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Soil sampling method

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https://www.readbyqxmd.com/read/28631592/blastomonas-quesadae-sp-nov-isolated-from-a-saline-soil-by-dilution-to-extinction-cultivation
#1
David J Castro, Inmaculada Llamas, Victoria Béjar, Fernando Martínez-Checa
We isolated a Gram-stain-negative, aerobic bacterial strain, 912T, from a soil sample taken from Rambla Salada (Murcia), south-eastern Spain, by using the dilution-to-extinction method. Cells of the strain were motile with a polar flagellum, short rod-shaped, catalase- and oxidase-positive and grew at NaCl concentrations within the range 0-5 % (w/v) (optimum 3 %, w/v), at 4-32 °C (optimum 30 °C) and at pH 6-9 (optimum pH 7); bacteriochlorophyll a was produced. Analysis of the 16S rRNA gene sequence indicated that this strain belonged to the genus Blastomonas in the class Alphaproteobacteria...
June 20, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28629168/assessing-statistically-significant-heavy-metal-concentrations-in-abandoned-mine-areas-via-hot-spot-analysis-of-portable-xrf-data
#2
Sung-Min Kim, Yosoon Choi
To develop appropriate measures to prevent soil contamination in abandoned mining areas, an understanding of the spatial variation of the potentially toxic trace elements (PTEs) in the soil is necessary. For the purpose of effective soil sampling, this study uses hot spot analysis, which calculates a z-score based on the Getis-Ord Gi* statistic to identify a statistically significant hot spot sample. To constitute a statistically significant hot spot, a feature with a high value should also be surrounded by other features with high values...
June 18, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28626294/optical-molecular-fluorescence-determination-of-ultra-trace-beryllium-in-occupational-and-environmental-samples-using-highly-alkaline-conditions
#3
Lori Adams, Anoop Agrawal, John P Cronin, Kevin Ashley
Exposures to beryllium (Be), even at extremely low levels, can cause severe health effects in a percentage of those exposed; consequently, occupational exposure limits (OELs) promulgated for this element are the lowest established for any element. This work describes the advantages of using highly alkaline dye solutions for determination of Be in occupational hygiene and environmental samples by means of an optical molecular fluorescence technique after sample extraction in 1-3% (w˖w(-1)) aqueous ammonium bifluoride (NH4HF2)...
2017: International Journal of Environmental Analytical Chemistry
https://www.readbyqxmd.com/read/28625159/dna-extraction-for-streamlined-metagenomics-of-diverse-environmental-samples
#4
Clarisse Marotz, Amnon Amir, Greg Humphrey, James Gaffney, Grant Gogul, Rob Knight
A major bottleneck for metagenomic sequencing is rapid and efficient DNA extraction. Here, we compare the extraction efficiencies of three magnetic bead-based platforms (KingFisher, epMotion, and Tecan) to a standardized column-based extraction platform across a variety of sample types, including feces, oral, skin, soil, and water. Replicate sample plates were extracted and prepared for 16S rRNA gene amplicon sequencing in parallel to assess extraction bias and DNA quality. The data demonstrate that any effect of extraction method on sequencing results was small compared with the variability across samples; however, the KingFisher platform produced the largest number of high-quality reads in the shortest amount of time...
June 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28624637/developing-a-new-bayesian-risk-index-for-risk-evaluation-of-soil-contamination
#5
M T D Albuquerque, S Gerassis, C Sierra, J Taboada, J E Martín, I M H R Antunes, J R Gallego
Industrial and agricultural activities heavily constrain soil quality. Potentially Toxic Elements (PTEs) are a threat to public health and the environment alike. In this regard, the identification of areas that require remediation is crucial. In the herein research a geochemical dataset (230 samples) comprising 14 elements (Cu, Pb, Zn, Ag, Ni, Mn, Fe, As, Cd, V, Cr, Ti, Al and S) was gathered throughout eight different zones distinguished by their main activity, namely, recreational, agriculture/livestock and heavy industry in the Avilés Estuary (North of Spain)...
June 15, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28620816/bioaccessibility-of-as-cu-pb-and-zn-in-mine-waste-urban-soil-and-road-dust-in-the-historical-mining-village-of-ka%C3%A5-k-czech-republic
#6
Petr Drahota, Karel Raus, Eva Rychlíková, Jan Rohovec
Historical mining activities in the village of Kaňk (in the northern part of the Kutná Hora ore district, Czech Republic) produced large amounts of mine wastes which contain significant amounts of metal(loid) contaminants such as As, Cu, Pb, and Zn. Given the proximity of residential communities to these mining residues, we investigated samples of mine waste (n = 5), urban soil (n = 6), and road dust (n = 5) with a special focus on the solid speciation of As, Cu, Pb, and Zn using a combination of methods (XRD, SEM/EDS, oxalate extractions), as well as on in vitro bioaccessibility in simulated gastric and lung fluids to assess the potential exposure risks for humans...
June 15, 2017: Environmental Geochemistry and Health
https://www.readbyqxmd.com/read/28620364/a-multiplex-rt-pcr-assay-for-s-aureus-l-monocytogenes-and-salmonella-spp-detection-in-raw-milk-with-pre-enrichment
#7
Tian Ding, Yuanjie Suo, Zhaohuan Zhang, Donghong Liu, Xingqian Ye, Shiguo Chen, Yong Zhao
This study firstly developed a multiplex real-time PCR (RT-PCR) technique combined with a pre-enrichment step to simultaneously detect Staphylococcus aureus (S. aureus), Listeria monocytogenes (L. monocytogenes) and Salmonella spp. in raw milk and the dairy farm environment (feces, soil, feed, water) in one reaction. Brain heart infusion (BHI) broth was selected for the enrichment step to increase the density of the target bacteria by using an incubation of 4 h before multiplex RT-PCR. The results showed that the detection limit of the multiplex real-time assay was approximately 10(2) CFU/mL for pure cultures and artificially contaminated milk without enrichment, while 12, 14, and 10 CFU/25 mL, respectively, for S...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28619671/combination-of-five-diagnostic-tests-to-estimate-the-prevalence-of-hookworm-infection-among-school-aged-children-from-a-rural-area-of-colombia
#8
Rafael E Barreto, Javier Narváez, Natalia A Sepúlveda, Fabián C Velásquez, Sandra C Díaz, Myriam Consuelo López, Patricia Reyes, Ligia I Moncada
BACKGROUND: Public health programs for the control of soil-transmitted helminthiases require valid diagnostic tests for surveillance and parasitic control evaluation. However, there is currently no agreement about what test should be used as a gold standard for the diagnosis of hookworm infection. Still, in presence of concurrent data for multiple tests it is possible to use statistical models to estimate measures of test performance and prevalence. The aim of this study was to estimate the diagnostic accuracy of five parallel tests (direct microscopic examination, Kato-Katz, Harada-Mori, modified Ritchie-Frick, and culture in agar plate) to detect hookworm infections in a sample of school-aged children from a rural area in Colombia...
June 12, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28616506/the-hookworm-ancylostoma-ceylanicum-an-emerging-public-health-risk-in-australian-tropical-rainforests-and-indigenous-communities
#9
Felicity A Smout, Lee F Skerratt, James R A Butler, Christopher N Johnson, Bradley C Congdon, R C Andrew Thompson
Ancylostoma ceylanicum is the common hookworm of domestic dogs and cats throughout Asia, and is an emerging but little understood public health risk in tropical northern Australia. We investigated the prevalence of A. ceylanicum in soil and free-ranging domestic dogs at six rainforest locations in Far North Queensland that are Indigenous Australian communities and popular tourist attractions within the Wet Tropics World Heritage Area. By combining PCR-based techniques with traditional methods of hookworm species identification, we found the prevalence of hookworm in Indigenous community dogs was high (96...
June 2017: One Health
https://www.readbyqxmd.com/read/28614606/antagonism-of-trichoderma-isolates-against-leucoagaricus-gongylophorus-singer-m%C3%A3-ller
#10
Mariela Otoni do Nascimento, Renato de Almeida Sarmento, Gil Rodrigues Dos Santos, Cléia Almeida de Oliveira, Danival José de Souza
Filamentous fungi from the genus Trichoderma are commonly found in soil. They are considered facultative mycoparasites, and are antagonists of other fungi such as the cultivar of leaf-cutting ants (Leucoagaricus gongylophorus). The aim of the present study was to bioprospect Trichoderma spp. from different soils collected from Gurupi, Tocantins, Brazil, for antagonistic effects against the mutualistic fungus of leaf-cutting ants. To isolate filamentous fungi, samples were collected from six locations. Preliminarily, isolates were identified by morphological analysis as belonging to Trichoderma...
June 14, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28609744/a-whole-cell-bioreporter-assay-for-quantitative-genotoxicity-evaluation-of-environmental-samples
#11
Bo Jiang, Guanghe Li, Yi Xing, Dayi Zhang, Jianli Jia, Zhisong Cui, Xiao Luan, Hui Tang
Whole-cell bioreporters have emerged as promising tools for genotoxicity evaluation, due to their rapidity, cost-effectiveness, sensitivity and selectivity. In this study, a method for detecting genotoxicity in environmental samples was developed using the bioluminescent whole-cell bioreporter Escherichia coli recA::luxCDABE. To further test its performance in a real world scenario, the E. coli bioreporter was applied in two cases: i) soil samples collected from chromium(VI) contaminated sites; ii) crude oil contaminated seawater collected after the Jiaozhou Bay oil spill which occurred in 2013...
June 7, 2017: Chemosphere
https://www.readbyqxmd.com/read/28608621/simultaneous-extraction-and-determination-of-antibiotics-in-soils-using-a-method-based-on-quick-easy-cheap-effective-rugged-and-safe-extraction-and-liquid-chromatography-with-tandem-mass-spectrometry
#12
Minghui Meng, Zeying He, Yaping Xu, Lu Wang, Yi Peng, Xiaowei Liu
The increasing use of antibiotics has caused substantial environmental problems, which proved to be a matter of great concern. The aim of this work was to develop a quick, easy, cheap, effective, rugged and safe method for 20 antibiotics residues in soil. The developed method was based on extraction with acetonitrile and phosphate buffer, clean-up with dispersive solid-phase extraction adsorbent using primary secondary amine, octadecylsilane, followed by liquid chromatography with tandem mass spectrometry determination...
June 13, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/28606424/influence-of-composition-and-degradation-on-the-shear-strength-of-municipal-solid-waste
#13
A E S Abreu, O M Vilar
This study aimed to evaluate the shear strength of municipal solid waste (MSW) of different landfilling ages exhumed from disposal sites in a subtropical humid environment. Wastes which had been landfilled from ages of 2 up to 25years were characterized using physical, chemical and biochemical tests and were tested in a large scale direct shear device. The results indicate that the tested wastes older than five years had reached similar decomposition stages, but showed different compositions in terms of soft plastics, incompressible material and reinforcing elements...
June 9, 2017: Waste Management
https://www.readbyqxmd.com/read/28602310/spatial-distribution-of-heavy-hydrocarbons-pahs-and-metals-in-polluted-areas-the-case-of-galicia-spain
#14
D Monaco, E Chianese, A Riccio, A Delgado-Sanchez, S Lacorte
The aim of this work is to verify the impact of anthropogenic activities and the effects of accidental events, e.g. oil spills, on the marine environment. For this reason, marine sediments and soil samples were collected in the inner part of Vigo and Pontevedra bays, in the Galicia region, northwest Spain, an area interested by many events of oil spills and also characterized by coastal areas with intense anthropic activities; also Cíes Islands, a natural protected area facing the Vigo bay, was investigated, as background site...
June 9, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28599671/is-there-a-difference-in-prevalence-of-helminths-between-households-using-ecological-sanitation-and-those-using-traditional-pit-latrines-a-latrine-based-cross-sectional-comparative-study-in-malawi
#15
Save Kumwenda, Chisomo Msefula, Wilfred Kadewa, Yohane Diness, Charles Kato, Tracy Morse, Bagrey Ngwira
BACKGROUND: Studies have shown that households using sludge from human excreta for agriculture are at an increased risk of soil transmitted helminths. However, while use of ecological sanitation (EcoSan) latrines is increasing in most African countries including Malawi, few studies have been done to check whether use of such sludge could potentially increase the prevalence of helminthic infections among household members as a results of exposure to faecal sludge/compared to use of traditional latrines...
June 9, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28599633/prevalence-of-intestinal-parasitic-infection-and-associated-risk-factors-among-village-health-volunteers-in-rural-communities-of-southern-thailand
#16
Chuchard Punsawad, Nonthapan Phasuk, Suchirat Bunratsami, Kanjana Thongtup, Niramon Siripakonuaong, Somchok Nongnaul
BACKGROUND: Intestinal parasitic infections remain prevalent and constitute a public health problem in certain rural areas of Thailand. Village health volunteers (VHVs), who are members of a Thai healthcare alliance, function as key providers of health prevention measures, disease control, and health education and share national health promotion campaigns with community members. This study is aimed at evaluating the prevalence, intensity, and risk factors for intestinal parasitic infection in VHVs in order to design community awareness and health education campaigns for the target population...
June 9, 2017: BMC Public Health
https://www.readbyqxmd.com/read/28597163/shift-in-microbial-group-during-remediation-by-enhanced-natural-attenuation-rena-of-a-crude-oil-impacted-soil-a-case-study-of-ikarama-community-bayelsa-nigeria
#17
Chioma Blaise Chikere, Christopher Chibueze Azubuike, Evan Miebaka Fubara
Acute and chronic pollution of environments with crude oil does not bode well for biota living within the vicinity of polluted environments. This is due to environmental and public health concerns on the negative impact of crude oil pollution on living organisms. Enhancing microbial activities by adding nutrients and other amendments had proved effective in pollutant removal during bioremediation. This study was carried out to determine how microbial group respond during remediation by enhanced natural attenuation (RENA) during a field-scale bioremediation...
June 2017: 3 Biotech
https://www.readbyqxmd.com/read/28597052/on-the-ground-or-in-the-air-a-methodological-experiment-on-crop-residue-cover-measurement-in-ethiopia
#18
Frédéric Kosmowski, James Stevenson, Jeff Campbell, Alemayehu Ambel, Asmelash Haile Tsegay
Maintaining permanent coverage of the soil using crop residues is an important and commonly recommended practice in conservation agriculture. Measuring this practice is an essential step in improving knowledge about the adoption and impact of conservation agriculture. Different data collection methods can be implemented to capture the field level crop residue coverage for a given plot, each with its own implication on survey budget, implementation speed and respondent and interviewer burden. In this paper, six alternative methods of crop residue coverage measurement are tested among the same sample of rural households in Ethiopia...
June 8, 2017: Environmental Management
https://www.readbyqxmd.com/read/28587142/spatial-distribution-of-heavy-metals-and-the-environmental-quality-of-soil-in-the-northern-plateau-of-spain-by-geostatistical-methods
#19
Fernando Santos-Francés, Antonio Martínez-Graña, Carmelo Ávila Zarza, Antonio García Sánchez, Pilar Alonso Rojo
The environmental quality of soil in the central part of the Northern Plateau of Spain has been analyzed by studying the heavy metal content of 166 samples belonging to the horizons A, B and C of 89 soil profiles. The analysis to assess the environmental risk of heavy metals in the soil was carried out by means of the spatial distribution of nine heavy metals and the use of several pollution indices. The results showed that the concentration values of heavy metals (x ± S) in the superficial soil horizons were the following: With a total of 6...
May 26, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28585590/isolation-of-potentially-pathogenic-fungi-from-selected-pigeons-feeding-sites-in-karachi-a-new-dimension-to-health-hazard
#20
Sehar Afshan Naz, Muhammad Yaseen, Nusrat Jabeen, Maryam Shafique
OBJECTIVE: To determine the presence of pathogenic fungal strains in areas where pigeons are present in a large number. METHODS: This study was conducted at the Federal Urdu University of Arts, Science and Technology, Karachi, from February 2015 to March2016, and comprised samples of soil contaminated with pigeons' excreta. The samples were collected from 20 different pigeon-feeding places in the city. These samples were processed for the isolation and identification of fungi by using standard conventional methods...
June 2017: JPMA. the Journal of the Pakistan Medical Association
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