Complexity and heterogeneity of soil samples have often implied the inclusion of purification steps in conventional DNA extraction for polymerase chain reaction (PCR) assays. Unfortunately the purification steps are also time and labor intensive. Therefore the necessity of DNA purification was re-visited and investigated for a variety of environmental soil samples that contained various amounts of PCR inhibitors. Bead beating and centrifugation was used as the baseline (without purification) method for DNA extraction. Its performance was compared with that of conventional DNA extraction kit (with purification). The necessity criteria for DNA purification were established with environmental soil samples. Using lysis conditions at 3000 rpm for 3 minutes with 0.1 mm glass beads, centrifugation time of 10 minutes and 1:10 dilution ratio, the baseline method outperformed conventional DNA extraction on cell seeded sand samples. Further investigation with PCR inhibitors (i.e., humic acids, clay, and magnesium [Mg]) showed that sand samples containing less than 10 μg/g humic acids and 70% clay may not require purifications. Interestingly, the inhibition pattern of Mg ion was different from other inhibitors due to the complexation interaction of Mg ion with DNA fragments. It was concluded that DNA extraction method without purification is suitable for soil samples that have less than 10 μg/g of humic acids, less than 70% clay content and less than 0.01% Mg ion content.
Centrifugation ; DNA ; DNA, Bacterial ; Glass ; Humic Substances ; Magnesium ; Methods ; Polymerase Chain Reaction ; Population Characteristics ; Soil

An archaeoparasitological analysis of the soil samples from Nadym Gorodok site of Western Siberia has been carried out in this study. The archaeological site was dated as the 13 to 18th century, being characterized as permafrost region ensuring good preservation of ancient parasite eggs. Parasite eggs as Opisthorchis felineus, Alaria alata, and Diphyllobothrium sp. were found in the archaeological soil samples, which made clear about the detailed aspects of Nadym Gorodok people's life. We found the Diphyllobothrium sp. eggs throughout the 14 to 18th century specimens, allowing us to presume that raw or undercooked fish might have been commonly used for the foods of Nadym Gorodok inhabitants and their dogs for at least the past 400 years. Our study on Nadym Gorodok specimens also demonstrate that there might have been migratory interactions and strong economic ties between the people and society in Western Siberia, based on archaeoparasitological results of Opisthorchis felineus in Western Siberia.
Animals ; Archaeology ; Asia, Northern ; Diphyllobothrium ; Dogs ; Eggs ; Humans ; Middle Aged ; Opisthorchis ; Ovum ; Parasites ; Permafrost ; Siberia ; Soil

Aims: The former Mamut Copper Mine, acid mine drainage site represents an anthropogenic altered landscape characterized by its acidic topsoil which is contaminated primarily with copper. Even though the mining operation was ceased at 1999, the bacterial diversity in this area has never been investigated. This study was conducted to ascertain the bacterial diversity of this abandoned copper mine and correlate it to the copper concentration in the soil. Methodology and results: Soil samples were collected from 7 sites near the mine pit and the vicinity. Soil samples were assessed for soil copper elemental concentration using inductively coupled plasma optical emission spectrometry and bacteria were isolated via serial dilution followed by culture on nutrient agar plates. Phylogenetic analysis was done based on the full-length sequences of 16S rRNA gene. Twenty-four phylotypes were obtained from the 7 locations which originated from the phyla Firmicutes, Actinobacteria, Bacteroidetes and Proteobacteria. The results of the study indicated that site 2 (6.030223°; 116.658030°), located in between the mine pit and the mine factory with a copper concentration of 88.96 ppm, possessed the most diverse bacterial community with a Shannon diversity index (H) of 1.68, evenness (EH) of 0.94 and richness (S) of 6. Conclusion, significance and impact of study Current study revealed that there was a positive correlation between the copper concentration and the H index and the richness, but this was not reflected in the evenness. This is the first report of bacterial diversity from the former Mamut Copper Mine site. The data provided a valuable insight for the future monitoring of the bacterial community in this ecologically important niche.
Soil Microbiology

Bioremediation is considered as a cost-effective, efficient and free-of-secondary-pollution technology for petroleum pollution remediation. Due to the limitation of soil environmental conditions and the nature of petroleum pollutants, the insufficient number and the low growth rate of indigenous petroleum-degrading microorganisms in soil lead to long remediation cycle and poor remediation efficiency. Bioaugmentation can effectively improve the biodegradation efficiency. By supplying functional microbes or microbial consortia, immobilized microbes, surfactants and growth substrates, the remediation effect of indigenous microorganisms on petroleum pollutants in soil can be boosted. This article summarizes the reported petroleum-degrading microbes and the main factors influencing microbial remediation of petroleum contaminated soil. Moreover, this article discusses a variety of effective strategies to enhance the bioremediation efficiency, as well as future directions of bioaugmentation strategies.
Biodegradation, Environmental ; Petroleum ; Soil ; Soil Microbiology ; Soil Pollutants

With continuous improvement of people's living standards, great efforts have been paid to environmental protection. Among those environmental issues, soil contamination by petroleum hydrocarbons has received widespread concerns due to the persistence and the degradation difficulty of the pollutants. Among the various remediation technologies, in-situ microbial remediation enhancement technologies have become the current hotspot because of its low cost, environmental friendliness, and in-situ availability. This review summarizes several in-situ microbial remediation technologies such as bioaugmentation, biostimulation, and integrated remediation, as well as their engineering applications, providing references for the selection of in-situ bioremediation technologies in engineering applications. Moreover, this review discusses future research directions in this area.
Biodegradation, Environmental ; Humans ; Hydrocarbons ; Petroleum ; Soil ; Soil Microbiology ; Soil Pollutants

The Cd stress of Chrysanthemum indicum was treated by different concentrations of Cd Cl2 solution in the culture substrate. The content of Cd in different parts of Ch. indicum and the content of buddleoside and the total flavonoids in Ch. indicum were determined. The absorption characteristics of Cd elements in Ch. indicum were analyzed. And the influence of Cd elements on the quality of the herbs. The results showed that the application of soil Cd in the range of 0-100 mg·kg~(-1) had no significant effect on the biomass of Ch. indicum,and the root-shoot ratio showed a decreasing-increasing-decreasing trend. The content of Cd in different parts of Ch. indicum was significantly different,and the content of aboveground part was higher than that of underground part. The enrichment factors of Cd elements in different parts of Ch. indicum are different. The enrichment coefficient of aboveground parts is larger than that of underground parts. The whole parts and plants show an increase first and then decrease,and the overall enrichment factor is greater than1. The transfer coefficient of the aerial part/underground part of Ch. indicum showed a decreasing-increasing-decreasing-increasing trend with the increase of the amount of Cd applied in the soil,and the transfer coefficient was higher than 1. The contents of buddleoside and total flavonoids in Ch. indicum after Cd stress treatment were lower than the control,and the overall performance was lower and then increased,but it was still significantly lower than the control,indicating that Cd pollution directly led to the decrease of chemical quality of Ch. indicum.
Cadmium ; Chrysanthemum ; Flavonoids ; Soil ; Soil Pollutants

Soil microorganisms are one of the important biological indictors of soil quality and can reflct the comprehensive ecological environment characteristics of the soil. The research of soil microbial diversity is the key to know the ecological functions and balance with soil. In this paper, high-throughput sequencing on PCR-amplified 16 S rRNA gene V3-V4 fragments was used to determine the bacterial diversity in rhizosphere soil of A. macrocephala under the treatment with BZJN1 or streptoprofen. The results showed that there were no significant differences of the bacteria in A. macrocephala rhizosphere soil of the streptoprofen treatment group and the biocontrol BZJN1 treatment group. All the soil bacteria was classified into 25 categories,67 classes, 108 orders, 167 families and 271 generas, except some unidentified bacteria. Proteobacteria(30.7%-34.8%) was the dominant phylum, of which Alphaproteobacteria(16.8%-18.5%) was the dominant subgroup. Compared with the control group, the relative abundance of multiple phylums bacteria in the rhizosphere soil of A. macrocephala was significantly changed in the streptoprofen treatment group and the biocontrol BZJN1 treatment group. In addition, RDA analysis showed that there was connection with different environmental factors and microbial communities. The abundance of the three genera in the rhizosphere soil of A. macrocephala was significantly positively correlated with Invertase, Urease and AP. PICRUSt function prediction results showed that BZNJ1 could enhance some bacterial functions and promote the plant growth. Biocontrol is a new type of green and safety control pest method. BZNJ1 significantly enhances some bacterial functions on the basis of effectively preventing root rot of A. macrocephala and promoting plant growth, and has no significant effect on the soil bacterial community structure. All the results can provide theoretical support for popularization of BZNJ1.
Atractylodes ; Bacteria ; Rhizosphere ; Soil ; Soil Microbiology

No abstract available.
Environmental Pollution* ; Soil*

Yersinia pestis is the cause for the acute infection and may be chosen for biological terrorism. Rapid diagnosis of this agent from infected soil - water is essential. Y. pestis habours 3 specific plasmids providing virulent factors to the bacterium. Objectives: (1) Testing the sensitivity and accurateness of PCR for Y. pestis. (2) Carrying out PCR using total genomic DNA serially diluted as a template. (3) Undertaking PCR on artificical experimentation by diluting Y. pestis in soil water as samples to test PCR based fast diagnostic approach. Methods: Yersinia pestis (inactivated) was used. Genomic DNA was extracted by DNeasy kit (Qiagen Inc). Using primer - pairs PLAF - PLAR (binding on pia gene of plasmid pPCP1) a specific product of PCR was 480 bp. After determination of the PCR sensitivity, a molecular based diagnostic kit was developed. Sensitivity and specificity of this kit was tested by PCR using diluted genomic DNA and bacterium itself; and mix of these templates in water and soil as samples. Results: With the diluted genomic DNA, it was successful to obtain specific PCR with 0.6ng template, which is equal to a single bacterium. Additionally, successful PCR amplification was obtained using the whole bacterium (without extraction of genomic DNA) and diluted quantity ranging from 101 to 102. Based on these results, the bacterium was artificially diluted with sample of soil - water as a natural isolate for PCR amplification. Conclusions: Evidently, approach for PCR-based diagnostic kit was successfully carried out from any template including soil - water samples with high fidelity, using the pia gene genetic marker of pPCR of Y. pestis.
Yersinia ; Water ; Soil

Parasitological and knowledge – attitude – practice (KAP) surveys were carried out in 200 schoolchildren of Tran Phu primary school, Tam Diep town, Ninh Binh province and 200 their parents in 1999-2000. Information, education and communication (IEC) campaign for control program of helminth diseases and regular deworming every 6 months with albendazole 400mg single dose for all primary school children were implemented. After 1 year, prevalence of infection of Ascaris and Trichuris were reduced by more 50%, intensity of infection of Ascaris, Trichuris and hookworm were reduced by 86.9%, 84%, 100%, respectively. KAP of school children and their parents was changed significantly. Model of soil-transmitted helminthiasis control based on school has effectiveness, practice and extended application
Helminthiasis ; Child ; Disease ; Soil