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https://www.readbyqxmd.com/read/28217901/the-choice-of-the-dna-extraction-method-may-influence-the-outcome-of-the-soil-microbial-community-structure-analysis
#1
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
#2
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-edna
#3
Joanna 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...
December 22, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28168105/successive-dna-extractions-improve-characterization-of-soil-microbial-communities
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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...
April 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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
COMPARATIVE STUDY
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
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