Browsing tag: bioróżnorodność

Metagenom – zródło nowej informacji o mikroorganizmach glebowych

Metagenome – a new source of information about soil microorganisms
J. Kozdrój

1. Wstęp. 2. Problemy z poznaniem mikrobiomu oraz próby ich przezwyciężania. 3. Metagenomika a specyficzny charakter gleby. 4. Analiza genetyczna mikrobiomu. 5. Analiza funkcjonalna metagenomu. 6. Strukturalna różnorodność mikroorganizmów w różnych środowiskach glebowych. 7. Podsumowanie

Abstract: Soil environment, due to its high heterogeneity, is considered as a major reservoir of microbial genetic and metabolic diversity in the biosphere. The knowledge on this diversity is limited, because most of the soil microorganisms cannot be cultured under the usual laboratory conditions. During the last two decades, development of methods to isolate nucleic acids from soil has opened a window to a previously unknown microbial world. In consequence, a new metagenomic approach based on the analyses of total microbial DNA has appeared in soil studies. Total microbial DNA extracted from soil by direct or indirect methods is mostly used for amplification of marker genes (e.g. SSU rRNA) which is further differentiated by fingerprinting (e.g. DGGE, T-RFLP) or sequenced directly. Until recently, sequencing was mainly performed after first cloning PCR products to produce a clone library of amplicons. Lately, another approach has been introduced to reduce costs and labour; it is commonly known as 454-pyrosequencing, the method that does not require cloning. These methods as well as DNA microarrays have demonstrated an unanticipated level of microbial diversity, especially in the newly discovered world of the biosphere. Thousands or even several hundred thousands of different bacterial phylotypes can be present in a gram of soil. They belong to dozens of phyla. The molecular approach changed the picture of structural diversity of soil microbiome, also indicating that bacteria, archaea, fungi and even viruses are diverse both globally and locally. Moreover, soil metagenomics, allows for a comprehensive search for gene expression and metabolic activity within microbiome.

1. Introduction. 2. Difficulties with microbiome analysis and attempts to overcome them. 3. Metagenomics vs. distict features of soil. 4. Genetic analysis of microbiome. 5. Functional analysis of microbiome. 6. Microbial structural diversity in different soil environments. 7. Summary

Genetyczne metody różnicowania mikroorganizmów w systemie gleba – roślina

Genetic differentiation methods of microorganisms in the soil – plant system
M. Łyszcz, A. Gałązka

1. Wstęp. 2. Elektroforeza w gradiencie czynnika denaturującego DGGE, elektroforeza w gradiencie temperatury TGGE. 3. Polimorfizm konformacji pojedynczej nici DNA SSCP. 4. Łańcuchowa reakcja polimerazy w czasie rzeczywistym (Real Time PCR). 5. Podsumowanie

Abstract: Biodiversity is a key concept in finding important features of new microorganisms. Microorganisms play an important role in the soil ecosystem and participate, among others, in such processes as the maintenance of soil structure, humification, release of organic compounds, disposal of pollutants and transformation of organic matter. The maintenance of competent state of soil microbial communities, i.e. the appropriate microorganism count, activity and diversity, is a necessary condition for the functioning of a highly complex system such as the soil. Phyllosphere bacteria have the potential to influence plant biogeography and ecosystem function through their influence on plant performance under different environmental conditions, but the drivers of variation in leaf-associated bacterial biodiversity among host plants are not well understood. Hence, undoubtedly, an important research aspect is the selection and development of indicators to evaluate microbial biodiversity of the soil and plant phyllosphere. In this publication, selected molecular methods used for the diversity assessment of microorganisms have been presented.

1. Introduction. 2. Denaturing Gradient Gel Electrophoresis DGGE, Temperature Gradient Gel Electrophoresis TGGE, 3. SSCP – single strand conformation polymorphism. 4. Real-Time Quantitative PCR. 5. Summary

Wybrane metody molekularne wykorzystywane w ocenie bioróżnorodności mikroorganizmów glebowych

Selected molecular methods used in assessing the biodiversity of soil organisms
M. Łyszcz, A. Gałązka

1. Wstęp. 2. Metody klasyczne stosowane do identyfikacji bakterii. 3. Metody molekularne stosowane do identyfikacji mikroorganizmów glebowych. 4. Analiza zawartości zasad G+C w DNA. 5. Hybrydyzacja kwasów nukleinowych. 6. Analiza sekwencji kwasów nukleinowych. 7. Podsumowanie

Abstract: Biodiversity and the identification of new important features of microorganisms is crucial for the development of biotechnology. The current knowledge about microbs in natural environments is limited, thus the analysis of the microbial diversity in nature is not an easy task. So far, only a small percentage of prokaryotic microorganisms has been identified. It is believed that the soil environment is one of the richest reservoirs of microorganisms, as approximately 2 000 to 18 000 prokaryotic genomes can be isolated from one gram of soil. In this publication the selected methods used to identify microorganisms are presented. The first molecular marker used in the genetic identification of soil microorganisms was the analysis of the G+C base content, sincemicroorganisms exhibit differences in the (G+C)/(A+T) relative factor. Another method used to identify bacteria is the nucleic acid hybridization. This technique involves a determination of the degree of similarity of DNA-DNA between two organisms. One of the most frequently used hybridization technique is FISH – fluorescent in situ hybridization. The most precise method for analyzing the nucleic acids is sequencing, i.e. determining the order of nucleotides which form the genetic information of the microorganism studied. Very often in molecular studies the 16S rDNA molecule is subjected to sequencing.

1. Introduction. 2. Classical methods used to identify bacteria. 3. Molecular methods used in the identification of soil microorganisms. 4. Analysis of the G+C DNA content. 5. Nucleic acid hybridization. 6. Analysis of nucleic acid sequences. 7. Summary