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Soil microbiology

Mariana Consiglio Kasemodel, Jacqueline Zanin Lima, Isabel Kimiko Sakamoto, Maria Bernadete Amancio Varesche, Julio Cesar Trofino, Valéria Guimarães Silvestre Rodrigues
Improper disposal of mining waste is still considered a global problem, and further details on the contamination by potentially toxic metals are required for a proper assessment. In this context, it is important to have a combined view of the chemical and biological changes in the mining dump area. Thus, the objective of this study was to evaluate the Pb, Zn and Cd contamination in a slag disposal area using the integration of geochemical and microbiological data. Analyses of soil organic matter (SOM), pH, Eh, pseudo-total concentration of metals, sequential extraction and microbial community by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) were conducted...
December 2016: Environmental Monitoring and Assessment
Claude Daou, Rony Nabbout, Amine Kassouf
Surface water quality monitoring constitutes a crucial and important step in any water quality management system. Twenty-three physicochemical and microbiological parameters were assessed in surface water samples collected from the Arka River located in the Akkar District, north of Lebanon. Eight sampling locations were considered along the river and seven sampling campaigns were performed in order to evaluate spatial and temporal influences. The extraction of relevant information from this relatively large data set was done using principal component analysis (PCA), being a very well established chemometric tool in this field...
December 0: Environmental Monitoring and Assessment
Rafał Strachel, Jadwiga Wyszkowska, Małgorzata Baćmaga
This study analyzed the relationship between nitrogen fertilization and the biological properties of soil contaminated with zinc. The influence of various concentrations of zinc and nitrogen on the microbiological and biochemical activity of soil was investigated. In a laboratory experiment, loamy sand with pHKCl 5.6 was contaminated with zinc (ZnCl2) and fertilized with urea as a source of nitrogen. The activity of acid phosphatase, alkaline phosphatase, urease and β-glucosidase, and microbial counts were determined in soil samples after 2 and 20 weeks of incubation...
November 21, 2016: Bulletin of Environmental Contamination and Toxicology
Andrew Stevenson, Philip G Hamill, Callum J O'Kane, Gerhard Kminek, John D Rummel, Mary A Voytek, Jan Dijksterhuis, John E Hallsworth
Water availability acts as the most-stringent constraint for life on Earth. Thus, understanding the water relations of microbial extremophiles is imperative to our ability to increase agricultural productivity (e.g., by enhancing the processing and turnover of dead organic matter in soils of arid regions); reduce human exposure to mycotoxins in buildings and our food-supply chain; prevent the spoilage of foods/animal feeds, books, museum specimens and artworks; and better control microbiology of industrial fermentations...
November 21, 2016: Environmental Microbiology
Gordana Racić, Péter Körmöczi, László Kredics, Vera Raičević, Beba Mutavdžić, Miroslav M Vrvić, Dejana Panković
Influence of edaphic factors and metal content on diversity of Trichoderma species at 14 different soil sampling locations, on two depths, was examined. Forty-one Trichoderma isolates from 14 sampling sites were determined as nine species based on their internal transcribed spacer (ITS) sequences. Our results indicate that weakly alkaline soils are rich sources of Trichoderma strains. Also, higher contents of available K and P are connected with higher Trichoderma diversity. Increased metal content in soil was not inhibiting factor for Trichoderma species occurrence...
November 19, 2016: Environmental Science and Pollution Research International
Petr Baldrian
Globally, forests represent highly productive ecosystems that act as carbon sinks where soil organic matter is formed from residuals after biomass decomposition as well as from rhizodeposited carbon. Forests exhibit a high level of spatial heterogeneity and the importance of trees, the dominant primary producers, for their structure and functioning. Fungi, bacteria and archaea inhabit various forest habitats: foliage, the wood of living trees, the bark surface, ground vegetation, roots and the rhizosphere, litter, soil, deadwood, rock surfaces, invertebrates, wetlands or the atmosphere, each of which has its own specific features, such as nutrient availability or temporal dynamicy and specific drivers that affect microbial abundance, the level of dominance of bacteria or fungi as well as the composition of their communities...
November 16, 2016: FEMS Microbiology Reviews
Ting Huang, Ying Xu, Jie Zeng, Dong-Hao Zhao, Liang Li, Xiao-Ping Liao, Ya-Hong Liu, Jian Sun
The spread of antimicrobial resistance in environment is promoted at least in part by the inappropriate use of antibiotics in animals and humans. The present study was designed to investigate the impact of different concentrations of ciprofloxacin in soil containing manure on the development of plasmid-mediated quinolone resistance (PMQR) - encoding genes and the abundance of soil bacterial communities. For these studies, high-throughput next-generation sequencing of 16S rRNA, real-time polymerase chain reaction and standard microbiologic culture methods were utilized...
2016: Frontiers in Microbiology
Cristina N Butterfield, Zhou Li, Peter F Andeer, Susan Spaulding, Brian C Thomas, Andrea Singh, Robert L Hettich, Kenwyn B Suttle, Alexander J Probst, Susannah G Tringe, Trent Northen, Chongle Pan, Jillian F Banfield
Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10-20 cm and 30-40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate...
2016: PeerJ
Ursula Hofer
No abstract text is available yet for this article.
November 11, 2016: Nature Reviews. Microbiology
Rosana Faria Vieira, Ricardo Antônio Almeida Pazianotto
BACKGROUND: One of the main concerns related to the increasing use of sewage sludge in the soil is the possible presence of excess nutrients, which could cause environmental problems and detrimental effects on the soil microorganisms, considered essential to soil nutrient cycling. Thus, the objective of this work was to evaluate the microbial biomass and activity and some chemical characteristics of one specific tropical soil, classified as Dark Red Distroferric Latosol, of a loamy/clayey texture, in a long-term field experiment using anaerobically digested household sludge amendment...
2016: SpringerPlus
Vania Elisabete Schneider, Roger Vasques Marques, Taison Anderson Bortolin, Gisele Cemin, Geise Macedo Dos Santos
Pig farming is one of the human activities carried out to meet the increasing food demand by the increasing population. South Brazil is the region with most intensive pig farming in the country, exerting pressure on the water and soil environments by the relevant pollutant emissions. Therefore, the main objective of this work was to assess pig farming pollution by monitoring superficial water qualities of the Taquari-Antas Watershed in South Brazil. The study area is about 8062 km(2) (south latitude 292,614, 282,624 and west longitude 520,802, 504,554)...
December 0: Environmental Monitoring and Assessment
R M Hernández-Hernández, A Roldán, F Caravaca, G Rodriguez-Caballero, M P Torres, F T Maestre, M M Alguacil
Knowledge of the arbuscular mycorrhizal fungal assemblages in the Trachypogon savanna ecosystems is very important to a better understanding of the ecological processes mediated by this soil microbial group that affects multiple ecosystem functions. Considering the hypothesis that the biocrusts can be linked to vegetation through the arbuscular fungi mycelial network, the objectives proposed in this study were to determine (i) whether there are arbuscular mycorrhizal fungi (AMF) in the biocrusts (ii) whether arbuscular mycorrhizal fungal assemblages are linked to the Trachypogon patches, and (iii) whether the composition of the assemblages is related to soil properties affected by microbiological activity...
September 30, 2016: Science of the Total Environment
Rasmus Hare Jensen
Antifungal drug resistance is a multifaceted clinical challenge, and when present, a primary cause of treatment failure in patients with severe fungal infections. Changing epidemiology, increasing resistance rates and a narrow antifungal armamentarium may further underline the required attention on resistance particularly within the most prevalent invasive fungal infections caused by Candida yeasts and Aspergillus moulds. In Denmark, the resistance epidemiology remains to be fully elucidated. This thesis sought to address this demand as well as provide insight into the landscape of underlying molecular resistance mechanisms...
October 2016: Danish Medical Journal
Tommaso Bardelli, María Gómez-Brandón, Judith Ascher-Jenull, Flavio Fornasier, Paola Arfaioli, Davide Francioli, Markus Egli, Giacomo Sartori, Heribert Insam, Giacomo Pietramellara
Due to their sensitivity to changing environmental conditions sub- and alpine soils are often monitored in the context of climate change, usually, however, neglecting slope exposure. Therefore, we set up a climosequence-approach to study the effect of exposure and, in general, climate, on the microbial biomass and microbial diversity and activity, comprising five pairs of north (N)- and south (S)-facing sites along an altitudinal gradient ranging from 1200 to 2400m a.s.l. in the Italian Alps (Trentino Alto Adige, Italy)...
September 28, 2016: Science of the Total Environment
Valeria Ancona, Anna Barra Caracciolo, Paola Grenni, Martina Di Lenola, Claudia Campanale, Angelantonio Calabrese, Vito Felice Uricchio, Giuseppe Mascolo, Angelo Massacci
A plant-assisted bioremediation strategy was applied in an area located in Southern Italy, close to the city of Taranto, historically contaminated by polychlorinated biphenyls (PCBs) and heavy metals. A specific poplar clone (Monviso) was selected for its ability to promote organic pollutant degradation in the rhizosphere, as demonstrated elsewhere. Chemical and microbiological analyses were performed at the time of poplar planting in selected plots at different distances from the trunk (0.25-1m) and at different soil depths (0-20 and 20-40cm), at day 420...
September 26, 2016: New Biotechnology
Aditi Sengupta, Yadi Wang, Antonio A Meira Neto, Katarena A Matos, Katerina Dontsova, Rob Root, Julie W Neilson, Raina M Maier, Jon Chorover, Peter A Troch
Studying co-evolution of hydrological and biogeochemical processes in the subsurface of natural landscapes can enhance the understanding of coupled Earth-system processes. Such knowledge is imperative in improving predictions of hydro-biogeochemical cycles, especially under climate change scenarios. We present an experimental method, designed to capture sub-surface heterogeneity of an initially homogeneous soil system. This method is based on destructive sampling of a soil lysimeter designed to simulate a small-scale hillslope...
2016: Journal of Visualized Experiments: JoVE
A S Gregory, K Ritz, S P McGrath, J N Quinton, K W T Goulding, R J A Jones, J A Harris, R Bol, P Wallace, E S Pilgrim, A P Whitmore
National governments are becoming increasingly aware of the importance of their soil resources and are shaping strategies accordingly. Implicit in any such strategy is that degradation threats and their potential effect on important soil properties and functions are defined and understood. In this paper, we aimed to review the principal degradation threats on important soil properties in the UK, seeking quantitative data where possible. Soil erosion results in the removal of important topsoil and, with it, nutrients, C and porosity...
October 2015: Soil Use and Management
Vikram Bhatia, Anu Gupta, Shweta Sharma, Rajeev Shandil, Manav Wadhawan, Nitesh Agrawal, Ajay Kumar
BACKGROUND AND AIM: Endoscopic ultrasound (EUS) aspiration needles are single-use devices. However, in many centers, because of cost-constraints, these devices are reused multiple times. We studied microbiological contamination and bioburden on reprocessed needles to evaluate whether these devices can be successfully sterilized. METHODS: We studied 10 EUS needles each of 19 G, 22 G, and 25 G in size, and five 22-G ProCore needles. After initial use, each needle was reprocessed by a standardized protocol...
September 16, 2016: Digestive Endoscopy: Official Journal of the Japan Gastroenterological Endoscopy Society
Cláudia Marques-Dos-Santos Cordovil, Tiago Filipe Alves, Pedro Mendes, Amarilis de Varennes, Sílvio César Sampaio, Renata Machado Dos Santos Pinto
BACKGROUND: biofuel crops are gaining importance due to the need to replace non renewable sources. Also, due to the increasing amounts of wastes generated there is the need to recycle them to the soil, both to fertilize crops and to improve soil physical properties through OM increase and microbiological changes in the ryzosphere. So, we studied the influence of six biofuel crops (elephant-grass, giant-cane, sugarcane, blue-gum, black-cottonwood, willow) on the decomposition rate and enzymatic activity of composted municipal solid waste and poultry manure...
September 13, 2016: Journal of the Science of Food and Agriculture
Simone Gwosdz, Julia M West, David Jones, Jana Rakoczy, Kay Green, Tom Barlow, Marco Blöthe, Karon Smith, Michael Steven, Martin Krüger
Impacts of long-term CO2 exposure on environmental processes and microbial populations of near-surface soils are poorly understood. This near-surface long-term CO2 injection study demonstrated that soil microbiology and geochemistry is influenced more by seasonal parameters than elevated CO2 Soil samples were taken during a 3-year field experiment including sampling campaigns before, during and after 24 months of continuous CO2 injection. CO2 concentrations within CO2-injected plots increased up to 23% during the injection period...
December 2016: FEMS Microbiology Ecology
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