Bacteria diversity and arsenic mobilization in rock biofilm from an ancient gold and arsenic mine

Tomczyk-Żak, Karolina; Kaczanowski, Szymon; Drewniak, Łukasz; Dmoch, Łukasz; Skłodowska, Aleksandra; Zielenkiewicz, Urszula

doi:10.1016/j.scitotenv.2013.04.087

Cited by 35 publications

(33 citation statements)

References 44 publications

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“…Total DNA was isolated according to the modified procedure for soil samples as described by Tomczyk-Żak et al (2013). In order to reduce the presence of humic substances and other soil impurities the crude total DNA was further purified by CsCl gradient centrifugation (16 h, 70 000 rpm, 20°C; Sorvall WX Ultra ThermoScietific) as described by Sambrook et al (1989).…”

Section: Methodsmentioning

confidence: 99%

Microbial biodiversity in arable soils is affected by agricultural practices

Wolińska¹,

Górniak²,

Zielenkiewicz³

et al. 2017

International Agrophysics

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A b s t r a c t. The aim of the study was to examine the differences in microbial community structure as a result of agricultural practices. Sixteen samples of cultivated and the same number of non-cultivated soils were selected. Gel bands were identified using the GelCompar software to create the presence-absence matrix, where each band represented a bacterial operational taxonomic unit. The data were used for principal-component analysis and additionally, the ShannonWeaver index of general diversity, Simpson index of dominance and Simpson index of diversity were calculated. Denaturing gradient gel electrophoresis profiles clearly indicated differentiation of tested samples into two clusters: cultivated and non-cultivated soils. Greater numbers of dominant operational taxonomic units (65) in non-cultivated soils were noted compared to cultivated soils (47 operational taxonomic units). This implies that there was a reduction of dominant bacterial operational taxonomic units by nearly 30% in cultivated soils. Simpson dominance index expressing the number of species weighted by their abundance amounted to 1.22 in cultivated soils, whereas a 3-fold higher value (3.38) was observed in non-cultivated soils. Land-use practices seemed to be a important factors affected on biodiversity, because more than soil type determined the clustering into groups.

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Section: Methodsmentioning

confidence: 99%

Microbial biodiversity in arable soils is affected by agricultural practices

Wolińska¹,

Górniak²,

Zielenkiewicz³

et al. 2017

International Agrophysics

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“…DNA extraction from soil was performed according the procedure developed by Tomczyk-Żak et al (2013) with own small modification, regarding purification of the isolate in caesium chloride. Shortly, soil samples (3 g) were mixed with several glass beads (0.4–0.6 mm, Sartorius) in 50 ml Falcon tubes filled with extraction buffer [100 mM Tris–HCl (pH 8.0), 100 mM sodium EDTA (pH 8.0), and 100 mM sodium phosphate (pH 8.0), 1.5 M NaCl] and shaken carefully for a short time.…”

Section: Methodsmentioning

confidence: 99%

Microbial biodiversity of meadows under different modes of land use: catabolic and genetic fingerprinting

Wolińska

Frąc

Oszust

et al. 2017

World J Microbiol Biotechnol

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The main goal of the study was to find differences in the bacterial community structure resulting from different ways of meadow management in order to get the first insight into microbial biodiversity in meadow samples. The next generation sequencing technique (454-pyrosequencing) was accompanied with the community level physiological profiling (CLPP) method in order to acquire combined knowledge of both genetic and catabolic bacterial fingerprinting of two studied meadows (hayland and pasture). Soil samples (FAO: Mollic Gleysol) were taken in April 2015 from the surface layer (0–20 cm). Significant differences of the bacterial community structure between the two analyzed meadows resulted from different land mode were evidenced by pyrosequencing and CLPP techniques. It was found that Alpha- and Gammaproteobacteria dominated in the hayland, whereas Delta- and Betaproteobacteria prevailed in the pasture. Additionally, the hayland displayed lower Firmicutes diversity than the pasture. Predominant bacterial taxa: Acidobacteria, together with Chloroflexi and Bacteroidetes seemed to be insensitive to the mode of land use, because their abundance remained at a similar level in the both studied meadows. The CLPP analysis confirmed much faster degradation of the carbon sources by microorganisms from the hayland rather than from the pasture. Amino acids were the most favoured carbon source groups utilized by microorganisms in contrast to carbohydrates, which were utilized to the lowest extent. The study clearly proved that the consequences of even moderate anthropogenic management are always changes in bacterial community structure and their metabolic activity. Bacterial taxa that are sensitive and resistant on modes of land use were determined.Electronic supplementary materialThe online version of this article (doi:10.1007/s11274-017-2318-2) contains supplementary material, which is available to authorized users.

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“…DNA was extracted within 24 h after sample collection according to the modified procedure elaborated for soil material as described by Tomczyk-Żak et al [40]. The modification included an additional purification step by CsCl gradient centrifugation (16 h, 70,000 rpm, 20 °C; Sorvall WX Ultra ThermoScietific).…”

Section: Methodsmentioning

confidence: 99%

Metagenomic Analysis of Some Potential Nitrogen-Fixing Bacteria in Arable Soils at Different Formation Processes

et al. 2016

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The main goal of the study was to determine the diversity of the potential nitrogen-fixing (PNF) bacteria inhabiting agricultural (A) soils versus wastelands serving as controls (C). The soils were classified into three groups based on the formation process: autogenic soils (Albic Luvisols, Brunic Arenosols, Haplic Phaeozem) formed on loess material, hydrogenic soils (Mollic Gleysols, Eutric Fluvisol, Eutric Histosol) formed under the effect of stagnant water and lithogenic soils (Rendzina Leptosols) formed on limestone. In order to determine the preferable conditions for PNF bacteria, the relationships between the soil chemical features and bacterial operational taxonomic units (OTUs) were tested. Additionally, the nitrogen content and fertilisation requirement of the lithogenic (LG), autogenic (AG) and hydrogenic (HG) soils were discussed. The composition of the bacterial communities was analysed with the next-generation sequencing (NGS) by the Ion Torrent™ technology. The sequences were clustered into OTU based on a 99 % similarity threshold. The arable soils tested were distinctly dominated by β-Proteobacteria representatives of PNF bacteria belonging to the genus Burkholderia. Bacteria from the α-Proteobacteria class and Devosia genus were subdominants. A free-living Cyanobacteria population dominated in A rather than in C soils. We have found that both soil agricultural management and soil formation processes are the most conducive factors for PNF bacteria, as a majority of these microorganisms inhabit the AG group of soils, whilst the LG soils with the lowest abundance of PNF bacteria revealed the need for additional mineral fertilisation. Our studies have also indicated that there are close relationships between soil classification with respect to soil formation processes and PNF bacteria preference for occupation of soil niches.Electronic supplementary materialThe online version of this article (doi:10.1007/s00248-016-0837-2) contains supplementary material, which is available to authorized users.

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Bacteria diversity and arsenic mobilization in rock biofilm from an ancient gold and arsenic mine

Cited by 35 publications

References 44 publications

Microbial biodiversity in arable soils is affected by agricultural practices

Microbial biodiversity in arable soils is affected by agricultural practices

Microbial biodiversity of meadows under different modes of land use: catabolic and genetic fingerprinting

Metagenomic Analysis of Some Potential Nitrogen-Fixing Bacteria in Arable Soils at Different Formation Processes

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