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https://www.readbyqxmd.com/read/28441441/a-novel-multiplexed-probe-based-quantitative-pcr-assay-for-the-soybean-root-and-stem-rot-pathogen-phytophthora-sojae-utilizes-its-transposable-element
#1
James S Haudenshield, Jeong Y Song, Glen L Hartman
Phytophthora root rot of soybean [Glycine max (L.) Merr.] is caused by the oomycete Phytophthora sojae (Kaufm. & Gerd.). P. sojae has a narrow host range, consisting primarily of soybean, and it is a serious pathogen worldwide. It exists in root and stem tissues as mycelium, wherein it can form oospores which subsequently germinate to release motile, infectious zoospores. Molecular assays detecting DNA of P. sojae are useful in disease diagnostics, and for determining the presence of the organism in host tissues, soils, and runoff or ponded water from potentially infested fields...
2017: PloS One
https://www.readbyqxmd.com/read/28421041/metagenome-wide-association-study-and-machine-learning-prediction-of-bulk-soil-microbiome-and-crop-productivity
#2
Hao-Xun Chang, James S Haudenshield, Charles R Bowen, Glen L Hartman
Areas within an agricultural field in the same season often differ in crop productivity despite having the same cropping history, crop genotype, and management practices. One hypothesis is that abiotic or biotic factors in the soils differ between areas resulting in these productivity differences. In this study, bulk soil samples collected from a high and a low productivity area from within six agronomic fields in Illinois were quantified for abiotic and biotic characteristics. Extracted DNA from these bulk soil samples were shotgun sequenced...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28410799/genomic-identification-and-characterization-of-the-elite-strains-bradyrhizobium-yuanmingense-br-3267-and-bradyrhizobium-pachyrhizi-br-3262-recommended-for-cowpea-inoculation-in-brazil
#3
Jakson Leite, Samuel Ribeiro Passos, Jean Luiz Simões-Araújo, Norma Gouvêa Rumjanek, Gustavo Ribeiro Xavier, Jerri Édson Zilli
The leguminous inoculation with nodule-inducing bacteria that perform biological nitrogen fixation is a good example of an "eco-friendly agricultural practice". Bradyrhizobium strains BR 3267 and BR 3262 are recommended for cowpea (Vigna unguiculata) inoculation in Brazil and showed remarkable responses; nevertheless neither strain was characterized at species level, which is our goal in the present work using a polyphasic approach. The strains presented the typical phenotype of Bradyrhizobium with a slow growth and a white colony on yeast extract-mannitol medium...
March 31, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/28397264/population-densities-of-indigenous-acidobacteria-change-in-the-presence-of-plant-growth-promoting-rhizobacteria-pgpr-in-rhizosphere
#4
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/28381965/development-and-evaluation-of-loop-mediated-isothermal-amplification-assay-for-rapid-detection-of-tylenchulus-semipenetrans-using-dna-extracted-from-soil
#5
Zhi-Qiang Song, Ju-E Cheng, Fei-Xue Cheng, De-Yong Zhang, Yong Liu
Tylenchulus semipenetrans is an important and widespread plant-parasitic nematode of citrus worldwide and can cause citrus slow decline disease leading to significant reduction in tree growth and yield. Rapid and accurate detection of T. semipenetrans in soil is important for the disease forecasting and management. In this study, a loop-mediated isothermal amplification (LAMP) assay was developed to detect T. semipenetrans using DNA extracted from soil. A set of five primers was designed from the internal transcribed spacer region (ITS1) of rDNA, and was highly specific to T...
April 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/28377928/quantitative-pcr-and-digital-pcr-for-detection-of-ascaris-lumbricoides-eggs-in-reclaimed-water
#6
Lucrecia Acosta Soto, Ana Belén Santísima-Trinidad, Fernando Jorge Bornay-Llinares, Marcos Martín González, José Antonio Pascual Valero, Margarita Ros Muñoz
The reuse of reclaimed water from wastewater depuration is a widespread and necessary practice in many areas around the world and must be accompanied by adequate and continuous quality control. Ascaris lumbricoides is one of the soil-transmitted helminths (STH) with risk for humans due to its high infectivity and an important determinant of transmission is the inadequacy of water supplies and sanitation. The World Health Organization (WHO) recommends a limit equal to or lower than one parasitic helminth egg per liter, to reuse reclaimed water for unrestricted irrigation...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28340454/pea-cultivar-and-wheat-residues-affect-carbon-nitrogen-dynamics-in-pea-triticale-intercropping-a-microcosms-approach
#7
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
#8
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
#9
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/28268038/comparison-of-different-commercial-dna-extraction-kits-and-pcr-protocols-for-the-detection-of-echinococcus-multilocularis-eggs-in-faecal-samples-from-foxes
#10
Pavlo Maksimov, Gereon Schares, Sebastian Press, Andreas Fröhlich, Walter Basso, Mandy Herzig, Franz J Conraths
Effective and sensitive methods for the molecular detection of Echinococcus multilocularis in faecal samples of final hosts are crucial for the prevention and control of human alveolar echinococcosis and for studies on the epidemiology of the parasite. Little is known about the suitability of commercial test kits for isolating DNA of E. multilocularis from fox faeces and the performance of standard Polymerase Chain Reaction (PCR) protocols in relation to the quality of DNA extracted by these kits. We compared four different kits: ZR Faecal DNA MiniPrep™ (Zymo Research), FastDNA(®) SPIN Kit for Soil (MP Biomedicals), QIAamp(®) Fast DNA Stool Mini Kit (QIAGEN) and NucleoSpin(®) Soil Kit (Macherey-Nagel) for the extraction of DNA from E...
February 24, 2017: Veterinary Parasitology
https://www.readbyqxmd.com/read/28260685/oxidative-stress-and-genotoxicity-of-an-organic-and-an-inorganic-nanomaterial-to-eisenia-andrei-sds-ddab-nano-vesicles-and-titanium-silicon-oxide
#11
Bruno Correia, Joana Lourenço, Sérgio Marques, Verónica Nogueira, Ana Gavina, Maria da Graça Rasteiro, Filipe Antunes, Sónia Mendo, Ruth Pereira
In the past few years the number of studies on the toxic effects of nanomaterials (NMs) in the environment increased significantly. Nonetheless, the data is still scarce, since there is a large number of NMs and new ones are being developed each day. Soils are extremely important for life, and are easily exposed to the released NMs, thus enhanced efforts are needed to study the impacts on soil biota. The objective of the present work was to determine if different concentrations of two NMs, one inorganic (TiSiO4) and other organic (nano-vesicles of sodium sodecyl sulfate/ didodecyl dimethylammonium bromide - SDS/DDAB), are genotoxic to soil invertebrates...
March 2, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28252174/molecular-marker-based-genetic-diversity-analysis-of-scantly-studied-brazilian-accessions-of-a-medicinal-plant-morinda-citrifolia-l-noni
#12
P N Bordallo, A M R Monteiro, J A Sousa, F A S Aragão
Morinda citrifolia L., commonly known as noni, has been used for the treatment of various diseases for over two centuries. It was introduced and widely disseminated in Brazil because of its high market value and ease of adaptation to the soil and climatic conditions of the country. The aim of this study was to estimate the genetic variability of noni accessions from the collection of Embrapa Agroindústria Tropical in Brazil. We evaluated 36 plants of the 13 accessions of noni from the germplasm collection of M...
February 23, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28238016/seasonal-pattern-of-mycobacterium-ulcerans-the-causative-agent-of-buruli-ulcer-in-the-environment-in-ghana
#13
Samuel Yaw Aboagye, Kobina Assan Ampah, Amanda Ross, Prince Asare, Isaac Darko Otchere, Janet Fyfe, Dorothy Yeboah-Manu
This study aimed to contribute to the understanding of Mycobacterium ulcerans (MU) ecology by analysing both clinical and environmental samples collected from ten communities along two major river basins (Offin and Densu) associated with Buruli ulcer (BU) at different seasons. We collected clinical samples from presumptive BU cases and environmental samples from ten communities. Following DNA extraction, clinical samples were confirmed by IS2404 PCR and environmental samples were confirmed by targeting MU-specific genes, IS2404, IS2606 and the ketoreductase (KR) using real-time PCR...
February 25, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28217901/the-choice-of-the-dna-extraction-method-may-influence-the-outcome-of-the-soil-microbial-community-structure-analysis
#14
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...
February 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28203533/modification-of-extraction-method-for-community-dna-isolation-from-salt-affected-compact-wasteland-soil-samples
#15
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/28177833/the-importance-of-molecular-markers-and-primer-design-when-characterizing-biodiversity-from-environmental-dna
#16
Joanna R Freeland
Environmental DNA (eDNA) comprises DNA fragments that have been shed into the environment by organisms, and which can be extracted from environmental samples such as water or soil. Characterization of eDNA can allow researchers to infer the presence or absence of species from a particular site without the need to locate and identify individuals, and therefore may provide an extremely valuable tool for quantifying biodiversity. However, as is often the case with relatively new protocols, methodological challenges remain...
April 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28168105/successive-dna-extractions-improve-characterization-of-soil-microbial-communities
#17
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/28141504/luteitalea-pratensis-gen-nov-sp-nov-a-new-member-of-subdivision-6-acidobacteria-isolated-from-temperate-grassland-soil
#18
Selma Vieira, Maja Luckner, Gerhard Wanner, Jorg Overmann
Albeit being widespread and abundant in soils worldwide, bacteria of the phylum Acidobacteria have remained grossly understudied due to difficulties in their cultivation and isolation. To date only 48 species have been validly described, including a single member of the phylogenetically diverse Acidobacteria subdivision 6. Here, we report the polyphasic characterization of strain HEG_-6_39T, a new representative of Acidobacteria subdivision 6 isolated from a grassland soil in Thuringia, Germany. Cells of HEG_-6_39T are Gram-negative, non-motile, non-spore-forming, non-capsulated short rods that form small dark yellow colonies...
January 31, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28096624/genetic-variability-and-discrimination-of-low-doses-of-toxocara-spp-from-public-areas-soil-inferred-by-loop-mediated-isothermal-amplification-assay-as-a-field-friendly-molecular-tool
#19
Maryam Ozlati, Adel Spotin, Abbas Shahbazi, Mahmoud Mahami-Oskouei, Teimour Hazratian, Mohammad Adibpor, Ehsan Ahmadpour, Afsaneh Dolatkhah, Paria Khoshakhlagh
ABSTRACT: Aim: One of the main diagnostic problems of conventional polymerase chain reaction (PCR) is indiscrimination of low parasitic loads in soil samples. The aim of this study is to determine the genetic diversity and identification of Toxocara spp. from public areas soil inferred by loop-mediated isothermal amplification (LAMP) assay. MATERIALS AND METHODS: A total of 180 soil samples were collected from various streets and public parks of northwest Iran. The DNA of recovered Toxocara eggs were extracted and amplified by PCR and LAMP following ZnSO4 flotation technique...
December 2016: Veterinary World
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
#20
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...
January 16, 2017: Environmental Science and Pollution Research International
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