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Soil microbiology

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https://www.readbyqxmd.com/read/28432990/influence-of-red-mud-on-soil-microbial-communities-application-and-comprehensive-evaluation-of-the-biolog-ecoplate-approach-as-a-tool-in-soil-microbiological-studies
#1
Viktória Feigl, Éva Ujaczki, Emese Vaszita, Mónika Molnár
Red mud can be applied as soil ameliorant to acidic, sandy and micronutrient deficient soils. There are still knowledge gaps regarding the effects of red mud on the soil microbial community. The Biolog EcoPlate technique is a promising tool for community level physiological profiling. This study presents a detailed evaluation of Biolog EcoPlate data from two case studies. In experiment "A" red mud from Ajka (Hungary) was mixed into acidic sandy soil in soil microcosms at 5-50 w/w%. In experiement "B" red mud soil mixture was mixed into low quality subsoil in a field experiment at 5-50 w/w%...
April 19, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28412024/prevalence-of-bacterial-contamination-in-platelet-concentrates-at-the-national-center-of-blood-transfusion-mexico
#2
G Ibáñez-Cervantes, J M Bello-López, V Fernández-Sánchez, C A Domínguez-Mendoza, L I Acevedo-Alfaro
OBJECTIVES: Most common bacterial sepsis associated with transfusion is caused by contaminated Platelet Concentrates (PC). The screening of PC to detect bacterial contamination is obligatory in Mexico, and it is carried out in quality control programs. In Mexico, the identification and molecular characterization of bacterial contaminants to detect contamination sources have not been implemented due to high costs; however, it is an actual current need. MATERIAL AND METHODS: One hundred PC were randomly selected and microbiologically analyzed...
April 12, 2017: Transfusion Clinique et Biologique: Journal de la Société Française de Transfusion Sanguine
https://www.readbyqxmd.com/read/28400755/comparative-evaluation-of-four-bacteria-specific-primer-pairs-for-16s-rrna-gene-surveys
#3
Sofie Thijs, Michiel Op De Beeck, Bram Beckers, Sascha Truyens, Vincent Stevens, Jonathan D Van Hamme, Nele Weyens, Jaco Vangronsveld
Bacterial taxonomic community analyses using PCR-amplification of the 16S rRNA gene and high-throughput sequencing has become a cornerstone in microbiology research. To reliably detect the members, or operational taxonomic units (OTUs), that make up bacterial communities, taxonomic surveys rely on the use of the most informative PCR primers to amplify the broad range of phylotypes present in up-to-date reference databases. However, primers specific for the domain Bacteria were often developed some time ago against database versions that are now out of date...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28393846/an-algorithm-of-association-rule-mining-for-microbial-energy-prospection
#4
Muhammad Shaheen, Muhammad Shahbaz
The presence of hydrocarbons beneath earth's surface produces some microbiological anomalies in soils and sediments. The detection of such microbial populations involves pure bio chemical processes which are specialized, expensive and time consuming. This paper proposes a new algorithm of context based association rule mining on non spatial data. The algorithm is a modified form of already developed algorithm which was for spatial database only. The algorithm is applied to mine context based association rules on microbial database to extract interesting and useful associations of microbial attributes with existence of hydrocarbon reserve...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28390702/low-effect-of-phenanthrene-bioaccessibility-on-its-biodegradation-in-diffusely-contaminated-soil
#5
M Crampon, A Cébron, F Portet-Koltalo, S Uroz, F Le Derf, J Bodilis
This study focused on the role of bioaccessibility in the phenanthrene (PHE) biodegradation in diffusely contaminated soil, by combining chemical and microbiological approaches. First, we determined PHE dissipation rates and PHE sorption/desorption isotherms for two soils (PPY and Pv) presenting similar chronic PAH contamination, but different physico-chemical properties. Our results revealed that the PHE dissipation rate was significantly higher in the Pv soil compared to the PPY soil, while PHE sorption/desorption isotherms were similar...
April 6, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28303476/a-review-of-clinical-cases-of-infection-with-photorhabdus-asymbiotica
#6
John G Gerrard, Robert P Stevens
The three recognised Photorhabdus species are bioluminescent Gram-negative bacilli of the family Enterobacteriaceae. They are all pathogenic to insects and form a symbiotic relationship with nematodes of the genus Heterorhabditis. P. luminescens and P. temperata are both harmless to humans whilst P. asymbiotica, on the other hand, is a human pathogen that is a symbiont of the newly described nematode vector, Heterorhabditis gerrardi. In this chapter, we review the epidemiological and clinical features of eighteen human cases of P...
March 17, 2017: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/28300153/brucella-spp-of-amphibians-comprise-genomically-diverse-motile-strains-competent-for-replication-in-macrophages-and-survival-in-mammalian-hosts
#7
Sascha Al Dahouk, Stephan Köhler, Alessandra Occhialini, María Pilar Jiménez de Bagüés, Jens Andre Hammerl, Tobias Eisenberg, Gilles Vergnaud, Axel Cloeckaert, Michel S Zygmunt, Adrian M Whatmore, Falk Melzer, Kevin P Drees, Jeffrey T Foster, Alice R Wattam, Holger C Scholz
Twenty-one small Gram-negative motile coccobacilli were isolated from 15 systemically diseased African bullfrogs (Pyxicephalus edulis), and were initially identified as Ochrobactrum anthropi by standard microbiological identification systems. Phylogenetic reconstructions using combined molecular analyses and comparative whole genome analysis of the most diverse of the bullfrog strains verified affiliation with the genus Brucella and placed the isolates in a cluster containing B. inopinata and the other non-classical Brucella species but also revealed significant genetic differences within the group...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28262753/soil-bacterial-and-fungal-diversity-differently-correlated-with-soil-biochemistry-in-alpine-grassland-ecosystems-in-response-to-environmental-changes
#8
Yong Zhang, Shikui Dong, Qingzhu Gao, Shiliang Liu, Hasbagan Ganjurjav, Xuexia Wang, Xukun Su, Xiaoyu Wu
To understand effects of soil microbes on soil biochemistry in alpine grassland ecosystems under environmental changes, we explored relationships between soil microbial diversity and soil total nitrogen, organic carbon, available nitrogen and phosphorus, soil microbial biomass and soil enzyme activities in alpine meadow, alpine steppe and cultivated grassland on the Qinghai-Tibetan plateau under three-year warming, enhanced precipitation and yak overgrazing. Soil total nitrogen, organic carbon and NH4-N were little affected by overgrazing, warming or enhanced precipitation in three types of alpine grasslands...
March 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28251888/increase-in-outbreaks-of-gastroenteritis-linked-to-bathing-water-in-finland-in-summer-2014
#9
Ari Kauppinen, Haider Al-Hello, Outi Zacheus, Jaana Kilponen, Leena Maunula, Sari Huusko, Maija Lappalainen, Ilkka Miettinen, Soile Blomqvist, Ruska Rimhanen-Finne
An increased number of suspected outbreaks of gastroenteritis linked to bathing water were reported to the Finnish food- and waterborne outbreak (FWO) registry in July and August 2014. The investigation reports were assessed by a national outbreak investigation panel. Eight confirmed outbreaks were identified among the 15 suspected outbreaks linked to bathing water that had been reported to the FWO registry. According to the outbreak investigation reports, 1,453 persons fell ill during these outbreaks. Epidemiological and microbiological data revealed noroviruses as the main causative agents...
February 23, 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/28213706/plant-microbial-association-in-petroleum-and-gas-exploration-sites-in-the-state-of-assam-north-east-india-significance-for-bioremediation
#10
Hemen Sarma, N F Islam, M N V Prasad
The state of Assam in north-east India gained popularity in Asia because of discovery of oil. Pollution due to petroleum and gas exploration is a serious problem in Assam. Oil and gas exploration by various agencies in Assam resulted in soil pollution due to hydrocarbons (HCs) and heavy metals (HMs). Bioremediation gained considerable significance in addressing petroleum hydrocarbon polluted sites in various parts of the world. In this investigation, we have observed 15 species of plants belonging to grass growing on the contaminated soils...
February 17, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28207180/assembly-of-the-outermost-spore-layer-pieces-of-the-puzzle-are-coming-together
#11
George C Stewart
Certain endospore-forming soil dwelling bacteria are important human, animal or insect pathogens. These organisms produce spores containing an outer layer, the exosporium. The exosporium is the site of interactions between the spore and the soil environment and between the spore and the infected host during the initial stages of infection. The composition and assembly process of the exosporium are poorly understood. This is partly due to the extreme stability of the exosporium that has proven to be refractive to existing methods to deconstruct the intact structure into its component parts...
February 16, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28199147/microbiological-safety-of-animal-wastes-processed-by-physical-heat-treatment-an-alternative-to-eliminate-human-pathogens-in-biological-soil-amendments-as-recommended-by-the-food-safety-modernization-act
#12
Zhao Chen, Xiuping Jiang
Animal wastes have high nutritional value as biological soil amendments of animal origin for plant cultivation in sustainable agriculture; however, they can be sources of some human pathogens. Although composting is an effective way to reduce pathogen levels in animal wastes, pathogens may still survive under certain conditions and persist in the composted products, which potentially could lead to fresh produce contamination. According to the U.S. Food and Drug Administration Food Safety Modernization Act, alternative treatments are recommended for reducing or eliminating human pathogens in raw animal manure...
February 15, 2017: Journal of Food Protection
https://www.readbyqxmd.com/read/28185617/mycobacterium-kansasii
#13
James C Johnston, Leslie Chiang, Kevin Elwood
The incidence of Mycobacterium kansasii varies widely over time and by region, but this organism remains one of the most clinically relevant isolated species of nontuberculous mycobacteria. In contrast to other common nontuberculous mycobacteria, M. kansasii is infrequently isolated from natural water sources or soil. The major reservoir appears to be tap water. Infection is likely acquired through the aerosol route, with low infectivity in regions of endemicity. Human-to-human transmission is thought not to occur...
January 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28162132/wohlfahrtiimonas-chitiniclastica-current-insights-into-an-emerging-human-pathogen
#14
P Schröttner, W W Rudolph, U Damme, C Lotz, E Jacobs, F Gunzer
Since the first description of Wohlfahrtiimonas chitiniclastica in 2008, a number of well described case reports demonstrating its pathogenic role in humans have been published. Infections may be closely linked to flies, such as Wohlfahrtia magnifica, Lucilia sericata, Chrysomya megacephala or Musca domestica. These insects are potent vectors for the distribution of W. chitiniclastica causing local or systemic infections originating from wounds infested with fly larvae. However, other potential sources of transmission of W...
May 2017: Epidemiology and Infection
https://www.readbyqxmd.com/read/28150819/legacy-of-contaminant-n-sources-to-the-no3-signature-in-rivers-a-combined-isotopic-%C3%AE-15-n-no3-%C3%AE-18-o-no3-%C3%AE-11-b-and-microbiological-investigation
#15
Cyrielle Briand, Mathieu Sebilo, Pascale Louvat, Thierry Chesnot, Véronique Vaury, Maude Schneider, Valérie Plagnes
Nitrate content of surface waters results from complex mixing of multiple sources, whose signatures can be modified through N reactions occurring within the different compartments of the whole catchment. Despite this complexity, the determination of nitrate origin is the first and crucial step for water resource preservation. Here, for the first time, we combined at the catchment scale stable isotopic tracers (δ(15)N and δ(18)O of nitrate and δ(11)B) and fecal indicators to trace nitrate sources and pathways to the stream...
February 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28144889/screening-of-filamentous-fungi-for-antimicrobial-silver-nanoparticles-synthesis
#16
Cristiane Angélica Ottoni, Marta Filipa Simões, Sara Fernandes, Jonas Gomes Dos Santos, Elda Sabino da Silva, Rodrigo Fernando Brambilla de Souza, Alfredo Eduardo Maiorano
The present work had the goal of screening a batch of 20 fungal strains, isolated from sugar cane plantation soil, in order to identify those capable of biosynthesis of silver nanoparticles. These nanoparticles are known to have a large and effective application in clinical microbiology. Four strains were found to be capable of biosynthesis of silver nanoparticles. The biosynthesised nanoparticles were characterised by UV-vis spectroscopy, scanning electron microscopy, EDX, and XRD. They were found to have an average size of 30-100 nm, a regular round shape, and potential antimicrobial activity against Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28124968/-accurate-diagnosis-of-pseudomonas-luteola-in-routine-microbiology-laboratory-on-the-occasion-of-two-isolates
#17
Muharrem Çiçek, Gülşen Hasçelik, H Kaan Müştak, K Serdar Diker, Burçin Şener
Pseudomonas luteola which was previously known as Chryseomonas luteola; is a gram-negative, non-fermentative, aerobic, motile, non-spore-forming bacillus. It is frequently found as a saprophyte in soil, water and other damp environments and is an opportunistic pathogen in patients with underlying medical disorders or with indwelling catheters. It has been reported as an uncommon cause of bacteremia, sepsis, septic arthritis, meningitis, endocarditis, and peritonitis. Thus, early and accurate identification of this rare species is important for the treatment and also to provide information about the epidemiology of P...
October 2016: Mikrobiyoloji Bülteni
https://www.readbyqxmd.com/read/28118998/differentiating-current-and-past-pcb-and-pcdd-f-sources-the-role-of-a-large-contaminated-soil-site-in-an-industrialized-city-area
#18
Antonio Di Guardo, Elisa Terzaghi, Giuseppe Raspa, Sara Borin, Francesca Mapelli, Bessem Chouaia, Elisabetta Zanardini, Cristiana Morosini, Andrea Colombo, Elena Fattore, Enrico Davoli, Stefano Armiraglio, Vanna M Sale, Simone Anelli, Paolo Nastasio
Cities and contaminated areas can be primary or secondary sources of polychlorinated biphenyls (PCBs), dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs), and other chemicals, into air and soil and can influence the regional level of some of these pollutants. In a contaminated site, the evaluation of such emissions can be crucial in the choice of the remediation technology to be adopted. In the city of Brescia (Northern Italy), more than 100 ha of agricultural areas were contaminated with PCBs, PCDD/Fs and heavy metals, originating from the activities of a former PCB factory...
April 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28100131/influence-of-activated-sewage-sludge-amendment-on-pah-removal-efficiency-from-a-naturally-contaminated-soil-application-of-the-landfarming-treatment
#19
Borislava Lukić, David Huguenot, Antonio Panico, Eric D van Hullebusch, Giovanni Esposito
The removal of polycyclic aromatic hydrocarbons (PAHs) from a naturally co-contaminated soil by PAHs and heavy metals with an initial concentration of 620 mg of total PAHs kg(-1) dry soil was investigated. The efficiency of landfarming in removing phenanthrene, pyrene, benzo(a)pyrene and the group of total 16 US EPA PAHs was evaluated. The process was biostimulated by adding centrifuged activated sewage sludge (SS) as an organic amendment. The tested ratios of contaminated soil to SS were 1:2, 1:1, 1:0.5 and 1:0 as wet weight basis...
February 10, 2017: Environmental Technology
https://www.readbyqxmd.com/read/28099457/comparing-and-evaluating-metagenome-assembly-tools-from-a-microbiologist-s-perspective-not-only-size-matters
#20
John Vollmers, Sandra Wiegand, Anne-Kristin Kaster
With the constant improvement in cost-efficiency and quality of Next Generation Sequencing technologies, shotgun-sequencing approaches -such as metagenomics- have nowadays become the methods of choice for studying and classifying microorganisms from various habitats. The production of data has dramatically increased over the past years and processing and analysis steps are becoming more and more of a bottleneck. Limiting factors are partly the availability of computational resources, but mainly the bioinformatics expertise in establishing and applying appropriate processing and analysis pipelines...
2017: PloS One
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