture (low Km, low Vmax) and an algal culture (Chlamydomonas sp., high Km, high Vmax).Km of bacteria is 27 nM; Km of algae is 27,000 nM. Note that uptake of algae resembles diffusion. Modified from Wright and Hobbie (1966).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Laboratory study of Michaelis–Menten kinetics from the incorporation of glucose at a variety of concentrations by a lake bacteria culture (low Km, low Vmax) and an algal culture (Chlamydomonas sp., high Km, high Vmax).Km of bacteria is 27 nM; Km of algae is 27,000 nM. Note that uptake of algae resembles diffusion. Modified from Wright and Hobbie (1966).
Mentions: In the literature, the present understanding is that LMW compounds are present in micromolar concentrations in the soil. What happens in experiments when these high concentrations of labeled amino acids or sugars are added and when plants or animals are present? Fundamental information on the topic comes from studies in aquatic systems and with aquatic organisms. For example, the kinetics of the uptake of glucose in freshwaters was investigated (Figure 5) with a bacterial culture (Km of 27 nM) and an algal culture of Chlamydomonas sp. (Km of 27 μM) over a range of low concentrations (Wright and Hobbie, 1966). The bacterial culture was freshly isolated; the algae grew either in the light or on high concentrations of glucose in the dark (Bennett and Hobbie, 1972). In the experiment in Figure 5, at low concentrations (<1 μM), the bacterial uptake rises to Vmax as the transport systems become saturated. Over the range 0.3 to 11 μM glucose (0.05–2 mg l-1) algal uptake increased linearly. This linear increase over the entire range of expected glucose concentrations indicates that a diffusion-like process is driving the uptake. Therefore, if the labeled glucose is added at only one relatively high concentration, which is typical of most soil measurements made, there is no recognition of the importance of concentration added and algal uptake is believed to outcompete bacterial uptake. However, the ecological question is not whether LMW compounds enter the cell but rather whether the contribution of sugars and amino acids is important to the energy and growth requirement of these cells? The value of studying uptake at a number of concentrations of the added substrate is obvious.

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