Mineralization of carbon from d- and l-amino acids and d-glucose in two contrasting soils
Introduction
The presence of an asymmetric carbon atom, i.e. one to which four different functional groups are attached, that acts as a chiral centre in the molecule means that all amino acids except glycine may exist as enantiomers (or d- and l-forms). Both isomeric forms of amino acids occur naturally, but in living organisms and their metabolites the l-isomers are far more abundant. The biological occurrence of d-amino acids is restricted to a few amino acids with a few specific roles, such as the d-alanine and d-glutamic acid in the cross-linking of bacterial peptidoglycan (Weidel and Pelzer, 1964) and some antibiotics (Kuhn and Somerville, 1971).
Amino acids are collectively an important component of the soil organic N pool (Stevenson, 1982) and they are likely, therefore, to be important natural sources of C and N for soil microorganisms. Most studies of amino acid biochemistry in soils have, quite correctly although implicitly, assumed that the l-amino acids are the predominant form. There have been very few studies of d-amino acid metabolism in soils. Waksman (1932)commented on chirality as a factor influencing the rate of amino acid mineralization but, tantalisingly, did not say which isomeric form he thought was mineralized the more rapidly. It has also been suggested that bacterially-produced d-amino acids accumulate during the transformations of organic compounds in soil because of their persistence relative to that of the corresponding l-amino acids (Wagner and Mutatkar, 1968). This suggestion has been supported by little direct evidence, although d-alanine has been used as biomarker for bacteria (Gunnarson and Tunlid, 1986). Hopkins and O'Dowd (1997)have discussed chirality as a factor influencing substrate utilization by soil microbial communities.
Our previous studies have shown that short-term (usually 0–6 h) substrate induced respiratory responses following l-amino acid additions to a range of soils are greater than those following the addition of the corresponding d-amino acids (Hopkins and Ferguson, 1994; Hopkins et al., 1994, Hopkins et al., 1997; O'Dowd et al., 1997). Prior exposure of the soil microbial community to d-amino acids enhanced the subsequent rate of metabolism of the same d-amino acid to a proportionately greater extent than was observed for l-amino acids (Hopkins and Ferguson, 1994). Although the short-term l-amino acid induced respiration rate correlates well with microbial biomass C, as determined by glucose-induced respiration (Hopkins et al., 1994, Hopkins et al., 1997), d-amino acid metabolism does not appear to be related to the activity of the bacterial component of the soil microbial community (O'Dowd et al., 1997), as we had earlier hypothesized (Hopkins and Ferguson, 1994). Using soils with a range of biological and chemical properties, Hopkins et al. (1997)showed that the ratio of the maximum short-term rate of l-amino acid metabolism to that of the corresponding d-amino acid (the l-to-d ratio) declined markedly with both increasing activity per unit of biomass (CO2 production/biomass C; qCO2) and declining soil pH. This has led to the suggestion that increased l-to-d ratio is associated with increasing energetic demand by the soil community, so that the organisms are less fastidious with respect to C sources and will use relatively exotic C sources more readily in the presence of environmentally-imposed stress (Hopkins et al., 1997). This suggestion may be consistent with the recent observations of Staddon et al. (1997)that organic soils showed greater metabolic diversity than mineral soils, and has been supported indirectly by the observation that in soils with similar pH, the l-to-d ratio was much greater for soil with small available inorganic nutrient contents and organic C inputs compared to one with much larger available nutrient contents and C inputs (Hopkins and O'Dowd, 1997).
To date our studies comparing d- and l-amino acid metabolism in soils have been restricted to short-term investigations in which only the immediate physiological response of the soil microbial community has been determined. The objectives of the work presented here were two-fold. First, to compare the patterns with time of CO2 production from soil following addition of d- and l-amino acids and d-glucose over a sufficient period for the pulse of additional CO2 production to have subsided thereby allowing the substrate-induced CO2 production to be estimated. This will show whether the smaller amino acid induced respiration rates for d-amino acids compared to l-amino acids is due to a lag before the onset of C mineralization from d-amino acids. Second, to determine how mineralization of C from the different isomeric forms of amino acids added to soils was affected by repeated prior exposure of the soil microbial community to the amino acid. Given that we have already shown that prior exposure of the soil microbial community to an amino acid increases the subsequent substrate induced respiration rate to a greater extent for d-amino acids than for l-amino acids, this second objective will show whether the prior exposure affects any lag period.
Section snippets
Soils
Soils from the 0–15 cm depth at a forest and an arable site were collected, sieved (<4 mm) in the field-moist state and stored at 4°C for 2 weeks prior to experimentation. These soils were from the same sites as those used by O'Dowd et al. (1997)and they were selected because of their contrasting biological and physico–chemical characteristics (Table 1). Despite marked differences in soil pH and organic matter content, both soils had similar microbial biomass C contents (d-glucose induced
Results
The initial pulses of elevated CO2 evolution from the unamended soils subsided after 160 h in the forest soil and 48 h in the arable soil (Fig. 1). The individual rates of CO2 production following this time were used to estimate the basal respiration rates, which were 41 nmol CO2 g−1 soil h−1 (sd=3.9; n=5) and 21 nmol CO2 g−1 soil h−1 (sd=9.6; n=5) for the forest and the arable soils, respectively. Given that the biomass C contents of the two soils were similar (Table 1), the qCO2 for the forest soil
Discussion
Dissolution of CO2 in the soil solution and its loss in the CO2/HCO3− equilibrium is a possible source of error in the arable soil, because of its neutral pH, which could have caused loss of CO2 from the head-space thereby leading to an apparent lag period. It seems, however, unlikely that this is a major source of error because although the bulk pH(water) was approximately 7.0, much of the soil solution would have been below pH 7.0. In addition, the buffering capacity, which would also be
Acknowledgements
We are grateful to the Departmentof Agriculture for Northern Ireland and the U.K. Biotechnology and Biological Sciences Research Council (Soil-Plant-Microbe Interactions initiative) for their respective contributions to a postgraduate studentship for RWO.
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Differential acquisition of amino acid and peptide enantiomers within the soil microbial community and its implications for carbon and nitrogen cycling in soil
2015, Soil Biology and BiochemistryCitation Excerpt :It is therefore possible that the metabolism of Gram-positive bacteria may be primed on first exposure to d-enantiomers, allowing for faster and more efficient utilisation on subsequent exogenous additions. It was also noted that there was a lag period before the maximal respiration rate was achieved, when soils were amended with d-amino acids (O'Dowd and Hopkins, 1998), suggesting that cells needed to modify gene expression to cope with d-isomers when added at high exogenous concentrations. This might be expected from the lower availability of d- than l-enantiomers in soil, with l-amino acids comprising on average 87% (excluding glycine) of the free amino acid pool, whilst d-amino acids formed just 8% (15% for d-alanine relative to l-alanine) in soil solutions.
Soil- and enantiomer-specific metabolism of amino acids and their peptides by Antarctic soil microorganisms
2011, Soil Biology and BiochemistryCitation Excerpt :Nevertheless, the capacity to metabolise d-amino acids appears to be present in a wide range of prokaryotic and eukaryotic organisms, although rates of metabolism tend to be reduced in comparison to those for l-enantiomers (D’Aniello et al., 1993; Hill et al., 2011b; Kreil, 1997; Martínez-Rodríguez et al., 2010; Pollegioni et al., 2007; Tonelli, 1985). Similarly, d-amino acids are metabolised by soil microorganisms, but existing evidence suggests that decomposition is slower than for l-enantiomers and may have a greater dependence upon soil type (Hopkins and Ferguson, 1994; Hopkins et al., 1997; O’Dowd and Hopkins, 1998; O’Dowd et al., 1997, 1999). Information on the biological decomposition of d-peptides is scarce in comparison to that on the decomposition of l-peptides.
Soil organic N - An under-rated player for C sequestration in soils?
2011, Soil Biology and BiochemistryCitation Excerpt :A further possibility to aggravate proteolysis represents the introduction of d-amino acids as they occur for example in the peptidoglucan skeleton of bacteria (Kimber et al., 1990; Amelung and Zhang, 2001; Amelung et al., 2006). It was shown that the rate of C mineralization from d-amino acids is initially less than from the corresponding l-amino acids in a range of soils (Hopkins et al., 1997; O’Dowd and Hopkins, 1998; O’Dowd et al., 1999). This suggests that cell wall residues of bacteria comprise a considerable fraction of the refractory SON pool in soils.
The response of organic matter mineralisation to nutrient and substrate additions in sub-arctic soils
2010, Soil Biology and BiochemistryCitation Excerpt :Glycine additions stimulated respiration rates for a longer time period than glucose additions did, and this resulted in more CO2 being produced over the course of the whole incubation. This is in agreement with previous studies in which amino acid additions have tended to stimulate microbial respiration rates to a greater extent than glucose additions (O'Dowd and Hopkins, 1998; Meli et al., 2003). The simplest explanation for this result is the fact that glycine is a source of both C and N. However, when the same amounts of C and N were added in the combined glucose and NH4NO3 additions, respiration rates were still not stimulated as much as when glycine was added.