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Applied and Environmental Microbiology

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https://www.readbyqxmd.com/read/28235879/experimental-manipulation-shows-a-greater-influence-of-population-than-dietary-perturbation-on-the-microbiome-of-tyrophagus-putrescentiae
#1
Tomas Erban, Ondrej Ledvinka, Marta Nesvorna, Jan Hubert
Tyrophagus putrescentiae (TP) is inhabited by bacteria that differ among mite populations (strains) and diets. Here, we investigated how the microbiome and fitness of TP are altered by dietary perturbations and mite populations. Four TP populations, referred to as Dog, Koppert, Laboratory and Phillips, underwent a perturbation, i.e., a dietary switch from a rearing diet to two experimental diets. The microbiome was investigated by sequencing the V1-V3 portion of the 16S rRNA gene, and selected bacterial taxa were quantified by qPCR using group/taxa-specific primers...
February 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28235878/botrytis-fragariae-a-new-species-causing-gray-mold-on-strawberries-shows-high-frequencies-of-specific-and-efflux-based-fungicide-resistance
#2
Sabrina Rupp, Cecilia Plesken, Sibylle Rumsey, Madeline Dowling, Guido Schnabel, Roland W S Weber, Matthias Hahn
Botrytis cinerea causes pre- and postharvest decay of many fruit and vegetable crops. A survey in German strawberry fields revealed Botrytis strains that differed from B. cinerea in diagnostic PCR markers and growth appearance. Phylogenetic analyses showed these strains to belong to an undescribed species in Botrytis clade 2, named Botrytis fragariae sp. nov. Isolates of B. fragariae were detected in strawberry fields throughout Germany, sometimes at similar frequencies as B. cinerea, and in the Southeastern United States...
February 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28235877/spread-from-the-sink-to-the-patient-in-situ-study-using-green-fluorescent-protein-gfp-expressing-escherichia-coli-to-model-bacterial-dispersion-from-hand-washing-sink-trap-reservoirs
#3
Shireen Kotay, Weidong Chai, William Guilford, Katie Barry, Amy J Mathers
There have been an increasing number of reports implicating Gammaproteobacteria often carrying genes of drug resistance from colonized sink traps to vulnerable hospitalized patients. However, the mechanism of transmission from the wastewater of the sink P-trap to patients remains poorly understood. Herein we report the use of a designated hand washing sink lab gallery to model dispersion of green fluorescent protein (GFP)- expressing Escherichia coli from sink wastewater to the surrounding environment. We found no dispersion of GFP-E...
February 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28235876/comparison-of-biochemical-properties-of-the-original-and-newly-identified-oleate-hydratases-from-stenotrophomonas-maltophilia
#4
Woo-Ri Kang, Min-Ju Seo, Kyung-Chul Shin, Jin-Byung Park, Deok-Kun Oh
Oleate hydratases (OhyAs) catalyze the conversion of unsaturated fatty acids to 10-hydroxy fatty acids, which are used as precursors of important industrial compounds, including lactones, and ω-hydroxycarboxylic and α,ω-dicarboxylic acids. The genes encoding OhyA and a putative fatty acid hydratase in Stenotrophomonas maltophilia were identified by genomic analysis. The putative fatty acid hydratase was purified and identified as an oleate hydratase (OhyA2) based on its substrate specificity. The activity of OhyA2 as a holoenzyme was not affected on adding cofactors, whereas the activity of the original oleate hydratase (OhyA1) showed an increase...
February 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28235875/engineering-cyanobacterial-cell-morphology-for-enhanced-recovery-and-processing-of-biomass
#5
Adam Jordan, Jenna Chandler, Joshua S MacCready, Jingcheng Huang, Katherine W Osteryoung, Daniel C Ducat
Cyanobacteria are emerging as alternative crop species for the production of fuels, chemicals, and biomass. Yet, the success of these microbes depends upon the development of cost-effective technologies that permit scaled cultivation and cell harvesting. Here, we investigate the feasibility of engineering cell morphology in order to improve biomass recovery and decrease energetic costs associated with lysing cyanobacterial cells. Specifically, we modify the levels of Min system proteins in Synechococcus elongatus sp...
February 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28235874/a-novel-subfamily-esterase-with-a-homoserine-transacetylase-like-fold-but-no-transferase-activity
#6
Ping-Yi Li, Qiong-Qiong Yao, Peng Wang, Yi Zhang, Yue Li, Yan-Qi Zhang, Jie Hao, Bai-Cheng Zhou, Xiu-Lan Chen, Mei Shi, Yu-Zhong Zhang, Xi-Ying Zhang
Microbial esterases play important roles in deep-sea organic carbon degradation and cycling. Though sharing similar catalytic triads and oxyanion holes, esterases are hydrolases, and homoserine transacetylases (HTAs) are transferases. Because two HTA homologs were identified as acetyl esterases, the HTA family was divided into the bonafide acetyltransferase subfamily and the acetyl esterase subfamily recently. Here, we identified and characterized a novel HTA-like esterase, Est22, from a deep-sea sedimentary metagenomic library...
February 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28235873/high-resolution-x-ray-structures-of-two-functionally-distinct-members-of-the-cyclic-amide-hydrolase-cyah-family-of-toblerone-fold-enzymes
#7
Thomas S Peat, Sahil Balotra, Matthew Wilding, Carol J Hartley, Janet Newman, Colin Scott
The Toblerone-fold was discovered recently when the first structure of the cyclic amide hydrolase, AtzD (a cyanuric acid hydrolase), was elucidated. We surveyed the cyclic amide hydrolase family finding a strong correlation between phylogenetic distribution and specificity for either cyanuric acid or barbituric acid; albeit, one of six classes (IV) could not be tested due to lack of expression of the proteins from it, and another class (V) had neither cyanuric acid nor barbituric acid hydrolase activity. High resolution X-ray structures were obtained for a class VI barbituric acid hydrolase (1...
February 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28235872/role-and-characterization-of-a-cyanide-induced-3-cyanoalanine-nitrilase-in-the-cyanide-assimilating-bacterium-pseudomonas-pseudoalcaligenes-cect-5344
#8
Felipe Acera, María Isabel Carmona, Francisco Castillo, Alberto Quesada, Rafael Blasco
Pseudomonas pseudoalcaligenes CECT 5344 is a bacterium able to assimilate cyanide as the sole nitrogen source. Under this growth conditions, a 3-cyanoalanine nitrilase enzymatic activity was induced. This activity was coded by nit4, one of the four nitrilases detected in the genome of this bacterium, and its expression in E. coli enabled the recombinant strain to fully assimilate 3-cyanoalanine. P. pseudoalcaligenes CECT 5344 showed a weak growth level with 3-cyanoalanine as N-source, unless KCN was also added...
February 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28235871/metatranscriptomic-profiling-reveals-linkages-between-the-active-rumen-microbiome-and-feed-efficiency-in-beef-cattle
#9
Fuyong Li, Le Luo Guan
Exploring compositional and functional characteristics of the rumen microbiome can improve the understanding of its role in rumen function and feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen microbiomes of beef cattle with different feed efficiencies (efficient, n=10; inefficient, n=10) using total RNA sequencing. Active bacterial and archaeal compositions were estimated based on 16S rRNAs, and active microbial metabolic functions including carbohydrate-active enzymes (CAZymes) were assessed based on mRNAs from the same metatranscriptomic datasets...
February 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213548/effects-of-gelling-agent-and-extracellular-signaling-molecules-on-the-culturability-of-marine-bacteria
#10
Anita Mac Rygaard, Mariane Schmidt Thøgersen, Kristian Fog Nielsen, Lone Gram, Mikkel Bentzon-Tilia
Only 1 % of marine bacteria are currently culturable using standard laboratory procedures and this is a major obstacle for our understanding of the biology of marine microorganisms and for the discovery of novel microbial natural products. Therefore, the purpose of the present study was to investigate if improved cultivation conditions, including the use of an alternative gelling agent, and supplementation with signaling molecules, could improve the culturability of bacteria from seawater. Substituting agar with gellan gum improved viable counts 3 - 40-fold, depending on medium composition and incubation conditions, with a maximum of 6...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213547/laboratory-selection-and-characterization-of-resistance-to-the-bacillus-thuringiensis-vip3aa-toxin-in-heliothis-virescens-lepidoptera-noctuidae
#11
Brian R Pickett, Asim Gulzar, Juan Ferré, Denis J Wright
Laboratory selection with Vip3Aa of a field-derived population of Heliothis virescens produced >2040-fold resistance in 12 generations of selection. The Vip-Sel resistant population showed little cross-resistance to Cry1Ab and no cross-resistance to Cry1Ac. Resistance was unstable after 15 generations without exposure to the toxin. F1 reciprocal crosses between Vip-Unsel and Vip-Sel indicated a strong paternal influence on the inheritance of resistance. Resistance ranged from almost completely recessive (mean h = 0...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213546/environmental-surveillance-of-norovirus-genogroups-i-and-ii-for-sensitive-detection-of-epidemic-variants
#12
Shinobu Kazama, Takayuki Miura, Yoshifumi Masago, Yoshimitsu Konta, Kentaro Tohma, Takafumi Manaka, Xiaofang Liu, Daisuke Nakayama, Takashi Tanno, Mayuko Saito, Hitoshi Oshitani, Tatsuo Omura
Sewage samples have been investigated to study the level of noroviruses concentration in sewage or the genotypes of noroviruses circulating in human populations. However, the statistical relationship between the concentration of the virus and the number of infected individuals, and the clinical importance of genotypes or strains detected in sewage are unclear. In this study, we carried out both environmental and clinical surveillance of noroviruses for three years: 2013-2016. We performed cross-correlation analysis between the concentrations of norovirus GI or GII in sewage samples collected weekly and the number of gastroenteritis cases...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213545/antifungal-bacteria-on-woodland-salamander-skin-exhibit-high-taxonomic-diversity-and-geographic-variability
#13
Carly R Muletz-Wolz, Graziella V DiRenzo, Stephanie A Yarwood, Evan H Campbell Grant, Robert C Fleischer, Karen R Lips
Diverse bacteria inhabit amphibian skin, some of which inhibit growth of the fungal pathogen, Batrachochytrium dendrobatidis (Bd). Yet, there has been no systematic survey of anti-Bd bacteria across localities, species and elevations. This is important given geographic and taxonomic variation in amphibian susceptibility to Bd. Our sites were within the Appalachian Mountains where previous sampling indicated low Bd prevalence. We determined the number and identity of anti-Bd bacteria on 61 Plethodon salamanders (37 P...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213544/isolation-and-characterization-of-a-unique-strain-of-rickettsia-parkeri-associated-with-the-hard-tick-dermacentor-parumapertus-neumann-in-the-western-united-states
#14
Christopher D Paddock, Michelle E J Allerdice, Sandor E Karpathy, William L Nicholson, Michael L Levin, Travis C Smith, Tom Becker, Robert J Delph, Robert N Knight, Jana M Ritter, Jeanine H Sanders, Jerome Goddard
In 1953, investigators at the Rocky Mountain Laboratories in Hamilton, Montana, described the isolation of a spotted fever group Rickettsia (SFGR) species from Dermacentor parumapertus collected from black-tailed jackrabbits (Lepus californicus) in northern Nevada. Several decades later, investigators characterized this SFGR by using mouse serotyping methods and determined that it represented a distinct rickettsial serotype, related closely to Rickettsia parkeri; nonetheless, the parumapertus agent was not further characterized or studied...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213543/functional-characterization-of-a-28-kb-catabolic-island-from-pseudomonas-sp-m1-involved-in-biotransformation-of-%C3%AE-myrcene-and-related-plant-derived-volatiles
#15
Pedro Soares-Castro, Pedro Montenegro-Silva, Hermann J Heipieper, Pedro M Santos
Pseudomonas sp. M1 is able to mineralize highly hydrophobic and recalcitrant compounds such as benzene, phenol and their methylated/halogenated derivatives, as well as the backbone of several monoterpenes. The ability to use such spectrum of compounds as sole carbon source is, most probably, associated with a genetic background evolved under different environmental constraints. The outstanding performance of M1 strain regarding β-myrcene catabolism was elucidated in this work, with focus on the biocatalytical potential of β-myrcene-associated core-code, comprised in a 28-kb genomic island (GI), predicted to be organized in 8 transcriptional units...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213542/plant-community-and-nitrogen-deposition-as-drivers-of-%C3%AE-and-%C3%AE-prokaryotic-diversity-in-reconstructed-oil-sands-soils-and-natural-boreal-forest-soils
#16
Jacynthe Masse, Cindy E Prescott, Sébastien Renaut, Yves Terrat, Sue J Grayston
The Athabasca Oil Sands deposit is one of the largest single oil deposits in the world. Following surface mining, companies are required to restore soil-like profiles that can support the previous land capabilities. The objective of this study was to assess if soil prokaryotic α- and β-diversity in oil-sands soils reconstructed 20-30 years previously, and planted to one of three vegetation types (coniferous or deciduous trees and grassland) were similar to those found in natural boreal-forest soils subject to wildfire disturbance...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213541/accurate-quantification-of-laminarin-in-marine-organic-matter-with-enzymes-from-marine-microbes
#17
Stefan Becker, André Scheffel, Martin F Polz, Jan-Hendrik Hehemann
Marine algae produce varieties of glycans, which fulfill diverse biological functions and fuel the carbon and energy demand of heterotrophic microbes. A common approach to analyze marine organic matter uses acid to hydrolyze its glycans into measurable monosaccharides. These, however, may derive from different glycans that are built with the same monosaccharides, hence this approach does not distinguish between glycans in natural samples. Here we use enzymes to selectively digest and thereby quantify laminarin in particulate organic matter...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213540/characterization-of-the-physical-and-functional-interplay-between-mazf1-bif-and-its-noncognate-antitoxins-from-bifidobacterium-longum
#18
Yanxia Wei, Yang Li, Fan Yang, Qiong Wu, Dianbin Liu, Xiangyang Li, Hui Hua, Xiaomei Liu, Yugang Wang, Kuiyang Zheng, Renxian Tang
Bifidobacterium longum strain JDM301, a widely used commercial strain in China, encodes at least two MazEF-like modules and one RelBE-like toxin-antitoxin (TA) systems in its chromosome, designated as MazE1F1(Bif), MazE2F2(Bif) and RelBE(Bif), respectively. Bacterial TA systems play an important role in several stress responses, but the relationship between these TA systems is largely unknown. In this study, the interaction between MazF1(Bif) and MazE2(Bif) or RelB(Bif) was assessed in B. longum strain JDM301...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213539/critical-concentration-of-lecithin-enhances-the-antimicrobial-activity-of-eugenol-against-escherichia-coli
#19
Haoshu Zhang, Edward G Dudley, P Michael Davidson, Federico Harte
Lecithin is a natural emulsifier used in a wide range of food and non-food applications to improve physical stability with no known bioactive effects. In this study, the effect of lecithin on the antimicrobial performance of a constant eugenol concentration was tested against three Escherichia coli strains (C600, 0.1229, and O157:H7 strain ATCC 700728). This was the first study focusing on lecithin at concentrations below those commonly used in foods to improve the stability of oil in water emulsions (≤ 10mg/100ml)...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213538/colonization-and-transmission-of-the-gut-microbiota-of-the-burying-beetle-nicrophorus-vespilloides-through-development
#20
Yin Wang, Daniel E Rozen
Carrion beetles in the genus Nicrophorus rear their offspring on decomposing carcasses where larvae are exposed to a diverse community of decomposer bacteria. Parents coat the carcass with antimicrobial secretions prior to egg hatch (defined as Pre-Hatch care) and also feed regurgitated food, and potentially bacteria, to larvae throughout development (defined as Full care). Here we partition the roles of pre- and post-hatch parental care in the transmission and persistence of culturable symbiotic bacteria to larvae...
February 17, 2017: Applied and Environmental Microbiology
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