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https://www.readbyqxmd.com/read/28803266/a-degradome-based-polymerase-chain-reaction-to-resolve-the-potential-of-environmental-samples-for-2-4-dichlorophenol-biodegradation
#1
Eslam S Ibrahim, Mona T Kashef, Tamer M Essam, Mohammed A Ramadan
A clean way to overcome environmental pollution is biodegradation. In this perspective, at the intersection of biodegradation and metagenomics, the degradome is defined as the totality of genes related to the biodegradation of a certain compound. It includes the genetic elements from both culturable and uncultured microorganisms. The possibility of assessing the biodegradation potential of an environmental samples, using a degradome-based polymerase chain reaction, was explored. 2,4-Dichlorophenol (2,4-DCP) was chosen as a model and the use of tfdB gene as a biodegradation marker was confirmed by bioinformatics study of TfdB protein...
August 12, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28798742/preservation-and-significance-of-extracellular-dna-in-ferruginous-sediments-from-lake-towuti-indonesia
#2
Aurèle Vuillemin, Fabian Horn, Mashal Alawi, Cynthia Henny, Dirk Wagner, Sean A Crowe, Jens Kallmeyer
Extracellular DNA is ubiquitous in soil and sediment and constitutes a dominant fraction of environmental DNA in aquatic systems. In theory, extracellular DNA is composed of genomic elements persisting at different degrees of preservation produced by processes occurring on land, in the water column and sediment. Extracellular DNA can be taken up as a nutrient source, excreted or degraded by microorganisms, or adsorbed onto mineral matrices, thus potentially preserving information from past environments. To test whether extracellular DNA records lacustrine conditions, we sequentially extracted extracellular and intracellular DNA from anoxic sediments of ferruginous Lake Towuti, Indonesia...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28793754/necessity-of-purification-during-bacterial-dna-extraction-with-environmental-soils
#3
Hyun Jeong Lim, Jung-Hyun Choi, Ahjeong Son
Objectives: Complexity and heterogeneity of soil samples have often implied the inclusion of purification steps in conventional DNA extraction for 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. Methods: Bead beating and centrifugation was used as the baseline (without purification) method for DNA extraction...
August 8, 2017: Environmental Health and Toxicology
https://www.readbyqxmd.com/read/28761476/prevalence-clinical-manifestations-and-genotyping-of-cryptosporidium-spp-in-patients-with-gastrointestinal-illnesses-in-western-iran
#4
Hamed Kiani, Ali Haghighi, Seyyed Javad Seyyedtabaei, Eznollah Azargashsb, Nozhat Zebardast, Niloofar Taghipour, Ali Rostami, Lihua Xiao
BACKGROUND: Cryptosporidium species are recognized as important gastrointestinal pathogens. This study was conducted to identify the prevalence, clinical manifestations and genotyping of Cryptosporidium spp. in patients with gastrointestinal illnesses (GIs) in western Iran. METHODS: Overall, 1301 fecal samples were collected from patients with GIs referred to the 12 clinical laboratories in Nahavand County, west of Iran. Modified Ziehl-Neelsen staining method was used to identify the oocysts...
April 2017: Iranian Journal of Parasitology
https://www.readbyqxmd.com/read/28737135/a-flotation-sieving-method-to-detect-echinococcus-multilocularis-and-toxocara-spp-eggs-in-soil-by-real-time-pcr
#5
Gérald Umhang, Matthieu Bastien, Camille Renault, Marine Faisse, Christophe Caillot, Jean-Marc Boucher, Vanessa Hormaz, Marie-Lazarine Poulle, Franck Boué
Soil can be a source of human infection by many zoonotic helminth species including Echinococcus multilocularis and Toxocara spp. The prevention of alveolar echinococcosis could be greatly improved through the identification of at-risk areas. Yet very few data are available about the detection of E. multilocularis in soil, while more studies have been reported for Toxocara spp. Identification of soil contamination by E. multilocularis eggs requires the use of specific methods. This study describes the development of a method for the detection of E...
2017: Parasite: Journal de la Société Française de Parasitologie
https://www.readbyqxmd.com/read/28732171/using-metagenomics-to-show-the-efficacy-of-forest-restoration-in-the-new-jersey-pine-barrens
#6
William D Eaton, Shadi Shokralla, Kathleen M McGee, Mehrdad Hajibabaei
The Franklin Parker Preserve within the New Jersey Pine Barrens contains 5,000 acres of wetlands habitat, including old-growth Atlantic White Cedar (or AWC; Chamaecyparis thyoides) swamps, cranberry bogs, and former cranberry bogs undergoing restoration into AWC forests. This study showed that the C-use efficiency was greater in the old-growth AWC soils than in soils from 8-year old mid-stage restored AWC stands, which were greater than found in soil from 4-year old AWC stands-the latter two stands being restored from long-term cranberry bogs...
July 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28728909/assessing-impacts-of-dna-extraction-methods-on-next-generation-sequencing-of-water-and-wastewater-samples
#7
Connie Walden, Franck Carbonero, Wen Zhang
Next Generation Sequencing (NGS) is increasingly affordable and easier to perform. However, standard protocols prior to the sequencing step are only available for few selected sample types. Here we investigated the impact of DNA extraction methods on the consistency of NGS results. Four commercial DNA extraction kits (QIAamp DNA Mini Kit, QIAamp DNA Stool Mini Kit, MO BIO Power Water Kit, and MO BIO Power Soil DNA Isolation Kit) were used on sample sources including lake water and wastewater, and sample types including planktonic and biofilm bacteria communities...
July 17, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28704064/nucleic-acid-extraction-from-synthetic-mars-analog-soils-for-in-situ-life-detection
#8
Angel Mojarro, Gary Ruvkun, Maria T Zuber, Christopher E Carr
Biological informational polymers such as nucleic acids have the potential to provide unambiguous evidence of life beyond Earth. To this end, we are developing an automated in situ life-detection instrument that integrates nucleic acid extraction and nanopore sequencing: the Search for Extra-Terrestrial Genomes (SETG) instrument. Our goal is to isolate and determine the sequence of nucleic acids from extant or preserved life on Mars, if, for example, there is common ancestry to life on Mars and Earth. As is true of metagenomic analysis of terrestrial environmental samples, the SETG instrument must isolate nucleic acids from crude samples and then determine the DNA sequence of the unknown nucleic acids...
July 13, 2017: Astrobiology
https://www.readbyqxmd.com/read/28702370/in-vitro-and-in-silico-characterization-of-metagenomic-soil-derived-cellulases-capable-of-hydrolyzing-oil-palm-empty-fruit-bunch
#9
Laura Marcela Palma Medina, Diana Catalina Ardila, María Mercedes Zambrano, Silvia Restrepo, Andrés Fernando González Barrios
Diversification of raw material for biofuel production is of interest to both academia and industry. One attractive substrate is a renewable lignocellulosic material such as oil palm (Elaeis guineensis Jacq.) empty fruit bunch (OPEFB), which is a byproduct of the palm oil industry. This study aimed to characterize cellulases active against this substrate. Cellulases with activity against OPEFB were identified from a metagenomic library obtained from DNA extracted from a high-Andean forest ecosystem. Our findings show that the highest cellulolytic activities were obtained at pH and temperature ranges of 4-10 and 30 °C-60 °C, respectively...
September 2017: Biotechnology Reports
https://www.readbyqxmd.com/read/28673033/comparison-of-four-dna-extraction-methods-for-comprehensive-assessment-of-16s-rrna-bacterial-diversity-in-marine-biofilms-using-high-throughput-sequencing
#10
Natàlia Corcoll, Tobias Österlund, Lucas Sinclair, Alexander Eiler, Erik Kristiansson, Thomas Backhaus, K Martin Eriksson
High-throughput DNA sequencing technologies are increasingly used for the metagenomic characterization of microbial biodiversity. However, basic issues, such as the choice of an appropriate DNA extraction method, are still not resolved for non-model microbial communities. This study evaluates four commonly used DNA extraction methods for marine periphyton biofilms in terms of DNA yield, efficiency, purity, integrity and resulting 16S rRNA bacterial diversity. Among the tested methods, the Plant DNAzol® Reagent (PlantDNAzol) and the Fast DNATM SPIN Kit for Soil (FastDNA Soil) methods were best suited to extract high quantities of DNA (77 - 130 μg g wet wt-1)...
June 29, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28667598/comparison-of-two-bacterial-dna-extraction-methods-from-non-polluted-and-polluted-soils
#11
Mélanie Mazziotti, Sonia Henry, Philippe Laval-Gilly, Antoine Bonnefoy, Jaïro Falla
DNA extraction from soil samples is a critical step for molecular biology analyses. The present study compared the efficiency of two DNA isolation methods from non-polluted and polluted soils with or without the presence of a plant. Both applied methods used chemical and physical lyses, but method 1 had an additional physical disruption. The main difference between these two methods was the humic acid purification technique as it was carried out during cell lysis for method 1 and after cell lysis for method 2...
July 1, 2017: Folia Microbiologica
https://www.readbyqxmd.com/read/28660454/an-improved-method-suitable-for-isolation-of-high-quality-metagenomic-dna-from-diverse-soils
#12
Sumit Kumar Verma, Himanshi Singh, Prakash C Sharma
Standardization of metagenomic DNA extraction protocol is a pre-requisite for a successful metagenomic study aiming to screen and exploit the variety of microorganisms inhabiting a particular soil environment. Six methods reported earlier were used for isolation of metagenomic DNA in the present study. These methods suffered with regard to either poor yield or quality of DNA. Therefore, we developed an improved method for isolation of high-molecular weight and good quality metagenomic DNA from different soil samples...
July 2017: 3 Biotech
https://www.readbyqxmd.com/read/28651337/preliminary-validation-of-a-method-combining-cultivation-and-cloning-based-approaches-to-monitor-airborne-bacteria
#13
Jenny Schäfer, Sarah Weiß, Udo Jäckel
It is already known that occupational exposure to bioaerosols or organic dust could be harmful for occupants, but mostly the correlation to occurring bacteria is missing. Especially, cultivation of bacteria from bioaerosols is important to get an insight on occurring and possibly infectious bacteria. These measures are highly time consuming and cost intensive. Therefore, to monitor bacterial diversity in bioaerosol samples and to avoid isolation procedures, an approach was applied using a combination of cultivation and cloning-based approach...
June 23, 2017: Annals of Work Exposures and Health
https://www.readbyqxmd.com/read/28646202/the-microbiome-of-endophytic-wood-colonizing-bacteria-from-pine-trees-as-affected-by-pine-wilt-disease
#14
Diogo Neves Proença, Romeu Francisco, Susanne Kublik, Anne Schöler, Gisle Vestergaard, Michael Schloter, Paula V Morais
Pine wilt disease (PWD) is a devastating forest disease present worldwide. In this study we analyzed the effects of the invasion of the pinewood nematode Bursaphelenchus xylophilus, the major pathogen causing PWD, on the endophytic microbiome of adult P. pinaster trees. Wood samples from trees with different degrees of PWD disease were collected at two sites (A and M) in Portugal. Endophytic bacteria were characterized based on directly extracted DNA by fingerprinting and barcoding using the 16S rRNA gene as marker...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28639891/antitumor-activity-of-a-rhodococcus-sp-lut0910-isolated-from-polluted-soil
#15
Xin-Guo Zhang, Zi-Yu Liu, Jin-Wen Liu, Yan-Long Zeng, Guang-Jun Guo, Qiao-Yun Sun
The actinomycetes strain, lut0910, was isolated from polluted soil and identified as the Rhodococcus species with 99% similarity based on the sequence analysis of 16S recombinant DNA. The extract of this strain demonstrated in vivo and in vitro antitumor activity. The treatment of two human cancer cell lines, hepatocellular carcinoma HepG2 and cervical carcinoma Hela cells, with the lut0910 extract caused the delay in cell propagation in a dose-dependent manner with an IC50 of 73.39 and 33.09 µg/mL, respectively...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28625159/dna-extraction-for-streamlined-metagenomics-of-diverse-environmental-samples
#16
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/28609744/a-whole-cell-bioreporter-assay-for-quantitative-genotoxicity-evaluation-of-environmental-samples
#17
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...
October 2017: Chemosphere
https://www.readbyqxmd.com/read/28567016/streptomyces-sp-mum212-as-a-source-of-antioxidants-with-radical-scavenging-and-metal-chelating-properties
#18
Loh Teng-Hern Tan, Kok-Gan Chan, Tahir Mehmood Khan, Sarah Ibrahim Bukhari, Surasak Saokaew, Acharaporn Duangjai, Priyia Pusparajah, Learn-Han Lee, Bey-Hing Goh
Reactive oxygen species and other radicals potentially cause oxidative damage to proteins, lipids, and DNA which may ultimately lead to various complications including mutations, carcinogenesis, neurodegeneration, cardiovascular disease, aging, and inflammatory disease. Recent reports demonstrate that Streptomyces bacteria produce metabolites with potent antioxidant activity that may be developed into therapeutic drugs to combat oxidative stress. This study shows that Streptomyces sp. MUM212 which was isolated from mangrove soil in Kuala Selangor, Malaysia, could be a potential source of antioxidants...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28559892/streptomyces-colonosanans-sp-nov-a-novel-actinobacterium-isolated-from-malaysia-mangrove-soil-exhibiting-antioxidative-activity-and-cytotoxic-potential-against-human-colon-cancer-cell-lines
#19
Jodi Woan-Fei Law, Hooi-Leng Ser, Acharaporn Duangjai, Surasak Saokaew, Sarah I Bukhari, Tahir M Khan, Nurul-Syakima Ab Mutalib, Kok-Gan Chan, Bey-Hing Goh, Learn-Han Lee
Streptomyces colonosanans MUSC 93J(T), a novel strain isolated from mangrove forest soil located at Sarawak, Malaysia. The bacterium was noted to be Gram-positive and to form light yellow aerial and vivid yellow substrate mycelium on ISP 2 agar. The polyphasic approach was used to determine the taxonomy of strain MUSC 93J(T) and the strain showed a range of phylogenetic and chemotaxonomic properties consistent with those of the members of the genus Streptomyces. Phylogenetic and 16S rRNA gene sequence analysis indicated that closely related strains include Streptomyces malachitofuscus NBRC 13059(T) (99...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28555427/optimization-of-high-yielding-protocol-for-dna-extraction-from-the-forest-rhizosphere-microbes
#20
Sadam D V Satyanarayana, M S R Krishna, Pindi Pavan Kumar
Soil is major reservoir for microbes and harbors a vast microbial diversity. Soil microbiota plays a pivotal role in biogeochemical cycles, bioremediation, and in health and disease states of humans, animals, and plants. It is imperative to understand the microbial signatures which are specific in such an ecosystem to unravel their potential role and impact on environment. During the recent years, exploration of soil microbial communities has been geared up with the advent of advanced sequencing technologies...
June 2017: 3 Biotech
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