scholarly journals Cadmium Pollution Impact on the Bacterial Community Structure of Arable Soil and the Isolation of the Cadmium Resistant Bacteria

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaoxia Yu ◽  
JinTong Zhao ◽  
Xiaoqing Liu ◽  
LiXin Sun ◽  
Jian Tian ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Contaminated Soils ◽  
Removal Rate ◽  
Illumina Miseq ◽  
Soil Samples ◽  
Arable Soil ◽  
Polluted Area ◽  
Resistant Bacteria ◽  
Cadmium Pollution ◽  
Different Seasons

Microorganisms play an important role in the remediation of cadmium pollution in the soil and their diversity can be affected by cadmium. In this study, the bacterial community in arable soil samples collected from two near geographical sites, with different degrees of cadmium pollution at three different seasons, were characterized using Illumina MiSeq sequencing. The result showed that cadmium is an important factor to affect the bacterial diversity and the microbial communities in the high cadmium polluted area (the site H) had significant differences compared with low cadmium polluted area (the site L). Especially, higher concentrations of Cd significantly increased the abundance of Proteobacteria and Gemmatimonas whereas decreased the abundance of Nitrospirae. Moreover, 42 Cd-resistant bacteria were isolated from six soil samples and evaluated for potential application in Cd bioremediation. Based on their Cd-MIC [minimum inhibitory concentration (MIC) of Cd2+], Cd2+ removal rate and 16S rDNA gene sequence analyses, three Burkholderia sp. strains (ha-1, hj-2, and ho-3) showed very high tolerance to Cd (5, 5, and 6 mM) and exhibited high Cd2+ removal rate (81.78, 79.37, and 63.05%), six Bacillus sp. strains (151-5,151-6,151-13, 151-20, and 151-21) showed moderate tolerance to Cd (0.8, 0.4, 0.8, 0.4, 0.6, and 0.4 mM) but high Cd2+ removal rate (84.78, 90.14, 82.82, 82.39, 81.79, and 84.17%). Those results indicated that Burkholderia sp. belonging to the phylum Proteobacteria and Bacillus sp. belonging to the phylum Firmicutes have developed a resistance for cadmium and may play an important role in Cd-contaminated soils. Our study provided baseline data for bacterial communities in cadmium polluted soils and concluded that Cd-resistant bacteria have potential for bioremediation of Cd-contaminated soils.

scholarly journals Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 569
Author(s):  
Chakriya Sansupa ◽  
Sara Fareed Mohamed Wahdan ◽  
Terd Disayathanoowat ◽  
Witoon Purahong
Keyword(s):  
Bacterial Community ◽  
Forest Soil ◽  
Culture Media ◽  
Enrichment Culture ◽  
Sequence Similarity ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Soil Samples ◽  
Enrichment Cultures ◽  
Total Community

This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.

scholarly journals Responses of the Anaerobic Bacterial Community to Addition of Organic C in Chromium(VI)- and Iron(III)-Amended Microcosms

2006 ◽  
Vol 72 (1) ◽  
pp. 628-637 ◽  
Author(s):  
Peter S. Kourtev ◽  
Cindy H. Nakatsu ◽  
Allan Konopka
Keyword(s):  
Bacterial Community ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
Community Change ◽  
Resistant Bacteria ◽  
Rrna Gene ◽  
Organic C ◽  
Iron Reducing Bacteria ◽  
Chromium Vi ◽  
Reducing Bacteria

ABSTRACT Chromium (VI) is toxic to microorganisms and can inhibit the biodegradation of organic pollutants in contaminated soils. We used microcosms amended with either glucose or protein (to drive bacterial community change) and Fe(III) (to stimulate iron-reducing bacteria) to study the effect of various concentrations of Cr(VI) on anaerobic bacterial communities. Microcosms were destructively sampled based on microbial activity (measured as evolution of CO2) and analyzed for the following: (i) dominant bacterial community by PCR-denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene; (ii) culturable Cr-resistant bacteria; and (iii) enrichment of iron-reducing bacteria of the Geobacteraceae family by real-time PCR. The addition of organic C stimulated the activities of anaerobic communities. Cr(VI) amendment resulted in lower rates of CO2 production in glucose microcosms and a slow mineralization phase in protein-amended microcosms. Glucose and protein amendments selected for different bacterial communities. This selection was modified by the addition of Cr(VI), since some DGGE bands were intensified and new bands appeared in Cr(VI)-amended microcosms. A second dose of Cr(VI), added after the onset of activity, had a strong inhibitory effect when higher levels of Cr were added, indicating that the developing Cr-resistant communities had a relatively low tolerance threshold. Most of the isolated Cr-resistant bacteria were closely related to previously studied Cr-resistant anaerobes, such as Pantoea, Pseudomonas, and Enterobacter species. Geobacteraceae were not enriched during the incubation. The studied Cr(VI)-contaminated soil contained a viable anaerobic bacterial community; however, Cr(VI) altered its composition, which could affect the soil biodegradation potential.

scholarly journals Characterization and comparison of the bacterial communities of rhizosphere and bulk soils from cadmium-polluted wheat fields

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10302
Author(s):  
Li Song ◽  
Zhenzhi Pan ◽  
Yi Dai ◽  
Lin Chen ◽  
Li Zhang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
Cadmium Concentration ◽  
Normal Growth ◽  
Amplicon Sequencing ◽  
Negative Influence ◽  
Cadmium Pollution ◽  
16S Rrna Amplicon Sequencing ◽  
The Impact

Cadmium pollution is becoming a serious problem due to its nondegradability and substantial negative influence on the normal growth of crops, thereby harming human health through the food chain. Rhizospheric bacteria play important roles in crop tolerance. However, there is little experimental evidence which demonstrates how various cadmium concentrations affect the bacterial community in wheat fields including rhizosphere microorganisms and nonrhizosphere (bulk) microorganisms. In this study, 16S rRNA amplicon sequencing technology was used to investigate bacterial communities in rhizosphere and bulk soils under different levels of pollution in terms of cadmium concentration. Both the richness and diversity of the rhizosphere microorganism community were higher under nonpolluted soil and very mild and mild cadmium-contaminated soils than compared with bulk soil, with a shift in community profile observed under severe cadmium pollution. Moreover, cadmium at various concentrations had greater influence on bacterial composition than for the nonpolluted site. In addition, redundancy analysis (RDA) and Spearman’s analysis elucidated the impact of exchangeable Cd and total Cd on bacterial community abundance and composition. This study suggests that cadmium imposes a distinct effect on bacterial community, both in bulk and rhizosphere soils of wheat fields. This study increases our understanding of how bacterial communities in wheat fields shaped under different concentrations of cadmium.

scholarly journals Chemical Properties of Heavy Metal-Contaminated Soils from a Korean Military Shooting Range: Evaluation of Pb Sources Using Pb Isotope Ratios

2021 ◽  
Vol 11 (15) ◽  
pp. 7099
Author(s):  
Inkyeong Moon ◽  
Honghyun Kim ◽  
Sangjo Jeong ◽  
Hyungjin Choi ◽  
Jungtae Park ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Contaminated Soils ◽  
Management Strategies ◽  
Chemical Properties ◽  
Heavy Metal Concentration ◽  
Soil Samples ◽  
Shooting Range ◽  
Geochemical Properties ◽  
Mineral Phases

In this study, the geochemical properties of heavy metal-contaminated soils from a Korean military shooting range were analyzed. The chemical behavior of heavy metals was determined by analyzing the soil pH, heavy metal concentration, mineral composition, and Pb isotopes. In total, 24 soil samples were collected from a Korean military shooting range. The soil samples consist of quartz, albite, microcline, muscovite/illite, kaolinite, chlorite, and calcite. Lead minerals, such as hydrocerussite and anglesite, which are indicative of a transformation into secondary mineral phases, were not observed. All soils were strongly contaminated with Pb with minor concentrations of Cu, Ni, Cd, and Zn. Arsenic was rarely detected. The obtained results are indicated that the soils from the shooting range are contaminated with heavy metals and have evidences of different degree of anthropogenic Pb sources. This study is crucial for the evaluation of heavy metal-contaminated soils in shooting ranges and their environmental effect as well as for the establishment of management strategies for the mitigation of environmental risks.

scholarly journals A Rapid Bacteriophage DNA Extraction Method

2018 ◽  
Vol 1 (3) ◽  
pp. 27 ◽  
Author(s):  
Džiuginta Jakočiūnė ◽  
Arshnee Moodley
Keyword(s):  
Dna Extraction ◽  
Illumina Miseq ◽  
Extraction Methods ◽  
Resistant Bacteria ◽  
Simple Method ◽  
Antibiotic Resistant ◽  
Phage Dna ◽  
Specialized Equipment ◽  
Miseq Platform ◽  
Dna Extraction Methods

Bacteriophages (phages) are intensely investigated as non-antibiotic alternatives to circumvent antibiotic resistance development as well as last resort therapeutic options against antibiotic resistant bacteria. As part of gaining a better understanding of phages and to determine if phages harbor putative virulence factors, whole genome sequencing is used, for which good quality phage DNA is needed. Traditional phage DNA extraction methods are tedious and time consuming, requiring specialized equipment e.g., an ultra-centrifuge. Here, we describe a quick and simple method (under four hours) to extract DNA from double stranded DNA (dsDNA) phages at titers above 1.0 × 1010 plaque-forming units (PFU)/mL. This DNA was suitable for library preparation using the Nextera XT kit and sequencing on the Illumina MiSeq platform.

Analysis of bacterial diversity of Chinese Luzhou-flavor liquor brewed in different seasons by Illumina Miseq sequencing

2016 ◽  
Vol 66 (3) ◽  
pp. 1293-1301 ◽  
Author(s):  
Weining Sun ◽  
Huazhi Xiao ◽  
Qian Peng ◽  
Qiaoge Zhang ◽  
Xingxing Li ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Different Seasons

scholarly journals Isolation and characterization of arsenic resistant soil bacteria and their effects on germination of rice under arsenic contamination

2015 ◽  
Vol 2 (2) ◽  
pp. 229-237
Author(s):  
Istiaq Ahmed ◽  
Md Tofazzal Islam ◽  
Md Akhter Hossain Chowdhury ◽  
Md Kamruzzaman
Keyword(s):  
Contaminated Soils ◽  
Sodium Arsenite ◽  
Agar Plate ◽  
Rice Seedling ◽  
Resistant Bacteria ◽  
Gram Staining ◽  
Isolation And Characterization ◽  
Resistant Strains

This study was carried out to isolate, screen and characterize arsenic (As) resistant bacteria from As contaminated soils of Dumrakandi and Matlab under Faridpur and Chandpur districts and to evaluate their efficiency in reducing As toxicity against rice seedlings during germination. Thirteen strains were isolated from the soils which showed resistance to different levels of sodium arsenite (viz. 5, 10, 20 and 40 mM) in both agar plate and broth assay using BSMY I media. Among the isolates, BTL0011, BTL0012, BTL0015 and BTL0022 showed highest resistance to 40 mM sodium arsenite. Gram staining and KOH solubility test revealed that five strains were gram positive and rest eight was gram negative. They grew well in the liquid media at pH 5.5 to 8.5. In-vitro rice seedling bioassay with two superior isolates (BTL0011 and BTL0022) revealed that As resistant strains significantly enhanced seed germination of BRRI dhan29 and BRRI dhan47 at 60 ppm As. This study was laid out in CRD with three replications. The performance of BTL 0022 was superior to BTL0011. The overall results suggest that BTL0011 and BTL0022 can be used for bioremediation of As contaminated soils and to increase the germination and seedling growth of rice in As contaminated soils.Res. Agric., Livest. Fish.2(2): 229-237, August 2015

Lead (II) Removal from Contaminated Soils by Electrokinetic Remediation Coupled with Modified Eggshell Waste

2018 ◽  
Vol 777 ◽  
pp. 256-261 ◽  
Author(s):  
André Ribeiro ◽  
André Mota ◽  
Margarida Soares ◽  
Carlos Castro ◽  
Jorge Araújo ◽  
...  
Keyword(s):  
Contaminated Soil ◽  
Contaminated Soils ◽  
Removal Rate ◽  
Electrokinetic Remediation ◽  
Permeable Reactive Barrier ◽  
Inorganic Contaminants ◽  
Reactive Barrier ◽  
Eggshell Waste ◽  
Inorganic Fraction ◽  
Maximum Removal

Electrokinetic remediation deserves particular attention in soil treatment due to its peculiar advantages, including the capability of treating fine and low permeability materials, and achieving consolidation, dewatering and removal of salts and inorganic contaminants like heavy metals in a single stage. In this study, the remediation of artificially lead (II) contaminated soil by electrokinetic process, coupled with Eggshell Inorganic Fraction Powder (EGGIF) permeable reactive barrier (PRB), was investigated. An electric field of 2 V cm-1was applied and was used an EGGIF/soil ratio of 30 g kg-1 of contaminated soil for the preparation of the permeable reactive barrier (PRB) in each test. It was obtained high removal rates of lead in both experiments, especially near the cathode. In the normalized distance to cathode of 0.2 it was achieved a maximum removal rate of lead (II) of 68, 78 and 83% in initial lead (II) concentration of 500 mg-1, 200 mg-1 and 100 mg-1, respectively. EGGIF (Eggshell Inorganic Fraction) proved that can be used as permeable reactive barrier (PRB) since in all the performed tests were achieved adsorptions yields higher than 90%.

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.

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