A new “direct extraction” method for measuring soil microbial biomass nitrogen (biomass N) is described. The new method (fumigation-extraction) is based on CHC13 fumigation, followed by immediate extraction with 0.5 M K2SO4 and measurement of total N released by CHC13 in the soil extracts. The amounts of NH4-N and total N extracted by K2SO4 immediately after fumigation increased with fumigation time up to 5 days. Total N released by CHC13 after 1 day fumigation (1 day CHC13-N) and after 5 days fumigation (5 day CHC13-N) were positively correlated with the flush of mineral N (FN) in 37 soils that had been fumigated, the fumigant removed and the soils incubated for 10 days (fumigation-incubation). The regression equations were 1 day CHC13-N = (0.79 ± 0.022) FN and 5 day CHC13-N = (1.01 ± 0.027) FN, both regressions accounting for 92% of the variance in the data. In field soils previously treated with 15N-labelled fertilizer, the amounts of labelled N, measured after fumigation-extraction, were very similar to the amounts of labelled N mineralized during fumigation-incubation; both were about 4 times as heavily labelled as the soil N as a whole. These results suggest that fumigation-extraction and fumigation-incubation both measure the same fraction of the soil organic N (probably the cytoplasmic component of the soil microbial biomass) and that measurement of the total N released by CHC13 fumigation for 24 h provides a rapid method for measuring biomass N.

Chloroform fumigation and the release of soil nitrogen: A rapid direct extraction method to measure microbial biomass nitrogen in soil

Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth.

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Soil bacterial and fungal communities across a pH gradient in an arable soil.

A method is described for the rapid and objective estimation of the amount of carbon in the living, non-resting microbial biomass of soils. The method, which is based on the initial respiratory response of microbial populations to amendment with an excess of a carbon and energy source, was quantified using an expanded version of Jenkinson's technique.

The simultaneous application of the two methods to 50 soil samples showed a highly significant correlation (r = 0.96) between both. From this correlation it could be deduced that at 22°C, a substrate-induced maximal respiratory rate of 1 ml CO2· h−1 corresponds to c. 40 mg microbial biomass C. Evidence supporting these results was obtained from pure culture studies. The various soil types investigated were collected from agricultural as well as forest sites and they contained between 15 and 240 mg microbial C·100g dry soil−1. The respiratory method provides reproducible estimates of biomass size within 1–3 h after soil amendment. It can be combined without difficulty with a selective inhibition method for determination of bacterial and fungal contributions to soil metabolism.

A physiological method for the quantitative measurement of microbial biomass in soils

An increasing body of evidence suggests that microorganisms are far more sensitive to heavy metal stress than soil animals or plants growing on the same soils. Not surprisingly, most studies of heavy metal toxicity to soil microorganisms have concentrated on effects where loss of microbial function can be observed and yet such studies may mask underlying effects on biodiversity within microbial populations and communities. The types of evidence which are available for determining critical metal concentrations or loadings for microbial processes and populations in agricultural soil are assessed, particularly in relation to the agricultural use of sewage sludge. Much of the confusion in deriving critical toxic concentrations of heavy metals in soils arises from comparison of experimental results based on short-term laboratory ecotoxicological studies with results from monitoring of long-term exposures of microbial populations to heavy metals in field experiments. The laboratory studies in effect measure responses to immediate, acute toxicity (disturbance) whereas the monitoring of field experiments measures responses to long-term chronic toxicity (stress) which accumulates gradually. Laboratory ecotoxicological studies are the most easily conducted and by far the most numerous, but are difficult to extrapolate meaningfully to toxic effects likely to occur in the field. Using evidence primarily derived from long-term field experiments, a hypothesis is formulated to explain how microorganisms may become affected by gradually increasing soil metal concentrations and this is discussed in relation to defining “safe” or “critical” soil metal loadings for soil protection.

Toxicity of heavy metals to microorganisms and microbial processes in agricultural soils: a review.

All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

Compendium of Soil Fungi

The ratio of microbial biomass carbon (C mic ) to total organic carbon (C org ) was measured in soils from long-term agricultural experiments located in the temperate climatic zone of Central Europe. One hundred and thirty-four plots located in 26 experimental sites were analysed. This survey of C mic -to-C org ratios indicated no universal equilibrium constant. In contrast, a comparative regression analysis of permanent monoculture plots (M) with continuous crop rotation plots (R) showed both to be highly significantly different at the P = 0.001 level: the regression line of continuous crop rotations shows a steeper slope, suggesting that a higher concentration of microbial carbon is characteristic of the crop rotation. The regressions accounted for 87% (M) and 94% (R) of the variances in the data, respectively. Mean % C mic in C org amounted to 2.3 for permanent monocultures and to 2.9 for continuous crop rotations, respectively, of the simplest, the mineral fertilizer management. The differences in C-to-C ratios between the two management systems is thought to be caused by the difference in cropping management rather than by soil texture, i.e. clay content. These C mic -to-C org ratios rose to 4 or 3.7% in both plots under monoculture and plots under rotation, when the plots had received organic fertilizer the year prior to sampling. This rise in C mic over C org is seen as a transient rather than an absolute phenomenon and is believed to be due to the easily available carbon fraction of the introduced organic materia. Linearity of the C mic -to-C org relationship seems to be expressed only up to 2.5% C org . Regressions of C mic -to-N t were as well highly significant ( P =0.001) and in addition, the comparative regression analysis between M and R plots.

Ratios of microbial biomass carbon to total organic carbon in arable soils

The metabolic quotient for CO2 (qCO2) as a specific activity parameter to assess the effects of environmental conditions, such as ph, on the microbial biomass of forest soils

Metabolic quotients for CO2C (qCO2C) and microbial-C-loss (qD) were studied on soil microbial communities under long-term monoculture (M) or continuous crop rotations (CR). Under defined laboratory conditions the mean qCO2C (unit CO2C unit−1 Cmic h−1) of different microbial biomasses from 17 M systems amounted to 1.097 μg CO2qCO2CC as compared to 0.645 μg CO2C of microbial biomasses from 19 CR systems. The 1.7 times higher CO2C release per unit biomass and time of microbial biomasses from M systems was significantly different at the P =0.001 level.

In addition, microbial C-loss in samples from M or CR plots was followed for 5 weeks. Again, mean qD per unit microbial biomass and time was 1.6 times higher (P = 0.01) for microbial biomasses from M systems (0.301 μg C, 14 soils) when compared with CR systems (0.188μg C, 14 soils).

These differences were not related to soil texture, Corg or pH of these soils. The effects of environmental influences (soil management) on the microbial pool in terms of a changing energy demand are discussed.

Klaus Heinz Domsch

Papers

Compendium of Soil Fungi

A physiological method for the quantitative measurement of microbial biomass in soils

Ratios of microbial biomass carbon to total organic carbon in arable soils

The metabolic quotient for CO2 (qCO2) as a specific activity parameter to assess the effects of environmental conditions, such as ph, on the microbial biomass of forest soils

Application of eco-physiological quotients (qCO2 and qD) on microbial biomasses from soils of different cropping histories