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

Soil respiration after addition of glucose, glycine, or water. 50 mM glucose (top), 50 mM glycine (middle), or rainwater (bottom) added to grassland soil at time 0. The basal respiration value of 209 μmol CO2 kg-1 h-1 has been subtracted from all treatments. From Jones and Murphy (2007) with permission.
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Figure 1: Soil respiration after addition of glucose, glycine, or water. 50 mM glucose (top), 50 mM glycine (middle), or rainwater (bottom) added to grassland soil at time 0. The basal respiration value of 209 μmol CO2 kg-1 h-1 has been subtracted from all treatments. From Jones and Murphy (2007) with permission.

Mentions: A major aspect of the starving-survival lifestyle is that large numbers of microbes with low activity are poised to respond quickly to added substrate (White, 1995). This aspect of the survival lifestyle is very important to consider when the response (such as CO2 release) of large numbers of activated soil microbes is measured. This response is less important for measurements in aquatic systems where there are many-fold fewer microbes. Soil microbes are physiologically adapted to respond rapidly. When soil was held in the laboratory for many months (Brookes et al., 1983; De Nobili et al., 2001) microbes maintained ATP and an adenylate charge ratio (AEC) of 0.8, typical of exponentially growing microbes in vitro. The AEC is defined as the quantity (ATP + 0.5 ADP)/(ATP + ADP + AMP). The rapidity of the respiration response of soil microbes, just a few minutes, to very high micromolar amounts of added glucose and glycine is illustrated in Figure 1 (Jones and Murphy, 2007).


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)

Soil respiration after addition of glucose, glycine, or water. 50 mM glucose (top), 50 mM glycine (middle), or rainwater (bottom) added to grassland soil at time 0. The basal respiration value of 209 μmol CO2 kg-1 h-1 has been subtracted from all treatments. From Jones and Murphy (2007) with permission.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Soil respiration after addition of glucose, glycine, or water. 50 mM glucose (top), 50 mM glycine (middle), or rainwater (bottom) added to grassland soil at time 0. The basal respiration value of 209 μmol CO2 kg-1 h-1 has been subtracted from all treatments. From Jones and Murphy (2007) with permission.
Mentions: A major aspect of the starving-survival lifestyle is that large numbers of microbes with low activity are poised to respond quickly to added substrate (White, 1995). This aspect of the survival lifestyle is very important to consider when the response (such as CO2 release) of large numbers of activated soil microbes is measured. This response is less important for measurements in aquatic systems where there are many-fold fewer microbes. Soil microbes are physiologically adapted to respond rapidly. When soil was held in the laboratory for many months (Brookes et al., 1983; De Nobili et al., 2001) microbes maintained ATP and an adenylate charge ratio (AEC) of 0.8, typical of exponentially growing microbes in vitro. The AEC is defined as the quantity (ATP + 0.5 ADP)/(ATP + ADP + AMP). The rapidity of the respiration response of soil microbes, just a few minutes, to very high micromolar amounts of added glucose and glycine is illustrated in Figure 1 (Jones and Murphy, 2007).

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