磷脂脂肪酸法在土壤微生物群落分析中的应用

土壤微生物群落的组成一直是土壤学、微生物学和生态学研究的热点问题。我国在这方面的研究处于国际前列,越来越多的研究成果在国际重要刊物上发表。而磷脂脂肪酸(PLFA)法在土壤微生物群落分析中占有举足轻重的地位,国内外学者都热衷于使用该方法。但是PLFA法的使用仍存在一些不足的地方,需要研究学者们慎重使用。本文综述了国际上相关研究,概述了PLFA方法使用的发展历史,应用及挑战。总结了使用和数据解读时需要注意的问题,整理了PLFA法相关的生物标记以及与新方法结合的设想,方便以后研究的开展。     

Use of microbial cells of Corynebacterium diphtheriae for preparing a nutrient medium]

Nutrient media prepared on the basis of microbial cells (Corynebacteria diphtheriae) proved to be no less nutrient in comparison with conventional media prepared on the full-value food products. Use of diphtheria bacilli (by-products of diphtheria toxoid production) as the basis for nutrient media permitted to use up to 30% less food products for this purpose.     

Evaluation of the state of soil microbial communities in two types of Siberian forest ecosystems

Microbial respiration and biomass were evaluated in soils of the Ermak Tree Nursery and Pogorel’skii Forest under different coniferous species. The degree of disturbance of each biocenosis was determined from the metabolic coefficient (qCO₂). The microbial investigation demonstrated a lower resistance to ecological factors of the tree nursery biocenosis as compared to those of the Pogorel’skii Forest.     

The restoration of the enzyme activity of chernozem soil after gamma-irradiation

The Influence of gamma-radiation by dozes 1, 5, 10 and 20 kGy on enzyme activity of ordinary chemozem were studied. Dynamics of the restoration of the enzyme activity after the influence of gamma-radiation in model experiments in 3, 30, 90 and 180 days was investigated. The doze 1 kGy did no statistically significant influence on the investigated enzymes. Dehydrogenase is more radiosensitive enzyme than catalase. Values of the saccharase activity differed a significant variation so in most cases it has not been registered statistically significant changes. In 90-180 days of the incubation enzymes activity was restored up to control values. Dehydrogenase activity in 180 days in variants with dozes 10 and 20 kGy was restored up to a level of the control, over variants with dozes 1 and 5 kGy--is higher than the control over 78% and 23% accordingly. Saccharase activity in 180 days after the influence of gamma-radiation with a doze 20 kGy was on 61% lower than the control.     

土壤微生物多样性研究方法

概述了研究土壤微生物多样性的主要方法．传统上,土壤微生物群落的分析依赖于培养技术,使用各种培养基最大限度地培养各种微生物群体,但仍只能培养和分离出一小部分土壤微生物群落．使用Biolog分析、磷脂脂肪酸分析和核酸分析等方法,可研究和表征那些现在还不能够被培养的土壤微生物。从而获取关于土壤微生物群落多样性的更多和更完整的信息．     

Use of 2-stage continuous culture for studying the physiological state of Candida utilis]

The effect of D2 (second stage) on the growth rate, the content of RNA, and the rate of its formation was studied during two-stage continuous cultivation of the yeast Candida utilis. At the same time, the effect of changes of D1 (first stage) on the properties of the yeast during the second stage was also investigated.     

Accessing the soil metagenome for studies of microbial diversity

Soil microbial communities contain the highest level of prokaryotic diversity of any environment, and metagenomic approaches involving the extraction of DNA from soil can improve our access to these communities. Most analyses of soil biodiversity and function assume that the DNA extracted represents the microbial community in the soil, but subsequent interpretations are limited by the DNA recovered from the soil. Unfortunately, extraction methods do not provide a uniform and unbiased subsample of metagenomic DNA, and as a consequence, accurate species distributions cannot be determined. Moreover, any bias will propagate errors in estimations of overall microbial diversity and may exclude some microbial classes from study and exploitation. To improve metagenomic approaches, investigate DNA extraction biases, and provide tools for assessing the relative abundances of different groups, we explored the biodiversity of the accessible community DNA by fractioning the metagenomic DNA as a function of (i) vertical soil sampling, (ii) density gradients (cell separation), (iii) cell lysis stringency, and (iv) DNA fragment size distribution. Each fraction had a unique genetic diversity, with different predominant and rare species (based on ribosomal intergenic spacer analysis [RISA] fingerprinting and phylochips). All fractions contributed to the number of bacterial groups uncovered in the metagenome, thus increasing the DNA pool for further applications. Indeed, we were able to access a more genetically diverse proportion of the metagenome (a gain of more than 80% compared to the best single extraction method), limit the predominance of a few genomes, and increase the species richness per sequencing effort. This work stresses the difference between extracted DNA pools and the currently inaccessible complete soil metagenome.     

Use of lectins as probes for analyzing embryonic induction

Summary Lectins were used as probes to investigate the mechanism of embryonic induction. Concanavalin (Con A) and gorse agglutinin out of 7 species of lectins tested were found to have strong neural-inducing effect on the presumptive ectoderm of newt gastrulae. Their effects were abolished by the addition of -methyl-D-mannoside and -L-fucose, respectively. Succinyl-Con A had a weak inducing activity in comparison to Con A. Autoradiography of³H-Con A-treated explants revealed that Con A bound to the inner surface, but not to the outer surface of ectoderm and was successively incorporated into cytoplasm.³H-Thymidine incorporation was lower in the first half and higher in the second half of the 60 h cultivation period in Con A-treated explants as compared to controls.Con A-Sepharose had a strong inductive effect. This suggests that neural induction is caused through Con A binding to the plasma membrane, but not through incorporation into the cytoplasm of the ectoderm cells.     

Use of genome-scale microbial models for metabolic engineering

Metabolic engineering serves as an integrated approach to design new cell factories by providing rational design procedures and valuable mathematical and experimental tools. Mathematical models have an important role for phenotypic analysis, but can also be used for the design of optimal metabolic network structures. The major challenge for metabolic engineering in the post-genomic era is to broaden its design methodologies to incorporate genome-scale biological data. Genome-scale stoichiometric models of microorganisms represent a first step in this direction.