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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
#1
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
#2
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
https://www.readbyqxmd.com/read/28078519/decrease-in-the-genotoxicity-of-metal-contaminated-soils-with-biochar-amendments
#3
Frédéric Rees, Adrien Dhyèvre, Jean Louis Morel, Sylvie Cotelle
Biochar amendments, i.e., the solid product of biomass pyrolysis, reduce soil metal availability, which may lower the toxicity of metal-contaminated soils. A direct link between the decrease in soil metal availability and improved plant development is however often difficult to establish, as biochar may induce undesirable side effects on plant growth, e.g., a modification to plant nutrition. In order to investigate toxicity processes at a cellular level, roots of Vicia faba were exposed for 7 days to three metal-contaminated substrates and one control soil, amended with a 0 or 5% (w/w) addition of a wood-derived biochar...
January 11, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28074923/bacterial-community-composition-in-costal-dunes-of-the-mediterranean-along-a-gradient-from-the-sea-shore-to-the-inland
#4
Haggai Wasserstrom, Susanne Kublik, Rachel Wasserstrom, Stefanie Schulz, Michael Schloter, Yosef Steinberger
Sand dunes are unique ecosystems with distinct features which limited the accumulation of biomass. The distance from seashore affects both the physical properties of the sand dunes and the biota living above- and below ground. The goal of the present study was to determine the effects of the distance from shore to inland on soil bacterial community composition during wet and dry season. We studied a chronosequence of sites close to the eastern Mediterranean coast. Bacterial diversity was assessed using directly extracted DNA from soil samples and 16 S ribosomal RNA gene fingerprinting...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28062407/symbiont-abundance-can-affect-host-plant-population-dynamics
#5
Rachel Rock-Blake, Melissa K McCormick, Hope E A Brooks, Cynthia S Jones, Dennis F Whigham
PREMISE OF THE STUDY: Symbioses are almost universal, but little is known about how symbiont abundance can affect host performance. Many orchids undergo vegetative dormancy and frequent and protracted dormancy have been associated with population declines. If mycorrhizal fungi affect host plant performance, those effects are likely to alter patterns of vegetative dormancy. The goal of this study was to determine whether the abundance of mycorrhizal fungi is related to the likelihood of entering dormancy and whether fungal abundance varied with dormancy duration in the federally listed threatened orchid Isotria medeoloides...
January 6, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28061412/nature-of-fly-ash-amendments-differently-influences-oxidative-stress-alleviation-in-four-forest-tree-species-and-metal-trace-element-phytostabilization-in-aged-contaminated-soil-a-long-term-field-experiment
#6
Sonia Labidi, Stéphane Firmin, Anthony Verdin, Géraldine Bidar, Frédéric Laruelle, Francis Douay, Pirouz Shirali, Joël Fontaine, Anissa Lounès-Hadj Sahraoui
Aided phytostabilization using coal fly ashes (CFAs) is an interesting technique to clean-up polluted soils and valorizing industrial wastes. In this context, our work aims to study the effect of two CFAs: silico-aluminous (CFA1) and sulfo-calcic (CFA2) ones, 10 years after their addition, on the phytostabilization of a highly Cd (cadmium), Pb (lead) and Zn (zinc) contaminated agricultural soil, with four forest tree species: Robinia pseudoacacia, Alnus glutinosa, Acer pseudoplatanus and Salix alba. To assess the effect of CFAs on trees, leaf fatty acid composition, malondialdehyde (MDA), oxidized and reduced glutathione contents ratio (GSSG: GSH), 8-hydroxy-2'-deoxyguanosine (8-OHdG), Peroxidase (PO) and Superoxide dismutase (SOD) activities were examined...
January 3, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28054984/detection-of-ribosomal-dna-sequence-polymorphisms-in-the-protist-plasmodiophora-brassicae-for-the-identification-of-geographical-isolates
#7
Rawnak Laila, Arif Hasan Khan Robin, Kiwoung Yang, Gyung Ja Choi, Jong-In Park, Ill-Sup Nou
Clubroot is a soil-borne disease caused by the protist Plasmodiophora brassicae (P. brassicae). It is one of the most economically important diseases of Brassica rapa and other cruciferous crops as it can cause remarkable yield reductions. Understanding P. brassicae genetics, and developing efficient molecular markers, is essential for effective detection of harmful races of this pathogen. Samples from 11 Korean field populations of P. brassicae (geographic isolates), collected from nine different locations in South Korea, were used in this study...
January 4, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28050848/microbial-communities-in-pyrene-amended-soil-compost-mixture-and-fertilized-soil
#8
Iris K U Adam, Márcia Duarte, Jananan Pathmanathan, Anja Miltner, Thomas Brüls, Matthias Kästner
Polycyclic aromatic hydrocarbons are distributed ubiquitously in the environment and form metabolites toxic to most organisms. Organic amendment of PAH contaminated soil with compost and farmyard manure has proven to be efficient for PAH bioremediation mediated by native microorganisms, even though information on the identity of PAH degraders in organic-amended soil is still scarce. Here we provide molecular insight into the bacterial communities in soil amended with compost or farmyard manure for which the degradation mass balances of (13)C-labeled pyrene have been recently published and assess the relevant bacterial genera capable of degrading pyrene as a model PAH...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28043561/identification-of-different-subtypes-of-rapid-growing-atypical-mycobacterium-from-water-and-soil-sources-using-pcr-rflp-using-hsp65-and-rrna-16s-23s-genes
#9
Mohammad Varahram, Parissa Farnia, Shima Saif, Mehran Marashian, Poopak Farnia, Jaladein Ghanavi, Ali Akbar Velayati
OBJECTIVE/BACKGROUND: Nontuberculosis mycobacteria (NTM) are a diverse group of microorganisms that cause a variety of diseases in humans including skin, respiratory, and gastrointestinal tract infection. Generally, NTM are classified into two categories: rapid (<7days) and slow growing (>7days). In this study, we aimed to investigate NTM frequency and prevalence in environmental samples. Additionally, we tried to identify various subtypes of isolated rapid growing mycobacteria (RGM)...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28028549/ssunique-detecting-sequence-novelty-in-microbiome-surveys
#10
Michael D J Lynch, Josh D Neufeld
High-throughput sequencing of small-subunit (SSU) rRNA genes has revolutionized understanding of microbial communities and facilitated investigations into ecological dynamics at unprecedented scales. Such extensive SSU rRNA gene sequence libraries, constructed from DNA extracts of environmental or host-associated samples, often contain a substantial proportion of unclassified sequences, many representing organisms with novel taxonomy (taxonomic "blind spots") and potentially unique ecology. Indeed, these novel taxonomic lineages are associated with so-called microbial "dark matter," which is the genomic potential of these lineages...
November 2016: MSystems
https://www.readbyqxmd.com/read/28024524/diversity-of-free-living-nitrogen-fixing-streptomyces-in-soils-of-the-badlands-of-south-dakota
#11
Bibha Dahal, Gitanjali NandaKafle, Lora Perkins, Volker S Brözel
Biological Nitrogen Fixation is critical for ecosystem productivity. Select members of Bacteria and Archaea express a nitrogenase enzyme complex that reduces atmospheric nitrogen to ammonia. Several nitrogen fixing bacteria form symbiotic associations with plants, but free-living diazotrophs also contribute a substantial amount of nitrogen to ecosystems. The aim of this study was to isolate and characterize free-living diazotrophs in arid lands of South Dakota Badlands. Samples were obtained from sod tables and the surrounding base in spring and fall...
January 2017: Microbiological Research
https://www.readbyqxmd.com/read/28018378/molecular-identification-of-broomrape-species-from-a-single-seed-by-high-resolution-melting-analysis
#12
Mathieu Rolland, Aurélie Dupuy, Aude Pelleray, Philippe Delavault
Broomrapes are holoparasitic plants spreading through seeds. Each plant produces hundreds of thousands of seeds which remain viable in the soils for decades. To limit their spread, drastic measures are being taken and the contamination of a commercial seed lot by a single broomrape seed can lead to its rejection. Considering that broomrapes species identification from a single seed is extremely difficult even for trained botanists and that among all the described species, only a few are really noxious for the crops, numerous seed lots are rejected because of the contamination by seeds of non-noxious broomrape species...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28004369/mycorrhizal-colonization-status-of-lowland-rice-oryza-sativa-l-in-the-southeastern-region-of-china
#13
Xun-Wen Chen, Fu-Yong Wu, Hui Li, Wai-Fung Chan, Sheng-Chun Wu, Ming-Hung Wong
The accumulation, distribution, and speciation of contaminants, such as arsenic, in rice can be affected by soil microorganisms such as arbuscular mycorrhizal fungi (AMF). As a potential measure to control contaminant acquisition in rice, the status and performance of AMF in the field need to be investigated. Root samples of rice plants were collected in seven different cities in Guangdong, Jiangxi, Hubei, and Jiangsu Provinces in China in order to investigate the colonization rate of AMF. The total DNA of the roots was extracted, followed by PCR and sequencing, and further confirmed the existence of AMF...
December 21, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27902281/acidicapsa-acidisoli-sp-nov-from-the-acidic-soil-of-a-deciduous-forest
#14
Heizo Matsuo, Chisaki Kudo, Juan Li, Akio Tonouchi
A bacterial strain designated strain SK-11T was isolated from the acidic soil of a deciduous forest in the Shirakami Mountains in Japan. Cells of strain SK-11T were aerobic, non-motile, Gram-stain-negative rods, 0.7-1.0 µm in width and 1.0-1.4 µm in length. The pH range for growth was between 4.0 and 5.5, with an optimum at 5.0. The temperature range for growth was between 10°C and 35°C, with an optimum at around 25-30°C. Strain SK-11T utilized various carbohydrates as growth substrates as well as yeast extract and protein hydrolysates...
November 23, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27844142/efficiency-and-sensitivity-of-the-digital-droplet-pcr-for-the-quantification-of-antibiotic-resistance-genes-in-soils-and-organic-residues
#15
Laura Cavé, Elisabeth Brothier, Danis Abrouk, Panignimyandé Salomon Bouda, Edmond Hien, Sylvie Nazaret
Droplet digital PCR (ddPCR) allows absolute quantification and tolerance to inhibitors and has been proposed as the method of choice to overcome limitations of qPCR. The aim of this study was to evaluate ddPCR and qPCR performances to detect low copy number and copy number variation of antibiotic resistance genes (sul1 and qnrB genes encoding for resistance to sulfonamides and quinolones, respectively) using bacterial genomic DNA (gDNA) and metagenomic DNA extracted from soil and organic residue samples. With gDNA, qPCR showed a better range of quantification but the lower limit of quantification was at 15 copies of qnrB target vs...
December 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27844108/transcriptional-responses-of-the-bacterium-burkholderia-terrae-bs001-to-the-fungal-host-lyophyllum-sp-strain-karsten-under-soil-mimicking-conditions
#16
Irshad Ul Haq, Francisco Dini-Andreote, Jan Dirk van Elsas
In this study, the mycosphere isolate Burkholderia terrae BS001 was confronted with the soil fungus Lyophyllum sp. strain Karsten on soil extract agar plates in order to examine its transcriptional responses over time. At the initial stages of the experiment (T1-day 3; T2-day 5), contact between both partner organisms was absent, whereas in the final stage (T3-day 8), the two populations made intimate physical contact. Overall, a strong modulation of the strain BS001 gene expression patterns was found. First, the stationary-phase sigma factor RpoS, and numerous genes under its control, were strongly expressed as a response to the soil extract agar, and this extended over the whole temporal regime...
January 2017: Microbial Ecology
https://www.readbyqxmd.com/read/27803690/transparent-dna-rna-co-extraction-workflow-protocol-suitable-for-inhibitor-rich-environmental-samples-that-focuses-on-complete-dna-removal-for-transcriptomic-analyses
#17
Natalie Y N Lim, Constance A Roco, Åsa Frostegård
Adequate comparisons of DNA and cDNA libraries from complex environments require methods for co-extraction of DNA and RNA due to the inherent heterogeneity of such samples, or risk bias caused by variations in lysis and extraction efficiencies. Still, there are few methods and kits allowing simultaneous extraction of DNA and RNA from the same sample, and the existing ones generally require optimization. The proprietary nature of kit components, however, makes modifications of individual steps in the manufacturer's recommended procedure difficult...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27779795/dna-extraction-from-benthic-cyanobacteria-comparative-assessment-and-optimization
#18
V Gaget, A Keulen, M Lau, P Monis, J D Brookes
AIMS: Benthic Cyanobacteria produce toxic and odorous compounds similar to their planktonic counterparts, challenging the quality of drinking water supplies. The biofilm that benthic algae and other micro-organisms produce is a complex and protective matrix. Monitoring to determine the abundance and identification of Cyanobacteria, therefore, relies on molecular techniques, with the choice of DNA isolation technique critical. This study investigated which DNA extraction method is optimal for DNA recovery in order to guarantee the best DNA yield for PCR-based analysis of benthic Cyanobacteria...
January 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27765986/first-report-of-the-spiral-nematode-rotylenchus-incultus-nematoda-hoplolaimidae-from-cultivated-olive-in-tunisia-with-additional-molecular-data-on-rotylenchus-eximius
#19
Ilhem Guesmi-Mzoughi, Antonio Archidona-Yuste, Carolina Cantalapiedra-Navarrete, Hajer Regaieg, Najet Horrigue-Raouani, Juan E Palomares-Rius, Pablo Castillo
Spiral nematode species of the genus Rotylenchus have been reported on olive (Olea europaea L.) in several Mediterranean countries (Castillo et al., 2010; Ali et al., 2014). Nematological surveys for plant-parasitic nematodes on olive trees were carried out in Tunisia between 2013 and 2014, and two nematode species of Rotylenchus were collected from the rhizosphere of olive cv. Chemlali in several localities of Tunisia (Tables 1,2 [Table: see text] [Table: see text] ). Twenty-two soil samples of 3 to 4 kg were collected with a shovel from the upper 50 cm of soil from arbitrarily chosen olive trees...
September 2016: Journal of Nematology
https://www.readbyqxmd.com/read/27765985/first-report-of-longidorus-kuiperi-and-rotylenchus-eximius-from-coastal-sand-dunes-in-crete-greece
#20
Emmanuel A Tzortzakakis, Carolina Cantalapiedra-Navarrete, Antonio Archidona-Yuste, Juan E Palomares-Rius, Pablo Castillo
Plant-parasitic nematode species have been reported on several occasions from coastal sand dunes, including Longidorus and Rotylenchus species (Vovlas et al., 2008; De Luca et al., 2009; Mateille et al., 2014). In April 2016, 10 soil samples of 3 to 4 kg from the rhizosphere of Tamarix smyrnensis with different vegetation around (viz. Elymus farctus, Lycium schweinfurthii, Crithmum maritimum, and Arthrocnemum sp.) were collected for diagnosis of plant-parasitic nematodes. The area of sampling was a coastal sand dune near the archeological site of Komos, southwest of Crete, Greece...
September 2016: Journal of Nematology
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