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Incidence of facultative bacterial endosymbionts in spider mites associated with local environment and host plant.
This study highlights that host-endosymbiont interactions may be associated with environmental factors, including climate and other geographically linked factors, as well as the host's food plant.IMPORTANCEThis study aims to study the incidence of endosymbiont distribution and infection patterns in spider mites. The main findings are that multiple endosymbiont infections were more common than expected, and that endosymbiont infection frequencies were associated with environmental factors. This work highlights that host-endosymbiont interactions need to be studied within an environmental and geographical context. PMID:...
Source: Applied and Environmental Microbiology - January 12, 2018 Category: Microbiology Authors: Zhu YX, Song YL, Zhang YK, Hoffmann AA, Zhou JC, Sun JT, Hong XY Tags: Appl Environ Microbiol Source Type: research

Development of an Efficient Genome Editing Tool in Bacillus licheniformis Using CRISPR-Cas9 Nickase.
In this study, an efficient genome editing method was developed for Bacillus licheniformis using a CRISPR-Cas9 nickase integrated into the genome of B. licheniformis DW2 with overexpression driven by the P43 promoter. The yvmC gene was deleted using the CRISPR-Cas9n technique with homology arms of 1.0 kb as a representative example and an efficiency of 100% was achieved. In addition, two genes were simultaneously disrupted with an efficiency of 11.6% and the large DNA fragment bacABC (42.7 kb) was deleted with an efficiency of 79.0%. Furthermore, the heterologous reporter gene aprN, which encodes for nattokinase in Bacillu...
Source: Applied and Environmental Microbiology - January 12, 2018 Category: Microbiology Authors: Li K, Cai D, Wang Z, He Z, Chen S Tags: Appl Environ Microbiol Source Type: research

Influence of type-I fimbriae and fluid shear stress on bacterial behavior and multicellular architecture of early Escherichia coli biofilms at single-cell resolution.
In this study we examine the specific role of type-I fimbriae in nascent stages of biofilm formation and the response of micro-colonies to environmental flow shear at single-cell resolution. The results show that type-I fimbriae are not required for reversible adhesion from plankton, but critical for irreversible adhesion of Escherichia coli (E.coli) MG1655 forming biofilms on polyethylene terephthalate (PET) surfaces. Besides establishing a firm cell-surface contact, the irreversible adhesion seems necessary to initiate the proliferation of E.coli on the surface. After application of shear stress, bacterial retention is d...
Source: Applied and Environmental Microbiology - January 12, 2018 Category: Microbiology Authors: Wang L, Keatch R, Zhao Q, Wright JA, Bryant CE, Redmann AL, Terentjev EM Tags: Appl Environ Microbiol Source Type: research

Genomic and phenotypic characterization of type strains and dairy-associated isolates in the Bacillus cereus group indicates considerable intra-clade variability in toxin production and cytotoxicity.
Abstract While some species in the B. cereus group are well-characterized human pathogens (e.g., B. anthracis and B. cereus s.s.), the pathogenicity of other species (e.g., B. pseudomycoides) either has not been characterized or is presently not well understood. To provide an updated characterization of the pathogenic potential of species in the B. cereus group, we classified a set of 52 isolates, including 8 type strains and 44 environmental isolates from dairy-associated sources, into 7 phylogenetic clades and characterized them for (i) the presence of toxin genes, (ii) phenotypic characteristics used for identi...
Source: Applied and Environmental Microbiology - January 12, 2018 Category: Microbiology Authors: Miller RA, Jian J, Beno SM, Wiedmann M, Kovac J Tags: Appl Environ Microbiol Source Type: research

A Novel l-Glutamate Exporter of Corynebacterium glutamicum.
Abstract Besides metabolic pathways and regulatory networks, transport systems are also pivotal for cellular metabolism and hyper-production of biochemicals using microbial cell factories. Identification and characterization of transporters are therefore of great significance for understanding and engineering of transport reactions. Herein, a novel l-glutamate exporter MscCG2 that extensively exists in Corynebacterium glutamicum strains but is distinct from the only known l-glutamate exporter MscCG was discovered in an industrial l-glutamate producing C. glutamicum MscCG2 was predicted to possess three transmembra...
Source: Applied and Environmental Microbiology - January 12, 2018 Category: Microbiology Authors: Wang Y, Cao G, Xu D, Fan L, Wu X, Ni X, Zhao S, Zheng P, Sun J, Ma Y Tags: Appl Environ Microbiol Source Type: research

Fluorescence recovery allows the implementation of a fluorescence reporter gene platform applicable for the detection and quantification of horizontal gene transfer in anoxic environments.
This study focused on the development and validation of an appropriate aerobic fluorescence recovery (AFR) method for this platform, as it embodies the missing technical link impeding its implementation in anoxic environments. PMID: 29330182 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - January 12, 2018 Category: Microbiology Authors: Pinilla R, Riber L, Sørensen SJ Tags: Appl Environ Microbiol Source Type: research

Campylobacter jejuni Colonization in the Crow Gut Involves High Deletion within the Cytolethal Distending Toxin Gene Cluster.
In this study two different species of the human-commensal crow, from two different geographical regions separated by 7000 miles of land and water, have been examined for their ability to cause disease by shedding campylobacter. Our results show that the crow, may not play a significant role in campylobacteriosis because the campylobacter they shed produce a non-functional toxin. PMID: 29330183 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - January 12, 2018 Category: Microbiology Authors: Sen K, Lu J, Mukherjee P, Berglund T, Varughese E, Mukhopadhyay AK Tags: Appl Environ Microbiol Source Type: research

Microbiomes in Dishwashers: Analysis of the microbial diversity and putative opportunistic pathogens in dishwasher biofilm communities.
This study showed how specific conditions of the dishwashers impact the abundance of microbial groups, and investigated on the inter- and intra-kingdom interactions that shape these biofilms. The age, the usage frequency and hardness of incoming tap water of dishwashers had significant impact on bacterial and fungal composition. Representatives of Candida spp. were found at highest prevalence (100%) in all dishwashers and are assumingly one of the first colonizers in recent dishwashers. Pairwise correlations in tested microbiome showed that certain bacterial groups co-occur and so did the fungal groups. In mixed bacterial-...
Source: Applied and Environmental Microbiology - January 12, 2018 Category: Microbiology Authors: Raghupathi PK, Zupančič J, Brejnrod AD, Jacquiod S, Houf K, Burmølle M, Gunde-Cimerman N, Sørensen SJ Tags: Appl Environ Microbiol Source Type: research

The MgtE homolog FicI acts as a secondary ferrous iron importer in Shewanella oneidensis strain MR-1.
Abstract The transport of metals into and out of cells is necessary for the maintenance of appropriate intracellular concentrations. Metals are needed for incorporation into metalloproteins but become toxic at higher concentrations. Many metal transport proteins have been discovered in bacteria, including the Mg2+ transporter-E (MgtE) family of passive Mg2+/Co2+ cation-selective channels. Low sequence identity exists between members of the MgtE family, indicating that substrate specificity may differ among MgtE transporters. Under anoxic conditions, dissimilatory metal-reducing bacteria such as Shewanella and Geob...
Source: Applied and Environmental Microbiology - January 12, 2018 Category: Microbiology Authors: Bennett BD, Redford KE, Gralnick JA Tags: Appl Environ Microbiol Source Type: research

Effect of plasmid design and type of integration event on recombinant protein expression in Pichia pastoris.
Abstract Pichia pastoris (syn. Komagataella phaffii) is one of the most common eukaryotic expression systems for heterologous protein production. Expression cassettes are typically integrated in the genome to obtain stable expression strains. In contrast to Saccharomyces cerevisiae, where short overhangs are sufficient to target highly specific integration, long overhangs are more efficient in P. pastoris and ectopic integration of foreign DNA can occur. Here, we aimed to elucidate the influence of ectopic integration by high throughput screening of>700 transformants and whole genome sequencing of 27 transforma...
Source: Applied and Environmental Microbiology - January 12, 2018 Category: Microbiology Authors: Vogl T, Gebbie L, Palfreyman RW, Speight R Tags: Appl Environ Microbiol Source Type: research

Acquisition of a novel sulfur-oxidizing symbiont in the gutless marine worm Inanidrilus exumae.
This study, thus, highlights the remarkable plasticity of both animals and bacteria in establishing beneficial associations: the phallodriline hosts were able to acquire and maintain symbionts from two very different lineages of bacteria, while sulfur-oxidizing bacteria from two very distantly related lineages were able to independently establish symbiotic relationships with phallodriline hosts. PMID: 29330187 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - January 12, 2018 Category: Microbiology Authors: Bergin C, Wentrup C, Brewig N, Blazejak A, Erséus C, Giere O, Schmid M, De Wit P, Dubilier N Tags: Appl Environ Microbiol Source Type: research

Germination, outgrowth and vegetative growth kinetics of dry heat-treated individual spores of Bacillus species.
Abstract DNA damage kills dry-heated spores of Bacillus subtilis, but dry heat-treatment effects on spore germination and outgrowth have not been studied. This is important, since if dry heat-killed spores germinate and undergo outgrowth, toxic proteins could be synthesized. Here, Raman spectroscopy and differential interference contrast microscopy were used to study germination and outgrowth of individual dry heat-treated B. subtilis and Bacillus megaterium spores. Major findings in this work were as follows. 1) Spores dry heat-treated at 140°C for 20 min nearly all lost viability but retained their Ca2+-dipi...
Source: Applied and Environmental Microbiology - January 12, 2018 Category: Microbiology Authors: He L, Chen Z, Wang S, Wu M, Setlow P, Li YQ Tags: Appl Environ Microbiol Source Type: research

Targeted synthesis and characterization of a gene-cluster encoding NAD(P)H-dependent 3 α-, 3β-, and 12α-hydroxysteroid dehydrogenases from Eggerthella CAG:298, a gut metagenomic sequence.
Targeted synthesis and characterization of a gene-cluster encoding NAD(P)H-dependent 3α-, 3β-, and 12α-hydroxysteroid dehydrogenases from Eggerthella CAG:298, a gut metagenomic sequence. Appl Environ Microbiol. 2018 Jan 12;: Authors: Mythen SM, Devendran S, Méndez-García C, Cann I, Ridlon JM Abstract Gut metagenomic sequences provide a rich source of microbial genes, the majority of which are annotated by homology or unknown. Genes and gene pathways that encode enzymes catalyzing biotransformation of host bile acids are important to identify in gut metagenomic sequences ...
Source: Applied and Environmental Microbiology - January 12, 2018 Category: Microbiology Authors: Mythen SM, Devendran S, Méndez-García C, Cann I, Ridlon JM Tags: Appl Environ Microbiol Source Type: research

Influence of pig farming on the human's nasal microbiota: The key role of the airborne microbial communities.
In this study we have simultaneously investigated the nasal microbiota of pigs, humans and the environment in pig farms. We reveal an enormous impact of pig farming on the human nasal microbiota which is far more pronounced as compared to cow farming. In addition, we have analyzed the airborne microbiota and found significant associations suggesting an animal-human transmission of the microbiota within pig farms. We also reveal that microbial patterns are farm-specific suggesting that the environment influences animals and humans in a similar manner. PMID: 29330190 [PubMed - as supplied by publisher] (Source: Applied ...
Source: Applied and Environmental Microbiology - January 12, 2018 Category: Microbiology Authors: Kraemer JG, Ramette A, Aebi S, Oppliger A, Hilty M Tags: Appl Environ Microbiol Source Type: research

Thermophilic alkaline fermentation followed by mesophilic anaerobic digestion for efficient hydrogen and methane production from waste activated sludge: Focusing on dynamics of bacterial pathogens as revealed by the combination of metagenomic and qPCR analysis.
Abstract Thermophilic alkaline fermentation followed by mesophilic anaerobic digestion (TM) for hydrogen and methane production from waste activated sludge (WAS) was investigated. TM process was also compared to mesophilic alkaline fermentation followed by mesophilic anaerobic digestion (MM) process and one-stage mesophilic anaerobic digestion (M) process. The results showed that both hydrogen yield (74.5 mLH2/gVS) and methane yield (150.7 mLCH4/gVS) in TM process were higher than those (6.7 mLH2/gVS and 127.8 mLCH4/gVS) in MM process. The lowest methane yield (101.2 mLCH4/gVS) was obtained in M process. Taxonomic...
Source: Applied and Environmental Microbiology - January 12, 2018 Category: Microbiology Authors: Wan J, Jing Y, Rao Y, Zhang S, Luo G Tags: Appl Environ Microbiol Source Type: research

Lactobacillus-deficient vaginal microbiota dominate post-partum women in rural Malawi.
In this study we sampled and characterised the vaginal microbiota from a cohort of 1107 women in rural Malawi found on vaginal swabs taken post-partum. We found a population dominated by Gardnerella vaginalis and devoid of the most common vaginal Lactobacillus species, even if the vagina was sampled over a year post-partum. The Lactobacillus-deficient anaerobic community commonly labelled community state type (CST) 4 could be sub-divided into four further communities. A Lactobacillus iners dominated vaginal microbiota became more common the longer after delivery the vagina was sampled, but G. vaginalis remained the dominan...
Source: Applied and Environmental Microbiology - January 5, 2018 Category: Microbiology Authors: Doyle R, Gondwe A, Fan YM, Maleta K, Ashorn P, Klein N, Harris K Tags: Appl Environ Microbiol Source Type: research

How much do rRNA gene surveys underestimate extant bacterial diversity?
Abstract The most common practice in studying and cataloguing prokaryotic diversity involves the grouping of sequences into Operational Taxonomic Units (or OTUs) at the 97% 16S rRNA gene sequence identity level, often using partial gene sequences such as PCR-generated amplicons. Due to the high sequence conservation of rRNA genes, organisms belonging to closely related yet distinct species may be grouped under the same OTU. However, it remains unclear how much diversity has been underestimated by this practice. To address this question, we compared OTUs of genomes defined at the 97% or 98.5% 16S rRNA gene identity...
Source: Applied and Environmental Microbiology - January 5, 2018 Category: Microbiology Authors: Rodriguez-R LM, Castro JC, Kyrpides NC, Cole JR, Tiedje JM, Konstantinidis KT Tags: Appl Environ Microbiol Source Type: research

Elucidating waterborne pathogen presence and aiding source apportionment in an impaired stream.
This study shows the use of this methodology in a historically impaired watershed that has successfully implemented total maximum daily load reductions to reduce risk. The results suggest that while the fecal indicators have been reduced over 96% and are nearing recreational water criteria levels, pathogens are still detectable in the watershed. Microbial source tracking results show that additional remediation efforts are needed to reduce the impact of human sewage in the watershed. PMID: 29305503 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - January 5, 2018 Category: Microbiology Authors: Weidhaas J, Anderson A, Jamal R Tags: Appl Environ Microbiol Source Type: research

An IgaA/UmoB-family protein from Serratia marcescens regulates motility, capsular polysaccharide, and secondary metabolite production.
This study introduces a new member of the IgaA/UmoB family and demonstrates a high degree of functional similarity between IgaA/UmoB family proteins. Moreover, this study extends the phenomena controlled by IgaA/UmoB family proteins to include the biosynthesis of antimicrobial secondary metabolites. PMID: 29305504 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - January 5, 2018 Category: Microbiology Authors: Stella NA, Brothers KM, Callaghan JD, Passerini AM, Sigindere C, Hill PJ, Liu X, Wozniak DJ, Shanks RMQ Tags: Appl Environ Microbiol Source Type: research

A unique autothermal thermophilic aerobic digestion process showing dynamic transition of physicochemical and bacterial characteristics from mesophilic to theromophilic phases.
This study investigated the physicochemical and bacterial community characteristic changes during the full-scale ATAD process operated for approximately 3 weeks in 2 different years. After initiating simultaneous aeration and mixing using an air-inducing circulator (aerator), the temperature autothermally increased rapidly in the first 1-2 d with exhaustive oxygen consumption, leading to a drastic decrease and gradual increase in oxidation-reduction potential in the first 2 d, which reached> 50°C in the middle 4-6 d and remained steady in the final phase. Volatile fatty acids were rapidly consumed and diminished in ...
Source: Applied and Environmental Microbiology - January 5, 2018 Category: Microbiology Authors: Tashiro Y, Kanda K, Asakura Y, Kii T, Cheng H, Poudel P, Okugawa Y, Tashiro K, Sakai K Tags: Appl Environ Microbiol Source Type: research

Contribution of YthA, a PspC family transcriptional regulator to Lactococcus lactis F44 acid tolerance and nisin yield: a transcriptomic approach.
This study shed light that YthA could increase acid resistance and nisin yield, and revealed a putative regulation mechanism of YthA.ImportanceNisin, produced by Lactococcus lactis subsp. Lactis, is widely used as a safe food preservative. Acid stress becomes the primary restrictive factor of cell growth and nisin yield. In this research, we found that the transcriptional regulator YthA was conducive to enhancing the acid-resistant ability in L. lactis F44. Overexpressing ythA could significantly improve the survival rate and nisin yield. The stability of intracellular pH and nisin resistance were also increased. Transcrip...
Source: Applied and Environmental Microbiology - January 5, 2018 Category: Microbiology Authors: Wu H, Liu J, Miao S, Zhao Y, Zhu H, Qiao M, Saris PEJ, Qiao J Tags: Appl Environ Microbiol Source Type: research

"Evolution of a dominant natural isolate of Escherichia coli in the human gut over a year suggests a neutral evolution with reduced effective population size".
In this study we follow the genomic fate of a dominant clone of Escherichia coli in the human gut of a healthy individual over about a year. We could compute a low annual mutation rate that supports a low diversity and we could not retrieve any clear signature of selection. These observations support a neutral evolution of E. coli in the human gut, compatible with a very limited effective population size that deviates drastically with the observations made previously in experimental evolution. PMID: 29305507 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - January 5, 2018 Category: Microbiology Authors: Ghalayini M, Launay A, Bridier-Nahmias A, Clermont O, Denamur E, Lescat M, Tenaillon O Tags: Appl Environ Microbiol Source Type: research

Comparative transcriptome analysis reveals the mechanism underlying 3,5-dibromo-4-hydroxybenzoate catabolism via a new oxidative-decarboxylation pathway.
In this study, a new oxidative-decarboxylation pathway for DBHB catabolism was identified in a DBHB-utilizing strain of Pigmentiphaga sp. H8. The genetic determinants underlying this pathway were elucidated based on comparative transcriptome analysis and subsequent experimental validation. A gene cluster comprising orf420-orf426, with transcripts that were about 33∼4400-fold up-regulated in DBHB-induced cells compared with those in uninduced cells, was suspected to be involved in DBHB catabolism. The gene odcA (orf420), which is essential for the initial catabolism of DBHB, encodes a novel NAD(P)H-dependent flavin mono...
Source: Applied and Environmental Microbiology - January 5, 2018 Category: Microbiology Authors: Chen K, Mu Y, Jian S, Zang X, Chen Q, Jia W, Ke Z, Gao Y, Jiang J Tags: Appl Environ Microbiol Source Type: research

Transcriptional responses of Pseudomonas aeruginosa to potable water and freshwater.
Abstract Many Pseudomonas aeruginosa infections are derived from residential, recreational, or surface water sources, thus, these environments represent an important pre-infection niche. To better understand P. aeruginosa biology in these environments, we quantified transcriptional changes by microarray after exposure to diluted LB, diluted R2B, potable tap water, and freshwater from a eutrophic pond. qRT-PCR confirmed conservation of these responses in other water sources, and competition experiments were used to test the importance of three implicated metabolic pathways. The global transcriptional responses in p...
Source: Applied and Environmental Microbiology - January 5, 2018 Category: Microbiology Authors: English EL, Schutz KC, Willsey GG, Wargo MJ Tags: Appl Environ Microbiol Source Type: research

Lipidomics of Thalassiosira pseudonana Under Phosphorus Stress Reveal Underlying Phospholipid Substitution Dynamics and Novel Diglycosylceramide Substitutes.
Abstract Phytoplankton substitute phosphorus (P) containing lipids with non-P analogues boosting growth in P-limited oceans. In the model diatom Thalassiosira pseudonana, lipid headgroup substitution dynamics are well described, but those of the individual lipids, varying in fatty acids, are unknown. Moreover, the behaviour of lipids outside of the common headgroup classes, and the relationship between lipid substitution and cellular particulate organic P (POP) are yet to be reported. We investigated these through the mass spectrometric lipidomics of P replete (P+) and depleted (P-) T. pseudonana cultures. Non-lip...
Source: Applied and Environmental Microbiology - January 5, 2018 Category: Microbiology Authors: Hunter JE, Brandsma J, Dymond MK, Koster G, Moore CM, Postle AD, Mills RA, Attard GS Tags: Appl Environ Microbiol Source Type: research

A cytoplasmic antiholin is embedded in-frame with the holin in a Lactobacillus fermentum bacteriophage.
Abstract In double-stranded DNA bacteriophages, infection cycles are ended by host cell lysis through the action of phage-encoded endolysins and holins. The precise timing of lysis is regulated by the holin inhibitors, named antiholins. Sequence analysis has revealed that holins with a single transmembrane domain (TMD) are prevalent in Lactobacillus bacteriophages. A temperate bacteriophage of Lbfermentum, ϕPYB5, has a two-component lysis cassette containing endolysin Lyb5 and holin Hyb5. The hyb5 gene is 465-bp long, encoding 154 amino acid residues with an N-terminal TMD and a large cytoplasmic C-terminal domai...
Source: Applied and Environmental Microbiology - January 5, 2018 Category: Microbiology Authors: Guo T, Xin Y, Zhang C, Kong J Tags: Appl Environ Microbiol Source Type: research

Molecular epidemiology of dairy cattle-associated Escherichia coli carrying blaCTX-M genes in Washington State.
Abstract An increase in prevalence of commensal Escherichia coli carrying blaCTX-M genes among dairy cattle was observed between 2008 and 2012 in Washington State. To study the molecular epidemiology of this change, we selected 126 blaCTX-M-positive and 126 blaCTX-M-negative isolates for multi-locus sequence typing (MLST) and antibiotic resistance phenotyping from E. coli obtained during a previous study. For 99 isolates we also determined the blaCTX-M alleles using PCR and sequencing and identified the replicon types of blaCTX-M carrying plasmids. The blaCTX-M-negative E. coli comprised 76 sequence types (STs) co...
Source: Applied and Environmental Microbiology - January 5, 2018 Category: Microbiology Authors: Afema JA, Ahmed S, Besser TE, Jones LP, Sischo WM, Davis MA Tags: Appl Environ Microbiol Source Type: research

Production of 4-Hydroxybenzoic Acid by an Aerobic Growth-Arrested Bioprocess using Metabolically Engineered Corynebacterium glutamicum.
In this study, we screened for a novel final reaction enzyme possessing characteristics superior to those of previously employed microbial 4-HBA production. We demonstrated that use of the highly 4-HBA-resistant UbiC from the intestinal bacterium P. rustigianii is very effective in increasing 4-HBA production. PMID: 29305513 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - January 5, 2018 Category: Microbiology Authors: Kitade Y, Hashimoto R, Suda M, Hiraga K, Inui M Tags: Appl Environ Microbiol Source Type: research

Metals and Methanotrophy.
Abstract Aerobic methanotrophs have long been known to play a critical role in the global carbon cycle, capable of converting methane to biomass and carbon dioxide. Interestingly, these microbes exhibit great sensitivity to copper and rare earth elements, with expression of key genes involved in the central pathway of methane oxidation controlled by the availability of these metals. That is, these microbes have a "copper-switch" that controls expression of alternative methane monooxygenases and a "rare earth element-switch" that controls expression of alternative methanol dehydrogenases. Furthe...
Source: Applied and Environmental Microbiology - January 5, 2018 Category: Microbiology Authors: Semrau JD, DiSpirito AA, Gu W, Yoon S Tags: Appl Environ Microbiol Source Type: research

Sapovirus in wastewater treatment plants in Tunisia: Prevalence, removal, and genetic characterization.
This study analyzed the incidence of human SaV in four wastewater treatment plants from Tunisia during a period of 13 months (December 2009 to December 2010). Detection and quantification were carried out using RT-qPCR methods, obtaining a prevalence of 39.9% (87/218). Sixty-one positive samples were detected in untreated water and 26 positive samples in processed water. Dekhila plant presented the highest contamination levels with 63.0% prevalence. A dominance of genotype I.2 was observed on 15 of the 24 positive samples that were genetically characterized. By a Bayesian estimation algorithm, the SaV density in wastewater...
Source: Applied and Environmental Microbiology - January 5, 2018 Category: Microbiology Authors: Varela MF, Ouardani I, Kato T, Kadoya S, Aouni M, Sano D, Romalde JL Tags: Appl Environ Microbiol Source Type: research

Erratum for Ito et al., "Identification of the hcb Gene Operon Involved in Catalyzing Aerobic Hexachlorobenzene Dechlorination in Nocardioides sp. Strain PD653".
Erratum for Ito et al., "Identification of the hcb Gene Operon Involved in Catalyzing Aerobic Hexachlorobenzene Dechlorination in Nocardioides sp. Strain PD653". Appl Environ Microbiol. 2018 Jan 01;84(1): Authors: Ito K, Takagi K, Iwasaki A, Tanaka N, Kanesaki Y, Martin-Laurent F, Igimi S PMID: 29247036 [PubMed - in process] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - December 20, 2017 Category: Microbiology Authors: Ito K, Takagi K, Iwasaki A, Tanaka N, Kanesaki Y, Martin-Laurent F, Igimi S Tags: Appl Environ Microbiol Source Type: research

Condensed tannins affect bacterial and fungal microbiomes and mycotoxin production during ensiling and upon aerobic exposure.
Abstract Purple prairie clover (PPC; Dalea purpurea Vent.) containing 84.5 g/kg DM of condensed tannin (CT) was ensiled without (Control) or with polyethylene glycol (PEG) for 76 days, followed by 14 days of aerobic exposure. Changes in fermentation characteristics were determined and bacterial and fungal communities were assessed using metagenomic sequencing. Addition of PEG that deactivated CT at ensiling increased (P
Source: Applied and Environmental Microbiology - December 15, 2017 Category: Microbiology Authors: Peng K, Jin L, Niu YD, Huang Q, McAllister TA, Yang HE, Denise H, Xu Z, Acharya S, Wang S, Wang Y Tags: Appl Environ Microbiol Source Type: research

The 14-3-3 homolog, ArtA, regulates development and secondary metabolism in the opportunistic plant pathogen Aspergillus flavus.
This study reports a 14-3-3 protein affecting secondary metabolism in filamentous fungi. Importantly, artA regulates the biosynthesis of the potent carcinogenic compound AFB1 as well as the production of other secondary metabolites. PMID: 29247055 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - December 15, 2017 Category: Microbiology Authors: Ibarra BA, Lohmar JM, Satterlee T, McDonald T, Cary JW, Calvo AM Tags: Appl Environ Microbiol Source Type: research

Genome sequencing links persistent outbreak of legionellosis in Sydney to an emerging clone of Legionella pneumophila ST211.
Abstract The city of Sydney, Australia, experienced a persistent outbreak of Legionella pneumophila serogroup 1 (Lp1) pneumonia in 2016. To elucidate the source and guide public health actions the genomes of clinical and environmental Lp1 isolates recovered over 7 weeks were examined. A total of 48 isolates from human cases and cooling towers were sequenced and compared using SNP-based, core-genome MLST and pangenome approaches. All three methods confirmed phylogenetic relatedness between isolates associated with outbreaks in the Central Business District (CBD) in March and May and Suburb 1. These isolates were de...
Source: Applied and Environmental Microbiology - December 15, 2017 Category: Microbiology Authors: Timms VJ, Rockett R, Bachmann NL, Martinez E, Wang Q, Chen SC, Jeoffreys N, Howard PJ, Smith A, Adamson S, Gilmour R, Sheppeard V, Sintchenko V Tags: Appl Environ Microbiol Source Type: research

Differential Engagement of Fermentative Taxa in Gut Contents of the Earthworm Lumbricus terrestris.
Abstract The earthworm gut is an anoxic, saccharide-rich microzone in aerated soils. The apparent degradation of diverse saccharides in the alimentary canal of the model earthworm Lumbricus terrestris is concomitant with the production of diverse organic acids, indicating that fermentation is an ongoing process in the earthworm gut. However, little is known about how different gut-associated saccharides are fermented. The hypothesis of this investigation was that different gut-associated saccharides differentially stimulate fermentative microorganisms in gut contents of L. terrestris This hypothesis was addressed ...
Source: Applied and Environmental Microbiology - December 15, 2017 Category: Microbiology Authors: Meier AB, Hunger S, Drake HL Tags: Appl Environ Microbiol Source Type: research

Frankia diversity in host-plant root nodules is independent of abundance or relative diversity of Frankia in corresponding rhizosphere soils.
Abstract Actinorhizal plants form nitrogen-fixing root nodules in symbiosis with soil-dwelling actinobacteria within the genus Frankia, and specific Frankia taxonomic clusters nodulate plants in corresponding host infection groups. In same-soil microcosms, we observed some host species were nodulated (Alnus glutinosa, Alnus cordata, Shepherdia argentea, Casuarina equisetifolia) while others were not (Alnus viridis, Hippophaë rhamnoides). Nodule populations were represented by eight different sequences of nifH gene fragments. Two of these sequences characterized frankiae in S. argentea nodules, and three other...
Source: Applied and Environmental Microbiology - December 15, 2017 Category: Microbiology Authors: Ben Tekaya S, Guerra T, Rodriguez D, Dawson JO, Hahn D Tags: Appl Environ Microbiol Source Type: research

Rice paddy Nitrospirae encode and express genes related to sulfate respiration: proposal of the new genus Candidatus Sulfobium.
Abstract Nitrospirae spp. distantly related to thermophilic, sulfate-reducing Thermodesulfovibrio species are regularly observed in environmental surveys of anoxic marine and freshwater habitats. Here, we present a metaproteogenomic analysis of Nitrospirae bacterium Nbg-4 as a representative of this clade. Its genome was assembled from replicated metagenomes of rice paddy soil that was used to grow rice in the presence and absence of gypsum (CaSO4×2H2O). Nbg-4 encoded the full pathway of dissimilatory sulfate reduction and showed expression thereof in gypsum-amended anoxic bulk soil as revealed by parallel m...
Source: Applied and Environmental Microbiology - December 15, 2017 Category: Microbiology Authors: Zecchin S, Mueller RC, Seifert J, Stingl U, Anantharaman K, von Bergen M, Cavalca L, Pester M Tags: Appl Environ Microbiol Source Type: research

Interactions of Salmonella enterica sv. Typhimurium and Pectobacterium carotovorum within a Tomato Soft Rot.
Abstract The human pathogen Salmonella is remarkably adaptable, and this trait allows these bacteria to thrive in a variety of environments and hosts. The mechanisms with which these pathogens establish within a niche amidst the native microbiota remains poorly understood. Here, we aimed to uncover the mechanisms that enable Salmonella enterica sv. Typhimurium to benefit from the degradation of plant tissue by a soft-rot plant pathogen Pectobacterium carotovorum. The hypothesis that in the soft rot, the liberation of starch (not utilized by P. carotovorum) makes this polymer available to Salmonella, thus allowing ...
Source: Applied and Environmental Microbiology - December 15, 2017 Category: Microbiology Authors: George AS, Cox CE, Desai P, Porwolik S, Chu W, de Moraes MH, McClelland M, Brandl MT, Teplitski M Tags: Appl Environ Microbiol Source Type: research

Impact of cell surface molecules on conjugative transfer of the integrative and conjugative element ICESt3 of Streptococcus thermophilus.
yot S Abstract Integrative Conjugative Elements (ICEs) are chromosomal elements that are widely distributed in bacterial genomes, hence contributing to genome plasticity, adaptation and evolution of bacteria. Conjugation requires a contact between both the donor and the recipient cells and thus likely depends on the composition of the cell surface envelope. In this work, we investigated the impact of different cell surface molecules including cell surface proteins, wall teichoic acids, lipoteichoic acids and exopolysaccharides on the transfer and acquisition of ICESt3 from Streptococcus thermophilus The transfer o...
Source: Applied and Environmental Microbiology - December 15, 2017 Category: Microbiology Authors: Dahmane N, Robert E, Deschamps J, Meylheuc T, Delorme C, Briandet R, Leblond-Bourget N, Guédon E, Payot S Tags: Appl Environ Microbiol Source Type: research

CerR, a Single-domain Regulatory Protein of the LuxR Family, Promotes the Cerecidin Production and Immunity in Bacillus cereus.
Abstract Cerecidins are small lantibiotics from Bacillus cereus that were obtained using a semi-in vitro biosynthesis strategy and showed prominent antimicrobial activities against certain Gram-positive bacteria. However, the parental strain B. cereus As 1.1846 is incapable of producing cerecidins, most probably due to the transcriptional repression of the cerecidin gene cluster. Located in the cerecidin gene cluster, cerR encodes a putative response regulator protein that belongs to LuxR-family transcriptional regulators. CerR (84 amino acids) only contains a conserved DNA binding domain but it lacks a convention...
Source: Applied and Environmental Microbiology - December 15, 2017 Category: Microbiology Authors: Zhang L, Teng K, Wang J, Zhang Z, Zhang J, Sun S, Li L, Yang X, Zhong J Tags: Appl Environ Microbiol Source Type: research

Aerobic transformation of 2,4-dinitrotoluene by Escherichia coli and its implications for the detection of trace explosives.
Abstract DNT (2,4-dinitrotoluene), a volatile impurity in military grade TNT-based explosives, is a potential tracer for the detection of buried landmines and other explosive devices. We have previously described an Escherichia coli bioreporter strain engineered to detect traces of DNT, and have demonstrated that the yqjF gene promoter, the sensing element of this bioreporter, is induced not by DNT but by at least one of its transformation products. In the present study we have characterized the initial stages of DNT biotransformation in E. coli, have identified the key metabolic products in this reductive pathway...
Source: Applied and Environmental Microbiology - December 8, 2017 Category: Microbiology Authors: Shemer B, Yagur-Kroll S, Hazan C, Belkin S Tags: Appl Environ Microbiol Source Type: research

A new niche for anoxygenic phototrophs as endoliths.
Abstract Anoxygenic phototrophic bacteria (APBs) occur in a wide range of aquatic habitats, from hot springs to freshwater lakes and intertidal microbial mats. Here we report the discovery of a novel niche for APBs: endoliths within marine littoral carbonates. In a study of 40 locations around Isla de Mona, Puerto Rico, and Menorca, Spain, 16S rRNA high-throughput sequencing of endolithic community DNA revealed the presence of abundant phylotypes potentially belonging to well-known APB clades. An ad hoc phylogenetic classification of these sequences allowed us to refine the assignments more stringently. Even then,...
Source: Applied and Environmental Microbiology - December 8, 2017 Category: Microbiology Authors: Roush D, Couradeau E, Guida B, Neuer S, Garcia-Pichel F Tags: Appl Environ Microbiol Source Type: research

Longitudinal study of the occurrence, persistence and contamination routes of Listeria monocytogenes genotypes on three Finnish dairy cattle farms.
m M Abstract The molecular epidemiology of Listeria monocytogenes was investigated in a longitudinal study of three Finnish dairy farms during 2013 -- 2016. Totals of 186 bulk tank milk (BTM) samples, 224 milk filter socks (MFS), and 1702 samples of the barn environment were analyzed and isolates of L. monocytogenes were genotyped using pulsed-field gel electrophoresis. L. monocytogenes occurred throughout the year in all sample types, and the prevalence in MFS increased significantly during the indoor season. L. monocytogenes was more prevalent in MFS (29%) than in BTM samples (13%). However, the prevalence of L....
Source: Applied and Environmental Microbiology - December 8, 2017 Category: Microbiology Authors: Castro H, Jaakkonen A, Hakkinen M, Korkeala H, Lindström M Tags: Appl Environ Microbiol Source Type: research

Isolation of the (+)-pinoresinol-mineralizing Pseudomonas sp. SG-MS2 and elucidation of its catabolic pathway.
Abstract Pinoresinol is a dimer of two β-β' linked coniferyl alcohol molecules. It is both a plant defence molecule synthesized from the shikimic acid pathway and a representative of several β-β linked dimers produced during the microbial degradation of lignin in dead plant material. Until now little has been known about the bacterial catabolism of such dimers. Here we report the isolation of an efficient (+)-pinoresinol mineralizing Pseudomonas sp. strain SG-MS2 and its catabolic pathway. Degradation of pinoresinol in this strain is inducible and proceeds via a novel oxidative route which is i...
Source: Applied and Environmental Microbiology - December 8, 2017 Category: Microbiology Authors: Shettigar M, Balotra S, Cahill D, Warden AC, Lacey MJ, Kohler HE, Rentsch D, Oakeshott JG, Pandey G Tags: Appl Environ Microbiol Source Type: research

Diversity of Lactococcus lactis in undefined mixed dairy starter cultures revealed by comparative genome analyses and targeted amplicon sequencing of epsD.
Abstract Undefined mesophilic mixed (DL) starter cultures are used in the production of continental cheeses and contain unknown strain mixtures of Lactococcus lactis and leuconostocs. The choice of starter culture affects the taste, aroma and quality of the final product. To gain insight into the diversity of Lactococcus lactis strains in starter cultures, we whole-genome sequenced 95 isolates from three different starter cultures. Pan-genomic analyses, which included 30 publically available complete genomes, grouped the strains into 21 subsp. lactis and 28 subsp. cremoris lineages. Only one of the 95 isolates gro...
Source: Applied and Environmental Microbiology - December 8, 2017 Category: Microbiology Authors: Frantzen CA, Kleppen HP, Holo H Tags: Appl Environ Microbiol Source Type: research

Divergence in gene regulation contributes to sympatric speciation of Shewanella baltica strains.
This study investigated genomic composition of two Shewanella baltica clades previously identified through multi-locus sequencing typing and recovered from the redox transition zone in the central Baltic Sea. Comparative genomic analysis revealed significantly higher inter- than intra-clade genomic dissimilarity, and that a subset of genes present in Clade A were associated with potential adaptation to respiration of sulfur compounds present in the redox-transition zone. Transcriptomic divergence between two representative strains of Clades A and D, OS185 and OS195, was also characterized and revealed marked regulatory dif...
Source: Applied and Environmental Microbiology - December 8, 2017 Category: Microbiology Authors: Deng J, Auchtung J, Konstantinidis KT, Caro-Quintero A, Brettar I, Höfle M, Tiedje JM Tags: Appl Environ Microbiol Source Type: research

Tracking the taxonomy of the genus Bifidobacterium based on a phylogenomic approach.
Abstract For decades, bacterial taxonomy has been based on in vitro molecular biology techniques and comparison of molecular marker sequences to measure the degree of genetic similarity and deduce phylogenetic relatedness of novel bacterial species with reference microbial taxa. Due to the advent of the genomic era, access to complete bacterial genome contents has become easier, thereby presenting the opportunity to precisely investigate the overall genetic diversity of microorganisms. Here, we describe a high-accuracy phylogenomic approach to assess the taxonomy of members of the genus Bifidobacterium and identif...
Source: Applied and Environmental Microbiology - December 8, 2017 Category: Microbiology Authors: Lugli GA, Milani C, Duranti S, Mancabelli L, Mangifesta M, Turroni F, Viappiani A, van Sinderen D, Ventura M Tags: Appl Environ Microbiol Source Type: research

A novel non-antibiotic, lgt-based selection system for stable maintenance of expression vectors in Escherichia coli and Vibrio cholerae.
We describe the construction of expression plasmids that are instead maintained by complementation of the lgt gene encoding a (pro)lipoprotein glyceryl transferase essential for biosynthesis of bacterial lipoprotein. Mutations in lgt are lethal in E. coli and other gram negative organisms. The lgt gene was deleted from E. coli and complemented by the V. cholerae derived gene provided in trans on a temperature sensitive plasmid allowing cells to grow at 30°C but not at 37°C. A temperature-insensitive expression vector carrying the V. cholerae-derived lgt gene was constructed whereby transformants were selected by gr...
Source: Applied and Environmental Microbiology - December 8, 2017 Category: Microbiology Authors: Terrinoni M, Nordqvist SL, Källgård S, Holmgren J, Lebens M Tags: Appl Environ Microbiol Source Type: research

Effect of start-up strategies and electrode materials on carbon dioxide reduction on bio-cathodes.
In this study, pre-enrichment of acetate-oxidizing bio-anodes did not facilitate start-up of bio-cathodes. It took about 170 days for the pre-enriched electrodes to generate substantial cathodic current compared to 83 days for the bare electrodes. Graphite foil and carbon felt cathodes produced higher current at the beginning of the experiment compared to graphite rods. However, all electrodes produced similar current densities at the end of the over 1-year long study (2.5 A/m2). Methane was the only product during operation of the bio-cathodes. Acetate was the only product detected after inhibition of the methanogens. Mic...
Source: Applied and Environmental Microbiology - December 8, 2017 Category: Microbiology Authors: Saheb-Alam S, Singh A, Hermansson M, Persson F, Schnürer A, Wilén BM, Modin O Tags: Appl Environ Microbiol Source Type: research

The Emergency Medical Service Microbiome.
Abstract Emergency medical services (EMS) personnel are an integral component of the healthcare framework and function to transport patients from various locations to and between care facilities. In addition to physical injury, EMS personnel are expected to be at high risk to acquire and transmit healthcare associated infections (HAIs) in the workplace. However, currently little is known about EMS biosafety risk factors and the epidemiological contribution of EMS to pathogen transmission within and outside of the healthcare sector. Our review summarizes literature surrounding pathogen prevalence and decontaminatio...
Source: Applied and Environmental Microbiology - December 8, 2017 Category: Microbiology Authors: Hudson AJ, Glaister GD, Wieden HJ Tags: Appl Environ Microbiol Source Type: research