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Soil microbial dna extraction

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https://www.readbyqxmd.com/read/29117585/metagenomics-profiling-for-assessing-microbial-diversity-in-both-active-and-closed-landfills
#1
Mohamad Yusof Zainun, Khanom Simarani
The municipal landfill is an example of human-made environment that harbours some complex diversity of microorganism communities. To evaluate this complexity, the structures of bacterial communities in active (operational) and closed (non-operational) landfills in Malaysia were analysed with culture independent metagenomics approaches. Several points of soil samples were collected from 0 to 20cm depth and were subjected to physicochemical test, such as temperature, pH, and moisture content. In addition, the heavy metal contamination was determined by using ICPMS...
November 5, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29106502/isolation-of-highly-thermostable-%C3%AE-xylosidases-from-a-hot-spring-soil-microbial-community-using-a-metagenomic-approach
#2
Masaru Sato, Migiwa Suda, Jiro Okuma, Tomohiko Kato, Yoshitsugu Hirose, Asuka Nishimura, Yasuhiko Kondo, Daisuke Shibata
The DNA extracted from a high-temperature environment in which micro-organisms are living will be a good source for the isolation of thermostable enzymes. Using a metagenomic approach, we aimed to isolate thermostable β-xylosidases that will be exploited for biofuel production from lignocellulosic biomass. DNA samples obtained from the soil near a spout of a hot spring (70°C, pH7.2) were subjected to sequencing, which generated a total of 84.2 Gbp with 967,925 contigs of >500 bp in length. Similarity search for β-xylosidase in the contigs revealed the presence of 168 candidate sequences, each of which may have arisen from more than one gene...
August 7, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29104570/characterization-of-bacterial-and-fungal-community-dynamics-by-high-throughput-sequencing-hts-metabarcoding-during-flax-dew-retting
#3
Christophe Djemiel, Sébastien Grec, Simon Hawkins
Flax dew-retting is a key step in the industrial extraction of fibers from flax stems and is dependent upon the production of a battery of hydrolytic enzymes produced by micro-organisms during this process. To explore the diversity and dynamics of bacterial and fungal communities involved in this process we applied a high-throughput sequencing (HTS) DNA metabarcoding approach (16S rRNA/ITS region, Illumina Miseq) on plant and soil samples obtained over a period of 7 weeks in July and August 2014. Twenty-three bacterial and six fungal phyla were identified in soil samples and 11 bacterial and four fungal phyla in plant samples...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28956398/-discovery-and-analysis-of-staphylococcus-aureus-biofilm-inhibitors-using-functional-metagenomics-approach
#4
Ying Zhu, Shumao Chai, Mingming Cao, Shaochen Wang, Zhiyang Feng
Although most microbes are not readily cultured in the lab, microbial DNA can be extracted directly from an environmental sample and be functionally expressed in a suitable host for natural products discovery, and this approach has been termed "metagenomics". An E'mei Mountain soil metagenomic library was constructed using an Escherichia coli-Streptomyces shuttle vector for functional based screening of anti-bacterial clones in Streptomyces albus host. Two active clones were obtained and their fermentation broths were studied for the inhibitory effect on Staphylococcus aureus biofilm...
September 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28919882/effects-of-soil-pre-treatment-with-basamid%C3%A2-granules-brassica-juncea-raphanus-sativus-and-tagetes-patula-on-bacterial-and-fungal-communities-at-two-apple-replant-disease-sites
#5
Bunlong Yim, Heike Nitt, Andreas Wrede, Samuel Jacquiod, Søren J Sørensen, Traud Winkelmann, Kornelia Smalla
Nurseries producing apple and rose rootstock plants, apple orchards as well as rose production often experience replanting problems after several cultivations at the same site when a chemical soil disinfectant is not applied. The etiology of apple and rose replanting problems is most likely caused by soil-borne pathogen complex, defined as "replant disease (RD)". Symptoms typical of RD are reduced shoot and root growth, a smaller leaf area, a significant decrease in plant biomass, yield and fruit quality and a shorter life span...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28892269/bacteria-utilising-plant-derived-carbon-in-the-rhizosphere-of-triticum-aestivum-change-in-different-depths-of-an-arable-soil
#6
Marie Uksa, Franz Buegger, Silvia Gschwendtner, Tillmann Lueders, Susanne Kublik, Timo Kautz, Miriam Athmann, Ulrich Köpke, Jean Charles Munch, Michael Schloter, Doreen Fischer
Root exudates shape microbial communities at the plant soil interface. Here we compared bacterial communities that utilise plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a green house using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant derived carbon, (13) C-CO2 labelling of plants was performed for two weeks at the EC50 stage, followed by stable isotope probing of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing...
September 11, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28861443/biochemical-characteristics-of-a-free-cyanide-and-total-nitrogen-assimilating-fusarium-oxysporum-ekt01-02-isolate-from-cyanide-contaminated-soil
#7
Enoch A Akinpelu, Adewole T Adetunji, Seteno K O Ntwampe, Felix Nchu, Lukhanyo Mekuto
Sustainability of nutrient requirements for microbial proliferation on a large scale is a challenge in bioremediation processes. This article presents data on biochemical properties of a free cyanide resistant and total nitrogen assimilating fungal isolate from the rhizosphere of Zeamays (maize) growing in soil contaminated with a cyanide-based pesticide. DNA extracted from this isolate were PCR amplified using universal primers; TEF1-α and ITS. The raw sequence files are available on the NCBI database. Characterisation using biochemical data was obtained using colorimetric reagents analysed with VITEK(®) 2 software version 7...
October 2017: Data in Brief
https://www.readbyqxmd.com/read/28803266/a-degradome-based-polymerase-chain-reaction-to-resolve-the-potential-of-environmental-samples-for-2-4-dichlorophenol-biodegradation
#8
Eslam S Ibrahim, Mona T Kashef, Tamer M Essam, Mohammed A Ramadan
A clean way to overcome environmental pollution is biodegradation. In this perspective, at the intersection of biodegradation and metagenomics, the degradome is defined as the totality of genes related to the biodegradation of a certain compound. It includes the genetic elements from both culturable and uncultured microorganisms. The possibility of assessing the biodegradation potential of an environmental samples, using a degradome-based polymerase chain reaction, was explored. 2,4-Dichlorophenol (2,4-DCP) was chosen as a model and the use of tfdB gene as a biodegradation marker was confirmed by bioinformatics study of TfdB protein...
December 2017: Current Microbiology
https://www.readbyqxmd.com/read/28798742/preservation-and-significance-of-extracellular-dna-in-ferruginous-sediments-from-lake-towuti-indonesia
#9
Aurèle Vuillemin, Fabian Horn, Mashal Alawi, Cynthia Henny, Dirk Wagner, Sean A Crowe, Jens Kallmeyer
Extracellular DNA is ubiquitous in soil and sediment and constitutes a dominant fraction of environmental DNA in aquatic systems. In theory, extracellular DNA is composed of genomic elements persisting at different degrees of preservation produced by processes occurring on land, in the water column and sediment. Extracellular DNA can be taken up as a nutrient source, excreted or degraded by microorganisms, or adsorbed onto mineral matrices, thus potentially preserving information from past environments. To test whether extracellular DNA records lacustrine conditions, we sequentially extracted extracellular and intracellular DNA from anoxic sediments of ferruginous Lake Towuti, Indonesia...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28673033/comparison-of-four-dna-extraction-methods-for-comprehensive-assessment-of-16s-rrna-bacterial-diversity-in-marine-biofilms-using-high-throughput-sequencing
#10
Natàlia Corcoll, Tobias Österlund, Lucas Sinclair, Alexander Eiler, Erik Kristiansson, Thomas Backhaus, K Martin Eriksson
High-throughput DNA sequencing technologies are increasingly used for the metagenomic characterisation of microbial biodiversity. However, basic issues, such as the choice of an appropriate DNA extraction method, are still not resolved for non-model microbial communities. This study evaluates four commonly used DNA extraction methods for marine periphyton biofilms in terms of DNA yield, efficiency, purity, integrity and resulting 16S rRNA bacterial diversity. Among the tested methods, the Plant DNAzol® Reagent (PlantDNAzol) and the FastDNA® SPIN Kit for Soil (FastDNA Soil) methods were best suited to extract high quantities of DNA (77-130 μg g wet wt-1)...
August 1, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28555427/optimization-of-high-yielding-protocol-for-dna-extraction-from-the-forest-rhizosphere-microbes
#11
Sadam D V Satyanarayana, M S R Krishna, Pindi Pavan Kumar
Soil is major reservoir for microbes and harbors a vast microbial diversity. Soil microbiota plays a pivotal role in biogeochemical cycles, bioremediation, and in health and disease states of humans, animals, and plants. It is imperative to understand the microbial signatures which are specific in such an ecosystem to unravel their potential role and impact on environment. During the recent years, exploration of soil microbial communities has been geared up with the advent of advanced sequencing technologies...
June 2017: 3 Biotech
https://www.readbyqxmd.com/read/28523377/mining-lipolytic-enzymes-in-community-dna-from-high-andean-soils-using-a-targeted-approach
#12
Daniel Borda-Molina, José Salvador Montaña, María Mercedes Zambrano, Sandra Baena
Microbial enrichments cultures are a useful strategy to speed up the search for enzymes that can be employed in industrial processes. Lipases have gained special attention because they show unique properties such as: broad substrate specificity, enantio- and regio-selectivity and stability in organic solvents. A major goal is to identify novel lipolytic enzymes from microorganisms living in cold extreme environments such as high Andean soils, of relevance to our study being their capability be used in industrial processes...
August 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28516483/capabilities-and-limitations-of-dgge-for-the-analysis-of-hydrocarbonoclastic-prokaryotic-communities-directly-in-environmental-samples
#13
Dina M Al-Mailem, Mayada K Kansour, Samir S Radwan
Prokaryotic communities in pristine and oil-contaminated desert soil, seawater, and hypersaline coastal soil were analyzed using culture-dependent and culture-independent approaches. The former technique was the dilution-plating method. For the latter, total genomic DNA was extracted and the 16S rRNA genes were amplified using a universal bacterial primer pair and primer pairs specific for Actinobacteria, Gammaproteobacteria, and Archaea. The amplicons were resolved using denaturing gradient gel electrophoresis (DGGE) and sequenced, and the sequences were compared to those in GenBank...
October 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28480140/high-diversity-and-suggested-endemicity-of-culturable-actinobacteria-in-an-extremely-oligotrophic-desert-oasis
#14
Hector Fernando Arocha-Garza, Ricardo Canales-Del Castillo, Luis E Eguiarte, Valeria Souza, Susana De la Torre-Zavala
The phylum Actinobacteria constitutes one of the largest and anciently divergent phyla within the Bacteria domain. Actinobacterial diversity has been thoroughly researched in various environments due to its unique biotechnological potential. Such studies have focused mostly on soil communities, but more recently marine and extreme environments have also been explored, finding rare taxa and demonstrating dispersal limitation and biogeographic patterns for Streptomyces. To test the distribution of Actinobacteria populations on a small scale, we chose the extremely oligotrophic and biodiverse Cuatro Cienegas Basin (CCB), an endangered oasis in the Chihuahuan desert to assess the diversity and uniqueness of Actinobacteria in the Churince System with a culture-dependent approach over a period of three years, using nine selective media...
2017: PeerJ
https://www.readbyqxmd.com/read/28397264/population-densities-of-indigenous-acidobacteria-change-in-the-presence-of-plant-growth-promoting-rhizobacteria-pgpr-in-rhizosphere
#15
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...
May 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28340454/pea-cultivar-and-wheat-residues-affect-carbon-nitrogen-dynamics-in-pea-triticale-intercropping-a-microcosms-approach
#16
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
#17
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
#18
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/28217901/the-choice-of-the-dna-extraction-method-may-influence-the-outcome-of-the-soil-microbial-community-structure-analysis
#19
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...
August 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28203533/modification-of-extraction-method-for-community-dna-isolation-from-salt-affected-compact-wasteland-soil-samples
#20
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
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