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 14CO2, 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 14CO2 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.
Highlights
A major goal of microbial ecology is to connect the processes or functions occurring in aquatic and terrestrial ecosystems with the microbes present in those systems
A major function of heterotrophic bacteria and fungi in nature is to break down large organic molecules, transport low molecular weight (LMW) compounds into microbial cells, and use a portion of the LMW compounds for respiration and growth
We suggest that it is possible that the microdialysis methods as well as other methods of sampling amino acids in soils, such as tension lysimeters, are measuring mostly amino acids released from fine roots and mycorrhizal hyphae
Summary
A major goal of microbial ecology is to connect the processes or functions occurring in aquatic and terrestrial ecosystems with the microbes present in those systems. There is agreement among authors that the concentration and supply rate of bioavailable organic material determine the growth of heterotrophic microbes (Coleman et al, 2004; Egli, 2010; Inselsbacher and Näsholm, 2012). These heterotrophic microbes and the methods used to study them are the subject of this review. This review deals with methods of measuring microbial rates of use of LMW compounds in soil and compares these with similar methods developed for aquatic ecosystems. Uptake and respiration rates in aquatic systems are measured by adding 14C- or 13C-labeled compounds to samples from nature and incubating for a few hours
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