Changes in fungal communities across a forest disturbance gradient.
This study suggests that changes in fungal functional group composition can be used as an indicator of the effects of forest disturbance on soil carbon and nutrients. PMID: 30979833 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - April 12, 2019 Category: Microbiology Authors: Shi L, Dossa GGO, Paudel E, Zang H, Xu J, Harrison RD Tags: Appl Environ Microbiol Source Type: research

Reversible Gene Expression Control in Yersinia pestis Using an Optimized CRISPRi System.
Abstract Many genes in the bacterial pathogen Yersinia pestis, the causative agent of three plague pandemics, remain uncharacterized, greatly hampering the development of measures for plague prevention and control. Clustered regularly interspaced short palindromic repeats interference (CRISPRi) has been shown to be an effective tool for gene knockdown in model bacteria. In this system, a catalytically-dead Cas9 (dCas9) and a small guide RNA (sgRNA) form a complex, binding to the specific DNA target through base pairing, thereby impeding RNA polymerase binding and causing target gene repression. Here, we introduce ...
Source: Applied and Environmental Microbiology - April 12, 2019 Category: Microbiology Authors: Wang T, Wang M, Zhang Q, Cao S, Li X, Qi Z, Tan Y, You Y, Bi Y, Song Y, Yang R, Du Z Tags: Appl Environ Microbiol Source Type: research

Following the Evolutionary Track of a Highly Specific L-Arginine Oxidase by Reconstruction and Biochemical Analysis of Ancestral and Native Enzymes.
In this study, we tried to follow the evolutionary track of L-arginine oxidase (AROD), an FAD-dependent amino acid oxidase (LAAO) that exhibits high specificity for L-arginine. The library was generated by selecting sequences in which the 15th, 50th, 332nd, and 580th residues are Gly, Ser, Trp, and Thr, respectively. We excluded sequences that are either extremely short or long and those with a low degree of sequence identity. Three ancestral ARODs (AncARODn0, AncARODn1, and AncARODn2) were designed using the library. Subsequently, we expressed the ancestral ARODs as well as native AROD (OkAROD) in bacteria. AncARODn0 is p...
Source: Applied and Environmental Microbiology - April 12, 2019 Category: Microbiology Authors: Nakano S, Niwa M, Asano Y, Ito S Tags: Appl Environ Microbiol Source Type: research

Level of spiked virus necessary to correctly assess enteric virus recovery in water matrices.
Abstract Quantitative microbial risk assessment (QMRA) identifies human enteric viruses in municipal wastewaters as the pathogen group requiring highest log-reductions for various reuse applications. When estimating virus concentration, however, method performance is not well understood, which without inclusion actual risks are likely severely underestimated. To evaluate recovery efficiency for viruses in water, 'known' amounts of virus are often spiked into a water sample and then recovered after a series of analytical procedures. Yet for water matrices such as wastewaters, due to the unknown background concentra...
Source: Applied and Environmental Microbiology - April 12, 2019 Category: Microbiology Authors: Li Q, Qiu Y, Pang XL, Ashbolt NJ Tags: Appl Environ Microbiol Source Type: research

Blue light photoreceptor Sfwc-1 gene regulates phototropic response and fruiting-body development in the homothallic ascomycete Sordaria fimicola.
In this study, we identified and characterized the blue light photoreceptor gene in S. fimicola S. fimicola white collar-1 photoreceptor (SfWC-1) contains light-oxygen-voltage-sensing (LOV), Per-Arnt-Sim (PAS) and other conserved domains and is homologous to the WC-1 blue-light photoreceptor of Neurospora crassa The LOV domain of Sfwc-1 was deleted by homologous recombination using Agrobacterium-mediated protoplast transformation. The Sfwc-1 (Δlov) mutant showed normal vegetative growth but produced less carotenoid pigment under illumination. The mutant showed delayed and less-pronounced fruiting body formation, was ...
Source: Applied and Environmental Microbiology - April 12, 2019 Category: Microbiology Authors: Krobanan K, Liang SW, Chiu HC, Shen WC Tags: Appl Environ Microbiol Source Type: research

Commensal Escherichia coli aggravates acute necrotizing pancreatitis through targeting intestinal epithelial cells.
In conclusion, our study shows that commensal E. coli MG1655 increases TLR4/MyD88/p38 MAPK and ERS signalling-induced intestinal epithelial injury and aggravates ANP in rats. To the best of our knowledge, this is the first study describing the harmful potential of commensal E. coli in ANP.IMPORTANCE To the best of our knowledge, this is the first study describing the harmful potential of commensal E. coli in ANP, which has never been demonstrated by previous studies. Our work provides new insights into the gut bacteria - ANP crosstalk, suggesting that non-pathogenic commensals could also exhibit adverse effects in the cont...
Source: Applied and Environmental Microbiology - April 12, 2019 Category: Microbiology Authors: Zheng J, Lou L, Fan J, Huang C, Mei Q, Wu J, Guo Y, Lu Y, Wang X, Zeng Y Tags: Appl Environ Microbiol Source Type: research

Biofilm formation and synthesis of antimicrobial compounds by the biocontrol agent Bacillus velezensis QST713 in Agaricus bisporus compost micromodel.
We report an over-expression of several genes of the biocontrol agent involved in biofilm formation in the compost compared to expression during growth in broth compost extract, either in the exponential growth phase (epsC, blsA and tapA genes) or in the stationary growth phase (tapA gene), while a gene encoding a flagellar protein (hag) was under-expressed. We also report an over-expression of Bacillus velezensis QST713 genes related to surfactin (srfAA) and fengycin (fenA) production in the presence of the fungal pathogen in the compost.ImportanceBiocontrol agents are increasingly used to replace chemical pesticides to p...
Source: Applied and Environmental Microbiology - April 12, 2019 Category: Microbiology Authors: Pandin C, Darsonval M, Mayeur C, Le Coq D, Aymerich S, Briandet R Tags: Appl Environ Microbiol Source Type: research

Deep Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium.
Abstract Bacterial Halanaerobium strains become the dominant persisting microbial community member in produced fluids across geographically distinct hydraulically fractured shales. Halanaerobium is believed to be inadvertently introduced into this environment during the drilling and fracturing process and must therefore tolerate large changes in pressure, temperature, and salinity. Here, we used a Halanaerobium strain isolated from a natural gas well in the Utica Point Pleasant formation to investigate metabolic and physiological responses to growth under high-pressure subsurface conditions. Laboratory incubations...
Source: Applied and Environmental Microbiology - April 12, 2019 Category: Microbiology Authors: Booker AE, Hoyt DW, Meulia T, Eder E, Nicora CD, Purvine SO, Daly RA, Moore JD, Wunch K, Pfiffner SM, Lipton MS, Mouser PJ, Wrighton KC, Wilkins MJ Tags: Appl Environ Microbiol Source Type: research

Wetland sediments host diverse microbial taxa capable of cycling alcohols.
Abstract Alcohols are commonly derived from the degradation of organic matter, and yet are rarely measured in environmental samples. Wetlands in the Prairie Pothole Region (PPR) support extremely high methane emissions and the highest sulfate reduction rates reported to date, likely contributing to a significant proportion of organic matter mineralization in this system. While ethanol and isopropanol concentrations up to 4-5 mM in PPR wetland pore fluids have been implicated in sustaining these high rates of microbial activity, the mechanisms that support alcohol cycling in this ecosystem are poorly understood. He...
Source: Applied and Environmental Microbiology - April 12, 2019 Category: Microbiology Authors: Dalcin Martins P, Frank J, Mitchell H, Markillie LM, Wilkins MJ Tags: Appl Environ Microbiol Source Type: research

Characterization of the bacteriophage φEf11 ORF 28 endolysin: A multi-functional lytic enzyme with properties distinct from all other identified Enterococcus. faecalis phage endolysins.
In this study, we have cloned, expressed, purified and characterized an endolysin produced by a bacteriophage infecting strains of Enterococcus faecalis The lysin is broadly active against most of the tested E. faecalis strains, and exhibits multifunctional enzymatic specificities that differ from all other characterized endolysins produced by E. faecalis bacteriophages. PMID: 30979842 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - April 12, 2019 Category: Microbiology Authors: Zhang H, Buttaro BA, Fouts DE, Sanjari S, Evans B, Stevens RH Tags: Appl Environ Microbiol Source Type: research

Insights into the phylogeny, nodule functioning and biogeographic distribution of microsymbionts nodulating the orphan Kersting's groundnut [Macrotyloma geocarpum (Harms) Marechal & Baudet] in African soils.
This study explored the morpho-genetic diversity, phylogenetic relationships and N2-fixing efficiency of Kersting's groundnut rhizobial isolates from contrasting environments in Ghana, South Africa and Mozambique. Box-PCR fingerprinting revealed high diversity among rhizobial populations which was influenced by geographic origin. Of the 164 isolates evaluated, 130 Box-PCR types were identified at 70% similarity coefficient, indicating that they were not clones. Soil pH and mineral concentrations were found to influence the distribution of bradyrhizobial populations in African soils. Phylogenetic analysis of 16S rRNA gene a...
Source: Applied and Environmental Microbiology - April 5, 2019 Category: Microbiology Authors: Mohammed M, Jaiswal SK, Dakora FD Tags: Appl Environ Microbiol Source Type: research

Development of a sensitive and specific whole-cell biosensor for arsenic detection.
In this study, we designed an arsenic WCB with a positive feedback amplifier. It is highly sensitive and able to detect arsenic below the WHO limit level. In addition, it also significantly improves the specificity of the biosensor toward arsenic, giving a signal about 10-20 times stronger in response to As(III) than to other metals. This work not only provides simple but effective arsenic biosensors but also demonstrates the importance of genetic engineering, particularly the use of positive feedback amplifiers, in designing WCBs. PMID: 30952659 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - April 5, 2019 Category: Microbiology Authors: Jia X, Bu R, Zhao T, Wu K Tags: Appl Environ Microbiol Source Type: research

Rapid and stable microbial community assembly in the headwaters of third-order stream.
We examined microbial community composition of a first- through third-order stream using fine-scale temporal and spatial regimes. Our results show that the bacterioplankton community develops rapidly and predictably from the headwater population with increasing total stream length. Along the length of the stream, the microbial community exhibits substantial diversity loss and enriches repeatedly for select taxa across days and years, although the relative abundances of individual taxa vary over time and space. This repeated enrichment of a stable stream community likely contributes to the stability and flexibility of downs...
Source: Applied and Environmental Microbiology - April 5, 2019 Category: Microbiology Authors: Teachey ME, McDonald JM, Ottesen EA Tags: Appl Environ Microbiol Source Type: research

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential After Two Years of Biochar Amendment in a Tropical Oxisol.
In this study, we utilized shotgun metagenomics in order to decipher changes in the microbial community in soil microcosms after 14 days of incubation at 23°C, which contained soils from biochar-amended and control plots cultivated with napiergrass. Our analyses revealed that biochar-amended soil microbiomes exhibited a significant shift in both community composition and predicted metabolism. Key metabolic pathways related to carbon turnover, such as the utilization of plant-derived carbohydrates as well as denitrification were enriched under biochar amendment. These community shifts were in part associated with increa...
Source: Applied and Environmental Microbiology - April 5, 2019 Category: Microbiology Authors: Yu J, Deem LM, Crow SE, Deenik J, Penton CR Tags: Appl Environ Microbiol Source Type: research

Functional Analysis of LanI Mediated Lantibiotic Immunity in Bacillus subtilis.
tian KD Abstract Lantibiotics subtilin and nisin are produced by Bacillus subtilis and Lactococcus lactis, respectively. To prevent toxicity of their own lantibiotic both bacteria express specific immunity proteins called SpaI and NisI. In addition, ABC-transporters SpaFEG and NisFEG prevent lantibiotic toxicity by transporting the respective peptides to the extracellular space. Although the 3D-structures of SpaI and NisI have been solved, very little is known about the molecular function of both lipoproteins. Using LILBID (laser induced liquid bead ion desorption) mass spectrometry we show in here that subtilin i...
Source: Applied and Environmental Microbiology - April 5, 2019 Category: Microbiology Authors: Geiger C, Korn SM, Häsler M, Peetz O, Martin J, Kötter P, Morgner N, Entian KD Tags: Appl Environ Microbiol Source Type: research

Decontamination effect of the Spindle and 222-nm krypton-chlorine excilamp combination against pathogens on apples (Malus domestica Borkh.) and bell peppers (Capsicum annuum L.).
This study demonstrates the potential of the Sp-Ex to replace conventional washing with sanitizers, and it can be used as baseline data for practical application by industry. In addition, implementation of the Sp-Ex developed in this study is expected to not only meet consumer preference for fresh, minimally-processed produce, but also reduces human exposure to harmful chemicals while being beneficial to the environment. PMID: 30952663 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - April 5, 2019 Category: Microbiology Authors: Kang JW, Kang DH Tags: Appl Environ Microbiol Source Type: research

Molecular Mechanism of N,N-Dimethylformamide Degradation in a Methylobacterium sp. Strain DM1.
This study provides insights in the molecular mechanism and evolutionary advantage of DMF degradation facilitated by plasmid pLVM1 and redundant genes in strain DM1, suggesting emergence of new ecotypes of Methylobacterium. PMID: 30952664 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - April 5, 2019 Category: Microbiology Authors: Lu X, Wang W, Zhang L, Hu H, Xu P, Wei T, Tang H Tags: Appl Environ Microbiol Source Type: research

Erratum for Hokynar et al., "Molecular Evidence of Chlamydia-Like Organisms in the Feces of Myotis daubentonii Bats".
Erratum for Hokynar et al., "Molecular Evidence of Chlamydia-Like Organisms in the Feces of Myotis daubentonii Bats". Appl Environ Microbiol. 2019 Apr 01;85(7): Authors: Hokynar K, Vesterinen EJ, Lilley TM, Pulliainen AT, Korhonen SJ, Paavonen J, Puolakkainen M PMID: 30902824 [PubMed - in process] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - March 25, 2019 Category: Microbiology Authors: Hokynar K, Vesterinen EJ, Lilley TM, Pulliainen AT, Korhonen SJ, Paavonen J, Puolakkainen M Tags: Appl Environ Microbiol Source Type: research

Differentiation of vegetative cells into spores: a kinetic model applied to Bacillus subtilis.
ler L Abstract Spore-forming bacteria are natural contaminants of food raw materials and sporulation can occur in many environments from farm to fork. In order to characterize and to predict spore formation over time, we developed a model that describes both the kinetics of growth and the differentiation of vegetative cells into spores. The model is based on a classical growth model and enables to describe the kinetic of sporulation with the addition of three parameters specific of the sporulation. Two parameters are related to the probability of each vegetative cell to commit to sporulation and to form a spore, a...
Source: Applied and Environmental Microbiology - March 22, 2019 Category: Microbiology Authors: Gauvry E, Mathot AG, Couvert O, Leguérinel I, Jules M, Coroller L Tags: Appl Environ Microbiol Source Type: research

Comparative Genomic Analyses of Municipal Wastewater Salmonella Isolates Detects a Clinically Unreported Salmonellosis Outbreak.
Abstract Municipal wastewater (MW) includes human waste that contains both commensal and pathogenic enteric microorganisms, and this collective community microbiome can be monitored for community diseases. In a previous study, we assessed salmonellosis disease burden using municipal wastewater from Honolulu, Hawaii, which was monitored over a 54-week period. During this time, a Salmonella serovar Paratyphi B var. L(+) tartrate (+) (also known as S. Java) strain was identified: this strain was detected simultaneously to a clinically-reported outbreak, and pulsed field gel electrophoresis (PFGE) patterns were identi...
Source: Applied and Environmental Microbiology - March 22, 2019 Category: Microbiology Authors: Diemert S, Yan T Tags: Appl Environ Microbiol Source Type: research

Characterization and genomic profiling of Klebsiella pneumoniae 2e, a newly isolated 1,3-propanediol-producing strain, revealed its adaptability to crude glycerol.
In this study, Klebsiella pneumoniae 2e was newly isolated for the conversion of crude glycerol into 1,3-PDO. Batch fermentation analysis confirmed that crude glycerol and its main impurities had slight impacts on the growth, key enzyme activity and 1,3-PDO production of K. pneumoniae 2e. The 1,3-PDO yield from crude glycerol by K. pneumoniae 2e reached 0.62 mol1,3-PDO/molglycerol, which was higher than that of most reported 1,3-PDO-producing Klebsiella strains. Genomic profiling revealed that K. pneumoniae 2e possesses 30 genes involved in glycerol anaerobic metabolism and 1,3-PDO biosynthesis. Quantitative real-time PCR ...
Source: Applied and Environmental Microbiology - March 22, 2019 Category: Microbiology Authors: Ma J, Jiang H, Hector SB, Xiao Z, Li J, Liu R, Li C, Zeng B, Liu GQ, Zhu Y Tags: Appl Environ Microbiol Source Type: research

An Osmoregulatory Mechanism Operating through OmpR and LrhA Controls the Motile-Sessile Switch in the Plant Growth-Promoting Bacterium Pantoea alhagi.
In this study, we report that the LrhA regulator is an osmoregulated transcription factor that directly binds to the promoters of the flhDC, eps and opgGH operons and differentially regulates their expression, thus inhibiting motility and promoting exopolysaccharides (EPS) production, synthesis of osmoregulated periplasmic glucans (OPGs), biofilm formation and root colonization of the plant growth-promoting bacterium Pantoea alhagi LTYR-11Z. Further, we observed that the LrhA-regulated OPGs control the RcsCD RcsB activation in a concentration-dependent manner, and a high concentration of OPGs induced by increased medium os...
Source: Applied and Environmental Microbiology - March 22, 2019 Category: Microbiology Authors: Li S, Liang H, Wei Z, Bai H, Li M, Li Q, Qu M, Shen X, Wang Y, Zhang L Tags: Appl Environ Microbiol Source Type: research

A Novel Antifungal Compound Z-705 Specifically Inhibits Protein Kinase C of Filamentous Fungi.
Abstract The cell wall integrity signaling (CWIS) pathway is involved in fungal cell-wall biogenesis. This pathway is composed of sensor proteins, protein kinase C (PKC), and the MAP kinase pathway, and controls the transcription of many cell-wall related genes. PKC plays a pivotal role in this pathway; deficiency in PkcA in the model filamentous fungus Aspergillus nidulans and in MgPkc1 in the rice blast fungus Magnaporthe grisea is lethal. This suggests that PKC in filamentous fungi is a potential target for antifungal agents. In the present study, to search for MgPkc1 inhibitors, we carried out in silico screen...
Source: Applied and Environmental Microbiology - March 22, 2019 Category: Microbiology Authors: Sugahara A, Yoshimi A, Shoji F, Fujioka T, Kawai K, Umeyama H, Komatsu K, Enomoto M, Kuwahara S, Hagiwara D, Katayama T, Horiuchi H, Miyazawa K, Nakayama M, Abe K Tags: Appl Environ Microbiol Source Type: research

Genomic characterization of candidate division LCP-89 reveals an atypical cell wall structure, microcompartment production, and dual respiratory and fermentative capacities.
This study provides a genomics-based analysis highlighting the structural features and metabolic capacities of a yet-uncultured bacterial phylum (LCP-89) previously identified in 16S rRNA surveys for which no prior genomes have been described. Our analysis identifies several interesting structural features for members of this phylum e.g. lack of peptidoglycan biosynthetic machinery and ability to form bacterial microcompartments. Predicted metabolic capabilities include degradation of a wide range of sugars, anaerobic respiratory capacity, as well as fermentative capacities. In addition to the detailed structural and metab...
Source: Applied and Environmental Microbiology - March 22, 2019 Category: Microbiology Authors: Youssef NH, Farag IF, Hahn CR, Jarett J, Becraft E, Eloe-Fadrosh E, Lightfoot J, Bourgeois A, Cole T, Ferrante S, Truelock M, Marsh W, Jamaleddine M, Ricketts S, Simpson R, McFadden A, Hoff W, Ravin NV, Sievert S, Stepanauskas R, Woyke T, Elshahed M Tags: Appl Environ Microbiol Source Type: research

Phototrophic lactate utilization by Rhodopseudomonas palustris is stimulated by co-utilization with additional substrates.
Abstract The phototrophic purple nonsulfur bacterium Rhodopseudomonas palustris is known for its metabolic versatility and is of interest for various industrial and environmental applications. Despite decades of research on R. palustris growth under diverse conditions, patterns of R. palustris growth and carbon utilization with mixtures of carbon substrates remain largely unknown. R. palustris readily utilizes most short chain organic acids but cannot readily use lactate as a sole carbon source. Here we investigated the influence of mixed-substrate utilization on phototrophic lactate consumption by R. palustris We...
Source: Applied and Environmental Microbiology - March 22, 2019 Category: Microbiology Authors: Govindaraju A, McKinlay JB, LaSarre B Tags: Appl Environ Microbiol Source Type: research

Conserved Pyridoxal 5'-Phosphate Binding Protein YggS Impacts Amino Acid Metabolism through Pyridoxine 5'-Phosphate in Escherichia coli.
In this study, we determined that the pyridoxine (PN) sensitivity observed in the yggS-deficient E. coli was caused by the pyridoxine 5'-phosphate (PNP)-dependent overproduction of Val, which is toxic to E. coli The data suggest that the yggS mutation impacts Val accumulation by perturbing the biosynthetic of Thr from homoserine (Hse). Exogenous Hse inhibited the growth of the yggS mutant, caused further accumulation of PNP, and increased some intermediates in the Thr-Ile-Val metabolic pathways. Blocking the Thr biosynthetic pathway or decreasing of the intracellular PNP levels, abolished the perturbations of amino acid me...
Source: Applied and Environmental Microbiology - March 22, 2019 Category: Microbiology Authors: Ito T, Yamamoto K, Hori R, Yamauchi A, Downs DM, Hemmi H, Yoshimura T Tags: Appl Environ Microbiol Source Type: research

Microcin PDI Inhibits Antibiotic-Resistant Strains of Escherichia coli and Shigella Through a Mechanism of Membrane Disruption and Protection by Homotrimer Self-Immunity.
ll DR Abstract Microcin PDI (MccPDI), a class IIa microcin that is produced by Escherichia coli strains 25 and 284, is known to inhibit foodborne pathogenic enterohemorrhagic E. coli (EHEC) serotypes O157:H7 and O26. Herein we demonstrate that MccPDI can inhibit Shigella strains and E. coli isolates that are multidrug resistant, the latter including strains known to cause urinary tract infections in people and companion animals. Two exceptions out of 17 strains were identified. One of the two resistant E. coli isolates (AR0349) has a mutation in a critical amino acid residue that was identified in prior work as re...
Source: Applied and Environmental Microbiology - March 22, 2019 Category: Microbiology Authors: Lu SY, Graça T, Avillan JJ, Zhao Z, Call DR Tags: Appl Environ Microbiol Source Type: research

Determinants of Phage Host Range in Staphylococcus Species.
Abstract Bacteria in the genus Staphylococcus are important targets for phage therapy due to their prevalence as pathogens and increasing antibiotic resistance. Here we review Staphylococcus outer surface features and specific phage resistance mechanisms that define host range - the set of strains an individual phage can potentially infect. Phage infection goes through five distinct phases - attachment, uptake, biosynthesis, assembly and lysis. Adsorption inhibition, encompassing outer surface teichoic acid receptor alteration, elimination, or occlusion, limits successful phage attachment and entry. Restriction-mo...
Source: Applied and Environmental Microbiology - March 22, 2019 Category: Microbiology Authors: Moller AG, Lindsay JA, Read TD Tags: Appl Environ Microbiol Source Type: research

Next Generation of Tn7-based single copy insertion elements for use in multi- and pandrug resistant strains of Acinetobacter baumannii.
This study demonstrates the practical potential of using apramycin and zeocin mini-Tn7 and Flp recombinase encoded constructs to carry out genomic manipulations in clinical isolates of A. baumannii displaying MDR and XDR phenotypes. PMID: 30902859 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - March 22, 2019 Category: Microbiology Authors: Ducas-Mowchun K, De Silva PM, Crisostomo L, Fernando DM, Chao TC, Pelka P, Schweizer HP, Kumar A Tags: Appl Environ Microbiol Source Type: research

The influence of plant species, tissue type and temperature on the capacity of Shigatoxigenic Escherichia coli to colonise, grow and internalise into plants.
Abstract Contamination of fresh produce with pathogenic Escherichia coli, including Shigatoxigenic E. coli (STEC), represents a serious risk to human health. Colonisation is governed by multiple bacterial and plant factors that can impact the probability and suitability of bacterial growth. Thus, we aimed to determine whether the growth potential of STEC for plants associated with foodborne outbreaks (two leafy vegetables and two sprouted seed species), is predictive for colonisation of living plants as assessed from growth kinetics and biofilm formation in plant extracts. Fitness of STEC was compared to environme...
Source: Applied and Environmental Microbiology - March 22, 2019 Category: Microbiology Authors: Merget B, Forbes KJ, Brennan F, McAteer S, Shepherd T, Strachan NJC, Holden NJ Tags: Appl Environ Microbiol Source Type: research

Composition and origin of the fermentation microbiota of mahewu, a Zimbabwean fermented cereal beverage.
In conclusion, mahewu microbiota is mainly derived from millet malt microbiota but minor components of malt microbiota rapidly outcompete Enterobacteriaceae and Bacillus species during fermentation.IMPORTANCE. This study provides insight into the composition and origin of the microbiota of mahewu and the composition of millet malt microbiota. Fermentation microbiota are often hypothesized to be derived from the environment but the evidence remains inconclusive. Our findings confirm that millet malt is the major source of mahewu microbiota. By complementing cultural methods with high throughput sequencing of 16S rRNA amplic...
Source: Applied and Environmental Microbiology - March 22, 2019 Category: Microbiology Authors: Pswarayi F, Gänzle MG Tags: Appl Environ Microbiol Source Type: research

Multilocus sequence analysis, a rapid and accurate tool for taxonomic classification, evolutionary relationship and population biology of the genus Shewanella.
In this study, a standard multilocus sequence analysis (MLSA) based on six protein-coding genes (gyrA, gyrB, infB, recN, rpoA and topA) was established as a rapid and accurate identification tool in fifty-nine type Shewanella strains. This method yielded sufficient resolving power in regard to enough informative sites, adequate sequence divergences and distinct interspecies branches. The stability of phylogenetic topology was supported by high bootstrap values and concordance with different methods. The reliability of the MLSA scheme was further validated by identical phylogenies and high correlations of genomes. The MLSA ...
Source: Applied and Environmental Microbiology - March 22, 2019 Category: Microbiology Authors: Fang Y, Wang Y, Liu Z, Dai H, Cai H, Li Z, Du Z, Wang X, Jing H, Wei Q, Kan B, Wang D Tags: Appl Environ Microbiol Source Type: research

Biofilm constructing variants of Paraburkholderia phytofirmans PsJN outcompete the wild-type form in free-living and static conditions but not in planta.
, Sanchez L Abstract Members of the genus Burkholderia colonize diverse ecological niches. Among the plant-associated strains, Paraburkholderia phytofirmans PsJN is an endophyte with a broad host range. In spatially structured environment (unshaken broth cultures), biofilm-constructing specialists of P. phytofirmans PsJN colonizing the air-liquid interface arose at high frequency. In addition to forming a robust biofilm in vitro and in planta on Arabidopsis roots, those mucoid phenotypic variants display a reduced swimming ability and modulate the expression of several Microbe Associated Molecular Pattern (MAMPs) ...
Source: Applied and Environmental Microbiology - March 22, 2019 Category: Microbiology Authors: Rondeau M, Esmaeel Q, Crouzet J, Blin P, Gosselin I, Sarazin C, Pernes M, Beaugrand J, Wisniewski-Dyé F, Vial L, Faure D, Clément C, Ait Barka E, Jacquard C, Sanchez L Tags: Appl Environ Microbiol Source Type: research

Salmonella Newport in soils amended with heat-treated poultry pellets survived longer and more readily transferred to and persisted on spinach.
Abstract Untreated biological soil amendments of animal origin (BSAAO) are commonly used as biological fertilizers, but can harbor foodborne pathogens like Salmonella enterica leading to potential transfer from soils to fruits and vegetables intended for human consumption. Heat-treated poultry pellets (HTPP) can provide produce growers a slow release fertilizer with minimized risk of pathogen contamination. Little is known about the impact of HTTP-amended soil on survival of Salmonella enterica The contributions of RpoS and formation of viable but non-culturable cells to Salmonella survival in soils are also inada...
Source: Applied and Environmental Microbiology - March 15, 2019 Category: Microbiology Authors: Shah MK, Bradshaw R, Nyarko E, Handy ET, East C, Millner PD, Bergholz TM, Sharma M Tags: Appl Environ Microbiol Source Type: research

Identification of a molecular switch that controls expression of the mannose-specific adhesin, Msa, in Lactobacillus plantarum.
In this study, we have analyzed the promoter regions upstream of the msa gene encoding a mannose-specific adhesin in these two strains. The promoter region was mapped by primer extension and DNA sequence analysis, and only a single nucleotide change was identified between the two strains. However, Northern blot analysis showed a stronger msa transcript band in 299v than in WCFS1 correlating with the different adhesion capacities. During establishment of a high-throughput yeast agglutination assay, we isolated variants of WCFS1 that displayed a very strong mannose-specific adhesion phenotype. The region upstream of the msa ...
Source: Applied and Environmental Microbiology - March 15, 2019 Category: Microbiology Authors: Holst B, Glenting J, Holmstrøm K, Israelsen H, Vrang A, Antonsson M, Ahrné S, Madsen SM Tags: Appl Environ Microbiol Source Type: research

Transposition of IS4 Family Insertion Sequences ISTeha3, ISTeha4 and ISTeha5 into arc Operon Disrupts Arginine Deiminase System in Tetragenococcus halophilus.
This report provides an example of insertion sequence-mediated generation and evolution of T. halophilus and primary information about their characteristics. PMID: 30877114 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - March 15, 2019 Category: Microbiology Authors: Wakinaka T, Watanabe J Tags: Appl Environ Microbiol Source Type: research

Bacterial analogs of plant tetrahydropyridine alkaloids mediate microbial interactions in a rhizosphere model system.
In this study, we characterized competition between Pseudomonas koreensis and Flavobacterium johnsoniae, two common rhizosphere inhabitants. We identified a widespread gene cluster in several Pseudomonas spp., which is necessary for the production of a novel family of tetrahydropyridine alkaloids that are structural analogs of plant alkaloids. We expand the known repertoire of antibiotics produced from Pseudomonas in the rhizosphere and demonstrate the role of the metabolites in interactions with other bacteria of the rhizosphere. PMID: 30877115 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - March 15, 2019 Category: Microbiology Authors: Lozano GL, Park HB, Bravo JI, Armstrong EA, Denu JM, Stabb EV, Broderick NA, Crawford JM, Handelsman J Tags: Appl Environ Microbiol Source Type: research

Cell aggregation and aerobic respiration are important for Zymomonas mobilis ZM4 survival in an aerobic minimal medium.
Abstract Zymomonas mobilis produces ethanol from glucose near the theoretical maximum yield, making it a potential alternative to yeast for industrial ethanol production. A potentially useful industrial feature is the ability to form multicellular aggregates called flocs, which can settle quickly and exhibit higher resistance to harmful chemicals. While spontaneous floc-forming Z. mobilis mutants have been described, little is known about the natural conditions that induce Z. mobilis floc formation and the genetic factors involved. Here we found that wild-type Z. mobilis forms flocs in response to aerobic growth c...
Source: Applied and Environmental Microbiology - March 15, 2019 Category: Microbiology Authors: Jones-Burrage SE, Kremer TA, McKinlay JB Tags: Appl Environ Microbiol Source Type: research

Genetic diversity of Flavescence dor ée phytoplasmas at vineyard scale.
Genetic diversity of Flavescence dorée phytoplasmas at vineyard scale. Appl Environ Microbiol. 2019 Mar 15;: Authors: Rossi M, Pegoraro M, Ripamonti M, Abbà S, Beal D, Giraudo A, Veratti F, Malembic-Maher S, Salar P, Bosco D, Marzachì C Abstract To study the role of wild areas around the vineyards in the epidemiology of Flavescence dorée (FD) and track origin of new foci, two phytoplasma genetic markers, dnaK and malG, were developed for FD phytoplasma characterization. The two genes and the vmpA locus were used to genetically characterize FDp populations at seven agroecosy...
Source: Applied and Environmental Microbiology - March 15, 2019 Category: Microbiology Authors: Rossi M, Pegoraro M, Ripamonti M, Abbà S, Beal D, Giraudo A, Veratti F, Malembic-Maher S, Salar P, Bosco D, Marzachì C Tags: Appl Environ Microbiol Source Type: research

Spatial heterogeneity of Vibrio spp. in sediments of Chinese marginal seas.
Abstract Vibrio spp. are ubiquitous marine bacteria with high metabolism flexibility and genome plasticity. Previous studies have revealed dynamics of planktonic vibrios in relation to environmental forces such as temperature and salinity. However, little is known about the Vibrio ecology in benthic environments. Here, we elucidated the abundance, diversity and spatial distribution of Vibrio spp. in sediments along the Chinese marginal seas, with a high spatial range from the north to south covering the Yellow Sea (YS), East China Sea (ECS) and South China Sea (SCS). Quantitative analysis showed that Vibrio was mo...
Source: Applied and Environmental Microbiology - March 15, 2019 Category: Microbiology Authors: Wang X, Liu J, Li B, Liang J, Sun H, Zhou S, Zhang XH Tags: Appl Environ Microbiol Source Type: research

Amino Sugars Modify Antagonistic Interactions between Commensal Oral Streptococci and Streptococcus mutans.
Abstract N-acetylglucosamine (GlcNAc) and glucosamine (GlcN) enhance the competitiveness of the laboratory strain DL1 of Streptococcus gordonii against the caries pathogen Streptococcus mutans Here we examine how amino sugars affect the interaction of five low-passage clinical isolates of abundant commensal streptococci with S. mutans utilizing a dual-species biofilm model. Compared to glucose, growth on GlcN or GlcNAc significantly reduced the viability of S. mutans in co-cultures with most commensals, shifting the proportions of species. Consistent with these results, production of H2O2 was increased in most com...
Source: Applied and Environmental Microbiology - March 15, 2019 Category: Microbiology Authors: Chen L, Chakraborty B, Zou J, Burne RA, Zeng L Tags: Appl Environ Microbiol Source Type: research

Influence of ammonium on the formation of mineral-associated organic carbon by an ectomycorrhizal fungus.
In this study, we examined how changes in nitrogen (N) availability affected the formation of mineral-associated carbon (C) from these two pathways. DOM was extracted from forest soils. The processing of this DOM by the ectomycorrhizal fungus Paxillus involutus was examined in laboratory-scale studies under different levels of ammonium. At low levels of ammonium (i.e. during N limited conditions), the DOM components were slightly oxidized and fungal C metabolites with iron reducing activity were secreted. Ammonium amendments decreased the amount of C metabolites and no additional oxidation of the organic matter was detecte...
Source: Applied and Environmental Microbiology - March 15, 2019 Category: Microbiology Authors: Wang T, Tian Z, Tunlid A, Persson P Tags: Appl Environ Microbiol Source Type: research

Swine-origin H1 influenza viruses isolated from humans exhibit sustained infectivity in an aerosol state.
In this study, we evaluated the longevity of influenza viruses in aerosols generated in the laboratory. We selected a panel of H1 viruses that exhibit diverse transmission profiles in the ferret model, including four human isolates of swine-origin (referred to as variant) and a seasonal strain. By measuring the ratio of viral RNA to infectious virus maintained in aerosols over time, we show that influenza viruses known to transmit efficiently through the air, display enhanced stability in an aerosol state for prolonged periods compared with those viruses that do not transmit as efficiently. We then assessed whether H1 infl...
Source: Applied and Environmental Microbiology - March 15, 2019 Category: Microbiology Authors: Pulit-Penaloza JA, Belser JA, Tumpey TM, Maines TR Tags: Appl Environ Microbiol Source Type: research

Characterization of the enterobactin-specific antibodies induced by a novel enterobactin conjugate vaccine.
In this study, we aimed to develop an innovative Ent conjugate vaccine that can induce high level of antibodies directed against Ent, and to provide solid evidence demonstrating siderophore-binding capacity of Ent-specific antibodies. Using a simple method, we successfully conjugated purified Ent to different carriers including keyhole limpet hemocyanin (KLH), bovine serum albumin, and CmeC, a vaccine candidate for Campylobacter control. Subcutaneous immunization of rabbits with the KLH-Ent conjugate triggered strong systemic IgG immune response with up to 16,384 fold increase in IgG titer directed against whole conjugate ...
Source: Applied and Environmental Microbiology - March 15, 2019 Category: Microbiology Authors: Wang H, Zeng X, Mo Y, He B, Lin H, Lin J Tags: Appl Environ Microbiol Source Type: research

Genome-wide Identification of Fitness Factors in Seawater for Edwardsiella piscicida.
In conclusion, we defined genes and processes related to metabolism and virulence that operate in E. piscicida to facilitate survival in low- and high-temperature seawater, which may underlie the infection outbreak mechanisms of E. piscicida and facilitate the development of improved vaccines against marine pathogens.IMPORTANCE E. piscicida is one of the most important marine pathogens and causes serious edwardsiellosis in farmed fish during the summer-autumn seasonal changes, resulting in enormous losses to aquaculture industries worldwide. Survival and transmission of the pathogen in seawater are critical steps that incr...
Source: Applied and Environmental Microbiology - March 15, 2019 Category: Microbiology Authors: Wei L, Wu Y, Yang G, Xu R, Liu X, Liu Q, Zhang Y, Ma Y, Wang Q Tags: Appl Environ Microbiol Source Type: research

The Pleiotropic Effects of c-di-GMP Content in Pseudomonas syringae.
Abstract Although the ubiquitous bacterial secondary messenger cyclic diguanylate (c-di-GMP) has important cellular functions in a wide range of bacteria, its function in the model plant pathogen Pseudomonas syringae (P. syringae) remains largely elusive. To this end, we overexpressed Escherichia coli diguanylate cyclase (YedQ) or phosphodiesterase (YhjH) in P. syringae, resulting in high or low in vivo levels of c-di-GMP. Via genome-wide RNA sequencing of these two strains, we found that c-di-GMP regulates (i) fliN, fliE, and flhA, which are associated with flagellar assembly; (ii) alg8 and alg44, which are relat...
Source: Applied and Environmental Microbiology - March 8, 2019 Category: Microbiology Authors: Wang T, Cai Z, Shao X, Zhang W, Xie Y, Zhang Y, Hua C, Schuster SC, Yang L, Deng X Tags: Appl Environ Microbiol Source Type: research

The PlyB Endolysin of Bacteriophage vB_BanS_Bcp1 Exhibits Broad-Spectrum Bactericidal Activity against Bacillus cereus sensu lato Isolates.
In this study, we isolated the Myoviridae phage vB_BanS_Bcp1 (herein referred to as Bcp1) from landfill soil using a Bacillus anthracis host. The antimicrobial activities of both Bcp1 and its encoded endolysin, PlyB, were examined across different B. cereus sensu lato (s.l.) group species, including B. cereus sensu stricto (s.s), B. thuringiensis and B. anthracis, with pathogenic potential in humans and multiple different uses in biotechnological applications. The Bcp1 phage infected only a subset (11-66%) of each B. cereus s.l. species group tested. In contrast, functional analysis of purified PlyB revealed a potent bacte...
Source: Applied and Environmental Microbiology - March 8, 2019 Category: Microbiology Authors: Schuch R, Pelzek AJ, Nelson DC, Fischetti VA Tags: Appl Environ Microbiol Source Type: research

Validation and stabilization of a prophage lysin of Clostridium perfringens by yeast surface display and co-evolutionary models.
Abstract Bacteriophage lysins are compelling antimicrobial proteins whose biotechnological utility and evolvability would be aided by elevated stability. Lysin catalytic domains, which evolved as modular entities distinct from cell wall binding domains, can be classified into one of several families with highly conserved structure and function, many of which contain thousands of annotated homologous sequences. Motivated by the quality of this evolutionary data, the performance of generative protein models incorporating co-evolutionary information was analyzed to predict the stability of variants in a collection of...
Source: Applied and Environmental Microbiology - March 8, 2019 Category: Microbiology Authors: Ritter SC, Hackel BJ Tags: Appl Environ Microbiol Source Type: research

New Insights into the Nature of Symbiotic Associations in Aphids: Infection Process, Biological Effects and Transmission Mode of Cultivable Serratia symbiotica Bacteria.
e T Abstract Symbiotic microorganisms are widespread in nature and can play a major role in the ecology and evolution of animals. The aphid-Serratia symbiotica bacterium interaction provides a valuable model to study mechanisms behind these symbiotic associations. The recent discovery of cultivable S. symbiotica strains having the possibility of free-living lifestyle allowed us to simulate their environmental acquisition by aphids to examine the mechanisms involved in this infection pathway. Here, after oral ingestion, we analyzed the infection dynamic of cultivable S. symbiotica during the host's lifetime using q...
Source: Applied and Environmental Microbiology - March 8, 2019 Category: Microbiology Authors: Pons I, Renoz F, Noël C, Hance T Tags: Appl Environ Microbiol Source Type: research

Evaluation of the natural attenuation potential of diluted bitumen by microbial communities in the Douglas Channel and Hecate Strait, British Columbia.
This study investigated the potential of microbial communities from these waters to mitigate the impacts of a potential dilbit spill. Microcosm experiments were set up with water samples representing different seasons, years, sampling stations, and dilbit blends. While the alkane fraction of the tested dilbit blends was almost completely degraded after 28 days, the majority of the polycyclic aromatic hydrocarbons (PAHs) remained. The addition of the dispersant Corexit 9500A most often had either no effect or an enhancing effect on dilbit degradation. Dilbit-degrading microbial communities were highly variable between seaso...
Source: Applied and Environmental Microbiology - March 8, 2019 Category: Microbiology Authors: Schreiber L, Fortin N, Tremblay J, Elias M, Mason J, Sanschagrin S, Cobanli S, King T, Lee K, Greer CW Tags: Appl Environ Microbiol Source Type: research