Bacterial Diversity at Abandoned Uranium Mining and Milling Sites in Bulgaria as Revealed by 16S rRNA Genetic Diversity Study

Radeva, Galina; Kenarova, Anelia; Bachvarova, Velina; Flemming, Katrin; Popov, Ivan; Vassilev, Dimitar; Selenska‐Pobell, Sonja

doi:10.1007/s11270-013-1748-1

Cited by 27 publications

(13 citation statements)

References 59 publications

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“…Other taxa first were identified in samples obtained from Au mines. Verrucomicrobia also have been linked to U mining environments (58), with the taxa identified here belonging to the ammonia-oxidizing group. The ubiquity and abundance of Acidobacteria and Verrucomicrobia in metalrich soils at the study sites, combined with their ability to survive in meal-polluted extreme environments, suggest that they serve functions important to biogeochemical metal cycling at the study sites, similar to those observed for other U-rich sites (59).…”

Section: Discussionmentioning

confidence: 78%

Geogenic Factors as Drivers of Microbial Community Diversity in Soils Overlying Polymetallic Deposits

Reith

Zammit

Pohrib

et al. 2015

Appl Environ Microbiol

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dThis study shows that the geogenic factors landform, lithology, and underlying mineral deposits (expressed by elevated metal concentrations in overlying soils) are key drivers of microbial community diversity in naturally metal-rich Australian soils with different land uses, i.e., agriculture versus natural bushland. One hundred sixty-eight soil samples were obtained from two metal-rich provinces in Australia, i.e., the Fifield Au-Pt field (New South Wales) and the Hillside Cu-Au-U rare-earth-element (REE) deposit (South Australia). Soils were analyzed using three-domain multiplex terminal-restriction-fragment-length-polymorphism (M-TRFLP) and PhyloChip microarrays. Geogenic factors were determined using field-mapping techniques and analyses of >50 geochemical parameters. At Fifield, microbial communities differed significantly with geogenic factors and equally with land use (P < 0.05). At Hillside, communities in surface soils (0.03-to 0.2-m depth) differed significantly with landform and land use (P < 0.05). Communities in deeper soils (>0.2 m) differed significantly with lithology and mineral deposit (P < 0.05). Across both sites, elevated metal contents in soils overlying mineral deposits were selective for a range of bacterial taxa, most importantly Acidobacteria, Bacilli, Betaproteobacteria, and Epsilonproteobacteria. In conclusion, long-term geogenic factors can be just as important as land use in determining soil microbial community diversity. Determining the drivers of microbial community composition in soils is challenging, because soils are complex ecosystems containing numerous ecological niches. This results in an immense diversity, with up to thousands of taxa per gram of soil (1). Land use, climate, vegetation, soil type, and anthropogenic pollution are strongly linked to soil microbial community structures, functions, and activities at many sites (2-4). In particular, agricultural practices are known to drive differences in soil microbial communities (5). Influences of geogenic factors, e.g., landform, underlying lithologies, and mineral deposits on soil microbial communities, have received little attention. However, three studies of soils from Switzerland and Nepal have shown that geological/mineralogical factors can significantly affect species assemblages and functions (6-8).A primary goal of geomicrobiological research is to link microbial communities and metal cycling in metallogenic environments and to determine how communities are structured due to metalassociated drivers (9). Microorganisms play a pivotal role in the biogeochemical cycling of many metals, particularly those essential for cell function, e.g., Co, Cu, Fe, Mg, Mn, Mo, Na, Ni, V, W, and Zn, and those oxidized or reduced in catabolic reactions to gain metabolic energy, e.g., As, Fe, Mn, Mo, Sb, Se, Sn, Te, U, and V (10). Therefore, metal-rich environments are useful model systems allowing links between microbial taxa and geochemical parameters to be identified (11).To date, mine tailing and acid mine drainage sites have been ...

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Section: Discussionmentioning

confidence: 78%

Geogenic Factors as Drivers of Microbial Community Diversity in Soils Overlying Polymetallic Deposits

Reith

Zammit

Pohrib

et al. 2015

Appl Environ Microbiol

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“…Similarly, Radeva et al (2013) and Dhal et al (2011) also suggested that the bacterial diversity was generally higher in uncontaminated soil than in radioactive soil. Meanwhile, beta diversity increased with an increase in the soil depth, indicating that the difference of species between the contaminated and uncontaminated soil increased with the increase in soil depth.…”

Section: Discussionmentioning

confidence: 90%

Metagenomic analysis of microbial community in uranium-contaminated soil

Yan

Luo

Zhao

2015

Appl Microbiol Biotechnol

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Uranium tailing is a serious pollution challenge for the environment. Based on metagenomic sequencing analysis, we explored the functional and structural diversity of the microbial community in six soil samples taken at different soil depths from uranium-contaminated and uncontaminated areas. Kyoto Encyclopedia of Genes and Genomes Orthology (KO) groups were obtained using a Basic Local Alignment Search Tool search based on the universal protein resource database. The KO-pathway network was then constructed using the selected KOs. Finally, alpha and beta diversity analyses were performed to explore the differences in soil bacterial diversity between the radioactive soil and uncontaminated soil. In total, 30-68 million high-quality reads were obtained. Sequence assembly yielded 286,615 contigs; and these contigs mostly annotated to 1699 KOs. The KO distributions were similar among the six soil samples. Moreover, the proportion of the metabolism of other amino acids (e.g., beta-alanine, taurine, and hypotaurine) and signal transduction was significantly lower in radioactive soil than in uncontaminated soil, whereas the proportion of membrane transport and carbohydrate metabolism was higher. Additionally, KOs were mostly enriched in ATP-binding cassette transporters and two-component systems. According to diversity analyses, Actinobacteria and Proteobacteria were the dominant phyla in radioactive and uncontaminated soil, and Robiginitalea, Microlunatus, and Alicyclobacillus were the dominant genera in radioactive soil. Taken together, these results demonstrate that soil microbial community, structure, and functions show significant changes in uranium-contaminated soil. The dominant categories such as Actinobacteria and Proteobacteria may be applied in environmental governance for uranium-contaminated soil in southern China.

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“…Our results are in line with Kumar et al (2013) who showed that 76 % of the culturable bacteria isolated from U deposits possessed constitutive phosphatase activity, and Yung and Yiao (2014), who reported that AlPA is an enzyme which was neither induced nor inhibited by U contamination. Among the most common AlPA producers are members of Gammaproteobacteria, Actinobacteria, and Bacteroidetes (Kumar et al 2013), and all of these taxa along Acidobacteria were found in Bulgarian U polluted Buhovo and Sliven (Radeva et al 2013), and Senokos (unpublished data) mining sites with increasing share in the bacterial communities along the U and HM gradient of contamination. Additionally, multi-metal (Cd, Co, Cr, Zn, and Ni (except DhA)) tolerance of AlPA and DhA is found than AcPA (Pb), determining the activities of AlPA and DhA as crucial for site cycling of OM and detoxification of metals, even in slightly acidic soils.…”

Section: Discussionmentioning

confidence: 95%

“…In the study, reference soil was not used due to our (Radeva et al 2013, Kenarova et al 2014) and Giller et al (1998) experience connected to the difficulties in finding a Breference^soil which differed only in the term of contamination from the studied ones. This challenge was overcome using multivariate analysis (see Statistical analysis) and interpreting the results on cause-effect relationships.…”

Section: Sampling Strategymentioning

confidence: 99%

Effects of long-term radionuclide and heavy metal contamination on the activity of microbial communities, inhabiting uranium mining impacted soils

Boteva

Radeva

Traykov

et al. 2015

Environ Sci Pollut Res

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Ore mining and processing have greatly altered ecosystems, often limiting their capacity to provide ecosystem services critical to our survival. The soil environments of two abandoned uranium mines were chosen to analyze the effects of long-term uranium and heavy metal contamination on soil microbial communities using dehydrogenase and phosphatase activities as indicators of metal stress. The levels of soil contamination were low, ranging from 'precaution' to 'moderate', calculated as Nemerow index. Multivariate analyses of enzyme activities revealed the following: (i) spatial pattern of microbial endpoints where the more contaminated soils had higher dehydrogenase and phosphatase activities, (ii) biological grouping of soils depended on both the level of soil contamination and management practice, (iii) significant correlations between both dehydrogenase and alkaline phosphatase activities and soil organic matter and metals (Cd, Co, Cr, and Zn, but not U), and (iv) multiple relationships between the alkaline than the acid phosphatase and the environmental factors. The results showed an evidence of microbial tolerance and adaptation to the soil contamination established during the long-term metal exposure and the key role of soil organic matter in maintaining high microbial enzyme activities and mitigating the metal toxicity. Additionally, the results suggested that the soil microbial communities are able to reduce the metal stress by intensive phosphatase synthesis, benefiting a passive environmental remediation and provision of vital ecosystem services.

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Bacterial Diversity at Abandoned Uranium Mining and Milling Sites in Bulgaria as Revealed by 16S rRNA Genetic Diversity Study

Cited by 27 publications

References 59 publications

Geogenic Factors as Drivers of Microbial Community Diversity in Soils Overlying Polymetallic Deposits

Geogenic Factors as Drivers of Microbial Community Diversity in Soils Overlying Polymetallic Deposits

Metagenomic analysis of microbial community in uranium-contaminated soil

Effects of long-term radionuclide and heavy metal contamination on the activity of microbial communities, inhabiting uranium mining impacted soils

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