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Dna extraction soil

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https://www.readbyqxmd.com/read/28919882/effects-of-soil-pre-treatment-with-basamid%C3%A2-granules-brassica-juncea-raphanus-sativus-and-tagetes-patula-on-bacterial-and-fungal-communities-at-two-apple-replant-disease-sites
#1
Bunlong Yim, Heike Nitt, Andreas Wrede, Samuel Jacquiod, Søren J Sørensen, Traud Winkelmann, Kornelia Smalla
Nurseries producing apple and rose rootstock plants, apple orchards as well as rose production often experience replanting problems after several cultivations at the same site when a chemical soil disinfectant is not applied. The etiology of apple and rose replanting problems is most likely caused by soil-borne pathogen complex, defined as "replant disease (RD)". Symptoms typical of RD are reduced shoot and root growth, a smaller leaf area, a significant decrease in plant biomass, yield and fruit quality and a shorter life span...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28892269/bacteria-utilising-plant-derived-carbon-in-the-rhizosphere-of-triticum-aestivum-change-in-different-depths-of-an-arable-soil
#2
Marie Uksa, Franz Buegger, Silvia Gschwendtner, Tillmann Lueders, Susanne Kublik, Timo Kautz, Miriam Athmann, Ulrich Köpke, Jean Charles Munch, Michael Schloter, Doreen Fischer
Root exudates shape microbial communities at the plant soil interface. Here we compared bacterial communities that utilise plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a green house using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant derived carbon, (13) C-CO2 labelling of plants was performed for two weeks at the EC50 stage, followed by stable isotope probing of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing...
September 11, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28861443/biochemical-characteristics-of-a-free-cyanide-and-total-nitrogen-assimilating-fusarium-oxysporum-ekt01-02-isolate-from-cyanide-contaminated-soil
#3
Enoch A Akinpelu, Adewole T Adetunji, Seteno K O Ntwampe, Felix Nchu, Lukhanyo Mekuto
Sustainability of nutrient requirements for microbial proliferation on a large scale is a challenge in bioremediation processes. This article presents data on biochemical properties of a free cyanide resistant and total nitrogen assimilating fungal isolate from the rhizosphere of Zeamays (maize) growing in soil contaminated with a cyanide-based pesticide. DNA extracted from this isolate were PCR amplified using universal primers; TEF1-α and ITS. The raw sequence files are available on the NCBI database. Characterisation using biochemical data was obtained using colorimetric reagents analysed with VITEK(®) 2 software version 7...
October 2017: Data in Brief
https://www.readbyqxmd.com/read/28818754/daily-thanatomicrobiome-changes-in-soil-as-an-approach-of-postmortem-interval-estimation-an-ecological-perspective
#4
Joe Adserias-Garriga, Marta Hernández, Narciso M Quijada, David Rodríguez Lázaro, Dawnie Steadman, Jesús Garcia-Gil
Understanding human decomposition is critical for its use in postmortem interval (PMI) estimation, having a significant impact on forensic investigations. In recognition of the need to establish the scientific basis for PMI estimation, several studies on decomposition have been carried out in the last years. The aims of the present study were: (i) to identify soil microbiota communities involved in human decomposition through high-throughput sequencing (HTS) of DNA sequences from the different bacteria, (ii) to monitor quantitatively and qualitatively the decay of such signature species, and (iii) to describe succesional changes in bacterial populations from the early putrefaction state until skeletonization...
September 2017: Forensic Science International
https://www.readbyqxmd.com/read/28817927/identification-of-biosynthetic-gene-clusters-from-metagenomic-libraries-using-pptase-complementation-in-a-streptomyces-host
#5
J Kipchirchir Bitok, Christophe Lemetre, Melinda A Ternei, Sean F Brady
The majority of environmental bacteria are not readily cultured in the lab, leaving the natural products they make inaccessible using culture-dependent discovery methods. Cloning and heterologous expression of DNA extracted from environmental samples (environmental DNA, eDNA) provides a means of circumventing this discovery bottleneck. To facilitate the identification of clones containing biosynthetic gene clusters, we developed a model heterologous expression reporter strain Streptomyces albus::bpsA ΔPPTase...
September 1, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28803266/a-degradome-based-polymerase-chain-reaction-to-resolve-the-potential-of-environmental-samples-for-2-4-dichlorophenol-biodegradation
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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...
August 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
#14
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
#15
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 characterisation 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 FastDNA® SPIN Kit for Soil (FastDNA Soil) methods were best suited to extract high quantities of DNA (77-130 μg g wet wt-1)...
August 1, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28667598/comparison-of-two-bacterial-dna-extraction-methods-from-non-polluted-and-polluted-soils
#16
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
#17
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
#18
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
#19
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
#20
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
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