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Soil microbial dna extraction

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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/28673033/comparison-of-four-dna-extraction-methods-for-comprehensive-assessment-of-16s-rrna-bacterial-diversity-in-marine-biofilms-using-high-throughput-sequencing
#3
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/28555427/optimization-of-high-yielding-protocol-for-dna-extraction-from-the-forest-rhizosphere-microbes
#4
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
https://www.readbyqxmd.com/read/28523377/mining-lipolytic-enzymes-in-community-dna-from-high-andean-soils-using-a-targeted-approach
#5
Daniel Borda-Molina, José Salvador Montaña, María Mercedes Zambrano, Sandra Baena
Microbial enrichments cultures are a useful strategy to speed up the search for enzymes that can be employed in industrial processes. Lipases have gained special attention because they show unique properties such as: broad substrate specificity, enantio- and regio-selectivity and stability in organic solvents. A major goal is to identify novel lipolytic enzymes from microorganisms living in cold extreme environments such as high Andean soils, of relevance to our study being their capability be used in industrial processes...
August 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28516483/capabilities-and-limitations-of-dgge-for-the-analysis-of-hydrocarbonoclastic-prokaryotic-communities-directly-in-environmental-samples
#6
Dina M Al-Mailem, Mayada K Kansour, Samir S Radwan
Prokaryotic communities in pristine and oil-contaminated desert soil, seawater, and hypersaline coastal soil were analyzed using culture-dependent and culture-independent approaches. The former technique was the dilution-plating method. For the latter, total genomic DNA was extracted and the 16S rRNA genes were amplified using a universal bacterial primer pair and primer pairs specific for Actinobacteria, Gammaproteobacteria, and Archaea. The amplicons were resolved using denaturing gradient gel electrophoresis (DGGE) and sequenced, and the sequences were compared to those in GenBank...
May 18, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28480140/high-diversity-and-suggested-endemicity-of-culturable-actinobacteria-in-an-extremely-oligotrophic-desert-oasis
#7
Hector Fernando Arocha-Garza, Ricardo Canales-Del Castillo, Luis E Eguiarte, Valeria Souza, Susana De la Torre-Zavala
The phylum Actinobacteria constitutes one of the largest and anciently divergent phyla within the Bacteria domain. Actinobacterial diversity has been thoroughly researched in various environments due to its unique biotechnological potential. Such studies have focused mostly on soil communities, but more recently marine and extreme environments have also been explored, finding rare taxa and demonstrating dispersal limitation and biogeographic patterns for Streptomyces. To test the distribution of Actinobacteria populations on a small scale, we chose the extremely oligotrophic and biodiverse Cuatro Cienegas Basin (CCB), an endangered oasis in the Chihuahuan desert to assess the diversity and uniqueness of Actinobacteria in the Churince System with a culture-dependent approach over a period of three years, using nine selective media...
2017: PeerJ
https://www.readbyqxmd.com/read/28397264/population-densities-of-indigenous-acidobacteria-change-in-the-presence-of-plant-growth-promoting-rhizobacteria-pgpr-in-rhizosphere
#8
Sadaf Kalam, Subha Narayan Das, Anirban Basu, Appa Rao Podile
Rhizosphere microbial community has diverse metabolic capabilities and plays a crucial role in maintaining plant health. Oligotrophic plant growth promoting rhizobacteria (PGPR), along with difficult-to-culture microbial fractions, might be involved synergistically in microbe-microbe and plant-microbe interactions in the rhizosphere. Among the difficult-to-culture microbial fractions, Acidobacteria constitutes the most dominant phylum thriving in rhizospheric soils. We selected effective PGPR for tomato and black gram and studied their effect on population densities of acidobacterial members...
April 11, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28340454/pea-cultivar-and-wheat-residues-affect-carbon-nitrogen-dynamics-in-pea-triticale-intercropping-a-microcosms-approach
#9
Antonella Scalise, Valentini A Pappa, Antonio Gelsomino, Robert M Rees
The underlying mechanisms by which legume cultivars contribute to nitrous oxide (N2O) generation are poorly understood. The aim of the present study was to explore the effects of two pea cultivars (Zero4 and Nitouche) intercropped with triticale, with or without wheat (Triticum aestivum) residues incorporation, on soil C and N dynamics, on bacterial community structure and their links with N2O emissions. Monocrops and bare soil (no plant) treatments were used as an additional control in order to account for the level of mineralisation between treatments...
March 21, 2017: Science of the Total Environment
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
#10
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/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
#11
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/28217901/the-choice-of-the-dna-extraction-method-may-influence-the-outcome-of-the-soil-microbial-community-structure-analysis
#12
Sylwia Zielińska, Piotr Radkowski, Aleksandra Blendowska, Agnieszka Ludwig-Gałęzowska, Joanna M Łoś, Marcin Łoś
Metagenomics approaches and recent improvements in the next-generation sequencing methods, have become a method of choice in establishing a microbial population structure. Many commercial soil DNA extraction kits are available and due to their efficiency they are replacing traditional extraction protocols. However, differences in the physicochemical properties of soil samples require optimization of DNA extraction techniques for each sample separately. The aim of this study was to compare the efficiency, quality, and diversity of genetic material extracted with the use of commonly used kits...
August 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28203533/modification-of-extraction-method-for-community-dna-isolation-from-salt-affected-compact-wasteland-soil-samples
#13
Purvi Zaveri, Rushika Patel, Meghavi Patel, Devki Sarodia, Nasreen S Munshi
To overcome the issue of interferences by salt and compactness in release of bacterial cell required for lysis, method described by Yeates et al. (1998), was optimized for isolation of genomic material (Deoxyribo Nucleic Acid, DNA) from soil microbial community by addition of Al(NH4)SO4. Very low total viable count was observed in the samples tested and hence use of higher amount of soil is required primarily for DNA isolation from wasteland soils. The method proves itself efficient where commercially available bead beating and enzymatic lysis methods could not give isolation of any amount of community genomic DNA due to compact nature and salt concentrations present in soil...
2017: MethodsX
https://www.readbyqxmd.com/read/28168105/successive-dna-extractions-improve-characterization-of-soil-microbial-communities
#14
Mauricio R Dimitrov, Annelies J Veraart, Mattias de Hollander, Hauke Smidt, Johannes A van Veen, Eiko E Kuramae
Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied...
2017: PeerJ
https://www.readbyqxmd.com/read/28093673/metagenomic-insights-into-effects-of-spent-engine-oil-perturbation-on-the-microbial-community-composition-and-function-in-a-tropical-agricultural-soil
#15
Lateef B Salam, Sunday O Obayori, Francisca O Nwaokorie, Aisha Suleiman, Raheemat Mustapha
Analyzing the microbial community structure and functions become imperative for ecological processes. To understand the impact of spent engine oil (SEO) contamination on microbial community structure of an agricultural soil, soil microcosms designated 1S (agricultural soil) and AB1 (agricultural soil polluted with SEO) were set up. Metagenomic DNA extracted from the soil microcosms and sequenced using Miseq Illumina sequencing were analyzed for their taxonomic and functional properties. Taxonomic profiling of the two microcosms by MG-RAST revealed the dominance of Actinobacteria (23...
March 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28074923/bacterial-community-composition-in-costal-dunes-of-the-mediterranean-along-a-gradient-from-the-sea-shore-to-the-inland
#16
Haggai Wasserstrom, Susanne Kublik, Rachel Wasserstrom, Stefanie Schulz, Michael Schloter, Yosef Steinberger
Sand dunes are unique ecosystems with distinct features which limited the accumulation of biomass. The distance from seashore affects both the physical properties of the sand dunes and the biota living above- and below ground. The goal of the present study was to determine the effects of the distance from shore to inland on soil bacterial community composition during wet and dry season. We studied a chronosequence of sites close to the eastern Mediterranean coast. Bacterial diversity was assessed using directly extracted DNA from soil samples and 16 S ribosomal RNA gene fingerprinting...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28050848/microbial-communities-in-pyrene-amended-soil-compost-mixture-and-fertilized-soil
#17
Iris K U Adam, Márcia Duarte, Jananan Pathmanathan, Anja Miltner, Thomas Brüls, Matthias Kästner
Polycyclic aromatic hydrocarbons are distributed ubiquitously in the environment and form metabolites toxic to most organisms. Organic amendment of PAH contaminated soil with compost and farmyard manure has proven to be efficient for PAH bioremediation mediated by native microorganisms, even though information on the identity of PAH degraders in organic-amended soil is still scarce. Here we provide molecular insight into the bacterial communities in soil amended with compost or farmyard manure for which the degradation mass balances of (13)C-labeled pyrene have been recently published and assess the relevant bacterial genera capable of degrading pyrene as a model PAH...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28028549/ssunique-detecting-sequence-novelty-in-microbiome-surveys
#18
Michael D J Lynch, Josh D Neufeld
High-throughput sequencing of small-subunit (SSU) rRNA genes has revolutionized understanding of microbial communities and facilitated investigations into ecological dynamics at unprecedented scales. Such extensive SSU rRNA gene sequence libraries, constructed from DNA extracts of environmental or host-associated samples, often contain a substantial proportion of unclassified sequences, many representing organisms with novel taxonomy (taxonomic "blind spots") and potentially unique ecology. Indeed, these novel taxonomic lineages are associated with so-called microbial "dark matter," which is the genomic potential of these lineages...
November 2016: MSystems
https://www.readbyqxmd.com/read/27660624/the-willow-microbiome-is-influenced-by-soil-petroleum-hydrocarbon-concentration-with-plant-compartment-specific-effects
#19
Stacie Tardif, Étienne Yergeau, Julien Tremblay, Pierre Legendre, Lyle G Whyte, Charles W Greer
The interaction between plants and microorganisms, which is the driving force behind the decontamination of petroleum hydrocarbon (PHC) contamination in phytoremediation technology, is poorly understood. Here, we aimed at characterizing the variations between plant compartments in the microbiome of two willow cultivars growing in contaminated soils. A field experiment was set-up at a former petrochemical plant in Canada and after two growing seasons, bulk soil, rhizosphere soil, roots, and stems samples of two willow cultivars (Salix purpurea cv...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27627898/modified-method-for-the%C3%A2-extraction-of-mrna-from-paddy-soils
#20
Hongling Qin, Xiangbi Chen, Yafang Tang, Haijun Hou, Rong Sheng, Jinlin Shen
OBJECTIVE: Paddy soils contain relatively greater organic matter and water contents than other soils thereby limiting effective mRNA extraction. A modification of the conventional mRNA soil extraction method specific to paddy soils is described. RESULTS: Two main modifications for co-extraction of DNA and RNA are: (1) addition of 20 % (w/v) sodium dodecyl sulphate to 10 % (w/v) hexadecyltrimethylammonium bromide extraction buffer, and (2) fresh soil, initially frozen at -80 °C, is immediately immersed in extraction buffer...
December 2016: Biotechnology Letters
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