Mechanisms of real and apparent priming effects and their dependence on soil microbial biomass and community structure: critical review

The number of studies on priming effects (PE) in soil has strongly increased during the last years. The information regarding real versus apparent PE as well as their mechanisms remains controversial. Based on a meta-analysis of studies published since 1980, we evaluated the intensity, direction, and the reality of PE in dependence on the amount and quality of added primers, the microbial biomass and community structure, enzyme activities, soil pH, and aggregate size. The meta-analysis allowed revealing quantitative relationships between the amounts of added substrates as related to microbial biomass C and induced PE. Additions of easily available organic C up to 15% of microbial biomass C induce a linear increase of extra CO₂. When the added amount of easily available organic C is higher than 50% of the microbial biomass C, an exponential decrease of the PE or even a switch to negative values is often observed. A new approach based on the assessment of changes in the production of extracellular enzymes is suggested to distinguish real and apparent PE. To distinguish real and apparent PE, we discuss approaches based on the C budget. The importance of fungi for long-term changes of SOM decomposition is underlined. Priming effects can be linked with microbial community structure only considering changes in functional diversity. We conclude that the PE involves not only one mechanism but a succession of processes partly connected with succession of microbial community and functions. An overview of the dynamics and intensity of these processes as related to microbial biomass changes and C and N availability is presented.     

Soil microbial biomass and its activity estimated by kinetic respiration analysis – Statistical guidelines

The use of kinetic respiration analysis to determine soil microbial biomass its active part and maximum specific growth rate has recently increased. With this method, the increase in soil respiration rate initiated by application of carbon growth substrate, e.g. glucose, and mineral nutrients is used to estimate parameters describing microbial growth in soil. This study refines the method by developing statistical guidelines for the data analysis and processing. The kinetic respiration analysis assumes that microbial growth is not limited by substrate and energy. That is why it is critically important to identify the time period corresponding to the unlimited growth. In this work, we studied how the unlimited growth phase can be identified in less subjective ways by examining 121 datasets of respiration time series of 44 different soil samples taken from field plots. Deflection of the respiratory curve from the exponential pattern indicates growth limitation. Subjective selection of the part of respiratory curve which fits to the exponential pattern resulted in a 30% bias in specific microbial growth rates. We propose rules that are based on inspecting the patterns in a series of plots of residuals of fitted respiration rate. By comparing those rules with a set of statistical criteria we find that the weighted-coefficient of determination (r²) can be used to objectively constrain the unlimited growth phase in those cases where double-limitation does not occur. Furthermore, we discuss how the uncertainty of estimated microbial parameters is influenced by a) measurement uncertainty, b) biased measurement at the beginning of the experiment, and c) the number and timing of respiration measurements. We recommend checking plots of fits and residuals as well as reporting uncertainty bounds together with the estimated microbial parameters. A free statistical package is provided to easily deal with those aspects.     

Mineralization of soil organic matter initiated by the application of an available substrate to the profiles of surface and buried podzolic soils

The priming effect (PE) initiated by the application of ¹⁴C-glucose was studied for copiotrophic microbial communities of organic horizons and for oligotrophic microbial communities of mineral soil horizons, as well as for mineral horizons of buried soils depleted in the input of fresh organic matter. The intensity of the PE depended on the reserves of C_org, the initial amount of the microbial biomass, and the enzymatic activity, which decreased from the organic to the mineral soil horizons. The ratio of the PE to the applied carbon was two times higher in the mineral horizons as compared with the organic horizons. This is explained by the predominance of K-strategists capable of decomposing difficultly available organic compounds in the mineral horizons, so that the turnover of the microbial biomass in the mineral horizons was more active than that in the organic horizons. The predominance of K-strategists was confirmed by the close correlation between the PE and the activity of the cellobiohydrolase enzyme decomposing cellulose (R = 0.96). In general, the absolute value of the PE was controlled by the soil organic matter content, whereas the specific PE was controlled by the functional features of the microorganisms. It was shown that the functional features of the soil microorganisms remained unchanged under the conditions of their preservation in the buried soil.     

Evaluation of the pathogenicity of microorganisms isolated from Egyptian broomrape (Orobanche aegyptiaca) in Israel

Diseased Egyptian broomrape ( Orobanche aegyptiaca ) inflorescences were collected from a heavily broomrape-infested tomato ( Lycopersicon esculentum ) field in Israel. The microorganisms that were isolated from the diseased inflorescences were passed through Koch's postulates on Egyptian broomrape-parasitizing tomato roots in a polyethylene bag system and pots under greenhouse conditions. The fungi, Alternaria alternata , Macrophomina phaseolina , Rhizoctonia solani , and Fusarium solani , and the bacterium, Bacillus sp., were newly isolated from the diseased inflorescences of Egyptian broomrape and were found to be pathogenic to the parasite. Fusarium solani damaged all of the developmental stages of broomrape and prevented the damage that Egyptian broomrape causes to tomato plants. The level of pathogenicity and the damage of M. phaseolina , A. alternata , and Bacillus sp. to Egyptian broomrape in greenhouse experiments were relatively low. All the tested microorganisms are known as pathogens of tomato, yet none caused disease symptoms on the tomato plants grown in the inoculated polyethylene bags or in the pots. Fusarium solani demonstrated the highest potential for further development as a mycoherbicide for Egyptian broomrape control in tomato.     

Determination of microbial mineralization activity in soil by modified Wright and Hobbie method

Summary The Wright and Hobbie (1966) procedure, originally proposed for measurements of microbial activity in water, was adapted for soil studies. It was critically assessed, both for technical details and for the theoretical background of the isotope dilution principle. The heterogeneity of the soil microbial community was taken into account by introducing a double Michaelis-Menten equation instead of the simple Michaelis-Menten form. More complicated models were unsuitable because the kinetic parameters were not sufficiently stable in view of fluctuations of the experimental data within the measurement error. An integrated form of kinetic equation was preferable to a differential one, and a non-linear regression was better than a linear analysis of transformed data. In grey forest soil the heterotrophic potential of microorganisms was estimated to be 1.31 and 4.26 mg C h^–1 kg^–1 of soil for oligotrophic and copiotrophic components, respectively. The turnover time of indigenous, readily available, soil organic matter was 2.82 h.     

Effect of lead on growth characteristics of microorganisms in soil and rhizosphere of Dactylis glomerata

The effects of lead oxide and lead nitrate on the growth strategies of microbial communities in the soil and in the rhizosphere of orchard grass (Dactylis glomerata L.) were studied. The maximum specific growth rate of the microorganisms (μ_m) changed significantly when the concentration of mobile forms of lead in the soil exceeded 170 mg Pb/kg, which corresponded to the addition of 400–1000 mg Pb/kg of soil in the form of lead nitrate. The addition of lead resulted in the suppression of a part of the r-strategists and in the more active development of the K-strategists in the adapted microbial community. It was demonstrated that the community of rhizosphere microorganisms could be a more sensitive indicator of lead pollution than the nonrhizosphere microbial community. The values of the auxotrophy index (the ratio between the μ_m values upon the growth on glucose and yeast extract) demonstrated a tendency towards a decrease in the metabolic diversity of the soil microbial community under the impact of lead.     

Substrate quality affects microbial‐ and enzyme activities in rooted soil

The rhizosphere reflects a sphere of high substrate input by means of rhizodeposits. Active microorganisms and extracellular enzymes are known to be responsible for substrate utilization in soil, especially in rooted soil. We tested for microbial‐ and enzyme activities in arable soil, in order to investigate the effects of continuous input of easily available organics (e.g., root‐exudates) to the microbial community. In a field experiment with maize, rooted and root‐free soil were analyzed and rhizosphere processes were linked to microbial activity indicators such as specific microbial growth rates and kinetics of six hydrolytic extracellular enzymes: β‐glucosidase, β‐cellobiohydrolase, β‐xylosidase, acid phosphatase, leucine‐ and tyrosine‐aminopeptidase. Higher potential activities of leucine‐aminopeptidase (2‐fold) for rooted vs. root‐free soil suggested increased costs of enzyme production, which retarded the specific microbial growth rates. Total microbial biomass determined by the substrate‐induced respiration technique and dsDNA extraction method was 23% and 42% higher in the rooted surface‐layer (0–10 cm) compared to the root‐free soil, respectively. For the rooted soil, potential enzyme activities of β‐glucosidase were reduced by 23% and acid phosphatase by 25%, and increased by 300% for β‐cellobiohydrolase at 10–20 cm depth compared to the surface‐layer. The actively growing microbial biomass increased by the 17‐fold in rooted soil in the 10–20 cm layer compared to the upper 10 cm. Despite the specific microbial growth rates showing no changes in the presence of roots, these rates decreased by 42% at 10–20 cm depth compared to the surface‐layer. This suggests the dominance in abundances of highly active but slower growing microbes with depth, reflecting also their slower turnover. Shifts in microbial growth strategy, upregulation of enzyme production and increased microbial respiration indicate strong root effects in maize planted soil.     

Model of apparent and real priming effects: Linking microbial activity with soil organic matter decomposition

The most frequently used models simulating soil organic matter (SOM) dynamics are based on first-order kinetics. These models fail to describe and predict such interactions as priming effects (PEs), which are short-term changes in SOM decomposition induced by easily available C or N sources. We hypothesized that if decomposition rate depends not only on size of the SOM pool, but also on microbial biomass and its activity, then PE can be simulated. A simple model that included these interactions and that consisted of three C pools - SOM, microbial biomass, and easily available C - was developed. The model was parameterized and evaluated using results of ¹²C-CO₂ and ¹⁴C-CO₂ efflux after adding ¹⁴C-labeled glucose to a loamy Haplic Luvisol. Experimentally measured PE, i.e., changes in SOM decomposition induced by glucose, was compared with simulated PE. The best agreement between measured and simulated CO₂ efflux was achieved by considering both the total amount of microbial biomass and its activity. Because it separately described microbial turnover and SOM decomposition, the model successfully simulated apparent and real PE.The proposed PE model was compared with three alternative approaches with similar complexity but lacking interactions between the pools and neglecting the activity of microbial biomass. The comparison showed that proposed new model best described typical PE dynamics in which the first peak of apparent PE lasted for 1 day and the subsequent real PE gradually increased during 60 days. This sequential decomposition scheme of the new model, with immediate microbial consumption only of soluble substrate, was superior to the parallel decomposition scheme with simultaneous microbial consumption of two substrates with different decomposability. Incorporating microbial activity function in the model improved the fit of simulation results with experimental data, by providing the flexibility necessary to properly describe PE dynamics. We conclude that microbial biomass should be considered in models of C and N dynamics in soil not only as a pool but also as an active driver of C and N turnover.     

Kinetics of the respiratory response of the soil and rhizosphere microbial communities in a field experiment with an elevated concentration of atmospheric CO2

The effect of an elevated concentration of atmospheric CO₂ and the application rate of nitrogen fertilizers on the microbial biomass and maximum specific growth rate of microorganisms in the soil and rhizosphere was studied in a long-term field experiment involving the growing of sugar beets and winter wheat. It was shown that the treatment of field plots with carbon dioxide at a concentration higher than that in the atmosphere (550 ppm) for three-four years resulted in the formation of a microbial community with a higher maximum specific growth rate and a larger share of R-strategy microorganisms as compared to the soil under the control plants. No reliable differences in the total microbial biomass in the soil under the winter wheat were revealed between the treatments with the ambient and elevated CO₂ concentrations; in the soil under the beet plants, a reliable increase in the total microbial biomass at the elevated CO₂ concentration was noted only in the close vicinity of the plant roots.