scholarly journals Extremophiles in Soil Communities of Former Copper Mining Sites of the East Harz Region (Germany) Reflected by Re-Analyzed 16S rRNA Data

2021 ◽  
Vol 9 (7) ◽  
pp. 1422
Author(s):  
J. Michael Köhler ◽  
Nancy Beetz ◽  
Peter Mike Günther ◽  
Frances Möller ◽  
Jialan Cao
Keyword(s):  
16S Rrna ◽  
Dna Sequences ◽  
Copper Slag ◽  
Soil Samples ◽  
Copper Mining ◽  
Late 20Th Century ◽  
Mining Sites ◽  
Degrading Bacterium ◽  
Promising Source ◽  
Mine Dump

The east and southeast rim of Harz mountains (Germany) are marked by a high density of former copper mining places dating back from the late 20th century to the middle age. A set of 18 soil samples from pre- and early industrial mining places and one sample from an industrial mine dump have been selected for investigation by 16S rRNA and compared with six samples from non-mining areas. Although most of the soil samples from the old mines show pH values around 7, RNA profiling reflects many operational taxonomical units (OTUs) belonging to acidophilic genera. For some of these OTUs, similarities were found with their abundances in the comparative samples, while others show significant differences. In addition to pH-dependent bacteria, thermophilic, psychrophilic, and halophilic types were observed. Among these OTUs, several DNA sequences are related to bacteria which are reported to show the ability to metabolize special substrates. Some OTUs absent in comparative samples from limestone substrates, among them Thaumarchaeota were present in the soil group from ancient mines with pH > 7. In contrast, acidophilic types have been found in a sample from a copper slag deposit, e.g., the polymer degrading bacterium Granulicella and Acidicaldus, which is thermophilic, too. Soil samples of the group of pre-industrial mines supplied some less abundant, interesting OTUs as the polymer-degrading Povalibacter and the halophilic Lewinella and Halobacteriovorax. A particularly high number of bacteria (OTUs) which had not been detected in other samples were found at an industrial copper mine dump, among them many halophilic and psychrophilic types. In summary, the results show that soil samples from the ancient copper mining places contain soil bacterial communities that could be a promising source in the search for microorganisms with valuable metabolic capabilities.

scholarly journals Distribution of Contaminated Soils along Transversal and Longitudinal Gradients in Dynamic Fluvial Environment (Southern Québec, Canada)

2015 ◽  
Vol 8 ◽  
pp. ASWR.S22465 ◽  
Author(s):  
Diane Saint-Laurent ◽  
Francis Baril ◽  
Ilias Bazier ◽  
Vernhar Gervais-Beaulac ◽  
Camille Chapados
Keyword(s):  
Spatial Distribution ◽  
Contaminated Soils ◽  
Soil Samples ◽  
Copper Mining ◽  
Mining Sites ◽  
Mining Areas ◽  
Pb Contamination ◽  
Flood Zone ◽  
Longitudinal Gradients ◽  
Mine Sites

This research combines a hydrological and pedological approach to better understand the spatial distribution of contaminated soils along the Massawippi River (southern Québec, Canada). This river crosses through former mines, which were some of the largest copper mining areas in North America from 1865 to 1939. To determine the spatial distribution and concentration of the metal elements, soil samples were taken in each flood recurrence zone appearing on official flood zone maps. The maximum values obtained for Cu and Pb are 380 and 200 mg kg−1, respectively, for the soils in the frequent flood zones (FFzs), while the values for soils in the moderate flood zones (MFzs) range from 700 to 540 (Cu) and 580 to 460 mg kg−1 (Pb). Contamination extends through several kilometers of the former mining sites (Eustis and Capleton), and concentration of metals in alluvial soils is slightly higher near the mine sites.

scholarly journals Description of Sphingobium fuliginis sp. nov., a phenanthrene-degrading bacterium from a fly ash dumping site, and reclassification of Sphingomonas cloacae as Sphingobium cloacae comb. nov.

2006 ◽  
Vol 56 (9) ◽  
pp. 2147-2152 ◽  
Author(s):  
Om Prakash ◽  
Rup Lal
Keyword(s):  
Phylogenetic Analysis ◽  
Fatty Acid ◽  
Fly Ash ◽  
16S Rrna ◽  
Dna Hybridization ◽  
Type Strain ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Dumping Site ◽  
Degrading Bacterium

A phenanthrene-degrading bacterium, strain TKPT, was isolated from a fly ash dumping site of the thermal power plant in Panki, Kanpur, India, by an enrichment culture method using phenanthrene as the sole source of carbon and energy. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus Sphingobium, as it showed highest sequence similarity to Sphingobium herbicidovorans DSM 11019T (97.3 %) and Sphingomonas cloacae JCM 10874T (96.5 %), compared with only 91–93 % similarity to members of other genera such as Sphingomonas sensu stricto, Novosphingobium, Sphingopyxis and Sphingosinicella. In DNA–DNA hybridization experiments with strains that were closely related phylogenetically and in terms of 16S rRNA gene sequences, i.e. Sphingobium herbicidovorans DSM 11019T and Sphingomonas cloacae JCM 10874T, strain TKPT showed less than 70 % relatedness. Strain TKPT contained sphingoglycolipids SGL-1 and SGL-2 and 18 : 1ω7c as the predominant fatty acid, with 16 : 0 as a minor component and 14 : 0 2-OH as the major 2-hydroxy fatty acid. Thus, phylogenetic analysis, DNA–DNA hybridization, fatty acid and polar lipid profiles and differences in physiological and morphological features from the most closely related members of the Sphingobium group showed that strain TKPT represents a distinct species of Sphingobium. The name Sphingobium fuliginis sp. nov. is proposed, with the type strain TKPT (=MTCC 7295T=CCM 7327T). Sphingomonas cloacae JCM 10874T formed a coherent cluster with members of Sphingobium, did not reduce nitrate to nitrite and had a fatty acid profile similar to those of Sphingobium species; hence Sphingomonas cloacae should be transferred to the genus Sphingobium as Sphingobium cloacae comb. nov., with the type strain JCM 10874T (=DSM 14926T).

MEASUREMENT OF RADON CONCENTRATION IN SOIL SAMPLES OF MAZAT AND KAFI-HABU MINING SITES, PLATEAU, NIGERIA

2021 ◽  
Vol 4 (4) ◽  
pp. 295-301
Author(s):  
Abubakar Sadiq Aliyu ◽  
Aminu Ismaila ◽  
A. M. Na'Inna ◽  
Ahmed Mohammed
Keyword(s):  
Dose Rate ◽  
Radon Concentration ◽  
Background Radiation ◽  
Average Concentration ◽  
Soil Samples ◽  
Radiological Protection ◽  
Sampling Point ◽  
Monitoring And Control ◽  
Tailing Dump ◽  
Mining Sites

Radon and its short-lived progenies contributed significantly to natural background radiation. Long-term exposure to such radiation increases the probability of lung cancer to persons. To assess the radiological hazards associated with the inhalation of radon gas from ore dust in Mazat and Kafi-Habu mining sites of Plateau, Nigeria, 12 soil samples from an abandoned tailing dump ground were collected and analysed for radon using RAD-7 electronic detector. The dose rate of each sampling point was directly measured using RADOS RDS -120 portable survey meter. The results gave a mean radon concentration ranging from 771.51 ± 21.9 Bq/m3 to 5666.13 ± 28.8 Bq/m3 with 3451.13 ± 42.9 Bq/m3as the average value for all measurements. The average concentration of measurements from Mazat and Kafi-Habu is 3671.6 ± 41.2 Bq/m3 and 3010.16 ± 46.5 Bq/m3 respectively. The average values obtained from the analysis are significantly higher than the upper limit of 300 Bq/m3 set by the International Commission on Radiological Protection (ICRP) suggesting quick remediation on the host communities. The geometrical mean value of Dose Rate (DR) and Annual Effective Dose Equivalent (AEDE) were 870 nGy/hr and 1.04 mSv/yr respectively. Again, these values are above the global average limits of 59 nGy/hr and 1 mSv/yr. The result indicates that miners working in those sites and dwellers of the study areas are at higher risk of getting exposed to radon and need to employ protective measures. This work is useful in monitoring and control of radon level for the on-site workers and the 

scholarly journals Aliiglaciecola aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium, isolated from a sea-tidal flat and emended description of the genus Aliiglaciecola Jean et al. 2013

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1550-1555 ◽  
Author(s):  
Hyun Mi Jin ◽  
Hye Im Jeong ◽  
Che Ok Jeon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Molecular Features ◽  
Degrading Bacterium ◽  
Emended Description

A Gram-stain-negative heterotrophic bacterium, designated GSD6T, capable of growth on aliphatic hydrocarbons as a sole carbon and energy source, was isolated from sea-tidal flat sediment of the Yellow Sea, South Korea. Cells were facultatively aerobic, catalase- and oxidase-positive, motile rods with a single polar flagellum. Growth of strain GSD6T was observed at 4–37 °C (optimum 30 °C), at pH 5.5–9.0 (optimum pH 6.5–7.5) and in the presence of 1–9 % (w/v) NaCl (optimum 2 %). Strain GSD6T contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c, C17 : 0 10-methyl and C17 : 1ω8c as the major fatty acids. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The G+C content of the genomic DNA was 44.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GSD6T formed a phylogenetic lineage with members of the genus Aliiglaciecola . Strain GSD6T was most closely related to Aliiglaciecola lipolytica E3T with a 16S rRNA gene sequence similarity of 97.4 %, but their DNA–DNA hybridization value was 39.1±7.1 %. On the basis of phenotypic, chemotaxonomic and molecular features, strain GSD6T represents a novel species of the genus Aliiglaciecola , for which the name Aliiglaciecola aliphaticivorans sp. nov. is proposed. The type strain is GSD6T ( = KACC 18129T = JCM 30133T). An emended description of the genus Aliiglaciecola is also proposed.

scholarly journals Assessment of Solid Mineral to Soil Radioactivity Contamination Index in Selected Mining Sites and their Radiological Risk Indices to the Public

2021 ◽  
Author(s):  
Ezekiel Oghenenyerhovwo Agbalagba ◽  
Mohammed S. Chaanda ◽  
Stephen Uloho U. Egarievwe
Keyword(s):  
Mean Value ◽  
Soil Samples ◽  
Permissible Limit ◽  
Radiation Hazard ◽  
Hazard Indices ◽  
Mean Values ◽  
Mining Sites ◽  
The Public ◽  
Risk Indices ◽  
Gamma Index

Abstract This study examined the radioactivity levels of soil samples within selected solid mining sites in Nigeria using high purity germanium (HpGe) detector. Sixty soil samples in all were collected from the ten solid mineral mining sites investigated and six samples were collected as control samples from non-mining environment for analyses. The results of the activity concentration values obtained for 40K, 226Ra and 232Th are 100.22 Bq kg-1, 33.15 Bq kg-1 and 77.31 Bq kg-1 respectively. The 226Ra and 40K activities were found to be within the United Nation Scientific Committee on the Effects of Atomic Radiation (UNSCEAR) acceptable permissible limit, but the 232Th mean value was above the permissible limit of 30 Bq kg-1 for the public. In comparison, 40K, 226Ra and 232Th soil samples mean activity concentrations were higher than the control soil samples values by 48.6%, 43.7% and 62.3% respectively. The results of estimated radiation hazard indices indicate average values of 150.72 Bq kg-1, 68.40T, 83.65µSvy-1 and 454.70µSvy-1 for the Radium Equivalent (h), iDose Equivalent (AEDE) and Annual Gonadal Equivalent Dose (AGED) respectively. The mean values for External Hazard Indices (Hex, Hin), Representative Gamma index (s) and Excess Life Cancer Risk (ELCR) were 0.41, 0.50, 1.06 and 0.29 x10-3 respectively. The statistical analysis shows positive skewness.

scholarly journals Isolation and Characterization of a Novel p,p’-DDT-Degrading Bacterium: Aeromonas sp. Strain MY1 from Agricultural Soil

2020 ◽  
pp. 12-22
Author(s):  
Y. Murtala ◽  
B. C. Nwanguma ◽  
L. U. S. Ezeanyika
Keyword(s):  
Carbon Source ◽  
16S Rrna ◽  
Agricultural Soil ◽  
Sole Carbon Source ◽  
Phylogenetic Analyses ◽  
Inhibitory Effect ◽  
Aerobic Conditions ◽  
Degrading Bacterium ◽  
Isolation And Characterization

Background: Despite the banned on the use of dichlorodiphenyltrichloroethane (DDT) and other Persistent Organic Pollutants (POPs) by the Stockholm Convention for their toxicity, emerging shreds of evidence have indicated that DDT is, however, still in use in developing countries. This might increase the global burden of DDT contamination and its hazardous effects. Aim: This study focused on the isolation and characterization of p,p’-DDT-degrading bacterium from a tropical agricultural soil. Methodology: Standard isolation procedure was used for the screening and isolation of the strain. The 16S rRNA and phylogenetic analyses were used to identify the isolate and established protocols were followed to characterize the strain. Results: A new strain belonging to the genus Aeromonas was isolated from agricultural soil using minimal salt-p,p’-DDT enrichment medium. The 16S rRNA sequencing was used to identify the strain and the partial sequence was deposited in the NCBI GenBank as Aeromonas sp. Strain MY1. This mesophilic isolate was capable of utilizing up to 50 mgL-1 of p,p’-DDT as the sole carbon source at an optimum pH of 7.5 and optimum temperature of 35 °C within 120 h under aerobic conditions. Fe2+ (0.2 mgL-1) demonstrated a stimulatory effect on the p,p’-DDT degradation capacity by the strain MY1. However, Zn, Cu, Pb, Hg, Ag and Cr ions have demonstrated various patterns of inhibitory effect on the p,p’-DDT degradation capacity of the isolate at 0.2 mgL-1. The strain MY1 could be a promising candidate for the bioremediation of p,p’-DDT contaminant. Conclusion: Aeromonas sp. strain MY1 was capable of utilizing p,p’-DDT as a sole carbon source under aerobic conditions. The utilization capacity of the strain was influenced by some heavy metals. Fe was found to enhance the p,p’-DDT utilization capacity of the isolate at a lower concentration. While Zn, Cu, Pb, Hg, Ag and Cr showed various patterns of inhibitory effect.

scholarly journals Levels of heavy metals in soils and food crops cultivated within selected mining sites in Ebonyi State, Nigeria

2021 ◽  
Vol 2 (1) ◽  
pp. 84-95
Author(s):  
David Okechukwu Okeke ◽  
◽  
Jonathan Chinenye Ifemeje ◽  
Keyword(s):  
Heavy Metals ◽  
Control Site ◽  
Soil Samples ◽  
World Health ◽  
Food Crops ◽  
Food Crop ◽  
Mining Site ◽  
Mining Sites ◽  
Health Association ◽  
Health Organization

The level of heavy metals (Fe, Cu, As, Pb, Cd, Mg, Ca, Hg, Ni, Cr, Zn, Ag, Co, Mo, Se and Al) in soils and food crops (okra, cassava and rice) cultivated within selected mining sites in Ebonyi State, Nigeria were determined using FS240AA Atomic Absorption Spectrophotometer (AAS) according to the method of American Public Health Association (APHA). Soil samples were collected from Enyigba mining site, Ikwo mining site, AmeriAmekamining site, Izza mining site, MkpumeAkwatakwa mining site and MpumeAkwaokuku mining site while the food crop samples (okra, cassava and rice) were collected from the farmlands within the mining sites. Control samples were collected 500m away from the mining destinations were there was no evidence of mining activities on the soils. A total of sixty sub-samples and six control soil samples were collected for this study. Generally, the values of all the heavy metals analyzed for soil and food crop samples were higher than the values recommended by the World Health Organization (WHO), and those from the control site suggesting possible mobility of the metals from mining sites to farmlands through leaching and runoffs. The findings in this study also revealed that the food crops contain heavy metals exceeding the maximum permissible concentration, and could be detrimental to human health when they are consumed.

scholarly journals Heavy Metals in the Soils of Placer Small-Scale Gold Mining Sites in Myanmar

2020 ◽  
Vol 10 (27) ◽  
pp. 200911
Author(s):  
Aung Zaw Tun ◽  
Pokkate Wongsasuluk ◽  
Wattasit Siriwong
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Gold Mining ◽  
Soil Samples ◽  
Small Scale ◽  
Mining Activities ◽  
Mining Operations ◽  
Metal Concentrations ◽  
Mining Sites ◽  
Heavy Metal Concentrations

Background. Artisanal and small-scale mining activities are widely practiced globally. Concentrations of heavy metals associated with gold, such as copper (Cu), zinc (Zn), arsenic (As), cadmium (Cd), mercury (Hg) and lead (Pb) can increase in the environment as a result of mining activities, leading to environmental pollution and pose toxicity risks to humans and animals. Objectives. The aim of the present study was to investigate soil concentrations of toxic heavy metals in placer small-scale gold mining operations in Myanmar. Methods. Soil samples were collected from three placer small-scale gold mining sites: Site A located in the Hmawbon public protected forest, Site B and Site C, situated in the Nant-Kyin reserved forest around Nar Nant Htun village. At each site, soil samples were collected from four gold mining stages (ore processing, sluicing, panning, and amalgamation). Atomic absorption spectroscopy was utilized to examine the concentrations of As, Cd, Pb, and Hg. Results. The highest heavy metal concentrations were generally found in the amalgamation stages across all the gold mining sites. Across the three mining sites, the maximum heavy metal concentrations in the amalgamation stage were 22.170 mg.kg−1 for As, 3.070 mg.kg−1 for Cd, 77.440 mg.kg−1 for Hg, and 210.000 mg.kg−1 for Pb. Conclusions. The present study examined the concentrations of As, Cd, Hg and Pb in the soil of several small-scale gold mining sites in Banmauk Township, Myanmar. The results demonstrated the presence of high concentrations of heavy metals in the soil of the gold mining sites. Miners in this area work without proper personal protective equipment, and frequent exposure to heavy metals in the soil may cause adverse health effects. The present study provides baseline data for future risk assessment studies of heavy metal contamination in gold mines. Competing Interests. The authors declare no competing financial interests

Soil aggregate-based nucleic acid analyses of the impact of maize roots and their root hairs on the structural diversity of microbial communities

2021 ◽  
Author(s):  
Christoph Tebbe ◽  
Damini Damini ◽  
Damien Finn ◽  
Nataliya Bilyera ◽  
Minh Ganther ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Root Hair ◽  
Soil Aggregates ◽  
Root Hairs ◽  
Soil Samples ◽  
Plant Roots ◽  
Bulk Soil ◽  
Rrna Gene ◽  
The Impact

<p>The deposition of energy rich carbon sources released by plant roots during their growth fuels microbially driven ecosystem processes in soil, but there is a lack of understanding how microorganisms interact and collaborate. The objective of this research was therefore to characterize microbial networks as they assemble under the influence of plant roots. To identify the specific importance of root hairs, we compared the impact of a maize wild-type to a root-air defective mutant (rth3; (1).</p><p>The microbial community structure was analyzed by qPCR and 16S rRNA gene amplicon sequencing from soil DNA. In order to increase the probability of detecting truly interacting microbial partners as a basis for network analyses, we first evaluated a new protocol to obtain DNA from as little as 1 mg instead of the usual 250 mg soil samples, thereby approaching the aggregate level (2). While the diversity of bacterial 16S rRNA gene amplicons of 250-mg samples taken from the same soil was not distinct, DNA analyses from individual aggregates clearly differed from each other underlining that soil aggregates represent distinct microbial habitats.</p><p>Soil column experiments with maize grown in a loam soil (3) revealed distinct communities between rhizosphere and bulk soil. The community composition of individual aggregates showed more differences in bulk soil compared to rhizosphere. Less elaborated networks were seen in bulk soil and a profound effect of root hairs could be unravelled. Null model testing demonstrated that Actinobacteria were equally important for network connectivity independent of the root hair mutation, but for networks of the wildtype, Acidobacteria were essential for synergistic interactions and overall network structure. In contrast, Proteobacteria and Firmicutes connectivity became more important. The observed differences in community composition and interactions suggests carbon cycling, and perhaps other microbially-driven functions, are markedly affected by the presence of root hairs.</p><p>Utilizing maize root soil microcosms for studying soil zymography in the rhizosphere allowed to obtain soil samples from regions with distinct specific enzyme activities. In order to enhance the detection of actively metabolizing bacterial community members, we studied rRNA sequences and compared it to rRNA gene sequences from the same samples. Currently the data are under analysis.</p><p>References</p><p>(1) Wen, T-J, Schnable PS (1994) Analyses of mutants of three genes that influence root hair development in Zea mays (Gramineae) suggest that root hairs are dispensable. Am. J. Bot. 81, 833–842.</p><p>(2) Szoboszlay M, Tebbe CC (2020) Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates. Microbiol. Open, e1144. DOI: 10.1002/mbo3.1144</p><p>(3) Vetterlein D et al. (2020) Experimental platforms for the investigation of spatiotemporal patterns in the rhizosphere – laboratory and field scale. J. Plant Nutr. Soil Sci., 000, 1–16 DOI: 10.1002/jpln.202000079</p>

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