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https://www.readbyqxmd.com/read/28932218/alleviation-of-heavy-metal-stress-in-plants-and-remediation-of-soil-by-rhizosphere-microorganisms
#1
REVIEW
Jitendra Mishra, Rachna Singh, Naveen K Arora
Increasing concentration of heavy metals (HM) due to various anthropogenic activities is a serious problem. Plants are very much affected by HM pollution particularly in contaminated soils. Survival of plants becomes tough and its overall health under HM stress is impaired. Remediation of HM in contaminated soil is done by physical and chemical processes which are costly, time-consuming, and non-sustainable. Metal-microbe interaction is an emerging but under-utilized technology that can be exploited to reduce HM stress in plants...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28929383/evaluation-of-the-impact-of-six-different-dna-extraction-methods-for-the-representation-of-the-microbial-community-associated-with-human-chronic-wound-infections-using-a-gel-based-dna-profiling-method
#2
Ayomi Dilhari, Asanga Sampath, Chinthika Gunasekara, Neluka Fernando, Deepaka Weerasekara, Chris Sissons, Andrew McBain, Manjula Weerasekera
Infected chronic wounds are polymicrobial in nature which include a diverse group of aerobic and anaerobic microorganisms. Majority of these communal microorganisms are difficult to grow in vitro. DNA fingerprinting methods such as polymerase chain reaction-denaturation gradient gel electrophoresis (PCR-DGGE) facilitate the microbial profiling of complex ecosystems including infected chronic wounds. Six different DNA extraction methods were compared for profiling of the microbial community associated with chronic wound infections using PCR-DGGE...
September 19, 2017: AMB Express
https://www.readbyqxmd.com/read/28918434/improved-dna-purification-with-quality-assurance-for-evaluation-of-the-microbial-genetic-content-of-constructed-wetlands
#3
Wenda Huang, Jingjing Guo, Ran Tao, Ying Man, Yunv Dai, Yang Yang
Efficient isolation of target DNA is a crucial first step of DNA-based metagenomic analyses of environmental samples. Insufficient quantity and purity of DNA isolated using commercial kits result in missing genetic information, especially for large-diameter substrates in constructed wetlands (CWs). Here, we addressed this problem by devising a cost-effective calcium chloride lysozyme-sodium dodecyl sulfate (SDS) method (CCLS), with key improvements in the steps of humic acid removal and cell lysis. The buffer comprising Tris, EDTA, Na2O2P7 and PVPP (TENP), and skim milk, could reduce adsorption between microorganisms and substrates, and calcium chloride precipitated and removed over 94% of humic acid...
September 16, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28910550/overview-of-craft-brewing-specificities-and-potentially-associated-microbiota
#4
Lindsey Rodhouse, Franck Carbonero
The brewing process differs slightly in craft breweries as compared to industrial breweries, as there are fewer control points. This arguably affects the microbiota of the final product. Beer contains several antimicrobial properties that protect it from pathogens, such as low pH, low oxygen and high carbon dioxide content, and the addition of hops. However, these hurdles have limited power controlling spoilage organisms. Contamination by these organisms can originate in the raw materials, persist in the environment, and be introduced by using flavoring ingredients later in the process...
September 14, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28910343/escherichia-coli-attachment-to-model-particulates-the-effects-of-bacterial-cell-characteristics-and-particulate-properties
#5
Xiao Liang, Chunyu Liao, Michelle L Soupir, Laura R Jarboe, Michael L Thompson, Philip M Dixon
E. coli bacteria move in streams freely in a planktonic state or attached to suspended particulates. Attachment is a dynamic process, and the fraction of attached microorganisms is thought to be affected by both bacterial characteristics and particulate properties. In this study, we investigated how the properties of cell surfaces and stream particulates influence attachment. Attachment assays were conducted for 77 E. coli strains and three model particulates (ferrihydrite, Ca-montmorillonite, or corn stover) under environmentally relevant conditions...
2017: PloS One
https://www.readbyqxmd.com/read/28906555/application-of-power-ultrasound-on-the-convective-drying-of-fruits-and-vegetables-effects-on-quality
#6
REVIEW
Óscar Rodríguez, Valeria Eim, Carmen Rosselló, Antoni Femenia, Juan A Cárcel, Susana Simal
Drying allows the obtaining of products with a long shelf life by reducing the water activity to a level low enough for the growth of microorganisms, enzymatic reactions, and other deteriorative reactions to be inhibited. Despite the benefits of this operation, the quality of heat sensitive products is diminished when high temperatures are used. The use of low drying temperatures reduces the heat damage but being the drying time longer, oxidation reactions occur and a reduction of the quality is also observed...
September 14, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28906493/rapid-curation-of-gene-disruption-collections-using-knockout-sudoku
#7
Isao A Anzai, Lev Shaket, Oluwakemi Adesina, Michael Baym, Buz Barstow
Knockout Sudoku is a method for the construction of whole-genome knockout collections for a wide range of microorganisms with as little as 3 weeks of dedicated labor and at a cost of ∼$10,000 for a collection for a single organism. The method uses manual 4D combinatorial pooling, next-generation sequencing, and a Bayesian inference algorithm to rapidly process and then accurately annotate the extremely large progenitor transposon insertion mutant collections needed to achieve saturating coverage of complex microbial genomes...
October 2017: Nature Protocols
https://www.readbyqxmd.com/read/28906012/pacbio-metabarcoding-of-fungi-and-other-eukaryotes-errors-biases-and-perspectives
#8
Leho Tedersoo, Ave Tooming-Klunderud, Sten Anslan
Second-generation, high-throughput sequencing methods have greatly improved our understanding of the ecology of soil microorganisms, yet the short barcodes (< 500 bp) provide limited taxonomic and phylogenetic information for species discrimination and taxonomic assignment. Here, we utilized the third-generation Pacific Biosciences (PacBio) RSII and Sequel instruments to evaluate the suitability of full-length internal transcribed spacer (ITS) barcodes and longer rRNA gene amplicons for metabarcoding Fungi, Oomycetes and other eukaryotes in soil samples...
September 14, 2017: New Phytologist
https://www.readbyqxmd.com/read/28899453/application-of-maldi-tof-ms-systems-in-the-rapid-identification-of-campylobacter-spp-of-public-health-importance
#9
Ying-Hsin Hsieh, Yun F Wang, Hercules Moura, Nancy Miranda, Steven Simpson, Ramnath Gowrishankar, John Barr, Khalil Kerdahi, Irshad M Sulaiman
Campylobacteriosis is an infectious gastrointestinal disease caused by Campylobacter spp.In most cases, it is either underdiagnosed or underreported due to poor diagnostics and limited databases. Several DNA-based molecular diagnostic techniques, including 16S ribosomal RNA (rRNA) sequence typing, have been widely used in the species identification of Campylobacter. Nevertheless, these assays are time-consuming and require a high quality of bacterial DNA. Matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) MS is an emerging diagnostic technology that can provide the rapid identification of microorganisms by using their intact cells without extraction or purification...
September 12, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28894894/advanced-microbial-analysis-for-wastewater-quality-monitoring-metagenomics-trend
#10
REVIEW
Jose Antonio Garrido-Cardenas, María Inmaculada Polo-López, Isabel Oller-Alberola
Urban Wastewater treatment plants (UWWTPs) have played an important and fundamental role in society for water purification of contaminated human wastewaters over the last decades. Microorganisms are very important in UWWTP as their metabolic activity significantly reduces the organic load of the UWW, although there is an uncertain gap in our knowledge regarding microbial consortium structure and their activity in UWWTP operation on a large scale. On the other hand, effluents of UWWTPs have come to be a new source of fresh water to ease water scarcity in many regions of the world, especially in intensive irrigation practices...
September 11, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28894102/recovery-of-nearly-8-000-metagenome-assembled-genomes-substantially-expands-the-tree-of-life
#11
Donovan H Parks, Christian Rinke, Maria Chuvochina, Pierre-Alain Chaumeil, Ben J Woodcroft, Paul N Evans, Philip Hugenholtz, Gene W Tyson
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination...
September 11, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28892512/grape-microbiome-as-a-reliable-and-persistent-signature-of-field-origin-and-environmental-conditions-in-cannonau-wine-production
#12
Valerio Mezzasalma, Anna Sandionigi, Ilaria Bruni, Antonia Bruno, Gianni Lovicu, Maurizio Casiraghi, Massimo Labra
Grape berries harbor a wide range of microbes originating from the vineyard environment, many of which are recognized for their role in the must fermentation process shaping wine quality. To better clarify the contribution of the microbiome of grape fruits during wine fermentation, we used high-throughput sequencing to identify bacterial and fungi communities associated with berries and musts of Cannonau. This is the most important cultivar-wine of Sardinia (Italy) where most vineyards are cultivated without phytochemical treatments...
2017: PloS One
https://www.readbyqxmd.com/read/28887415/inactivation-of-human-norovirus-gi-gii-and-surrogates-by-free-chlorine-in-postharvest-leafy-green-wash-water
#13
Nathan Dunkin, Shih-Chi Weng, Joseph G Jacangelo, Kellogg J Schwab
Human noroviruses (hNoVs) are a known public health concern associated with the consumption of leafy green vegetables. While a number of studies have investigated pathogen reduction on the surfaces of leafy greens during the postharvest washing process, there remains a paucity of data on the level of treatment needed to inactivate viruses in the wash water, which is critical for preventing cross-contamination. The objective of this study was to quantify the susceptibility of hNoV GI, hNoV GII, murine norovirus (MNV), and bacteriophage MS2 to free chlorine in whole leaf, chopped romaine, and shredded iceberg lettuce industrial leafy green wash waters, each sampled three times over a 4-month period...
September 8, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28884130/drinking-water-quality-status-and-contamination-in-pakistan
#14
REVIEW
M K Daud, Muhammad Nafees, Shafaqat Ali, Muhammad Rizwan, Raees Ahmad Bajwa, Muhammad Bilal Shakoor, Muhammad Umair Arshad, Shahzad Ali Shahid Chatha, Farah Deeba, Waheed Murad, Ijaz Malook, Shui Jin Zhu
Due to alarming increase in population and rapid industrialization, drinking water quality is being deteriorated day by day in Pakistan. This review sums up the outcomes of various research studies conducted for drinking water quality status of different areas of Pakistan by taking into account the physicochemical properties of drinking water as well as the presence of various pathogenic microorganisms. About 20% of the whole population of Pakistan has access to safe drinking water. The remaining 80% of population is forced to use unsafe drinking water due to the scarcity of safe and healthy drinking water sources...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28870406/probiotics-and-gastrointestinal-conditions-an-overview-of-evidence-from-the-cochrane-collaboration
#15
REVIEW
Elizabeth A Parker, Tina Roy, Christopher R D'Adamo, L Susan Wieland
Alterations in the composition of the gut microbiota are associated with a number of gastrointestinal (GI) conditions, including diarrhea, inflammatory bowel diseases (IBD), and liver diseases. Probiotics, live microorganisms that may confer a health benefit to the host when consumed, are commonly used as a therapy for treating these GI conditions by means of modifying the composition or activity of the microbiota. The purpose of this review was to summarize the evidence on probiotics and GI conditions available from Cochrane, a nonprofit organization that produces rigorous and high-quality systematic reviews of health interventions...
July 6, 2017: Nutrition
https://www.readbyqxmd.com/read/28870194/a-yeast-fermentate-improves-gastrointestinal-discomfort-and-constipation-by-modulation-of-the-gut-microbiome-results-from-a-randomized-double-blind-placebo-controlled-pilot-trial
#16
RANDOMIZED CONTROLLED TRIAL
Iris Pinheiro, Larry Robinson, An Verhelst, Massimo Marzorati, Björn Winkens, Pieter Van den Abbeele, Sam Possemiers
BACKGROUND: Constipation and symptoms of gastrointestinal discomfort such as bloating are common among otherwise healthy individuals, but with significant impact on quality of life. Despite the recognized contribution of the gut microbiome to this pathology, little is known about which group(s) of microorganism(s) are playing a role. A previous study performed in vitro suggests that EpiCor® fermentate has prebiotic-like properties, being able to favorably modulate the composition of the gut microbiome...
September 4, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28869549/microbiological-impact-of-the-use-of-reclaimed-wastewater-in-recreational-parks
#17
Oskar A Palacios, Francisco J Zavala-Díaz de la Serna, María de Lourdes Ballinas-Casarrubias, María S Espino-Valdés, Guadalupe V Nevárez-Moorillón
Reclaimed wastewater for irrigation is an opportunity for recovery of this natural resource. In this study, microbial risk from the use of treated wastewater for irrigation of recreational parks in the city of Chihuahua, evaluating the effect of distribution distance, season, and presence of storage tanks, was analyzed. Escherichia coli, Salmonella, and multidrug-resistant bacteria were recovered from samples of reclaimed water and soils at recreational parks in Chihuahua by the membrane filtration method, using selected agars for microbial growth...
September 4, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28867644/fracture-related-infection-a-consensus-on-definition-from-an-international-expert-group
#18
W J Metsemakers, M Morgenstern, M A McNally, T F Moriarty, I McFadyen, M Scarborough, N A Athanasou, P E Ochsner, R Kuehl, M Raschke, O Borens, Z Xie, S Velkes, S Hungerer, S L Kates, C Zalavras, P V Giannoudis, R G Richards, M H J Verhofstad
Fracture-related infection (FRI) is a common and serious complication in trauma surgery. Accurately estimating the impact of this complication has been hampered by the lack of a clear definition. The absence of a working definition of FRI renders existing studies difficult to evaluate or compare. In order to address this issue, an expert group comprised of a number of scientific and medical organizations has been convened, with the support of the AO Foundation, in order to develop a consensus definition. The process that led to this proposed definition started with a systematic literature review, which revealed that the majority of randomized controlled trials in fracture care do not use a standardized definition of FRI...
August 24, 2017: Injury
https://www.readbyqxmd.com/read/28866114/traditional-approaches-versus-mass-spectrometry-in-bacterial-identification-and-typing
#19
REVIEW
Angela Sloan, Gehua Wang, Keding Cheng
Biochemical methods such as metabolite testing and serotyping are traditionally used in clinical microbiology laboratories to identify and categorize microorganisms. Due to the large variety of bacteria, identifying representative metabolites is tedious, while raising high-quality antisera or antibodies unique to specific biomarkers used in serotyping is very challenging, sometimes even impossible. Although serotyping is a certified approach for differentiating bacteria such as E. coli and Salmonella at the subspecies level, the method is tedious, laborious, and not practical during an infectious disease outbreak...
October 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28861246/leaf-and-root-litter-decomposition-is-discontinued-at-high-altitude-tropical-montane-rainforests-contributing-to-carbon-sequestration
#20
Franca Marian, Dorothee Sandmann, Valentyna Krashevska, Mark Maraun, Stefan Scheu
We investigated how altitude affects the decomposition of leaf and root litter in the Andean tropical montane rainforest of southern Ecuador, that is, through changes in the litter quality between altitudes or other site-specific differences in microenvironmental conditions. Leaf litter from three abundant tree species and roots of different diameter from sites at 1,000, 2,000, and 3,000 m were placed in litterbags and incubated for 6, 12, 24, 36, and 48 months. Environmental conditions at the three altitudes and the sampling time were the main factors driving litter decomposition, while origin, and therefore quality of the litter, was of minor importance...
August 2017: Ecology and Evolution
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