Amino sugars are important indices for the contribution of soil microorganisms to soil organic matter. Consequently, the past decade has seen a great increase in the number of studies measuring amino ...sugars. However, some uncertainties remain in the interpretation of amino sugar data. The objective of the current opinion paper is to summarize current knowledge on amino sugars in soils, to give some advice for future research objectives, and to make a plea for the correct use of information. The study gives an overview on the origin of muramic acid (MurN), glucosamine (GlcN), galactosamine (GalN), and mannosamine (ManN). Information is also provided on measuring total amino sugars in soil but also on compound-specific δ
13
C and δ
15
N determination. Special attention is given to the turnover of microbial cell-wall residues, to the interpretation of the GlcN/GalN ratio, and to the reasons for converting fungal GlcN and MurN to microbial residue C. There is no evidence to suggest that the turnover of fungal residues generally differs from that of bacterial residues. On average, MurN contributes 7% to total amino sugars in soil, GlcN 60%, GalN 30%, and ManN 4%. MurN is highly specific for bacteria, GlcN for fungi if corrected for the contribution of bacterial GlcN, whereas GalN and ManN are unspecific microbial markers.
The current opinion and position paper highlights (1) correct assignation of indicator phospholipid fatty acids (PLFA), (2) specificity and recycling of PLFA in microorganisms, and (3) complete ...extraction and detection of PLFA. The straight-chain PLFA 14:0, 15:0, 16:0, and 17:0 occur in all microorganisms, i.e., also in fungi and not only in bacteria. If the phylum Actinobacteria is excluded from the group of Gram-positive bacteria, all remaining bacteria belong to the bacterial phylum Firmicutes, which should be considered. The PLFA 16:1ω5 should be used as an indicator for the biomass of arbuscular mycorrhizal fungi (AMF) as there is no experimental evidence that they occur in marked amounts in Gram-negative bacteria. Fungal PLFA should embrace the AMF-specific 16:1ω5. In the presence of plants, ergosterol should be used instead of the PLFA 18:2ω6,9 and 18:1ω9 as fungal indicators for Mucoromycotina, Ascomycota, and Basidiomycota. The majority of indicator PLFA are not fully specific for a certain microbial group. This problem might be intensified by recycling processes during decomposition to an unknown extent. Soil handling and extraction conditions should be further optimized. The reliability and accuracy of gas chromatographic separation need to be regularly checked against unintentional variations. PLFA analysis will still be of interest over the next decades as an important independent control of DNA-based methods.
Microorganisms are able to utilize nitrogen (N) from a wide range of organic and mineral compounds. In this paper, we review the current knowledge about the regulation of the enzyme systems involved ...in the acquisition of N and propose a conceptual model on the factors affecting the relative importance of organic and mineral N uptake. Most of the N input into soil is in the form of polymers, which first have to be broken down into smaller units by extracellular enzymes. The small organic molecules released by the enzymes can then be taken up directly or degraded further and the N taken up as ammonium (NH
4
+). When NH
4
+ is available at high concentrations, the utilization of alternative N sources, such as nitrate (NO
3
−) and organic molecules, is generally repressed. In contrast, when the NH
4
+ availability is low, enzyme systems for the acquisition of alternative N sources are de-repressed and the presence of a substrate can induce their synthesis. These mechanisms are known as N regulation. It is often assumed that most organic N is mineralized to NH
4
+ before uptake in soil. This pathway is generally known as the mineralization-immobilization-turnover (MIT) route. An advantage of the MIT route is that only one transporter system for N uptake is required. However, organic N uptake has the advantage that, in addition to N, it supplies energy and carbon (C) to sustain growth. Recent studies have shown that the direct uptake of organic molecules can significantly contribute to the N nutrition of soil microorganisms. We hypothesize that the relative importance of the direct and MIT route during the decomposition of residues is determined by three factors, namely the form of N available, the source of C, and the availability of N relative to C. The regulation system of soil microorganisms controls key steps in the soil N cycle and is central to determining the outcome of the competition for N between soil microorganisms and plants. More research is needed to determine the relative importance of the direct and MIT route in soil as well as the factors affecting the enzyme systems required for these two pathways.
The interrelations between the microbial biomass, total N, organic P, and organic S in the accumulation of soil organic C (SOC) and the contribution of fungal and bacterial residues to SOC, based on ...amino sugar data, were investigated in the current study. The soils had been developed under humid temperate, arid sub-tropical, and tropical climatic conditions and were used as arable, grass, and forest land. They covered a wide range in soil pH, in salinity as well as in the contents of clay and SOC. An increased microbial biomass C/N ratio due to nutrient limitation is not reflected by any increase in SOM elemental C/N/P/S ratio within the total nutrient pool or within the organic fraction. Increased SOC/total N and SOC/organic S ratios reduced the contribution of microbial biomass C to SOC, whereas neutral soil pH and high clay contents had positive effects. An increased formation of microbial biomass C also enlarged the contribution of microbial residue C to SOC, which accounted on average for 48% SOC in the neutral arable and moderate acidic grassland soils and for 30% in the saline arable and strongly acidic forest soils. The fungal C to bacterial C ratio increased with increasing acidity from 0.9 in the saline arable soils to 4.5 in the strongly acidic forest soils. Consequently, the relationship of the fungal C to bacterial C ratio was not simply related to the contribution of microbial residues to SOC. The lower the ergosterol to fungal GlcN ratio, the higher the contribution of microbial residues to SOC. This means the higher the contribution of arbuscular mycorrhizal fungi and the lower the contribution of saprotrophic fungi to the microbial community, the more fungal residues can be sequestered to SOC.
•Median SOC/total N and SOC/organic P ratios were similar in agricultural soils.•Median SOC/organic S ratios were more variable, especially in saline arable soils.•All elemental ratios were roughly doubled in strongly acidic forest soils.•Microbial residues contributed roughly 50% to SOC in arable and grassland soils.•Microbial residues contributed only 30% to SOC in saline arable and forest soils.
Soil salinity, as an increasingly important process of land degradation, is a major threat to microbial communities and thus strongly alters organic matter turnover processes. This study was ...conducted to determine the influence of salinity on the decomposition of maize and on the response of soil microbial communities. Soil samples were collected from two pasture sites in Heringen (Germany). One of the sites has previously been influenced by salinity caused by saline effluent from a potassium mine. These sandy soils were washed, resulting in equal levels of electrical conductivity. Moist soils were then incubated with 2% incorporated maize straw and at three levels of salinity (0, 15, 50 mg NaCl g
−
1
soil) for almost 7 weeks at 25 °C. The amount of recovered maize derived particulate organic matter (POM) increased with increasing salinity, exhibiting reduced decomposition of substrate. Furthermore, inorganic N, which consisted almost exclusively of NH
4
+, increased with increasing levels of salinity. Corresponding to this, biological indices like soil respiration and microbial biomass decreased with increasing levels of salinity, underlining the detrimental effect of salinity on soil microorganisms. This effect was reduced after addition of maize straw, documenting the importance of organic matter amendment in counteracting the negative effects of salinity on microbial communities and related mineralisation processes. Addition of organic matter also led to a spatial differentiation of the microbial community in the soil, with bacteria dominating the surface of the substrate, indicated by a low glucosamine-to-muramic acid ratio. This ratio, however, was not altered by salinity. On the other hand, the ergosterol-to-microbial biomass C ratio was an evidence of fungal dominance in the soil. The ratio increased with elevated salt content, either showing a shift towards fungi, a change in fungal cell morphology, or accumulation of ergosterol in the soil. The metabolic quotient
qCO
2 was higher in the soil previously subjected to osmotic stress, showing a physiologically more active population that is using substrate less efficiently. We assume that it might further reflect adaptation mechanisms to the increased osmotic pressure.
An incubation experiment with organic soil amendments was carried out with the aim to determine whether formation and use of microbial tissue (biomass and residues) could be monitored by measuring ...glucosamine and muramic acid. Living fungal tissue was additionally determined by the cell-membrane component ergosterol. The organic amendments were fibrous maize cellulose and sugarcane sucrose adjusted to the same C/N ratio of 15. In a subsequent step, spherical cellulose was added without N to determine whether the microbial residues formed initially were preferentially decomposed. In the non-amended control treatment, ergosterol remained constant at 0.44
μg
g
−1 soil throughout the 67-day incubation. It increased to a highest value of 1.9
μg
g
−1 soil at day 5 in the sucrose treatment and to 5.0
μg
g
−1 soil at day 33 in the fibrous cellulose treatment. Then, the ergosterol content declined again. The addition of spherical cellulose had no further significant effects on the ergosterol content in these two treatments. The non-amended control treatment contained 48
μg muramic acid and 650
μg
glucosamine
g
−1 soil at day 5. During incubation, these contents decreased by 17% and 19%, respectively. A 33% increase in muramic acid and an 8% increase in glucosamine were observed after adding sucrose. Consequently, the ratio of fungal C to bacterial C based on bacterial muramic acid and fungal glucosamine was lowered in comparison with the other two treatments. No effect on the two amino sugars was observed after adding cellulose initially or subsequently during the second incubation period. This indicates that the differences in quality between sucrose and cellulose had a strong impact on the formation of microbial residues. However, the amino sugars did not indicate a preferential decomposition of microbial residues as N sources.
A study was carried out to gain quantitative information on the diet-dependent faecal microbial biomass of dairy cows, especially on the biomass fractions of fungi, Gram-positive (G+) and ...Gram-negative (G-) bacteria. Groups of high-yield, low-yield and non-lactating cows were investigated at four different farms. A mean faecal microbial biomass C (MBC) concentration of 33.5 mg g-1 DM was obtained by the chloroform fumigation extraction method. This is similar to a mean microbial C concentration of 31.8 mg g-1 DM, which is the sum of bacterial C and fungal C, estimated by cell-wall derived muramic acid (MurN) and fungal glucosamine (GlcN), respectively. However, the response of these two approaches to the feeding regime was contradictory, due to feeding effects on the conversion values. The higher neutral detergent fibre (NDF) and acid detergent fibre (ADF) concentrations in the non-lactating group led to higher (P < 0.05) concentrations of cellulose and lignin in their faeces in comparison with the lactating cows. This change in faecal chemical composition in the non-lactating group was accompanied by usually higher ratios of G+/G- phospholipid fatty acids (PLFA), ergosterol/MBC and fungal C/bacterial C. Although bacteria dominate the faecal microbial biomass, fungi contribute a considerable mean percentage of roughly 20% to the faecal microbiome, according to PLFA and amino sugar data, which requires more attention in the future. Near-infra red spectroscopic estimates of organic N and C fractions of cow faeces were able to model microbial biomarkers successfully, which might be useful in the future to predict its N2O emission potential and fertilizer value.
To improve soil structure and take advantage of several accompanying ecological benefits, it is necessary to understand the underlying processes of aggregate dynamics in soils. Our objective was to ...quantify macroaggregate (> 250 μm) rebuilding in soils from loess (Haplic Luvisol) with different initial soil organic C (SOC) contents and different amendments of organic matter (OM) in a short term incubation experiment. Two soils differing in C content and sampled at 0–5 and 5–25 cm soil depths were incubated after macroaggregate destruction. The following treatments were applied: (1) control (without any addition), (2) OM₁ (addition of OM: preincubated wheat straw < 10 mm, C : N 40.6 at a rate of 4.1 g C kg soil–¹), and (3) OM₂ (same as (2) at a rate of 8.2 g C kg soil–¹). Evolution of CO₂ released from the treatments was measured continuously, and contents of different water‐stable aggregate‐size classes (> 250 μm, 250–53 μm, < 53 μm), microbial biomass, and ergosterol were determined after 7 and 28 d of incubation. Highest microbial activity was observed in the first 3 d after the OM application. With one exception, > 50% of the rebuilt macroaggregates were formed within the first 7 d after rewetting and addition of OM. However, the amount of organic C within the new macroaggregates was ≈ 2‐ to 3‐fold higher than in the original soil. The process of aggregate formation was still proceeding after 7 d of incubation, however at a lower rate. Contents of organic C within macroaggregates were decreased markedly after 28 d of incubation in the OM₁ and OM₂ treatments, suggesting that the microbial biomass (bacteria and fungi) used organic C within the newly built macroaggregates. Overall, the results confirmed for all treatments that macroaggregate formation is a rapid process and highly connected with the amount of OM added and microbial activity. However, the time of maximum aggregation after C addition depends on the soil and substrate investigated. Moreover, the results suggest that the primary macroaggregates, formed within the first 7 d, are still unstable and oversaturated with OM and therefore act as C source for microbial decomposition processes.
The current review investigates the hypothesis that dormant soil microorganisms are relevant for microbial processes and community changes. Dormant soil microorganisms are C limited and do not grow. ...However, they still have a basic metabolism, which requires organic C uptake, resulting in a slow biomass turnover. Dormant soil microorganisms respond to substrate limitation by recycling own cell components and by down-regulating enzyme-expressing genes. The adsorption of microbial cells to clay and soil organic matter, intensified by limited water availability under unsaturated conditions, reduces microbial requirements for maintenance energy but causes immobility. For this reason, soil microorganisms cannot move rapidly towards places of demand for a certain microbial ability. Consequently, it can be assumed that subsoils and deeper vadose zone sediments must have been predominantly colonized by microorganisms during periods near to the surface, with access to autotrophic C inputs. Being remote from hotspots of C input, dormant microorganisms are an important reservoir of biodiversity and potential activity if an organic substrate arrives. The turnover of the whole microbial biomass C (MBC) is the product of C use efficiency (CUE) and a maintenance coefficient. For complex osmotrophic soil microbial communities, the CUE accounts for all biomass and metabolites synthesized during growth, i.e. especially exo-enzymes but also extracellular polymeric substances. This results in a mean CUE of 0.59 for easily soluble glucose and sucrose components and a mean CUE of 0.45 for more complex organic polymers such as cellulose, straw and MBC. The annual C input limits the MBC turnover time, which varies roughly around 365 days, assuming a CUE of 0.4 for soil organic matter.
•Turnover of is the product of microbial CUE and maintenance energy requirements.•CUE should account for all microbial metabolites synthesized during growth.•The C budget required for turnover should not exceed annual C input rates into soil.•Recycling of and dormancy helps soil microorganisms to survive starvation periods.•Dormant microorganisms are a reservoir of biodiversity and potential activity.
The interacting effects of N, P, and S limitation were investigated by applying four different organic components, i.e., cysteine, chitosan, glucose-6-phosphate, and glucose, to a soil at two ...different clearly defined N, P, and S levels in a 5-fold range, one with sufficient and one with limited nutrient supply. Initially, MB-CN, MB-CP, and MB-CS ratios were lower after organic substrate amendments with the higher concentration of N, P, and S. The close relationship between the nutrient supply and elemental MB ratios was strongly modified within the next 14 days for the MB-CN ratio, probably due to a strong shift in the microbial community composition towards fungi, determined by the ergosterol content of soil. This shift was promoted by high N and low P and S availability, contrasting the view that S is important for the formation of fungal biomass. However, the negative interactions between P limitation and MB-CS ratio suggest that the microbial S metabolism has specific importance under P-limiting conditions. Low substrate CN ratio increased carbon use efficiency (CUE) by 20% in comparison with high substrate CN ratio, calculated at day 5, solely due to an increased formation of microbial residues, as the formation of MBC was not affected by differences in substrate CN ratio. In contrast, high substrate CP and CS ratios reduced MBC formation but did not affect CUE values.
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