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Applied and Environmental Microbiology

Yu Wang, Shanshan Wang, Weizhong Chen, Liqiang Song, Yifei Zhang, Zhen Shen, Fangyou Yu, Min Li, Quanjiang Ji
Klebsiella pneumoniae is a promising industrial microorganism as well as a major human pathogen. The recent emergence of carbapenem-resistant K. pneumoniae has posed a serious threat to public health worldwide, emphasizing a dire need for novel therapeutic means against drug-resistant K. pneumoniae Despite the critical importance of genetics in bioengineering, physiology study, and therapeutic-means development, genome editing, in particular, the highly desirable scarless genetic manipulation in K. pneumoniae is often time-consuming and laborious...
September 14, 2018: Applied and Environmental Microbiology
G Schwob, M Roy, C A Pozzi, A Herrera-Belaroussi, M P Fernandez
Alnus genus forms symbiosis with the actinobacteria Frankia and ectomycorrhizal fungi. Two types of Frankia lineages can be distinguished based on their ability to sporulate in planta. Spore-positive (Sp+) strains are predominant on Alnus incana ( Ai ) and Alnus viridis ( Av ) in highlands, while spore-negative (Sp-) strains are mainly associated with Alnus glutinosa ( Ag ) in lowlands. Here, we investigated whether the Sp+ predominance in nodules is due to host selection of certain Frankia genotypes from soil communities or the result of the ecological history of the alder stand soil, and the effect of the sporulation genotype on the ECM communities...
September 14, 2018: Applied and Environmental Microbiology
Shalev Gihaz, Margarita Kanteev, Yael Pazy, Ayelet Fishman
Enhanced stability in organic solvents is a desirable feature for enzymes implemented under industrial conditions. Lipases potential as biocatalysts is mainly limited by denaturation in polar alcohols. In this study we focused on selected solvent tunnels in lipase from Geobacillus stearothermophilus T6 to improve its stability in methanol during biodiesel synthesis. Using rational mutagenesis, bulky aromatic residues were incorporated in order to occupy solvent channels and induce aromatic interactions leading to a better inner core packing...
September 14, 2018: Applied and Environmental Microbiology
Joshua M A Stough, Max Kolton, Joel E Kostka, David J Weston, Dale A Pelletier, Steven W Wilhelm
Sphagnum -dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the Sphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnum peat bog. The vegetative portions of 6 Sphagnum plants were obtained from a peatland in northern Minnesota and total RNA extracted and sequenced...
September 14, 2018: Applied and Environmental Microbiology
Chloé Dupont, Estelle Jumas-Bilak, Clara Doisy, Fabien Aujoulat, Raphaël Chiron, Hélène Marchandin
Achromobacter are non-fermentative Gram-negative bacilli considered as emergent pathogens in Cystic Fibrosis (CF). Although some cross-transmission events have been described between CF patients, Achromobacter strains were mostly patient-specific, suggesting sporadic acquisitions from non-human reservoirs. However, sources of this emergent CF pathogen remain unknown. A large collection of specimens (n=273) was sampled in the home of 3 CF patients chronically colonized by Achromobacter xylosoxidans with the aim to evaluate the potential role of domestic reservoirs in sustaining airway colonization of the patients...
September 14, 2018: Applied and Environmental Microbiology
Ashutosh Kumar Rai, Sudhir Singh, Sushil Kumar Dwivedi, Amit Srivastava, Parul Pandey, Santosh Kumar, Bhupendra Narain Singh, Anil Kumar Tripathi
The genome of Azospirillum brasilense encodes 5 RpoH sigma factors, two OxyR transcription regulator and three catalases. The aim of this study was to understand the role they play during oxidative stress and their regulatory interconnection. Out of the 5 paralogs of RpoH present in A. brasilense, inactivation of only rpoH1 renders A. brasilense heat sensitive. While transcript levels of rpoH1 were elevated by heat stress those of rpoH3 and rpoH5 were upregulated by H2 O2 Catalase activity was upregulated in A...
September 14, 2018: Applied and Environmental Microbiology
Hamza Mbareche, Marc Veillette, Guillaume J Bilodeau, Caroline Duchaine
Bioaerosol studies tend to describe the microbial content and understand the aerosolization processes linked to diseases. Air samplers are used to collect, identify and quantify bioaerosols. Studies comparing the performance of air samplers have typically used a culture approach or have targeted a specific microorganism in laboratory settings. The objective of this study was to use environmental field samples to compare the efficiency of 3 high airflow rate samplers for describing bioaerosol diversity using a next-generation sequencing approach...
September 14, 2018: Applied and Environmental Microbiology
Xiu-Lan Chen, Fang Zhao, Yong-Sheng Yue, Xi-Ying Zhang, Yu-Zhong Zhang, Ping-Yi Li
Xylanases play a crucial role in the degradation of xylan in both terrestrial and marine environments. Endo-xylanase XynB from marine bacterium Glaciecola mesophila KMM 241 is a modular enzyme comprising a long N-terminal domain (NTD, E44-T562) with xylan-binding ability and a catalytic domain (CD, T563-E912) of glycoside hydrolase (GH) family 8. In this study, the long NTD is confirmed to contain three different functional regions, which are NTD1 (E44-D136), NTD2 (Y137-A193) and NTD3 (L194-T562). NTD1 mainly composed of eight β-strands functions as a new type of carbohydrate-binding module (CBM), which has xylan-binding ability but no sequence similarity to any known CBM...
September 14, 2018: Applied and Environmental Microbiology
Derese Getnet, Aarti Gautam, Raina Kumar, Allison Hoke, Amrita K Cheema, Franco Rossetti, Caroline R Schultz, Rasha Hammamieh, Lucille A Lumley, Marti Jett
The experimental pathophysiology of organophosphorus (OP) chemical exposure has been extensively reported. Here, we describe an altered fecal bacterial biota and urine metabolome that follows intoxication with soman, a lipophilic G class chemical warfare nerve agent. Non-anaesthetized Sprague-Dawley male rats were subcutaneously administered soman at 0.8 (sub-seizurogenic) or 1.0 (seizurogenic) of the median lethal dose (LD50 ) and evaluated for signs of toxicity. Animals were stratified based on seizing activity to evaluate effects of soman exposure on fecal bacterial biota and urine metabolites...
September 14, 2018: Applied and Environmental Microbiology
Zhigang Chen, Xi Zhang, Huanjie Li, Huaiwei Liu, Yongzhen Xia, Luying Xun
Saccharomyces cerevisiae is known to grow with thiosulfate as a sulfur source, and it produces more ethanol when using thiosulfate than using sulfate. Here we report how it assimilates thiosulfate. S. cerevisiae absorbed thiosulfate into the cell through two sulfate permeases, Sul1 and Sul2. Two rhodaneses, Rdl1 and Rdl2, converted thiosulfate to a persulfide and sulfite. The persulfide was reduced by cellular thiols to H2 S, and sulfite was reduced by sulfite reductase to H2 S. Cysteine synthase incorporated H2 S into O -acetyl-L-homoserine to produce L-homocysteine, which is the precursor for cysteine and methionine in S...
September 14, 2018: Applied and Environmental Microbiology
Minjin Kim, Yunyeol Jo, Yoon Jung Hwang, Hye Won Hong, Sung Sik Hong, Kwangseo Park, Heejoon Myung
When phages infect bacteria cultured in the presence of sub-lethal doses of antibiotics, the sizes of the phage plaques are significantly increased. This phenomenon is known as phage-antibiotic synergy (PAS). In this study, the observation of PAS was extended to a wide variety of bacteria-phage pairs using different classes of antibiotics. PAS was shown in both Gram-positive and Gram-negative bacteria. Cells stressed with β-lactam antibiotics filamented or swelled extensively, resulting in increased phage production...
September 14, 2018: Applied and Environmental Microbiology
Gudan Xu, Liyuan Kong, Rong Gong, Liudong Xu, Yaojie Gao, Ming Jiang, You-Sheng Cai, Kui Hong, Youcai Hu, Peng Liu, Zixin Deng, Neil P J Price, Wenqing Chen
Purine nucleoside antibiotic pairs, concomitantly produced by a single strain, are an important group of microbial natural products. Here, we report a target-directed genome mining approach to elucidate the biosynthesis of the purine nucleoside antibiotic pair aristeromycin (ARM) and coformycin (COF) in Micromonospora haikouensis DSM 45626 (a new producer for ARM and COF) and Streptomyces citricolor NBRC 13005 (a new COF producer). We also provided biochemical data that MacI and MacT function as unusual phosphorylases, catalyzing an irreversible reaction for the tailoring assembly of neplanocin A (NEP-A) and ARM...
September 14, 2018: Applied and Environmental Microbiology
Juliane Korp, Lea Winand, Angela Sester, Markus Nett
Myxobacteria utilize the catechol natural products myxochelin A and B in order to maintain their iron homeostasis. Recently, the production of these siderophores was reported from the marine bacterium Pseudoalteromonas piscicida S2040, along with a new myxochelin derivative named pseudochelin A. The latter features a characteristic imidazoline moiety, which was proposed to originate from an intramolecular condensation reaction of the β-aminoethyl amide group in myxochelin B. To identify the enzyme catalyzing this conversion, we compared the myxochelin regulons of two myxobacterial strains, which solely produce myxochelin A and B, with P...
September 14, 2018: Applied and Environmental Microbiology
Jacob H Cecil, David C Garcia, Richard J Giannone, Joshua K Michener
Transposon mutagenesis is a powerful technique in microbial genetics for the identification of genes in uncharacterized pathways. Recently, the throughput of transposon mutagenesis techniques has been dramatically increased through the combination of DNA barcoding and high-throughput sequencing. Here we show that, when applied to catabolic pathways, barcoded transposon libraries can be used to distinguish redundant pathways, decompose complex pathways into substituent modules, discriminate between enzyme homologs, and rapidly identify previously-hypothetical enzymes in an unbiased genome-scale search...
September 14, 2018: Applied and Environmental Microbiology
Ana K Pitol, Heather N Bischel, Alexandria B Boehm, Tamar Kohn, Timothy R Julian
Indirect exposure to waterborne viruses increases risk of infection, especially amongst children with frequent hand-to-mouth contacts. Here, we quantified the transfer of one bacteriophage (MS2) and two enteric viruses (adenovirus and coxsackievirus) from liquid-to-skin. MS2, a commonly used enteric virus surrogate, was used to compare virus transfer rates in a volunteer trial to those obtained using human cadaver skin and synthetic skin. MS2 transfer to volunteer skin was similar to cadaver skin, but significantly different than to synthetic skin...
September 14, 2018: Applied and Environmental Microbiology
Wenhao Han, Pinjing He, Liming Shao, Fan Lü
Carbon chain elongation (CCE), a reaction within the carboxylate platform that elongates short-chain to medium-chain carboxylates by mixed culture, has attracted worldwide interest. The present study provides insights into the microbial diversity and predictive microbial metabolic pathways of a mixed-culture CCE microbiome based on comparative analysis of the metagenome and metatranscriptome. We found that the acclimated chain elongation microbiome shared a highly similar microbial structure with the original inoculating biogas reactor culture; however, the metabolic activities were completely different, demonstrating the high stability of the microbial structure and flexibility of its functions...
September 14, 2018: Applied and Environmental Microbiology
Jordan A Berg, Bryan D Merrill, Donald P Breakwell, Sandra Hope, Julianne H Grose
Paenibacillus larvae and Brevibacillus laterosporus are two bacteria that are members of the Paenibacillaceae family. Both are commonly found in beehives and have historically been difficult to distinguish from each other due to related genetic and phenotypic characteristics and a shared ecological niche. Herein, we discuss the likely mischaracterization of three 16S rRNA sequences previously published as P. larvae and provide the phylogenetic evidence that supported the GenBank re-assignment of the sequences as B...
September 14, 2018: Applied and Environmental Microbiology
Wenqian Yuan, Zi Jing Seng, Gurjeet Singh Kohli, Liang Yang, Hyun-Gyun Yuk
Thymol, carvacrol and trans-cinnamaldehyde are essential oil (EO) compounds with broad-spectrum antimicrobial activities against foodborne pathogens, including Escherichia coli O157:H7. However, little is known regarding the direct- and cross-resistance development in E. coli O157:H7 after adaptation to sublethal levels of these compounds, and information is scarce on microbial adaptive responses at a molecular level. The present study demonstrated that E. coli O157:H7 was able to grow in the presence of sublethal thymol (1/2T), carvacrol (1/2C) or trans-cinnamaldehyde (1/2TC), displaying an extended lag phase duration and a lower maximum growth rate...
September 14, 2018: Applied and Environmental Microbiology
Dingrong Xue, Fang Tian, Fenghuan Yang, Huamin Chen, Xiaochen Yuan, Ching-Hong Yang, Yihua Chen, Qi Wang, Chenyang He
In Xanthomonas oryzae pv. oryzae (Xoo), the bacterial blight pathogen of rice, there are over twenty genes encoding GGDEF, EAL or HD-GYP domains, which are potentially involved in the metabolism of second messenger c-di-GMP. In this study, we focused on characterization of an EAL-domain protein EdpX1. Deletion of edpX1 resulted in a two-fold increase of the intracellular c-di-GMP levels, which was restored to the wild-type levels in the complemented strain Δ edpX1 (pB- edpX1 ), demonstrating EdpX1 is an active phosphodiesterase (PDE) in Xoo...
September 14, 2018: Applied and Environmental Microbiology
Yang-Hua Xu, Kai-Zhi Jia, Ya-Jie Tang
Adaptation to environmental perturbations requires living systems to coordinately regulate signaling pathways, gene expression and metabolism. To better understand the mechanisms underlying adaptation, the regulatory nodes within networks must be elucidated. Here, ARO8-2, which encodes an aminotransferase; PDC , which encodes a decarboxylase; and STR3 , which encodes a demethiolase, were identified as key genes involved in the catabolism of methionine (Met) in the mycoparasitic fungus Clonostachys rosea isolated from Tuber melanosporum ascocarps...
September 14, 2018: Applied and Environmental Microbiology
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