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Soil sampling method

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https://www.readbyqxmd.com/read/28330298/biodegradation-of-used-engine-oil-by-novel-strains-of-ochrobactrum-anthropi-hm-1-and-citrobacter-freundii-hm-2-isolated-from-oil-contaminated-soil
#1
Haytham M M Ibrahim
Used engine oil (UEO) constitutes a serious environmental problem due to the difficulty of disposal off or reuse. Ten bacterial strains with biodegradation potential were isolated from UEO-contaminated soil sample using enrichment technique. Two strains which exhibited the highest degradation %, 51 ± 1.2 and 48 ± 1.5, respectively, were selected. Based on the morphological, biochemical characteristics and 16S rRNA sequence analysis, they were identified as Ochrobactrum anthropi HM-1 (accession no: KR360745) and Citrobacter freundii HM-2 (accession no: KR360746)...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330292/comparative-assessment-of-methods-for-metagenomic-dna-isolation-from-soils-of-different-crop-growing-fields
#2
Aiman Tanveer, Sangeeta Yadav, Dinesh Yadav
The isolation of good quality metagenomic DNA from diverse soil, in appreciable amount, is a prerequisite for metagenomics. The availability of commercial kits for isolation of genomic DNAs from soil has drastically expedited the application of metagenomics approach for identifying novel sources of industrially important enzymes. The quantitative and qualitative assessment of metagenomic DNA isolated using either the manual method or the kit-based method should be performed prior to its use in downstream applications...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330132/an-efficient-and-cost-effective-method-for-dna-extraction-from-athalassohaline-soil-using-a-newly-formulated-cell-extraction-buffer
#3
Avinash Narayan, Kunal Jain, Amita R Shah, Datta Madamwar
The present study describes the rapid and efficient indirect lysis method for environmental DNA extraction from athalassohaline soil by newly formulated cell extraction buffer. The available methods are mostly based on direct lysis which leads to DNA shearing and co-extraction of extra cellular DNA that influences the community and functional analysis. Moreover, during extraction of DNA by direct lysis from athalassohaline soil, it was observed that, upon addition of poly ethylene glycol (PEG), isopropanol or absolute ethanol for precipitation of DNA, salt precipitates out and affecting DNA yield significantly...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28320455/a-systematic-review-of-taeniasis-cysticercosis-and-trichinellosis-in-vietnam
#4
REVIEW
Dinh Ng-Nguyen, Mark A Stevenson, Rebecca J Traub
Taeniasis, cysticercosis and trichinellosis have been ranked as the most important food-borne parasites of humans in terms of public health, socioeconomic and trade impact. Despite this, information on these food-borne zoonoses in Vietnam is scarce and fragmented, and many local reports remain inaccessible to the international research community. This study aims to conduct comprehensive literature searches to report on the incidence and estimate the true prevalence of taeniasis in humans and T. solium cysticercosis in humans and pigs in Vietnam utilizing Bayesian models; in addition, to report the incidence and the distribution of trichinellosis...
March 21, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28316413/detection-and-genotyping-of-toxoplasma-gondii-isolated-from-soil-in-ahvaz-southwest-of-iran
#5
J Saki, S Khademvatan, E Yousefi, M Tavalla, R Abdizadeh
To detection and genotype of Toxoplasma gondii isolated from soil in Ahvaz, southwest of Iran. Between August 2011 and May 2012 at different sites located in the area of the Ahvaz city south west Iran. A total of 200 soil samples were taken from different points of the region. Oocysts were recovered using the flotation method. Then, PCR reactions targeting the GRA6 gene were performed for specific T. gondii detection. The positive samples were studied by RFLP (random amplified fragment length polymorphism) using MseI enzymes to confirm the parasite linage...
March 2017: Journal of Parasitic Diseases: Official Organ of the Indian Society for Parasitology
https://www.readbyqxmd.com/read/28315821/1-3-propanediol-production-by-a-newly-isolated-strain-clostridium-perfringens-gyl
#6
Yali Guo, Lu Dai, Bo Xin, Fei Tao, Hongzhi Tang, Yaling Shen, Ping Xu
1,3-Propanediol (1,3-PD), a valuable bulk industrial material, has attracted increasing interest in recent years. A novel strain GYL isolated from soil samples could efficiently convert glycerol to 1,3-PD anaerobically. The physiological and biochemical characteristics of strain GYL were determined, indicating that strain GYL is a member of Clostridium perfringens with the neighbor-joining method of 16S rRNA gene sequences. The fermentation properties of strain GYL were also investigated systematically, which showed that the strain has a fast growth speed and high tolerance to 200g/L glycerol...
February 28, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28302147/soil-transmitted-helminths-and-plasmodium-falciparum-malaria-among-individuals-living-in-different-agroecosystems-in-two-rural-communities-in-the-mount-cameroon-area-a-cross-sectional-study
#7
Irene Ule Ngole Sumbele, Gladys Belanka Nkemnji, Helen Kuokuo Kimbi
BACKGROUND: Soil-transmitted helminths (STHs) and Plasmodium falciparum infections remain public health problems in Cameroon. A cross-sectional study was carried out in the Mount Cameroon area to determine the prevalence and intensity of STHs and P. falciparum infections in individuals living in different agroecosystems; to assess the influence of these infections on haematological parameters; and to identify the risk factors associated with STH infections. METHODS: STH and malaria parasites were detected using the Kato-Katz method and Giemsa staining of blood films, respectively...
March 16, 2017: Infectious Diseases of Poverty
https://www.readbyqxmd.com/read/28299980/penixanthones-a-and-b-two-new-xanthone-derivatives-from-fungus-penicillium-sp-syfz-1-derived-of-mangrove-soil-sample
#8
Huaming Tao, Xiaoyi Wei, Xiuping Lin, Xuefeng Zhou, Junde Dong, Bin Yang
Two new xanthone derivatives, penixanthones A (1) and B (2), together with three known compounds, aspenicillide (3), 1,5-dihydroxy-3-methoxy-7-methyl-anthracene-9,10-dione (4) and 1,2-indandiol (5), were isolated from the ethyl acetate extract of a culture of the fungus Penicillium sp. SYFz-1, which was separated from a mangrove soil sample. The structures of these compounds were elucidated by spectroscopic methods including NMR and mass spectrometry. The absolute configurations of penixanthones A (1) and B (2) were determined on the basis of electronic circular dichroism (ECD) data analysis...
March 16, 2017: Natural Product Research
https://www.readbyqxmd.com/read/28299568/time-lapse-effect-of-ancient-plant-coal-biochar-on-some-soil-agrochemical-parameters-and-soil-characteristics
#9
Tamás Kocsis, Borbála Biró, Ákos Ulmer, Mónika Szántó, Zsolt Kotroczó
Biochar is a solid material obtained from reductive, oxygen-free processes, i.e. the thermo-chemical conversion of biomass in oxygen-limited environment. The obtained products have high carbon sequestration potential and strong nutrient-water absorption capacities because of the enlarged carbon surfaces. It is not yet clear how carbon stimulates agrochemical parameters in soil and how those characteristics are developing as time goes on a long-term basis. Samples of ancient (25, 35, 80 years old) plant coal-affected soils were collected in a temperate deciduous forest site located in the south part of the Bükk Mountains (in North Eastern Hungary)...
March 15, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28296353/methodological-considerations-for-detection-of-terrestrial-small-body-salamander-edna-and-implications-for-biodiversity-conservation
#10
Donald M Walker, Jacob E Leys, Kelly E Dunham, Joshua C Oliver, Emily E Schiller, Kelsey S Stephenson, John T Kimrey, Jessica Wooten, Mark W Rogers
Environmental DNA (eDNA) can be used as an assessment tool to detect populations of threatened species and provide fine-scale data required to make management decisions. The objectives of this project were to use quantitative PCR (qPCR) to: 1) detect spiked salamander DNA in soil, 2) quantify eDNA degradation over time, 3) determine detectability of salamander eDNA in a terrestrial environment using soil, feces, and skin swabs, 4) detect salamander eDNA in a mesocosm experiment. Salamander eDNA was positively detected in 100% of skin swabs and 66% of fecal samples and concentrations did not differ between the two sources...
March 15, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28294490/the-determination-and-application-of-87-sr-86-sr-ratio-in-verifying-geographical-origin-of-wheat
#11
Hongyan Liu, Yimin Wei, Hai Lu, Shuai Wei, Tao Jiang, Yingquan Zhang, Jinfu Ban, Boli Guo
RATIONALE: As (87) Sr/(86) Sr ratio plays a significant role in authenticating the geographical origin of foodstuff, it is important to identify where the (87) Sr/(86) Sr signature in food comes from, and the methods of (87) Sr/(86) Sr ratio analysis in food and environmental samples. METHODS: Wheat with three genotypes, soil and groundwater samples were collected from three regions of China during harvest time of 2014. The (87) Sr/(86) Sr ratios in the samples were determined by thermal ionization mass spectrometer in order to investigate the possible source of (87) Sr/(86) Sr in wheat, and the concentrations of Rb and Sr in wheat and soils were also detected by inductively coupled plasma mass spectrometry and combined with (87) Sr/(86) Sr ratio in order to trace the geographical origin of wheat...
March 14, 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28294483/the-detection-and-quantification-of-bacillus-thuringiensis-spores-from-soil-and-swabs-using-quantitative-pcr-as-a-model-system-for-routine-diagnostics-of-bacillus-anthracis
#12
Vera Sedlackova, Radka Dziedzinska, Vladimir Babak, Petr Kralik
AIMS: To optimize the DNA isolation for the routine detection and quantification of bacillary spores in soil and swabs. The procedure is primarily intended for diagnostics of Bacillus anthracis spores, but due to its high pathogenicity B. thuringiensis served as its surrogate organism. METHODS AND RESULTS: Various commercial kits for soils and swabs in combination with quantitative PCR were tested with different results. The PowerSoil DNA kit and the Ultra Clean Microbial DNA kit gave the best results for the extraction from soil and swabs, respectively...
March 10, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28292322/revealing-large-metagenomic-regions-through-long-dna-fragment-hybridization-capture
#13
Cyrielle Gasc, Pierre Peyret
BACKGROUND: High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes from single organisms or metagenomic samples. However, due to the limited capacity of short-read sequence data to assemble complex or low coverage regions, genomes are typically fragmented, leading to draft genomes with numerous underexplored large genomic regions. Revealing these missing sequences is a major goal to resolve concerns in numerous biological studies...
March 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28291815/residue-analysis-and-persistence-evaluation-of-fipronil-and-its-metabolites-in-cotton-using-high-performance-liquid-chromatography-tandem-mass-spectrometry
#14
Xiaohu Wu, Yang Yu, Jun Xu, Fengshou Dong, Xingang Liu, Pengqiang Du, Dongmei Wei, Yongquan Zheng
A simple residue analytical method based on the QuEChERS approach and high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) detection was developed for the analysis of fipronil and its three metabolites in cottonseed, cotton plant and soil. The average recoveries of four test compounds from all three matrices were 78.6-108.9% at the level of 0.005 to 0.5 mg/kg, with an RSD in the range of 0.6 to 13.7%. The limit of quantification (LOQ) of the four test compounds ranged from 0.005 to 0...
2017: PloS One
https://www.readbyqxmd.com/read/28290090/evaluation-of-atrazine-degradation-applied-to-different-energy-systems
#15
EDITORIAL
Ailton J Moreira, Bianca S Pinheiro, André F Araújo, Gian P G Freschi
Atrazine is an herbicide widely used in crops and has drawn attention due to potential pollution present in soil, sediment, water, and food. Since conventional methods are not potentially efficient to persistent degradation of organic compounds, new technology has been developed to remove them, especially practices utilizing advanced oxidation processes (AOPs). This work aims to evaluate the use of different energies (ultraviolet (UV), microwaves (MW), and radiations (MW-UV)) to the herbicide atrazine through the process of photo-oxidation...
March 14, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28289558/phylogenetic-factorization-of-compositional-data-yields-lineage-level-associations-in-microbiome-datasets
#16
Alex D Washburne, Justin D Silverman, Jonathan W Leff, Dominic J Bennett, John L Darcy, Sayan Mukherjee, Noah Fierer, Lawrence A David
Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to investigate how shared evolutionary history affects microbial abundance patterns. Here, we present a method to identify the phylogenetic factors driving patterns in microbial community composition. We use the method, "phylofactorization," to re-analyze datasets from the human body and soil microbial communities, demonstrating how phylofactorization is a dimensionality-reducing tool, an ordination-visualization tool, and an inferential tool for identifying edges in the phylogeny along which putative functional ecological traits may have arisen...
2017: PeerJ
https://www.readbyqxmd.com/read/28289269/epidemiological-investigation-of-parasitic-infection-of-schoolchildren-from-six-elementary-schools-in-sakon-nakhon-province-thailand
#17
Ryuichi Doi, Makoto Itoh, Somchai Chakhatrakan, Shoji Uga
We conducted an epidemiological study of intestinal parasitic infection in 572 schoolchildren aged 4 to 12 years old from six elementary schools in Sakon Nakhon Province, Thailand from June 2013 to August 2014. We collected fecal, blood, and urine samples to investigate parasitic infection and conducted a questionnaire survey. Soil samples were examined for egg contamination. Fecal examination, using the formalin-ether sedimentation method, revealed that 39% of schoolchildren were infected with eight genera and eight species of parasites; three nematodes, two trematodes, one cestode, and two protozoa...
February 15, 2017: Kobe Journal of Medical Sciences
https://www.readbyqxmd.com/read/28287500/the-evaluation-on-the-cadmium-net-concentration-for-soil-ecosystems
#18
Yu Yao, Pei-Fang Wang, Chao Wang, Jun Hou, Ling-Zhan Miao
Yixing, known as the "City of Ceramics", is facing a new dilemma: a raw material crisis. Cadmium (Cd) exists in extremely high concentrations in soil due to the considerable input of industrial wastewater into the soil ecosystem. The in situ technique of diffusive gradients in thin film (DGT), the ex situ static equilibrium approach (HAc, EDTA and CaCl2), and the dissolved concentration in soil solution, as well as microwave digestion, were applied to predict the Cd bioavailability of soil, aiming to provide a robust and accurate method for Cd bioavailability evaluation in Yixing...
March 12, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28286303/uncertainty-assessment-method-for-the-cs-137-fallout-inventory-and-penetration-depth
#19
G N Papadakos, D J Karangelos, N P Petropoulos, M J Anagnostakis, E P Hinis, S E Simopoulos
Within the presented study, soil samples were collected in year 2007 at 20 different locations of the Greek terrain, both from the surface and also from depths down to 26 cm. Sampling locations were selected primarily from areas where high levels of (137)Cs deposition after the Chernobyl accident had already been identified by the Nuclear Engineering Laboratory of the National Technical University of Athens during and after the year of 1986. At one location of relatively higher deposition, soil core samples were collected following a 60 m by 60 m Cartesian grid with a 20 m node-to-node distance...
March 9, 2017: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/28285437/application-of-magnetic-methods-for-assessment-of-soil-restoration-in-the-vicinity-of-metallurgical-copper-processing-plant-in-bulgaria
#20
N Jordanova, E Petrovský, A Kapicka, D Jordanova, P Petrov
Copper ore mining and processing are among the most harmful anthropogenic influences for the environment and they are a subject of international and national law regulations. Recultivation of areas influenced by mining and processing industry is commonly applied and monitored in order to restore as much as possible the natural environment. In this study, environmental magnetic methods are applied in order to assess the degree of soil restoration in terms of soil development, after remediation of waste dump from Cu-processing plant...
April 2017: Environmental Monitoring and Assessment
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