keyword
MENU ▼
Read by QxMD icon Read
search

Soil microbial dna extraction

keyword
https://www.readbyqxmd.com/read/29921664/how-when-and-where-relic-dna-affects-microbial-diversity
#1
J T Lennon, M E Muscarella, S A Placella, B K Lehmkuhl
Extracellular or "relic" DNA is one of the largest pools of nucleic acids in the biosphere. Relic DNA can influence a number of important ecological and evolutionary processes, but it may also affect estimates of microbial abundance and diversity, which has implications for understanding environmental, engineered, and host-associated ecosystems. We developed models capturing the fundamental processes that regulate the size and composition of the relic DNA pools to identify scenarios leading to biased estimates of biodiversity...
June 19, 2018: MBio
https://www.readbyqxmd.com/read/29849646/illumina-miseq-sequencing-for-preliminary-analysis-of-microbiome-causing-primary-endodontic-infections-in-egypt
#2
Sally Ali Tawfik, Marwa Mohamed Azab, Ali Abdellah Abdelrahman Ahmed, Dalia Mukhtar Fayyad
The use of high throughput next generation technologies has allowed more comprehensive analysis than traditional Sanger sequencing. The specific aim of this study was to investigate the microbial diversity of primary endodontic infections using Illumina MiSeq sequencing platform in Egyptian patients. Samples were collected from 19 patients in Suez Canal University Hospital (Endodontic Department) using sterile # 15K file and paper points. DNA was extracted using Mo Bio power soil DNA isolation extraction kit followed by PCR amplification and agarose gel electrophoresis...
2018: International Journal of Microbiology
https://www.readbyqxmd.com/read/29846778/isolation-of-high-molecular-weight-and-humic-acid-free-metagenomic-dna-from-lignocellulose-rich-samples-compatible-for-direct-fosmid-cloning
#3
Abhijit Sar, Srikanta Pal, Bomba Dam
Activity-based screening of metagenomic DNA libraries is a promising approach to fish out genes encoding novel bioactive compounds/enzymes of industrial importance. The starting point of such functional screening in fosmid vectors is isolation of high molecular weight (HMW) DNA of sufficient purity from diverse environments. Metagenomic DNA isolation protocols mostly employ mechanical cell lysis that yields fragmented DNA. Those established for HMW DNA using enzymatic lysis have not considered samples with high lignocellulose or humic acid content...
May 30, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29807296/microbial-functional-responses-to-long-term-anthropogenic-impact-in-mangrove-soils
#4
Lucélia Cabral, Sanderson Tarciso Pereira de Sousa, Gileno Vieira Lacerda Júnior, Erik Hawley, Fernando Dini Andreote, Matthias Hess, Valéria Maia de Oliveira
Mangroves are coastal ecosystems of transition between terrestrial and marine environments, that have been particularly contaminated in the last decades. Organic compounds are part of these contaminants, which have increased in the environment due to industrial activities and accidental oil spills. These contaminants are toxic to higher organisms, but microorganisms can metabolize most of these compounds and thus offer a tool for bioremediation purposes. The aim of the present study was to characterize the microbial potential and activity for degradation of aromatic compounds in sediment samples from mangroves using metagenomic and metatranscriptomic approaches...
May 25, 2018: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/29782021/exploring-the-root-microbiome-extracting-bacterial-community-data-from-the-soil-rhizosphere-and-root-endosphere
#5
Tuesday Simmons, Daniel F Caddell, Siwen Deng, Devin Coleman-Derr
The intimate interaction between plant host and associated microorganisms is crucial in determining plant fitness, and can foster improved tolerance to abiotic stresses and diseases. As the plant microbiome can be highly complex, low-cost, high-throughput methods such as amplicon-based sequencing of the 16S rRNA gene are often preferred for characterizing its microbial composition and diversity. However, the selection of appropriate methodology when conducting such experiments is critical for reducing biases that can make analysis and comparisons between samples and studies difficult...
May 2, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29727935/recycling-organic-residues-in-agriculture-impacts-soil-borne-microbial-community-structure-function-and-n-2-o-emissions
#6
Afnan Khalil Ahmad Suleiman, Késia Silva Lourenço, Leonardo Machado Pitombo, Lucas William Mendes, Luiz Fernando Wurdig Roesch, Agata Pijl, Janaína Braga Carmo, Heitor Cantarella, Eiko Eurya Kuramae
Recycling residues is a sustainable alternative to improve soil structure and increase the stock of nutrients. However, information about the magnitude and duration of disturbances caused by crop and industrial wastes on soil microbial community structure and function is still scarce. The objective of this study was to investigate how added residues from industry and crops together with nitrogen (N) fertiliser affect the microbial community structure and function, and nitrous oxide (N2 O) emissions. The experimental sugarcane field had the following treatments: (I) control with nitrogen, phosphorus, and potassium (NPK), (II) sugarcane straw with NPK, (III) vinasse (by-product of ethanol industry) with NP, and (IV) vinasse plus sugarcane straw with NP...
August 1, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29656601/culture-independent-analysis-of-hydrocarbonoclastic-bacterial-communities-in-environmental-samples-during-oil-bioremediation
#7
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
#8
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...
May 2018: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/29527192/bacterial-preferences-for-specific-soil-particle-size-fractions-revealed-by-community-analyses
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
keyword
keyword
56890
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"