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Dna extraction soil

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
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
Christopher M Prosser, Bryan M Hedgpeth
Extracting and identifying genetic material from environmental media (i.e. water and soil) presents a unique opportunity for researchers to assess biotic diversity and ecosystem health with increased speed and decreased cost as compared to traditional methods (e.g. trapping). The heterogeneity of soil mineralogy, spatial and temporal variations however present unique challenges to sampling and interpreting results. Specifically, fate/transport of genetic material in the terrestrial environment represents a substantial data gap...
2018: PloS One
David Bass, D V Tikhonenkov, R Foster, P Dyal, J Janouskovec, P J Keeling, M Gardner, S Neuhauser, H Hartikainen, A P Mylnikov, C Berney
Rhizarian 'Novel Clade 10' (NC10) is frequently detected by 18S rRNA gene sequencing studies in freshwater planktonic samples. We describe a new genus and two species of eukaryovorous biflagellate protists, Aquavolon hoantrani n. gen. n. sp., and A. dientrani n. gen. n. sp., which represent the first morphologically characterized members of NC10, here named Aquavolonida ord. nov.. The slightly metabolic cells possess naked heterodynamic flagella, whose kinetosomes lie at a right angle to each other and are connected by at least one fibril...
April 15, 2018: Journal of Eukaryotic Microbiology
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
Sui Sheng T Hua, Jeffrey D Palumbo, Dan E Parfitt, Siov Bouy L Sarreal, Teresa L O'Keeffe
Aflatoxin B1 is a potent hepatotoxin and carcinogen that poses a serious safety hazard to both humans and animals. Aspergillus flavus is the most common aflatoxin-producing species on corn, cotton, peanuts, and tree nuts. Application of atoxigenic strains to compete against aflatoxigenic strains of A. flavus has emerged as one of the most practical strategies for ameliorating aflatoxin contamination in food. Genes directly involved in aflatoxin biosynthesis are clustered on an 82-kb region of the genome. Three atoxigenic strains (CA12, M34, and AF123) were each paired with each of four aflatoxigenic strains (CA28, CA42, CA90, and M52), inoculated into soil and incubated at 28 °C for 2 weeks and 1 month...
March 26, 2018: Mycotoxin Research
Ihsanul Khaliq, Giles E St J Hardy, Diane White, Treena I Burgess
Proper isolation and identification of Phytophthora species is critical due to their broad distribution and huge impact on natural ecosystems throughout the world. In this study, five different sites were sampled and seven methods were compared to determine the Phytophthora community. Three traditional isolation methods were conducted (1) soil baiting, (2) filtering of the bait water, and (3) isolation from field roots using Granny Smith apples. These were compared to four sources of eDNA used for metabarcoding using Phytophthora specific primers on (1) sieved field soil, (2) roots from field, (3) filtered baiting water, and (4) roots from bait plants grown in the glasshouse in soil collected from these sites...
March 20, 2018: FEMS Microbiology Ecology
Rodrigo Pinheiro Araldi, Maristela Oliveira Dos Santos, Fabiane Faria Barbon, Bruna Aparecida Manjerona, Bruno Rosa Meirelles, Pedro de Oliva Neto, Pedro Ismael da Silva, Lucinéia Dos Santos, Isabel Cristina Cherici Camargo, Edislane Barreiros de Souza
Brazilian Northeast is the world's largest producer of Agave sisalana Perrine for the supply of the sisal fiber. About 95% of plant biomass, which comprise the mucilage and sisal juice, is considered a waste residual is discarded in the soil. However, the sisal juice is rich in steroidal saponins, which exhibits different pharmacological properties. Despite this, natural products are not necessarily safe. Based on this, this study analyzed the antioxidant, cytotoxic and mutagenic potential of three extracts derived from acid hydrolysis (AHAS), dried precipitate (DPAS) and hexanic of A...
February 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
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...
May 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 worldwide 1 . 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...
April 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 macroorganisms 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...
March 1, 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
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