The ecoresponsive genome of Daphnia pulex

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.     

Oospores associated with tomato seed may lead to seedborne transmission of<Emphasis Type="Italic">Phytophthora infestans</Emphasis>

Tomato fruits at the green mature stage were inoculated with a mixed sporangial suspension of A₁ and A₂ isolates ofPhytophthora infestans. Other fruits were inoculated with either A₁ or A₂ sporangia. Seeds were extracted from the blighted fruits and sown in soil or on agar media to test for the transmission of late blight to the emerging seedlings. Only 23 (0.09%) of approximately 25,000 seedlings developed symptoms. All blighted seedlings originated from fruits inoculated with mixed A₁ + A₂ sporangia. Isolates ofP. infestans recovered from the emerging blighted seedlings were seemingly of oosporic origin, as they differed phenotypically (mating type, virulence, sensitivity to metalaxyl) from the parent isolates used to inoculate the fruits. The results suggest that transmission ofP. infestans might occur by seeds extracted from fruits carrying oospores and less probably by seeds extracted from fruits having no oospores. http://www.phytoparasitica.org posting April 30, 2004.     

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.     

Fusarium verticillioides as a new pathogen of the parasitic weed Orobanche spp.

A strain of Fusarium verticillioides was isolated from the tubercles of the parasitic weed Orobanche cumana in Israel. The pathogenicity was tested in polyethylene bags on O. cumana, O. crenata, O. aegyptiaca and O. ramosa and in pots on O. cumana and O. crenata. F. verticillioides was highly pathogenic to O. aegyptiaca, O. ramosa and O. cumana in the polyethylene bags. In pots, the fungus caused wilting and necrotic areas on flowering shoots of O. cumana, but did not cause disease symptoms on O. crenata. F. verticillioides grown on liquid Czapek growth medium produced a phytotoxic metabolite, which in leaf-puncture bioassay caused large necrotic areas on Orobanche shoots and on leaves of various crops. An extract of the fungal growth medium caused complete mortality of O. cumana and O. aegyptiaca seedlings in vitro. The toxic metabolite was isolated and identified by spectroscopic methods as fusaric acid. The identity of the compound was confirmed by conversion into the corresponding methyl ester, and by TLC comparison against authentic fusaric acid. No other phytotoxic metabolites could be detected in the growth medium extracts.     

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.