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Dna extraction soil

Joseph B DeShields, Rachel A Bomberger, James W Woodhall, David L Wheeler, Natalia Moroz, Dennis A Johnson, Kiwamu Tanaka
On-site diagnosis of plant diseases can be a useful tool for growers for timely decisions enabling the earlier implementation of disease management strategies that reduce the impact of the disease. Presently in many diagnostic laboratories, the polymerase chain reaction (PCR), particularly real-time PCR, is considered the most sensitive and accurate method for plant pathogen detection. However, laboratory-based PCRs typically require expensive laboratory equipment and skilled personnel. In this study, soil-borne pathogens of potato are used to demonstrate the potential for on-site molecular detection...
February 23, 2018: Journal of Visualized Experiments: JoVE
Hector Urbina, Martin F Breed, Weizhou Zhao, Kanaka Lakshmi Gurrala, Siv G E Andersson, Jon Ågren, Sandra Baldauf, Anna Rosling
Biotic and abiotic conditions in soil pose major constraints on growth and reproductive success of plants. Fungi are important agents in plant soil interactions but the belowground mycobiota associated with plants remains poorly understood. We grew one genotype each from Sweden and Italy of the widely-studied plant model Arabidopsis thaliana. Plants were grown under controlled conditions in organic topsoil local to the Swedish genotype, and harvested after ten weeks. Total DNA was extracted from three belowground compartments: endosphere (sonicated roots), rhizosphere and bulk soil, and fungal communities were characterized from each by amplification and sequencing of the fungal barcode region ITS2...
April 2018: Fungal Biology
J R Bowers, K L Parise, E J Kelley, D Lemmer, J M Schupp, E M Driebe, D M Engelthaler, P Keim, B M Barker
Coccidioides immitis and Coccidioides posadasii are soil fungi endemic to desert regions of the southwestern United States, and the causative agents of valley fever, or coccidioidomycosis. Studies have shown that the distribution of Coccidioides in soils is sporadic and cannot be explained by soil characteristics alone, suggesting that biotic and other abiotic factors should be examined. However, tools to reliably and robustly screen the large number of soils needed to investigate these potential associations have not been available...
March 8, 2018: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
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
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
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
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
Bradley M Hover, Seong-Hwan Kim, Micah Katz, Zachary Charlop-Powers, Jeremy G Owen, Melinda A Ternei, Jeffrey Maniko, Andreia B Estrela, Henrik Molina, Steven Park, David S Perlin, Sean F Brady
Despite the wide availability of antibiotics, infectious diseases remain a leading cause of death worldwide1 . In the absence of new therapies, mortality rates due to untreatable infections are predicted to rise more than tenfold by 2050. Natural products (NPs) made by cultured bacteria have been a major source of clinically useful antibiotics. In spite of decades of productivity, the use of bacteria in the search for new antibiotics was largely abandoned due to high rediscovery rates2,3 . As only a fraction of bacterial diversity is regularly cultivated in the laboratory and just a fraction of the chemistries encoded by cultured bacteria are detected in fermentation experiments, most bacterial NPs remain hidden in the global microbiome...
February 12, 2018: Nature Microbiology
Kelly A Meiklejohn, Megan L Jackson, Libby A Stern, James M Robertson
Soil is often collected from a suspect's tire, vehicle, or shoes during a criminal investigation and subsequently submitted to a forensic laboratory for analysis. Plant and insect material recovered in such samples is rarely analyzed, as morphological identification is difficult. In this study, DNA barcoding was used for taxonomic identifications by targeting the gene regions known to permit discrimination in plants [maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL)] and insects [cytochrome oxidase subunit I (COI)]...
February 8, 2018: International Journal of Legal Medicine
Syrie M Hermans, Hannah L Buckley, Gavin Lear
Using environmental DNA (eDNA) to assess the distribution of micro- and macro-organisms is becoming increasingly popular. However, the comparability and reliability of these studies is not well understood as we lack evidence on how different DNA extraction methods affect the detection of different organisms, and how this varies among sample types. Our aim was to quantify biases associated with six DNA extraction methods, and identify one which is optimal for eDNA research targeting multiple organisms and sample types...
February 2, 2018: Molecular Ecology Resources
Chad W McKinney, Robert S Dungan, Amber Moore, April B Leytem
Animal manures are commonly used to enhance soil fertility, but there are growing concerns over the impact of this practice on the development and dissemination of antibiotic resistance. The aim of this field study was to determine the effect of annual dairy manure applications on the occurrence and abundance of antibiotic resistance genes (ARGs) in an agricultural soil during four years of crop production. Treatments included: i) control (no fertilizer or manure); ii) inorganic fertilizer; and iii) dairy manure at three application rates...
January 19, 2018: FEMS Microbiology Ecology
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
Solomia Susulovska, Pablo Castillo, Antonio Archidona-Yuste
Seven needle nematode species of the genus Longidorus have been reported in Ukraine. Nematological surveys for needle nematodes were carried out in Ukraine between 2016 and 2017 and two nematode species of Longidorus (L. caespiticola and L. poessneckensis) were collected from natural and anthropogenically altered habitats on the territory of Opillia and Zakarpattia in Ukraine. Nematodes were extracted from 500 cm3 of soil by modified sieving and decanting method. Extracted specimens were processed to glycerol and mounted on permanent slides and subsequently identified morphologically and molecularly...
December 2017: Journal of Nematology
Marina Papaiakovou, Nils Pilotte, Ben Baumer, Jessica Grant, Kristjana Asbjornsdottir, Fabian Schaer, Yan Hu, Raffi Aroian, Judd Walson, Steven A Williams
BACKGROUND: Proper collection and storage of fecal samples is necessary to guarantee the subsequent reliability of DNA-based soil-transmitted helminth diagnostic procedures. Previous research has examined various methods to preserve fecal samples for subsequent microscopic analysis or for subsequent determination of overall DNA yields obtained following DNA extraction. However, only limited research has focused on the preservation of soil-transmitted helminth DNA in stool samples stored at ambient temperature or maintained in a cold chain for extended periods of time...
January 2018: PLoS Neglected Tropical Diseases
Andrew Scott, Yuan-Ching Tien, Craig F Drury, W Daniel Reynolds, Edward Topp
The impact of amendment with swine manure composts (SMC), yard waste compost (YWC), or food waste compost (FWC) on the abundance of antibiotic resistance genes in soil was evaluated. Following a commercial-scale application of the composts in a field experiment, soils were sampled periodically for a decade, and archived air-dried. Soil DNA was extracted and gene targets quantified by qPCR. Compared to untreated control soil, all three amendment types increased the abundance of gene targets for up to four years post-application...
January 17, 2018: Canadian Journal of Microbiology
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
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
I Ghiaie Asl, M Motamedi, G R Shokuhi, N Jalalizand, A Farhang, H Mirhendi
Background and Purpose: Cladosporium species are ubiquitous, saprobic, dematiaceous fungi, only infrequently associated with human and animal opportunistic infections. Materials and Methods: Airborne samples were collected using the settle plate method, and soil samples were obtained from a depth of 5-10 cm of the superficial soil layer. Samples were cultured on Sabouraud dextrose agar (SDA) plates, incubated at 25°C, and examined daily for fungal colonies for two to three weeks...
March 2017: Advances in Medical Mycology (Iran)
An-Dong Li, Jacob W Metch, Yulin Wang, Emily Garner, An Ni Zhang, Maria V Riquelme, Peter J Vikesland, Amy Pruden, Tong Zhang
With the growing application of high-throughput sequencing-based metagenomics for profiling antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), comparison of sample pretreatment and DNA extraction methods are needed to move towards standardized comparisons among laboratories. Three widely employed DNA extraction methods (FastDNA® Spin Kit for Soil, PowerSoil® DNA Isolation Kit, and ZR Fecal DNA MiniPrep™), with and without preservation in 50% ethanol and freezing, were applied to the influent, activated sludge and effluent of two WWTPs, in Hong Kong and in the USA...
December 27, 2017: FEMS Microbiology Ecology
Ramdas G Kanissery, Allana Welsh, Andres Gomez, Lynn Connor, Gerald K Sims
The influence of soil environmental factors such as aeration on the ecology of microorganisms involved in the mineralization and degradation of the popular soil-applied pre-emergent herbicide, metolachlor is unknown. To address this knowledge gap, we utilized DNA-based stable isotope probing (SIP) where soil microcosms were incubated aerobically or anaerobically and received herbicide treatments with unlabeled metolachlor or 13C-metolachlor. Mineralization of metolachlor was confirmed as noted from the evolution of 14CO2 from 14C-metolachlor-treated microcosms and clearly demonstrated the efficient utilization of the herbicide as a carbon source...
December 28, 2017: Biodegradation
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