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https://www.readbyqxmd.com/read/27902281/acidicapsa-acidisoli-sp-nov-from-the-acidic-soil-of-a-deciduous-forest
#1
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
#2
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...
November 14, 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
#3
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...
November 14, 2016: 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
#4
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-optimisation
#5
Virginie Gaget, Angela Keulen, Melody Lau, Paul Monis, Justin 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...
October 25, 2016: 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
#6
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
#7
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
https://www.readbyqxmd.com/read/27660624/the-willow-microbiome-is-influenced-by-soil-petroleum-hydrocarbon-concentration-with-plant-compartment-specific-effects
#8
Stacie Tardif, Étienne Yergeau, Julien Tremblay, Pierre Legendre, Lyle G Whyte, Charles W Greer
The interaction between plants and microorganisms, which is the driving force behind the decontamination of petroleum hydrocarbon (PHC) contamination in phytoremediation technology, is poorly understood. Here, we aimed at characterizing the variations between plant compartments in the microbiome of two willow cultivars growing in contaminated soils. A field experiment was set-up at a former petrochemical plant in Canada and after two growing seasons, bulk soil, rhizosphere soil, roots, and stems samples of two willow cultivars (Salix purpurea cv...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27627898/modified-method-for-the%C3%A2-extraction-of-mrna-from-paddy-soils
#9
Hongling Qin, Xiangbi Chen, Yafang Tang, Haijun Hou, Rong Sheng, Jinlin Shen
OBJECTIVE: Paddy soils contain relatively greater organic matter and water contents than other soils thereby limiting effective mRNA extraction. A modification of the conventional mRNA soil extraction method specific to paddy soils is described. RESULTS: Two main modifications for co-extraction of DNA and RNA are: (1) addition of 20 % (w/v) sodium dodecyl sulphate to 10 % (w/v) hexadecyltrimethylammonium bromide extraction buffer, and (2) fresh soil, initially frozen at -80 °C, is immediately immersed in extraction buffer...
September 15, 2016: Biotechnology Letters
https://www.readbyqxmd.com/read/27611697/a-quantitative-protocol-for-dna-metabarcoding-of-springtails-collembola
#10
Seikoh Saitoh, Hiroaki Aoyama, Saori Fujii, Haruki Sunagawa, Hideki Nagahama, Masako Akutsu, Naoya Shinzato, Nobuhiro Kaneko, Taizo Nakamori
We developed a novel protocol with superior quantitative analysis results for DNA metabarcoding of Collembola, a major soil microarthropod order. Degenerate PCR primers were designed for conserved regions in the mitochondrial cytochrome c oxidase subunit I (mtCOI) and 16S ribosomal RNA (mt16S) genes based on published collembolan mitogenomes. The best primer pair was selected based on its ability to amplify each gene, irrespective of the species. DNA was extracted from 10 natural communities sampled in a temperate forest (with typically 25-30 collembolan species per 10 soil samples) and 10 mock communities (with seven cultured collembolan species)...
September 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/27596590/current-and-projected-global-distribution-of-phytophthora-cinnamomi-one-of-the-world-s-worst-plant-pathogens
#11
Treena I Burgess, John K Scott, Keith L Mcdougall, Michael J C Stukely, Colin Crane, William A Dunstan, Frances Brigg, Vera Andjic, Diane White, Tim Rudman, Frans Arentz, Noboru Ota, Giles E St J Hardy
Globally, Phytophthora cinnamomi is listed as one of the 100 worst invasive alien species and active management is required to reduce impact and prevent spread in both horticulture and natural ecosystems. Conversely, there are regions thought to be suitable for the pathogen where no disease is observed. We developed a climex model for the global distribution of P. cinnamomi based on the pathogen's response to temperature and moisture and by incorporating extensive empirical evidence on the presence and absence of the pathogen...
September 6, 2016: Global Change Biology
https://www.readbyqxmd.com/read/27580466/solanum-lycopersicum-tomato-hosts-robust-phyllosphere-and-rhizosphere-bacterial-communities-when-grown-in-soil-amended-with-various-organic-and-synthetic-fertilizers
#12
Sarah M Allard, Christopher S Walsh, Anna E Wallis, Andrea R Ottesen, Eric W Brown, Shirley A Micallef
Due to the intimate association between plants and their microbial symbionts, an examination of the influence of agricultural practices on phytobiome structure and diversity could foster a more comprehensive understanding of plant health and produce safety. Indeed, the impact of upstream crop producti006Fn practices cannot be overstated in their role in assuring an abundant and safe food supply. To assess whether fertilizer type impacted rhizosphere and phyllosphere bacterial communities associating with tomato plants, the bacterial microbiome of tomato cv...
August 28, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/27567126/quinazoline-derivative-from-indigenous-isolate-nocardiopsis-alba-inhibits-human-telomerase-enzyme
#13
K G Kiran, M Thandeeswaran, K A Ayub Nawaz, M Easwaran, K K Jayagopi, L Ebrahimi, M Palaniswamy, R Mahendran, J Angayarkanni
AIM: Aim of this study was isolation and screening of various secondary metabolites produced by indigenous isolates of soil Actinomycetes for human telomerase inhibitory activity. METHODS AND RESULTS: Extracellular extract from culture suspension of various soil Actinomycetes species were tested for telomerase inhibitory activity. The organism which produced telomerase inhibitor was identified by 16S rRNA gene sequencing. The active fraction was purified by HPLC and analysed by GC-MS to identify the compound...
December 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27528083/soil-pretreatment-and-fast-cell-lysis-for-direct-polymerase-chain-reaction-from-forest-soils-for-terminal-restriction-fragment-length-polymorphism-analysis-of-fungal-communities
#14
Fei Cheng, Lin Hou, Keith Woeste, Zhengchun Shang, Xiaobang Peng, Peng Zhao, Shuoxin Zhang
Humic substances in soil DNA samples can influence the assessment of microbial diversity and community composition. Using multiple steps during or after cell lysis adds expenses, is time-consuming, and causes DNA loss. A pretreatment of soil samples and a single step DNA extraction may improve experimental results. In order to optimize a protocol for obtaining high purity DNA from soil microbiota, five prewashing agents were compared in terms of their efficiency and effectiveness in removing soil contaminants...
October 2016: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/27524249/potential-risks-of-the-residue-from-samarco-s-mine-dam-burst-bento-rodrigues-brazil
#15
Fabiana Roberta Segura, Emilene Arusievicz Nunes, Fernanda Pollo Paniz, Ana Carolina Cavalheiro Paulelli, Gabriela Braga Rodrigues, Gilberto Úbida Leite Braga, Walter Dos Reis Pedreira Filho, Fernando Barbosa, Giselle Cerchiaro, Fábio Ferreira Silva, Bruno Lemos Batista
On November 5th, 2015, Samarco's iron mine dam - called Fundão - spilled 50-60 million m(3) of mud into Gualaxo do Norte, a river that belongs to Rio Doce Basin. Approximately 15 km(2) were flooded along the rivers Gualaxo do Norte, Carmo and Doce, reaching the Atlantic Ocean on November 22nd, 2015. Six days after, our group collected mud, soil and water samples in Bento Rodrigues (Minas Gerais, Brazil), which was the first impacted area. Overall, the results, water samples - potable and surface water from river - presented chemical elements concentration according to Brazilian environmental legislations, except silver concentration in surface water that ranged from 1...
November 2016: Environmental Pollution
https://www.readbyqxmd.com/read/27508881/pigments-from-uv-resistant-antarctic-bacteria-as-photosensitizers-in-dye-sensitized-solar-cells
#16
N Órdenes-Aenishanslins, G Anziani-Ostuni, M Vargas-Reyes, J Alarcón, A Tello, J M Pérez-Donoso
Here we report the use of pigments produced by UV-resistant Antarctic bacteria as photosensitizers in Dye Sensitized Solar Cells (DSSCs). Pigments were obtained from red and yellow colored psychrotolerant bacteria isolated from soils of King George Island, Antarctica. Based on metabolic characteristics and 16s DNA sequence, pigmented bacteria were identified as Hymenobacter sp. (red) and Chryseobacterium sp. (yellow). Pigments produced by these microorganisms were extracted and classified as carotenoids based on their spectroscopic and structural characteristics, determined by UV-Vis spectrophotometry and infrared spectroscopy (FTIR), respectively...
September 2016: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/27454095/ecological-restoration-of-a-copper-polluted-vineyard-long-term-impact-of-farmland-abandonment-on-soil-bio-chemical-properties-and-microbial-communities
#17
Luciano Cavani, Luisa M Manici, Francesco Caputo, Elisabetta Peruzzi, Claudio Ciavatta
This study aimed at investigating the degree of interference of high soil copper (Cu) contamination when an old vineyard is converted into a protected area. This study was performed within an intensive agricultural system; it was organized into a two-factorial nested design to analyze the impact of management (conventional vs re-naturalized orchard) and position within each orchard (tree-rows and strips). Chemical and biochemical properties along with bacterial and fungal communities, evaluated with PCR-DGGE starting from total soil DNA, were analyzed...
November 1, 2016: Journal of Environmental Management
https://www.readbyqxmd.com/read/27450478/desert-perennial-shrubs-shape-the-microbial-community-miscellany-in-laimosphere-and-phyllosphere-space
#18
Varsik Martirosyan, Adrian Unc, Gad Miller, Tirza Doniger, Chaim Wachtel, Yosef Steinberger
Microbial function, composition, and distribution play a fundamental role in ecosystem ecology. The interaction between desert plants and their associated microbes is expected to greatly affect their response to changes in this harsh environment. Using comparative analyses, we studied the impact of three desert shrubs, Atriplex halimus (A), Artemisia herba-alba (AHA), and Hammada scoparia (HS), on soil- and leaf-associated microbial communities. DNA extracted from the leaf surface and soil samples collected beneath the shrubs were used to study associated microbial diversity using a sequencing survey of variable regions of bacterial 16S rRNA and fungal ribosomal internal transcribed spacer (ITS1)...
October 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27446009/flow-cytometric-and-16s-sequencing-methodologies-for-monitoring-the-physiological-status-of-the-microbiome-in-powdered-infant-formula-production
#19
Amir H P Anvarian, Yu Cao, Shabarinath Srikumar, Séamus Fanning, Kieran Jordan
The aim of this study was to develop appropriate protocols for flow cytometric (FCM) and 16S rDNA sequencing investigation of the microbiome in a powdered infant formula (PIF) production facility. Twenty swabs were collected from each of the three care zones of a PIF production facility and used for preparing composite samples. For FCM studies, the swabs were washed in 200 mL phosphate buffer saline (PBS). The cells were harvested by three-step centrifugation followed by a single stage filtration. Cells were dispersed in fresh PBS and analyzed with a flow cytometer for membrane integrity, metabolic activity, respiratory activity and Gram characteristics of the microbiome using various fluorophores...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27411981/cyanobacterial-diversity-of-western-european-biological-soil-crusts-along-a-latitudinal-gradient
#20
Laura Williams, Katharina Loewen-Schneider, Stefanie Maier, Burkhard Büdel
Cyanobacteria associated with biological soil crusts (BSCs) have important attributes, such as nitrogen fixation and soil stabilisation. However, research on these organisms has been minimal, and their diversity and distribution throughout temperate Europe is currently unknown. The SCIN (Soil Crust International) project is a multidisciplinary research initiative that aims to achieve improved understanding of the BSCs of Europe, one facet being an investigation into the cyanobacterial communities of BSCs across a latitudinal gradient...
October 2016: FEMS Microbiology Ecology
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