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Applied and Environmental Microbiology

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https://www.readbyqxmd.com/read/28314730/genome-wide-single-nucleotide-polymorphism-analysis-identified-clonal-lineages-of-erysipelothrix-rhusiopathiae-responsible-for-the-recent-increased-incidence-of-acute-swine-erysipelas-in-japan
#1
Yohsuke Ogawa, Kazumasa Shiraiwa, Yoshitoshi Ogura, Tadasuke Ooka, Sayaka Nishikawa, Masahiro Eguchi, Tetsuya Hayashi, Yoshihiro Shimoji
Erysipelothrix rhusiopathiae causes swine erysipelas, an important infectious disease in the swine industry. In Japan, the incidence of acute swine erysipelas due to serovar 1a has recently increased markedly. To study the genetic relatedness of the strains from the recent cases, we analyzed 34 E. rhusiopathiae serovar 1a swine isolates collected between 1990 and 2011 and further investigated the possible association of the live Koganei 65-0.15 vaccine strain (serovar 1a) with the increase in cases. Pulsed-field gel electrophoresis analysis revealed no marked variation among the isolates; however, sequencing analysis of a hypervariable region in the surface protective antigen A (spaA) gene revealed that the strains isolated after 2007 exhibited the same spaA genotype and could be differentiated from older strains...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28314729/efficacy-of-a-sonicating-swab-for-removal-and-capture-of-listeria-monocytogenes-in-biofilm-on-stainless-steel
#2
Tobyn A Branck, Matthew J Hurley, Gianna N Prata, Christina A Crivello, Patrick J Marek
Listeria monocytogenes is of great concern in food processing facilities because it persists in biofilms, potentiating biotransfer. Stainless steel is commonly used for food contact surfaces and transport containers. L. monocytogenes biofilm on stainless steel served as a model system for surface sampling to test the performance of a sonicating swab in comparison to a standard cotton swab. Swab performance and consistency were determined using total viable counts. Stainless steel coupons sampled with both swabs were examined with SEM to visualize biofilms and surface structures (i...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28314728/competitive-exclusion-reduces-transmission-and-excretion-of-extended-spectrum-%C3%AE-lactamase-producing-escherichia-coli-in-broilers
#3
Daniela Ceccarelli, Alieda van Essen-Zandbergen, Bregtje Smid, Kees T Veldman, Gert Jan Boender, Egil A J Fischer, Dik J Mevius, Jeanet A van der Goot
Extended-spectrum β-lactamases (ESBLs) and plasmid mediated AmpC β-lactamases (pAmpC) are enzymes able to hydrolyze a large variety of β-lactam antibiotics, including 3(rd) generation cephalosporins and monobactams. Broilers and broiler meat products can be highly contaminated with ESBL and pAmpC-producing Escherichia coli, also known as extended-spectrum cephalosporins (ESC)-resistant E. coli, and can be a source for human infections. As few data are available on interventions to reduce ESC-resistant E...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28314727/transcriptomic-analyses-elucidate-adaptive-differences-of-closely-related-strains-of-p-aeruginosa-in-fuel
#4
Thusitha S Gunasekera, Loryn L Bowen, Carol E Zhou, Susan C Howard-Byerly, William S Foley, Richard C Striebich, Larry C Dugan, Oscar N Ruiz
Pseudomonas aeruginosa can utilize hydrocarbons, but different strains have varying degrees of adaptation despite their highly conserved genome. P. aeruginosa ATCC 33988 is highly adapted to hydrocarbons while strain PAO1, a human pathogen, is less-adapted and degrades jet fuel at a slower rate than does ATCC 33988. We investigated fuel specific transcriptomic differences between these strains in order to ascertain the underling mechanisms utilized by the adapted strain to proliferate in fuel. During growth in fuel, the genes related to alkane degradation, heat-shock response, membrane proteins, efflux pumps and several novel genes were upregulated in ATCC 33988...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28314726/global-distribution-patterns-and-pangenomic-diversity-of-the-candidate-phylum-latescibacteria-ws3
#5
Ibrahim F Farag, Noha H Youssef, Mostafa S Elshahed
We investigated the global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3) in 16S rRNA gene as well as metagenomic datasets. We document distinct distribution patterns for various "Latescibacteria" orders in 16S rRNA gene datasets, with prevalence of orders sediment_1 in terrestrial, PBSIII_9 in groundwater and temperate freshwater, and GN03 in pelagic marine, saline-hypersaline, and wastewater habitats. Using a fragment recruitment approach, we identified 68.9 Mb of "Latescibacteria"-affiliated contigs in publicly available metagenomic datasets comprising 73,079 proteins...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28314725/a-genome-survey-and-postharvest-transcriptome-analysis-in-lentinula-edodes
#6
Yuichi Sakamoto, Keiko Nakade, Shiho Sato, Kentaro Yoshida, Kazuhiro Miyazaki, Satoshi Natsume, Naotake Konno
Lentinula edodes is a popular cultivated edible and medicinal mushroom. Lentinula edodes is susceptible to postharvest problems such as gill browning, fruiting body softening, and lentinan degradation. We constructed a de novo assembly draft genome sequence and performed gene prediction of Lentinula edodesDe novo assembly was carried out using short reads from paired-end and mate-paired libraries and long reads by PacBio, resulting in a contig number of 1951 and an N50 of 1 Mb. Further, we predicted genes by Augustus using RNA-seq data from the whole life cycle of Lentinula edodes, resulting in 12,959 predicted genes...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28314724/impact-of-seasonal-hypoxia-on-activity-and-community-structure-of-chemolithoautotrophic-bacteria-in-a-coastal-sediment
#7
Yvonne A Lipsewers, Diana Vasquez-Cardenas, Dorina Seitaj, Regina Schauer, Silvia Hidalgo Martinez, Jaap S Sinninghe Damsté, Filip J R Meysman, Laura Villanueva, Henricus T S Boschker
Seasonal hypoxia in coastal systems drastically changes the availability of electron acceptors in bottom water, which alters the sedimentary reoxidation of reduced compounds. However, the effect of seasonal hypoxia on the chemolithoautotrophic community that catalyze these reoxidation reactions, is rarely studied. Here we examine the changes in activity and structure of the sedimentary chemolithoautotrophic bacterial community of a seasonally hypoxic saline basin under oxic (spring) and hypoxic (summer) conditions...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28283527/corexit-9500-enhances-oil-biodegradation-and-changes-microbial-community-structure-of-oil-enriched-microcosms
#8
Stephen M Techtmann, Mobing Zhuang, Pablo Campo, Edith Holder, Michael Elk, Terry C Hazen, Robyn Conmy, Jorge W Santo Domingo
To better understand the impact of COREXIT 9500 on the structure and activity levels of hydrocarbon degrading microbial communities, we analyzed next-generation 16S rRNA gene sequencing libraries of hydrocarbon enrichments grown at 5 and 25 °C by using both DNA and RNA extracts as sequencing templates. Oil biodegradation patterns in both 5 and 25°C enrichments were consistent with those reported in the literature (i.e., aliphatics were degraded faster than aromatics). A slight increase in biodegradation was observed in the presence of COREXIT at both temperatures...
March 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28283526/mechanisms-of-inactivation-of-dry-escherichia-coli-by-high-pressure-carbon-dioxide
#9
Yuan Yao Chen, Feral Temelli, Michael G Gänzle
High pressure carbon dioxide processing is a promising technology for non-thermal food preservation. However, few studies determined the lethality of high pressure CO2 on dry bacterial cells, and the mechanism of inactivation remains unknown. This study explored mechanisms of inactivation by using Escherichia coli AW1.7 and mutant strains differing in heat and acid resistance, and in membrane composition based on disruption of the locus of heat resistance, and genes coding for glutamate decarboxylases and cyclopropane fatty acid synthase, respectively...
March 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28283525/molecular-viability-testing-of-uv-inactivated-bacteria
#10
Kris M Weigel, Felicia K Nguyen, Moira R Kearney, John S Meschke, Gerard A Cangelosi
The polymerase chain reaction (PCR) is effective at detecting bacterial DNA in samples, but it is unable to differentiate viable bacteria from inactivated cells or free DNA fragments. New PCR-based analytical strategies have been developed to address this limitation. Molecular viability testing (MVT) correlates bacterial viability with the ability to rapidly synthesize species-specific ribosomal RNA precursor (pre-rRNA) in response to brief nutritional stimulation. Previous studies demonstrated that MVT can assess bacterial inactivation by chlorine, serum, and low-temperature pasteurization...
March 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28283524/pirated-siderophores-promote-sporulation-in-bacillus-subtilis
#11
Gabrielle M Grandchamp, Lews Caro, Elizabeth A Shank
In microbial communities bacteria chemically and physically interact with one another. Some of these interactions are mediated by secreted specialized metabolites that act as either intra- or inter-species signals to alter gene expression and change cell physiology. Bacillus subtilis is a well-characterized soil microbe that can differentiate into multiple cell types including metabolically dormant endospores. We were interested in identifying microbial interactions that affected sporulation in B. subtilis...
March 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28283523/requirement-of-a-functional-fmn-prenyltransferase-for-the-activity-of-a-bacterial-decarboxylase-in-a-heterologous-muconic-acid-pathway-in-saccharomyces-cerevisiae
#12
Heike E Weber, Manuela Gottardi, Christine Brückner, Mislav Oreb, Eckhard Boles, Joanna Tripp
Biotechnological production of cis, cis-muconic acid from renewable feedstocks is an environmentally sustainable alternative to conventional, petroleum-based methods. Even though a heterologous production pathway for cis, cis-muconic acid has already been established in the host organism Saccharomyces cerevisiae, the generation of industrially relevant amounts of cis, cis-muconic acid is hampered by the low activity of the bacterial protocatechuic acid (PCA) decarboxylase AroY subunit C(iso) (AroY-C(iso)), leading to secretion of high amounts of the intermediate PCA to the medium...
March 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28283522/use-of-bacteria-to-stabilize-archaeological-iron
#13
Lucrezia Comensoli, Julien Maillard, Monica Albini, Frederic Sandoz, Pilar Junier, Edith Joseph
Iron artifacts are common among the findings of archaeological excavations. The corrosion layer formed on these objected requires stabilization after their recovery, without which the destruction of the item due to physicochemical damage is likely. Current technologies for the stabilization of the corrosion layer are lengthy and generate hazardous waste products. There is therefore a pressing need for an alternative method to stabilize the corrosion layer on iron objects. The aim of this study was to evaluate an alternative conservation-restoration method using bacteria...
March 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28283521/an-amoebal-grazer-of-cyanobacteria-requires-cobalamin-produced-by-heterotrophic-bacteria
#14
Amy T Ma, Joris Beld, Bianca Brahamsha
Amoebae are unicellular eukaryotes that consume microbial prey through phagocytosis, playing a role in shaping microbial foodwebs. Many amoebal species can be cultivated axenically in rich media or monoxenically with single bacterial prey species. Here we characterize heterolobosean amoeba LPG3, a recent natural isolate, which is unable to grow on unicellular cyanobacteria, its primary food source, in the absence of a heterotrophic bacterium, a Pseudomonas species coisolate. To investigate the molecular basis of this requirement for heterotrophic bacteria, we performed a screen using a defined non-redundant transposon library of Vibrio cholerae which implicated genes in corrinoid uptake and biosynthesis...
March 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28283520/biogeography-of-a-novel-clade-of-ensifer-meliloti-associated-with-the-australian-legume-trigonella-suavissima
#15
Bertrand Eardly, Patrick Elia, John Brockwell, Daniel Golemboski, Peter van Berkum
Here we describe a novel clade within Ensifer meliloti and consider how geographic and ecological isolation contributed to the limited distribution of this group. Members of the genus Ensifer are best known for their ability to form nitrogen-fixing symbioses with forage legumes of three related genera, Medicago L., Melilotus Mill., and Trigonella L., which are members of the tribe Trifoleae. They have a natural distribution extending from the Mediterranean basin through west Asia, where there is an unsurpassed number of species belonging to these genera...
March 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28283519/degradation-of-diphenyl-ether-in-sphingobium-phenoxybenzoativorans-sc_3-is-initiated-by-a-novel-ring-cleavage-dioxygenase
#16
Shu Cai, Li-Wei Chen, Yu-Chun Ai, Ji-Guo Qiu, Cheng-Hong Wang, Chao Shi, Jian He, Tian-Ming Cai
Sphingobium phenoxybenzoativorans SC_3 degrades and utilizes diphenyl ether (DE) and 2-carboxy DE as its sole carbon and energy source. In this study, we report the degradation of DE and 2-carboxy DE initiated by a novel ring-cleavage angular dioxygenase (Dpe) in the strain. Dpe functions at the angular carbon and its adjacent carbon (C1a, C2) of a benzene ring in DE (or the 2-carboxy benzene ring in 2-carboxy DE) and cleaves the C1a-C2 bond (decarboxylation is simultaneously happened for 2-carboxy DE), yielding 2,4-hexadienal phenyl ester, which is subsequently hydrolyzed to muconic acid semialdehyde and phenol...
March 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28283518/simultaneous-decolorization-and-biohydrogen-production-from-xylose-by-klebsiella-oxytoca-gs-4-08-in-presence-of-azo-dyes-with-sulfonate-and-carboxyl-groups
#17
Lei Yu, Ming-Yue Cao, Peng-Tao Wang, Shi Wang, Ying-Rong Yue, Wen-Duo Yuan, Wei-Chuan Qiao, Fei Wang, Xin Song
Biohydrogen production from the pulp and paper effluent containing rich lignocellulosic material could be achieved by the fermentation process. Xylose, an important hemicellulose hydrolysis product, is used less efficiently as a substrate for biohydrogen production. Moreover, azo dyes are usually added to fabricate anti-counterfeiting paper, which further increases the complexity of wastewater. This study is the first paper to report that xylose could serve as the sole carbon source for a pure culture-Klebsiella oxytoca GS-4-08 to achieve simultaneous decolorization and biohydrogen production...
March 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28258150/tm0416-is-a-hyperthermophilic-promiscuous-non-phosphorylated-sugar-isomerase-that-catalyzes-various-c5-and-c6-epimerization-reactions
#18
Sun-Mi Shin, Thinh-Phat Cao, Jin Myung Choi, Seong-Bo Kim, Sang-Jae Lee, Sung Haeng Lee, Dong-Woo Lee
There is currently little information on non-phosphorylated sugar epimerases, which are of potential interest for producing rare sugars. Herein, we found a gene (TM0416) encoding a putative d-tagatose 3-epimerase-related protein from a hyperthermophilic bacterium Thermotoga maritima We overexpressed the TM0416 gene in Escherichia coli and purified the resulting recombinant protein for detailed characterization. Amino acid sequence alignment and a structural similarity search revealed that TM0416 is a putative non-phosphorylated sugar epimerase...
March 3, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28258149/salmonella-senftenberg-adaptation-to-linalool-and-its-association-with-antibiotic-resistance-and-environmental-persistence
#19
Emmanuel Kalily, Amit Hollander, Ben Korin, Itamar Cymerman, Sima Yaron
A clinical isolate of Salmonella enterica serovar Senftenberg, isolated from an outbreak linked to the herb Ocimum basilicum L. (basil), has been shown resistance to basil oil and to the terpene alcohol linalool. To better understand how human pathogens might develop resistance to linalool and to investigate the association of this resistance with resistance to different antimicrobial agents, selective pressure was applied to the wild-type strain by sequential exposure to increasing concentrations of linalool...
March 3, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28258148/biosynthesis-of-2-chloropentostatin-and-2-amino-2-deoxyadenosine-highlights-a-single-gene-cluster-performing-two-independent-pathways-in-actinomadura-sp-atcc-39365
#20
Yaojie Gao, Gudan Xu, Pan Wu, Jin Liu, You-Sheng Cai, Zixin Deng, Wenqing Chen
2' -chloropentostatin (2' -Cl PTN, 2' -chloro-2' -deoxycoformycin) and 2' -amino-2' -deoxyadenosine (2' -Amino dA) are two adenosine-derived nucleoside antibiotics co-produced by Actinomadura sp. ATCC 39365. 2' -Cl PTN is a potent adenosine deaminase (ADA) inhibitor featuring an intriguing 1,3-diazepine ring as well as a chlorination at C-2' of ribose, and 2' -Amino dA is an adenosine analog showing bioactivity against RNA-type virus infection. However, the biosynthetic logic of them has remained poorly understood...
March 3, 2017: Applied and Environmental Microbiology
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