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1

Sampling, metadata and DNA extraction - important steps in metagenomic studies

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Felczykowska A., Krajewska A., Zielińska S., Łoś J.

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2015

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vol. 62

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issue 1

151-160

EN

Metagenomic studies have become increasingly popular. They allow for the estimation of biodiversity in complex populations. This diversity presents an enormous but largely unexpected genetic and biological pool and can be exploited for the recovery of novel genes, entire metabolic pathways and their products. Generally metagenomic study is a genomic analysis of organisms by direct extraction and cloning of DNA from their natural environment. The most common problems of modern metagenomics are as follows: majority of the microorganisms present in the environment cannot be cultivated by standard techniques, DNA extraction methods are not very effective, isolated DNA is contaminated with various compounds, a choice for a screening method is not obvious.

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The most widespread problems in the function-based microbial metagenomics

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Felczykowska A., Krajewska A., Zielińska S., Łoś J., Bloch S., Nejman-Faleńczyk B.

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2015

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vol. 62

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issue 1

161-166

EN

Metagenomics is a powerful tool to better understand the microbial niches, especially these from extreme habitats like oceans and seas, hot springs or deserts. However, one who is going to face the metagenomic studies should realize the challenges which might occur in the course of experiments. This manuscript indicates common problems in function-driven metagenomics, especially factors that influence gene expression are taken into account. Codon usage bias, internal cell accumulation, correct protein folding or presence of proper initiation factors are discussed and possible ways to overcome these problems are proposed. Finally, the annotation process is described, including possible limitations that one should take under consideration. What is more, the most popular databases for metagenomic data are mentioned and discussed.

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First insight into microbial community composition in a phosphogypsum waste heap soil

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Zielińska S., Radkowski P., Ossowski T., Ludwig-Gałęzowska A., Łoś J., Łoś M.

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2017

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vol. 64

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issue 4

693-698

EN

The aim of this study was to investigate the soil microbial communities of a phosphogypsum waste heap. The soil microbial community structures can differ over time, as they are affected by the changing environmental conditions caused by a long-term exposure to different kinds of pollutions, like is the case of soil in the post-production waste area in Wiślinka (in the northern part of Poland) currently undergoing restoration. Our analyses indicated that the most abundant phyla were Proteobacteria, Acidobacteria, and Actinobacteria, and generally such an abundance is common for most of the studied soils. The most dominant class were Alphaproteobacteria, with their participation in 33.46% of the total reads. Among this class, the most numbered order was Sphingomonadales, whereas among this order the Sphingomonadaceae family was the most abundant one. The Sphingomonadaceae family is currently in the center of interest of many researchers, due to the ability of some of its members to utilize a wide range of naturally occurring organic compounds and many types of environmental contaminants. This kind of knowledge about microbial populations can support efforts in bioremediation and can improve monitoring changes in the contaminated environments.

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3 Acta Biochimica Polonica

1 2017

2 2015

3 Zielińska S.

3 Łoś J.

2 Felczykowska A.

2 Krajewska A.

1 Bloch S.

1 Ludwig-Gałęzowska A.

1 Nejman-Faleńczyk B.

1 Ossowski T.

1 Radkowski P.

1 Łoś M.

Sampling, metadata and DNA extraction - important steps in metagenomic studies

The most widespread problems in the function-based microbial metagenomics

First insight into microbial community composition in a phosphogypsum waste heap soil