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Applied and Environmental Microbiology

Elizabeth A Miller, Timothy J Johnson, George Omondi, Edward R Atwill, Lynne A Isbell, Brenda McCowan, Kimberly VanderWaal
There is growing evidence that anthropogenic sources of antibiotics and antimicrobial resistant bacteria can spillover into natural ecosystems, raising questions about the role wild animals play in the emergence, maintenance, and dispersal of antibiotic resistance genes. In particular, we lack an understanding of how resistance genes circulate within wild animal populations, including whether specific host characteristics such as social associations promote inter-host transmission of these genes. Here, we use social network analysis to explore the forces shaping population-level patterns of resistant Escherichia coli in wild giraffe ( Giraffa camelopardalis ) and assess the relative importance of social contact for the dissemination of resistant E...
November 9, 2018: Applied and Environmental Microbiology
Lauren S McKee, Antonio Martínez-Abad, Andrea C Ruthes, Francisco Vilaplana, Harry Brumer
The genome and natural habitat of Chitinophaga pinensis suggest the ability to degrade a wide variety of carbohydrate-based biomass. Complementing our earlier investigations into the hydrolysis of some plant polysaccharides, we now show that C. pinensis can grow directly on spruce wood and fungal fruiting body. Growth was stronger on fungal material, although secreted enzyme activity was high in both cases, and all biomass-induced secretomes showed a predominance of β-glucanase activities. We therefore conducted a screen of growth on and hydrolysis of β-glucans isolated from different sources...
November 9, 2018: Applied and Environmental Microbiology
Ravin Poudel, Ari Jumpponen, Megan M Kennelly, Cary L Rivard, Lorena Gomez-Montano, Karen A Garrett
Root-associated microbes are critical to plant health and performance, although understanding of the factors that structure these microbial communities and theory to predict microbial assemblages are still limited. Here we use a grafted tomato system to study the effects of rootstock genotypes and grafting in endosphere and rhizosphere microbiomes that were evaluated by sequencing 16S rRNA. We compared the microbiomes of nongrafted tomato cultivar BHN589, selfgrafted BHN589, and BHN589 grafted to Maxifort or RST-04-106 hybrid rootstocks...
November 9, 2018: Applied and Environmental Microbiology
Daniel Bellieny-Rabelo, Collins K Tanui, Nikki Miguel, Stanford Kwenda, Divine Y Shyntum, Lucy N Moleleki
<u>S</u>oft-<u>r</u>ot Enterobacteriaceae (SRE) typified by Pectobacterium and Dickeya genera are phytopathogenic bacteria inflicting soft-rot disease in crops worldwide. By combining genomic information from 100 SRE with whole-transcriptome datasets, we identified novel genomic and transcriptional associations amongst key pathogenicity themes in this group. Comparative genomics revealed solid linkage between the <u>t</u>ype I <u>s</u>ecretion <u>s</u>ystem (T1SS) and the carotovoricin bacteriophage (Ctv) conserved in 96...
November 9, 2018: Applied and Environmental Microbiology
Fan Yang, He Li, Jie Sun, Xiaoyu Guo, Xinyu Zhang, Min Tao, Xiaoyi Chen, Xianzhen Li
Under general aqueous conditions, xanthan appears in an ordered conformation, which makes its backbone largely resistant to degradation by known cellulases. Therefore, the xanthan degradation mechanism is still unclear because of the lack of an efficient hydrolase. Herein, we report the catalytic properties of Mi Xen, a xanthan-degrading enzyme identified from the genus Microbacterium Mi Xen is a 952-amino-acid protein that is unique to strain XT11. Both the sequence and structural features suggested that MiXen probably belongs to a new branch of GH9 family and has a multi-modular structure, in which a catalytic (α/α)6 barrel is flanked by an N-terminal Ig-like domain and by a C-terminal domain that has very few homologues in sequence databases and functions as a carbohydrate-binding module (CBM)...
November 9, 2018: Applied and Environmental Microbiology
Christian Zerfaß, Joseph A Christie-Oleza, Orkun S Soyer
Manganese bio-mineralization is a widespread process among bacteria and fungi. To date there is no conclusive experimental evidence for, how and if this process impacts microbial fitness in the environment. Here we show how a model organism for manganese oxidation is growth-inhibited by nitrite, and that this inhibition is mitigated in presence of manganese. We show that such manganese-mediated mitigation of nitrite-inhibition is dependent on the culture inoculum size and that manganese oxide (MnOX ) forms granular precipitates in the culture, rather than sheaths around individual cells...
November 9, 2018: Applied and Environmental Microbiology
David Aerts, Stijn G van den Bergh, Harm Post, Maarten A F Altelaar, Mark Arentshorst, Arthur F J Ram, Robin A Ohm, Han A B Wösten
Proteins are secreted throughout the mycelium of Aspergillus niger except for the sporulating zone. A link between sporulation and repression of protein secretion was underlined by the finding that inactivation of the sporulation gene flbA results in mycelial colonies that secrete proteins throughout the colony. However, Δ flbA hyphae also lyse and have thinner cell walls. This pleiotropic phenotype is associated with differential expression of 36 predicted transcription factor genes, of which rpnR was inactivated in this study...
November 9, 2018: Applied and Environmental Microbiology
Cristina Coscolín, Nadine Katzke, Antonio García-Moyano, José Navarro-Fernández, David Almendral, Mónica Martínez-Martínez, Alexander Bollinger, Rafael Bargiela, Christoph Gerler, Tatyana N Chernikova, David Rojo, Coral Barbas, Tran Hai, Olga V Golyshina, Rainhard Koch, Michail M Yakimov, Gro E K Bjerga, Peter N Golyshin, Karl-Erich Jaeger, Manuel Ferrer
Amination of bulky ketones, particularly in ( R )-configuration, is an attractive chemical conversion, however known ω-transaminases (ω-TAs) show insufficient performances. By applying two screening methods we discovered 10 amine transaminases from the class III ω-TAs family, 38% to 76% identical to homologues. We present examples of such enzymes preferring bulky ketones over keto acids and aldehydes with stringent ( S )-selectivity. We also report representatives from the class III ω-TAs capable of converting ( R ) and ( S ) amines and bulky ketones, and one converting amines with longer alkyl substituents...
November 9, 2018: Applied and Environmental Microbiology
Tetsu Shimizu, Haruhiko Teramoto, Masayuki Inui
Rhodobacter sphaeroides produces hydrogen gas (H2 ) from organic compounds via nitrogenase under anaerobic-light conditions in the presence of poor nitrogen sources such as l-glutamate. R. sphaeroides utilizes the ethylmalonyl-CoA (EMC) pathway for acetate assimilation but its H2 yield from acetate in the presence of l-glutamate has been reported to be low. In this study, deletion of ccr encoding crotonyl-CoA carboxylase/reductase, a key enzyme for the EMC pathway in R. sphaeroides , revealed that the EMC pathway is essential for H2 production from acetate and l-glutamate but not for the growth and acetate consumption in the presence of l-glutamate...
November 9, 2018: Applied and Environmental Microbiology
Jeonghwan Jang, Yoriko Sakai, Keishi Senoo, Satoshi Ishii
Denitrification ability is sporadically distributed among diverse bacteria, archaea, and fungi. In addition, disagreement has been found between denitrification functional gene phylogenies and the 16S rRNA gene phylogeny. These facts have suggested the potential occurrences of horizontal gene transfer (HGT) for the denitrification functional genes. However, evidence of HGT has not been clearly presented thus far. In this study, we identified the sequences and the localization of the nitrite reductase genes in the genomes of 41 Azospirillum sp...
November 9, 2018: Applied and Environmental Microbiology
Christina M Ferraro, Steven E Finkel
When Escherichia coli K-12 is inoculated into rich medium in batch culture, cells experience five phases. While the lag and logarithmic phases are mechanistically fairly well-defined, stationary phase, death phase, and long-term stationary phase are less well understood. Here, we characterize a mechanism of delaying death, a phenomenon we call the "alcohol effect," where the addition of small amounts of certain alcohols prolongs stationary phase for at least 10 days longer than in untreated conditions...
November 2, 2018: Applied and Environmental Microbiology
Wenjing Zhao, Tao Yuan, Christine Piva, Edward J Spinard, Christian Schuttert, David C Rowley, David R Nelson
Phaeobacter inhibens S4Sm acts as a probiotic bacterium against the oyster pathogen, Vibrio coralliilyticus Here we report that P. inhibens S4Sm secretes three molecules that down-regulate transcription of major virulence factors, metalloprotease genes, in V. coralliilyticus cultures. The effects of S4Sm culture supernatant on the transcription of three genes involved in protease activity, vcpA, vcpB , and vcpR (encoding metalloproteases A and B and their transcriptional regulator, respectively), were examined by qRT-PCR...
November 2, 2018: Applied and Environmental Microbiology
Daniel Pacheco-Sánchez, Águeda Molina-Fuentes, Patricia Marín, Alberto Díaz-Romero, Silvia Marqués
The facultative anaerobe Thauera aromatica strain AR-1 uses 3,5-dihydroxybenzoate (3,5-DHB) as sole carbon and energy source under anoxic conditions using an unusual oxidative strategy to overcome aromatic ring stability. A 25 kb gene cluster organized in four main operons encodes the anaerobic degradation pathway for this aromatic. The dbdR gene coding for a LysR-type transcriptional regulator (LTTR) which is present at the foremost end of the cluster is required for anaerobic growth on 3,5-DHB and for expression of the main pathway operons...
November 2, 2018: Applied and Environmental Microbiology
Liangzhi Li, Zhenghua Liu, Delong Meng, Xueduan Liu, Xing Li, Ming Zhang, Jiemeng Tao, Yabing Gu, Shuiping Zhong, Huaqun Yin
Members of genus Acidithiobacillus which can adapt up to extremely high concentration of heavy metals are universally found at acid mine drainage (AMD) sites. We here perform comparative genomic analysis of 37 strains within the genus Acidithiobacillus to answer the untouched questions as to the mechanisms and the evolutionary history of metal resistance genes in Acidithiobacillus spp. Results showed that the evolutionary history of metal resistance genes in Acidithiobacillus spp. involved a combination of gene gains and losses, HGT and gene duplication...
November 2, 2018: Applied and Environmental Microbiology
J De Roos, D Van der Veken, L De Vuyst
Traditional lambic beer production takes place through wort inoculation with environmental air and fermentation and maturation in wooden barrels. These wooden casks or foeders are possible additional inoculation sources of microorganisms for lambic worts. However, up to now, these lambic barrels have only been examined with culture-dependent techniques, thereby missing a part of the microorganisms present. Moreover, the effect of the cleaning procedures (involving high-pressurized water and/or fumigation) and the barrel type on the microbial community structures of the interior surfaces of wooden lambic barrels was unclear...
November 2, 2018: Applied and Environmental Microbiology
Andrew J Sommer, Peter D Newell
Interactions between species shape the formation and function of microbial communities. In the gut microbiota of animals, cross-feeding of metabolites between microbes can enhance colonization and influence host physiology. We examined a mutually beneficial interaction between two bacteria isolated from the gut microbiota of Drosophila : Acetobacter fabarum and Lactobacillus brevis After developing an in vitro co-culture assay, we utilized a genetic screen to identify A. fabarum genes required for enhanced growth with L...
November 2, 2018: Applied and Environmental Microbiology
Mustafa Özçam, Restituto Tocmo, Jee-Hwan Oh, Amin Afrazi, Joshua D Mezrich, Stefan Roos, Jan Claesen, Jan-Peter van Pijkeren
Mechanistic understanding of microbe-host interactions is critical to developing therapeutic strategies for targeted modulation of the host immune system. Different members of the gut symbiont species Lactobacillus reuteri modulate host health by, for example, reduction of intestinal inflammation. Previously, it was shown that L. reuteri activates the aryl-hydrocarbon receptor (AhR)-a ligand-activated transcription factor that plays an important role in the mucosal immune system-by production of tryptophan catabolites...
November 2, 2018: Applied and Environmental Microbiology
R Junges, K Sturød, G Salvadori, H A Åmdal, T Chen, F C Petersen
Streptococcus mitis is found in the oral cavity and nasopharynx and forms a significant portion of the human microbiome. In this study, in silico analyses indicated the presence of an Rgg/SHP cell-to-cell communication system in S. mitis Although Rgg presented higher similarity to a repressor in Streptococcus pyogenes , auto-inducing assays and an rgg deletion mutant revealed that in S. mitis Rgg acts as an activator. Transcriptome analysis showed that in addition to shp , the system regulates two other downstream genes, comprising a segment of a putative lantibiotic gene cluster that is in a conjugative element locus in different members of the mitis group...
November 2, 2018: Applied and Environmental Microbiology
Kruti B Patel, Shuowei Cai, Michael Adler, Brajendra K Singh, Virinder S Parmar, Bal Ram Singh
Botulinum neurotoxins (BoNTs), the most poisonous proteins known to mankind, are a family of seven (A-G) immunologically distinct proteins synthesized primarily by different strains of the anaerobic bacteria, Clostridium botulinum Being the causative agents of botulism, the toxins block neurotransmitter release by specifically cleaving one of the three SNARE proteins thereby inducing flaccid paralysis. Developing countermeasures and therapeutics against BoNTs are high priority research areas for public health because of their extreme toxicity and potential as bio-warfare agents...
November 2, 2018: Applied and Environmental Microbiology
Wenwen Huo, Hannah M Adams, Cristian Trejo, Rohit Badia, Kelli L Palmer
The gastrointestinal colonizer Enterococcus faecium is a leading cause of hospital-acquired infections. Multidrug-resistant (MDR) E. faecium are particularly concerning for infection treatment. Previous comparative genomic studies revealed that subspecies referred to as Clade A and Clade B exist within E. faecium MDR E. faecium belong to Clade A, while Clade B consists of drug-susceptible fecal commensal E. faecium Isolates from Clade A are further grouped into two sub-clades, A1 and A2. In general, Clade A1 isolates are hospital epidemic isolates whereas Clade A2 isolates are isolates from animals and sporadic human infections...
November 2, 2018: Applied and Environmental Microbiology
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