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Soil microbiology

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https://www.readbyqxmd.com/read/28100131/influence-of-activated-sewage-sludge-amendment-on-pahs-removal-efficiency-from-a-naturally-contaminated-soil-application-of-the-landfarming-treatment
#1
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. Experimental activities were conducted in four laboratory scale reactors filled with corn cobs as bulking agent to reach bulk density of 640 kg/m(3)...
January 18, 2017: Environmental Technology
https://www.readbyqxmd.com/read/28099457/comparing-and-evaluating-metagenome-assembly-tools-from-a-microbiologist-s-perspective-not-only-size-matters
#2
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
https://www.readbyqxmd.com/read/28066816/from-genomes-to-phenotypes-traitar-the-microbial-trait-analyzer
#3
Aaron Weimann, Kyra Mooren, Jeremy Frank, Phillip B Pope, Andreas Bremges, Alice C McHardy
The number of sequenced genomes is growing exponentially, profoundly shifting the bottleneck from data generation to genome interpretation. Traits are often used to characterize and distinguish bacteria and are likely a driving factor in microbial community composition, yet little is known about the traits of most microbes. We describe Traitar, the microbial trait analyzer, which is a fully automated software package for deriving phenotypes from a genome sequence. Traitar provides phenotype classifiers to predict 67 traits related to the use of various substrates as carbon and energy sources, oxygen requirement, morphology, antibiotic susceptibility, proteolysis, and enzymatic activities...
November 2016: MSystems
https://www.readbyqxmd.com/read/28063834/statistical-assessment-of-dumpsite-soil-suitability-to-enhance-methane-bio-oxidation-under-interactive-influence-of-substrates-and-temperature
#4
Somvir Bajar, Anita Singh, C P Kaushik, Anubha Kaushik
Biocovers are considered as the most effective and efficient way to treat methane (CH4) emission from dumpsites and landfills. Active methanotrophs in the biocovers play a crucial role in reduction of emissions through microbiological methane oxidation. Several factors affecting methane bio-oxidation (MOX) have been well documented, however, their interactive effect on the oxidation process needs to be explored. Therefore, the present study was undertaken to investigate the suitability of a dumpsite soil to be employed as biocover, under the influence of substrate concentrations (CH4 and O2) and temperature at variable incubation periods...
January 4, 2017: Waste Management
https://www.readbyqxmd.com/read/28030923/microbiological-characterization-of-vegetables-and-their-rhizosphere-soil-in-eastern-poland
#5
Teresa Kłapeć, Angelina Wójcik-Fatla, Alicja Cholewa, Grażyna Cholewa, Jacek Dutkiewicz
The aim of this study was to investigate the bacteriological quality of 5 kinds of vegetables (lettuce, dill, radish, beetroot, carrot) and their rhizosphere soil, originating from conventional farms located in the Lublin Province of Eastern Poland. A total number of 35 samples of fresh vegetables (FV) taken immediately from soil, 35 samples of soil from rhizosphere of these vegetables (SR) and 35 samples of vegetables sold at retail in the markets in Lublin (VR) were examined. The samples were analysed for the content of: aerobic mesophilic bacteria (AMB) grown at 30°C and 37°C, Gram-negative bacteria of Enterobacteriaceae family, faecal coliform (FC) bacteria, Salmonella spp...
23, 2016: Annals of Agricultural and Environmental Medicine: AAEM
https://www.readbyqxmd.com/read/27992819/a-comparative-study-on-the-influence-of-different-organic-amendments-on-trace-element-mobility-and-microbial-functionality-of-a-polluted-mine-soil
#6
P Abad-Valle, E Iglesias-Jiménez, E Álvarez-Ayuso
A mine soil heavily polluted with zinc and cadmium was employed to evaluate the capacity of organic amendments of different origin to simultaneously reduce soil trace element mobility and enhance soil microbial functionality. With this aim, four organic products, namely olive processing solid waste (OPSW), municipal solid waste compost (MSWC), leonardite and peat, were applied individually at different doses (0, 1, 2 and 5%) to mine soil under controlled laboratory conditions. Extraction studies and analysis of soil microbiological parameters (basal soil respiration and dehydrogenase, β-glucosidase, urease, arylsulfatase and acid and alkaline phosphatase activities) were performed to assess the effect of such amendments on soil restoration...
March 1, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/27975077/microbial-ecology-where-are-we-now
#7
Lisa A Boughner, Pallavi Singh
Conventional microbiological methods have been readily taken over by newer molecular techniques due to the ease of use, reproducibility, sensitivity and speed of working with nucleic acids. These tools allow high throughput analysis of complex and diverse microbial communities, such as those in soil, freshwater, saltwater, or the microbiota living in collaboration with a host organism (plant, mouse, human, etc). For instance, these methods have been robustly used for characterizing the plant (rhizosphere), animal and human microbiome specifically the complex intestinal microbiota...
November 2016: Postdoc Journal: a Journal of Postdoctoral Research and Postdoctoral Affairs
https://www.readbyqxmd.com/read/27966086/procedures-of-determining-organic-trace-compounds-in-municipal-sewage-sludge-a-review
#8
Petra C Lindholm-Lehto, Heidi S J Ahkola, Juha S Knuutinen
Sewage sludge is the largest by-product generated during the wastewater treatment process. Since large amounts of sludge are being produced, different ways of disposal have been introduced. One tempting option is to use it as fertilizer in agricultural fields due to its high contents of inorganic nutrients. This, however, can be limited by the amount of trace contaminants in the sewage sludge, containing a variety of microbiological pollutants and pathogens but also inorganic and organic contaminants. The bioavailability and the effects of trace contaminants on the microorganisms of soil are still largely unknown as well as their mixture effects...
December 13, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27966037/microbiology-meets-archaeology-soil-microbial-communities-reveal-different-human-activities-at-archaic-monte-iato-sixth-century-bc
#9
Rosa Margesin, José A Siles, Tomas Cajthaml, Birgit Öhlinger, Erich Kistler
Microbial ecology has been recognized as useful in archaeological studies. At Archaic Monte Iato in Western Sicily, a native (indigenous) building was discovered. The objective of this study was the first examination of soil microbial communities related to this building. Soil samples were collected from archaeological layers at a ritual deposit (food waste disposal) in the main room and above the fireplace in the annex. Microbial soil characterization included abundance (cellular phospholipid fatty acids (PLFA), viable bacterial counts), activity (physiological profiles, enzyme activities of viable bacteria), diversity, and community structure (bacterial and fungal Illumina amplicon sequencing, identification of viable bacteria)...
December 13, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27964987/analysis-of-the-contaminants-released-from-municipal-solid-waste-landfill-site-a-case-study
#10
S R Samadder, R Prabhakar, D Khan, D Kishan, M S Chauhan
Release and transport of leachate from municipal solid waste landfills pose a potential hazard to both surrounding ecosystems and human populations. In the present study, soil, groundwater, and surface water samples were collected from the periphery of a municipal solid waste landfill (located at Ranital of Jabalpur, Madhya Pradesh, India) for laboratory analysis to understand the release of contaminants. The landfill does not receive any solid wastes for dumping now as the same is under a landfill closure plan...
December 10, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/27912981/examining-the-association-between-surface-bioburden-and-frequently-touched-sites-in-intensive-care
#11
C E Adams, J Smith, V Watson, C Robertson, S J Dancer
BACKGROUND: Critical care patients are at increased risk of infection. Near-patient surfaces act as reservoirs of microbial soil, which may contain pathogens. AIM: To correlate soil levels with hand-touch frequency of near-patient sites in an intensive care unit (ICU). METHODS: Five sites around each bed in a 10-bed ICU were screened for total microbial soil (cfu/cm(2)) and Staphylococcus aureus every month for 10 months. Selected sites were infusion pump and cardiac monitor, left and right bedrails, and bed table...
January 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/27896584/soil-contamination-assessment-for-pb-zn-and-cd-in-a-slag-disposal-area-using-the-integration-of-geochemical-and-microbiological-data
#12
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
https://www.readbyqxmd.com/read/27878544/spatial-and-temporal-assessment-of-surface-water-quality-in-the-arka-river-akkar-lebanon
#13
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 2016: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/27872971/the-influence-of-nitrogen-on-the-biological-properties-of-soil-contaminated-with-zinc
#14
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
https://www.readbyqxmd.com/read/27871132/aspergillus-penicillioides-differentiation-and-cell-division-at-0-585-water-activity
#15
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
https://www.readbyqxmd.com/read/27866360/effect-of-the-edaphic-factors-and-metal-content-in-soil-on-the-diversity-of-trichoderma-spp
#16
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
https://www.readbyqxmd.com/read/27856492/forest-microbiome-diversity-complexity-and-dynamics
#17
REVIEW
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
https://www.readbyqxmd.com/read/27847506/low-concentration-ciprofloxacin-selects-plasmid-mediated-quinolone-resistance-encoding-genes-and-affects-bacterial-taxa-in-soil-containing-manure
#18
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
https://www.readbyqxmd.com/read/27843720/proteogenomic-analyses-indicate-bacterial-methylotrophy-and-archaeal-heterotrophy-are-prevalent-below-the-grass-root-zone
#19
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
https://www.readbyqxmd.com/read/27833105/environmental-microbiology-a-small-soil-bacterium-dominates
#20
Ursula Hofer
No abstract text is available yet for this article.
November 11, 2016: Nature Reviews. Microbiology
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