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Soil microbial dna extraction

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https://www.readbyqxmd.com/read/29656601/culture-independent-analysis-of-hydrocarbonoclastic-bacterial-communities-in-environmental-samples-during-oil-bioremediation
#1
Narjes Dashti, Nedaa Ali, Samar Salamah, Majida Khanafer, Ghada Al-Shamy, Husain Al-Awadhi, Samir S Radwan
To analyze microbial communities in environmental samples, this study combined Denaturing Gradient Gel Electrophoresis of amplified 16S rRNA-genes in total genomic DNA extracts from those samples with gene sequencing. The environmental samples studied were oily seawater and soil samples, that had been bioaugmented with natural materials rich in hydrocarbonoclastic bacteria. This molecular approach revealed much more diverse bacterial taxa than the culture-dependent method we had used in an earlier study for the analysis of the same samples...
April 15, 2018: MicrobiologyOpen
https://www.readbyqxmd.com/read/29530467/tick-microbial-communities-within-enriched-extracts-of-amblyomma-maculatum
#2
A S Varela-Stokes, S H Park, J V Stokes, N A Gavron, S I Lee, G M Moraru, S C Ricke
Our objective of this study was to explore the bacterial microbiome in fresh or fresh-frozen adult Amblyomma maculatum (Gulf Coast ticks) using extracts enriched for microbial DNA. We collected 100 questing adult A. maculatum, surface disinfected them, and extracted DNA from individual ticks collected the same day or after storage at -80 °C. Because only extracts with microbial DNA concentrations above 2 ng/μL were considered suitable for individual analysis, we expected fewer samples to meet these requirements...
March 1, 2018: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/29527192/bacterial-preferences-for-specific-soil-particle-size-fractions-revealed-by-community-analyses
#3
Michael Hemkemeyer, Anja B Dohrmann, Bent T Christensen, Christoph C Tebbe
Genetic fingerprinting demonstrated in previous studies that differently sized soil particle fractions (PSFs; clay, silt, and sand with particulate organic matter (POM)) harbor microbial communities that differ in structure, functional potentials and sensitivity to environmental conditions. To elucidate whether specific bacterial or archaeal taxa exhibit preference for specific PSFs, we examined the diversity of PCR-amplified 16S rRNA genes by high-throughput sequencing using total DNA extracted from three long-term fertilization variants (unfertilized, fertilized with minerals, and fertilized with animal manure) of an agricultural loamy sand soil and their PSFs...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29497412/metagenomic-analysis-of-a-biphenyl-degrading-soil-bacterial-consortium-reveals-the-metabolic-roles-of-specific-populations
#4
Daniel Garrido-Sanz, Javier Manzano, Marta Martín, Miguel Redondo-Nieto, Rafael Rivilla
Polychlorinated biphenyls (PCBs) are widespread persistent pollutants that cause several adverse health effects. Aerobic bioremediation of PCBs involves the activity of either one bacterial species or a microbial consortium. Using multiple species will enhance the range of PCB congeners co-metabolized since different PCB-degrading microorganisms exhibit different substrate specificity. We have isolated a bacterial consortium by successive enrichment culture using biphenyl (analog of PCBs) as the sole carbon and energy source...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29453765/statistical-assessment-of-dna-extraction-methodology-for-culture-independent-analysis-of-microbial-community-associated-with-diverse-environmental-samples
#5
Rishi Mahajan, Sampan Attri, Kavita Sharma, Niharika Singh, Deepika Sharma, Gunjan Goel
Cost-effectiveness, quality, time-effectiveness and ease of the methodology are the most crucial factors in isolating quality DNA from wide variety of samples. Thus, research efforts focusing on the development of an efficient DNA extraction protocol is the need of the hour. The present study therefore, focuses on development of an efficient, rapid and free of inhibitory substances based methodology for extracting metagenomic DNA from diverse environmental samples viz. anaerobic biogas digesta, ruminant stomach, human feces, soil, and microbial starter cultures used for preparation of fermented food...
February 16, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29359695/use-of-amplification-fragment-length-polymorphism-to-genotype-pseudomonas-stutzeri-strains-following-exposure-to-ultraviolet-light-a
#6
Lisa Lombardi, Marina Zoppo, Cosmeri Rizzato, Colin Gerard Egan, Roberto Scarpato, Arianna Tavanti
Changes in ultraviolet light radiation can act as a selective force on the genetic and physiological traits of a microbial community. Two strains of the common soil bacterium Pseudomonas stutzeri, isolated from aquifer cores and from human spinal fluid were exposed to ultraviolet light. Amplification length polymorphism analysis (AFLP) was used to genotype this bacterial species and evaluate the effect of UVA-exposure on genomic DNA extracted from 18 survival colonies of the two strains compared to unexposed controls...
March 30, 2017: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/29322917/identification-of-natural-antimicrobial-peptides-from-bacteria-through-metagenomic-and-metatranscriptomic-analysis-of-high-throughput-transcriptome-data-of-taiwanese-oolong-teas
#7
Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K Robert Lai, Tzong-Yi Lee
BACKGROUND: Anti-microbial peptides (AMPs), naturally encoded by genes and generally containing 12-100 amino acids, are crucial components of the innate immune system and can protect the host from various pathogenic bacteria and viruses. In recent years, the widespread use of antibiotics has resulted in the rapid growth of antibiotic-resistant microorganisms that often induce critical infection and pathogenesis. Recently, the advent of high-throughput technologies has led molecular biology into a data surge in both the amount and scope of data...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29319522/characterization-of-microbial-communities-in-acidified-sulfur-containing-soils
#8
Grzegorz Czerwonka, Iwona Konieczna, Paulina Żarnowiec, Artur Zieliński, Agnieszka Malinowska-Gniewosz, Agnieszka Gałuszka, Zdzisław Migaszewski, Wiesław Kaca
Over a period of three years, microbial communities in acidified soil with high sulfur content were analyzed. In soil water extracts ureolytic, proteolytic, oxidoreductive, and lipolytic activity were detected. The presented results indicate that the enzymatic activity of soil microbial communities varied considerably over time. Isolated 26 (80%) bacterial strains belonged to genus Bacillus sp. and were identified by cultivation and 16S rRNA methods. The commercially available procedures for bacterial DNA isolation from acidified soil failed, therefore a new, specific DNA isolation method was established...
December 4, 2017: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/29117585/metagenomics-profiling-for-assessing-microbial-diversity-in-both-active-and-closed-landfills
#9
Mohamad Yusof Zainun, Khanom Simarani
The municipal landfill is an example of human-made environment that harbours some complex diversity of microorganism communities. To evaluate this complexity, the structures of bacterial communities in active (operational) and closed (non-operational) landfills in Malaysia were analysed with culture independent metagenomics approaches. Several points of soil samples were collected from 0 to 20cm depth and were subjected to physicochemical test, such as temperature, pH, and moisture content. In addition, the heavy metal contamination was determined by using ICPMS...
March 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29106502/isolation-of-highly-thermostable-%C3%AE-xylosidases-from-a-hot-spring-soil-microbial-community-using-a-metagenomic-approach
#10
Masaru Sato, Migiwa Suda, Jiro Okuma, Tomohiko Kato, Yoshitsugu Hirose, Asuka Nishimura, Yasuhiko Kondo, Daisuke Shibata
The DNA extracted from a high-temperature environment in which micro-organisms are living will be a good source for the isolation of thermostable enzymes. Using a metagenomic approach, we aimed to isolate thermostable β-xylosidases that will be exploited for biofuel production from lignocellulosic biomass. DNA samples obtained from the soil near a spout of a hot spring (70°C, pH7.2) were subjected to sequencing, which generated a total of 84.2 Gbp with 967,925 contigs of >500 bp in length. Similarity search for β-xylosidase in the contigs revealed the presence of 168 candidate sequences, each of which may have arisen from more than one gene...
December 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29104570/characterization-of-bacterial-and-fungal-community-dynamics-by-high-throughput-sequencing-hts-metabarcoding-during-flax-dew-retting
#11
Christophe Djemiel, Sébastien Grec, Simon Hawkins
Flax dew-retting is a key step in the industrial extraction of fibers from flax stems and is dependent upon the production of a battery of hydrolytic enzymes produced by micro-organisms during this process. To explore the diversity and dynamics of bacterial and fungal communities involved in this process we applied a high-throughput sequencing (HTS) DNA metabarcoding approach (16S rRNA/ITS region, Illumina Miseq) on plant and soil samples obtained over a period of 7 weeks in July and August 2014. Twenty-three bacterial and six fungal phyla were identified in soil samples and 11 bacterial and four fungal phyla in plant samples...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28956398/-discovery-and-analysis-of-staphylococcus-aureus-biofilm-inhibitors-using-functional-metagenomics-approach
#12
Ying Zhu, Shumao Chai, Mingming Cao, Shaochen Wang, Zhiyang Feng
Although most microbes are not readily cultured in the lab, microbial DNA can be extracted directly from an environmental sample and be functionally expressed in a suitable host for natural products discovery, and this approach has been termed "metagenomics". An E'mei Mountain soil metagenomic library was constructed using an Escherichia coli-Streptomyces shuttle vector for functional based screening of anti-bacterial clones in Streptomyces albus host. Two active clones were obtained and their fermentation broths were studied for the inhibitory effect on Staphylococcus aureus biofilm...
September 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
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
#13
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-utilizing-plant-derived-carbon-in-the-rhizosphere-of-triticum-aestivum-change-in-different-depths-of-an-arable-soil
#14
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 utilize 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 greenhouse 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 isopycnic density gradient centrifugation of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing...
December 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
#15
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/28803266/a-degradome-based-polymerase-chain-reaction-to-resolve-the-potential-of-environmental-samples-for-2-4-dichlorophenol-biodegradation
#16
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...
December 2017: Current Microbiology
https://www.readbyqxmd.com/read/28798742/preservation-and-significance-of-extracellular-dna-in-ferruginous-sediments-from-lake-towuti-indonesia
#17
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
#18
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/28555427/optimization-of-high-yielding-protocol-for-dna-extraction-from-the-forest-rhizosphere-microbes
#19
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
#20
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
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