Viral and Bacterial Fecal Indicators in Untreated Wastewater Across the Contiguous United States Exhibit Geospatial Trends.
This study provides multiple insights to consider for the application of bacterial and viral indicators of sewage to surface water quality monitoring across the contiguous U.S. ranging from method selection considerations to future research directions. Systematic testing of a large collection of sewage samples confirms that crAssphage genetic markers occur at a higher concentration than key human-associated Bacteroides spp. concentrations on a national scale. Geospatial testing also suggests that some methods may be more suitable than others for widespread implementation. Nationwide characterization of indicator geospatial...
Source: Applied and Environmental Microbiology - February 14, 2020 Category: Microbiology Authors: Korajkic A, McMinn B, Herrmann MP, Sivaganesan M, Kelty CA, Clinton P, Nash MS, Shanks OC Tags: Appl Environ Microbiol Source Type: research

Candidatus Desulfobulbus rimicarensis, an uncultivated deltaproteobacterial epibionts from the deep-sea hydrothermal vent shrimp Rimicaris exoculata.
This study is a genomic and transcriptomic analysis of a deltaproteobacterial epibiont and largely expands the understanding of its metabolism and adaptation to the R. exoculata host. PMID: 32060020 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - February 14, 2020 Category: Microbiology Authors: Jiang L, Liu X, Dong C, Huang Z, Cambon-Bonavita MA, Alain K, Gu L, Wang S, Shao Z Tags: Appl Environ Microbiol Source Type: research

Synergistic Effect of Multi-Saccharifying Enzymes on Alcoholic Fermentation for Chinese Baijiu Production.
In this study, we identified 51 carbohydrate hydrolyses in the baijiu fermentation by metaproteomics analysis. Through source tracking analysis, approximately 80% of carbohydrate hydrolyses in the baijiu fermentation were provided by Jiuqu Among these enzymes, alpha-amylase (EC 3.2.1.1) and glucoamylase (EC 3.2.1.3), from Aspergillus, Rhizomucor and Rhizopus, were positively related to starch hydrolysis and ethanol production, indicating that they were the key saccharifying enzymes associated with alcoholic fermentation in the baijiu fermentation. Moreover, a combined mixture of alpha-amylase and glucoamylase (in a ratio o...
Source: Applied and Environmental Microbiology - February 14, 2020 Category: Microbiology Authors: Wang B, Wu Q, Xu Y, Sun B Tags: Appl Environ Microbiol Source Type: research

Laccaria bicolor Mobilizes both Labile Aluminum and Inorganic Phosphate in Rhizosphere Soil of Pinus massoniana Seedlings Field-grown in a Yellow Acidic Soil.
This study advances our understanding of the contribution of ECM fungi in the plant-ECM fungus symbiosis and highlights the vital role of ECM fungus inoculation in plant Al-tolerance. In addition, the results described in the present study confirm the importance to carry out studies in field compared to the previous results from in vitro study. Our findings strengthen the role of ECM fungus association in exploring, utilizing and transporting the unavailable nutrients in the soil to enhance the host plant growth and adaptability in response to adverse habitats. PMID: 32060022 [PubMed - as supplied by publisher] (Sourc...
Source: Applied and Environmental Microbiology - February 14, 2020 Category: Microbiology Authors: Gu X, Li J, Wang X, He X, Cui Y Tags: Appl Environ Microbiol Source Type: research

Cultivable, Host-Specific Bacteroidetes Symbionts Exhibit Diverse Polysaccharolytic Strategies.
, Sabree ZL Abstract Beneficial gut microbes can facilitate insect growth on diverse diets. The omnivorous American cockroach, Periplaneta americana (Insecta: Blattodea), thrives on a diet rich in plant polysaccharides and harbors a species-rich gut microbiota responsive to host diet. Bacteroidetes are among the most abundant taxa in P. americana and other cockroaches based on cultivation-independent gut community profiling and these potentially polysaccharolytic bacteria may contribute to host diet processing. Eleven Bacteroidetes isolates were cultivated from P. americana digestive tracts and phylogenomic analys...
Source: Applied and Environmental Microbiology - February 14, 2020 Category: Microbiology Authors: Vera-Ponce de León A, Jahnes BC, Duan J, Camuy-Vélez LA, Sabree ZL Tags: Appl Environ Microbiol Source Type: research

Engineering Bacillus subtilis as a Versatile and Stable Platform for Production of Nanobodies.
Abstract There is a growing need for a highly stable system to allow the production of biologics for diagnoses and therapeutic interventions on demand that could be used in extreme environments. Among the variety of biologics, nanobodies (Nbs) derived from single-chain variable antibody fragments from camelids, have attracted great attention in recent years due to their small size and great stability with translational potentials in whole-body imaging and the development of new drugs. Intracellular expression using the bacterium Escherichia coli has been the predominant system to produce Nbs, and this requires len...
Source: Applied and Environmental Microbiology - February 14, 2020 Category: Microbiology Authors: Yang M, Zhu G, Korza G, Sun X, Setlow P, Li J Tags: Appl Environ Microbiol Source Type: research

Acidocalcisomes and Polyphosphate Granules Are Different Subcellular Structures in Agrobacterium tumefaciens.
In conclusion, A. tumefaciens forms polyP granules that are free of a surrounding membrane and thus resemble polyP granules of Ralstonia eutropha and other bacteria. The composition, contents and function of the subcellular structures that are stainable with MitoTracker and harbor eYFP-HppA remain unclear.IMPORTANCE The uptake of α-proteobacterial-like cells by ancestors of eukaryotic cells and subsequent conversion of these α-proteobacterial-like cells to mitochondria are thought to be a key step in the evolution of the first eukaryotic cells. The identification of acidocalcisomes in two α-proteobacteria...
Source: Applied and Environmental Microbiology - February 14, 2020 Category: Microbiology Authors: Frank C, Jendrossek D Tags: Appl Environ Microbiol Source Type: research

Proteomic characterization of lignocellulolytic enzymes secreted by the insect-associated fungus, Daldinia decipiens oita, isolated from the forest in northern Japan.
In this study, an insect-associated fungus, Daldinia decipiens oita was isolated as a potential symbiotic fungus of female Xiphydria albopicta captured from Hokkaido forest. This fungus was grown in seven different media containing a single carbon source, glucose, cellulose, xylan, mannan, pectin, poplar, or larch, and the secreted proteins were identified by LC-MS/MS. 128 CAZymes including domains of 92 glycoside hydrolases (GHs), 15 carbohydrate esterases (CEs), 5 polysaccharide lyases (PLs), 17 auxiliary activities (AAs), and 11 carbohydrate-binding modules (CBMs) were identified, and these are involved in degradation o...
Source: Applied and Environmental Microbiology - February 14, 2020 Category: Microbiology Authors: Hori C, Song R, Matsumoto K, Matsumoto R, Minkoff BB, Oita S, Hara H, Takasuka TE Tags: Appl Environ Microbiol Source Type: research

Identification of genes required for glucan exopolysaccharide production in Lactobacillus johnsonii suggests a novel mechanism of biosynthesis.
Abstract Lactobacillus johnsonii FI9785 makes two capsular exopolysaccharides -a heteropolysaccharide (EPS2) encoded by the eps operon, and a branched glucan homopolysaccharide (EPS1). The homopolysaccharide is synthesised in the absence of sucrose and there are no typical glucansucrase genes in the genome. Quantitative proteomics was used to compare the wild type to a mutant where EPS production was reduced, to attempt to identify proteins associated with EPS1 biosynthesis. A putative bactoprenol glycosyltransferase, 242, was less abundant in the Δeps_cluster mutant than in the wild type. NMR analysis of is...
Source: Applied and Environmental Microbiology - February 14, 2020 Category: Microbiology Authors: Mayer MJ, D'Amato A, Colquhoun IJ, Le Gall G, Narbad A Tags: Appl Environ Microbiol Source Type: research

PII signal transduction protein GlnK alleviates the feedback inhibition of N-acetyl-l-glutamate kinase by l-arginine in Corynebacterium glutamicum.
In conclusion, this study provides a new strategy for modifying amino acid biosynthesis in C. glutamicum. PMID: 32060028 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - February 14, 2020 Category: Microbiology Authors: Xu M, Tang M, Chen J, Yang T, Zhang X, Shao M, Xu Z, Rao Z Tags: Appl Environ Microbiol Source Type: research

Fitness and productivity increase with ecotypic diversity among E. coli coevolved in a simple, constant environment.
Abstract The productivity of a biological community often correlates with its diversity. In the microbial world this phenomenon can sometimes be explained by positive, density-dependent interactions such as cross-feeding and syntrophy. These metabolic interactions help account for the astonishing variety of microbial life, and drive many of the biogeochemical cycles without which life as we know it could not exist. While it is difficult to recapitulate experimentally how these interactions evolved among multiple taxa, we can explore in the laboratory how they arise within one. These experiments provide insight int...
Source: Applied and Environmental Microbiology - February 14, 2020 Category: Microbiology Authors: Yang DD, Alexander A, Kinnersley M, Cook E, Caudy A, Rosebrock A, Rosenzweig F Tags: Appl Environ Microbiol Source Type: research

Enhancement of sphingolipids synthesis improves osmotic tolerance of Saccharomyces cerevisiae.
This study demonstrated a novel strategy for manipulation membrane complex sphingolipids to enhance S. cerevisiae tolerance to osmotic stress. Elo2, a sphingolipid acyl chain elongase, was related to osmotic tolerance, through transcriptome analysis of the wild-type strain and an osmotic tolerant strain generated from ALE. Overexpression of ELO2 increased the content of complex sphingolipid with longer acyl chain, thus membrane integrity and osmotic tolerance improved. PMID: 32033944 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - February 7, 2020 Category: Microbiology Authors: Zhu G, Yin N, Luo Q, Liu J, Chen X, Liu L, Wu J Tags: Appl Environ Microbiol Source Type: research

Neutral processes dominate microbial community assembly in Atlantic salmon, Salmo salar.
In this study, the intestinal microbiota of Atlantic salmon, Salmo salar, sampled from farmed and wild environments was first characterised using 16s rDNA MiSeq sequencing analysis. We used neutral community models to determine the balance of stochastic and deterministic processes that underpin microbial community assembly and transfer across lifecycle stage and between gut compartments. Across gut compartments in farmed fish, neutral models suggest that most microbes are transient with no evidence of adaptation to their environment. In wild fish, we find declining taxonomic and functional microbial community richness as f...
Source: Applied and Environmental Microbiology - February 7, 2020 Category: Microbiology Authors: Heys C, Cheaib B, Busetti A, Kazlauskaite R, Maier L, Sloan WT, Ijaz UZ, Kaufmann J, McGinnity P, Llewellyn MS Tags: Appl Environ Microbiol Source Type: research

Performance of a geosynthetic clay-liner cover system at a Cu/Zn mine tailings impoundment: microbiological characterization.
This study assesses the performance and utility of geosynthetic clay liner cover systems for management of acid-generating mine wastes. Analyses of the microbial communities in tailings isolated beneath an engineered cover system provide a better understanding of the complex biogeochemical processes involved in the redox cycling of key elements, contribute to the remediation of mine wastes, and provide a valuable tool for assessment of the effectiveness of the remediation system. PMID: 32033946 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - February 7, 2020 Category: Microbiology Authors: Pakostova E, Schmall AJ, Holland SP, White H, Ptacek CJ, Blowes DW Tags: Appl Environ Microbiol Source Type: research

Fecal carriage of Extended Spectrum ß-Lactamase (ESBL)/AmpC-producing Escherichia coli in horses.
Fecal carriage of Extended Spectrum ß-Lactamase (ESBL)/AmpC-producing Escherichia coli in horses. Appl Environ Microbiol. 2020 Feb 07;: Authors: Hordijk J, Farmakioti E, Smit LAM, Duim B, Graveland H, Theelen MJP, Wagenaar JA Abstract A nationwide study on the occurrence of ESBL/AmpC in non-hospitalized horses in the Netherlands was performed. Molecular characterization was done and questionnaires were analyzed to identify factors associated with carriage.In total, 796 horse owners were approached, of which 281 submitted a fecal sample of their horse(s), resulting in 362 samples. All samples wer...
Source: Applied and Environmental Microbiology - February 7, 2020 Category: Microbiology Authors: Hordijk J, Farmakioti E, Smit LAM, Duim B, Graveland H, Theelen MJP, Wagenaar JA Tags: Appl Environ Microbiol Source Type: research

DNA damage Kills Bacterial Spores and Cells Exposed to 222 nm UV Radiation.
This study examined the microbicidal activity of 222 nm UV radiation (UV222), which is potentially a safer alternative to the 254 nm UV radiation (UV254) that is often used for surface decontamination. Spores and/or growing and stationary phase cells of Bacillus cereus, Bacillus subtilis, Bacillus thuringiensis, Staphylococcus aureus and Clostridioides difficile, and a Herpes virus were all killed or inactivated by UV222, and at lower fluences than with UV254 B. subtilis spores and cells lacking the major DNA repair protein RecA were more sensitive to UV222, as were spores lacking their DNA protective proteins, the α...
Source: Applied and Environmental Microbiology - February 7, 2020 Category: Microbiology Authors: Taylor W, Camilleri E, Craft DL, Korza G, Rocha Granados M, Peterson J, Szczpaniak R, Weller SK, Moeller R, Douki T, Mok WWK, Setlow P Tags: Appl Environ Microbiol Source Type: research

Genomic Evidence for Formate Metabolism by Chloroflexi as the Key to Unlocking Deep Carbon in Lost City Microbial Ecosystems.
Abstract The Lost City hydrothermal field on the Mid-Atlantic Ridge supports dense microbial life on the lofty calcium carbonate chimney structures. The vent field is fueled by chemical reactions between the ultramafic rock under the chimneys and ambient seawater. These serpentinization reactions provide reducing power (as hydrogen gas) and organic compounds that can serve as microbial food; the most abundant of these are methane and formate. Previous studies have characterized the interior of the chimneys as a single-species biofilm inhabited by the Lost City Methanosarcinales, but also indicated that this methan...
Source: Applied and Environmental Microbiology - February 7, 2020 Category: Microbiology Authors: McGonigle JM, Lang SQ, Brazelton WJ Tags: Appl Environ Microbiol Source Type: research

Isolation and characterization of ESKAPE-bacteria and ESBL-producing E. coli from waste- and process water of German poultry slaughterhouses.
In conclusion, wastewater effluents from the investigated poultry slaughterhouses exhibited clinically relevant bacteria (E. coli, MRSA, K. pneumoniae, species of the ACB-and E. cloacae-complexes) that contribute to the dissemination of clinically relevant resistances (i.e. bla CTX-M/SHV, mcr-1) in the environment.Importance Bacteria from livestock may be opportunistic pathogens and carriers of clinically relevant resistance genes, as many antimicrobials are used both in veterinary and human medicine. They may be released into the environment from wastewater treatment plants (WWTPs) that are influenced by wastewater from s...
Source: Applied and Environmental Microbiology - February 7, 2020 Category: Microbiology Authors: Savin M, Bierbaum G, Hammerl JA, Heinemann C, Parcina M, Sib E, Voigt A, Kreyenschmidt J Tags: Appl Environ Microbiol Source Type: research

Systematic analyses of factors required for adhesion of Salmonella enterica serovar Typhimurium to corn salad (Valerianella locusta).
l M Abstract Salmonella enterica is a foodborne pathogen often leading to gastroenteritis and is commonly acquired by consumption of contaminated food of animal origin. However, frequency of outbreaks linked to the consumption of fresh or minimally processed food of non-animal origin is increasing. New infection routes of S. enterica by vegetables, fruits, nuts and herbs have to be considered. This leads to special interest in S. enterica interactions with leafy products, e.g. salads, that are mainly consumed in minimally processed form. The attachment of S. enterica to salad is a crucial step in contamination, bu...
Source: Applied and Environmental Microbiology - February 7, 2020 Category: Microbiology Authors: Elpers L, Kretzschmar J, Nuccio SP, Bäumler AJ, Hensel M Tags: Appl Environ Microbiol Source Type: research

Identification and Functional Analysis of Photoreceptors in Blakeslea trispora.
In this study, we isolated and characterized three photoreceptor genes, btwc-1a, btwc-1b and btwc-1c in B. trispora Bioinformatics analyses of these genes and their protein sequences revealed that their functional domains (PAS/LOV domain and zinc finger structure) have significant homology to other fungal blue-light regulator proteins from Mucor circinelloides and Neurospora crassa The photoreceptor proteins were synthesized by heterologous expression in Escherichia coli The chromogenic groups FAD and FMN were detected to accompany BTWC-1 proteins by using high performance liquid chromatography (HPLC) and fluorescence spec...
Source: Applied and Environmental Microbiology - February 7, 2020 Category: Microbiology Authors: Luo W, Xue C, Zhao Y, Zhang H, Rao Z, Yu X Tags: Appl Environ Microbiol Source Type: research

Metabolic exchange with alkane non-consumer Pseudomonas stutzeri SLG510A3-8 improves the n-alkane biodegradation of the alkane degrader Dietzia sp. DQ12-45-1b.
Abstract Biodegradation of alkanes by microbial communities is ubiquitous in nature. Interestingly, the microbial communities with high hydrocarbon-degrading performances are sometimes composed of not only hydrocarbon degraders but also non-consumers, but the synergistic mechanisms remain unknown. Here, we found that two bacterial strains isolated from Chinese oilfields, Dietzia sp. DQ12-45-1b and Pseudomonas stutzeri SLG510A3-8, had a synergistic effect on hexadecane (C16) biodegradation, even though P. stutzeri could not utilize C16 individually. To gain a better understanding of the roles of the alkane non-cons...
Source: Applied and Environmental Microbiology - February 7, 2020 Category: Microbiology Authors: Hu B, Wang M, Geng S, Wen L, Wu M, Nie Y, Tang YQ, Wu XL Tags: Appl Environ Microbiol Source Type: research

A Disulfide Oxidoreductase CHU_1165 is Essential for Cellulose Degradation by Affecting Outer Membrane Proteins in Cytophaga hutchinsonii.
In this study, the deletion of a gene locus chu_1165, which encodes a hypothetical protein with a 32% identity with TlpB, a disulfide oxidoreductase in Flavobacterium psychrophilum, caused a complete cellulolytic defect in C. hutchinsonii Further study showed that the cells of Δ1165 could not bind to cellulose and many outer membrane proteins that can bind to cellulose were significantly decreased. The N-terminal region of CHU_1165 is anchored to the cytoplasmic membrane with five predicted transmembrane helices, and the C-terminal region is predicted to stretch to the periplasm and has a similar Trx-fold containing ...
Source: Applied and Environmental Microbiology - February 7, 2020 Category: Microbiology Authors: Zhao D, Wang Y, Wang S, Zhang W, Qi Q, Lu X Tags: Appl Environ Microbiol Source Type: research

Emergence of fluoroquinolone resistant Campylobacter jejuni and Campylobacter coli among Australian chickens in the absence of fluoroquinolone use.
This study also demonstrates the need for vigilance in the form of surveillance for AMR based on robust sampling to manage AMR risks in the food-chain.ImportanceCampylobacter is one of the most common causes of gastroenteritis in humans with infections frequently resulting from exposure to under-cooked poultry products. Although human illness is typically self-limiting, a minority of cases do require antimicrobial therapy. Ensuring that Campylobacter originating from meat-chickens do not acquire resistance to fluoroquinolones is therefore a valuable outcome for public-health. Australia has never legalised the use of fluoro...
Source: Applied and Environmental Microbiology - February 7, 2020 Category: Microbiology Authors: Abraham S, Sahibzada S, Hewson K, Laird T, Abraham R, Pavic A, Truswell A, Lee T, O'Dea M, Jordan D Tags: Appl Environ Microbiol Source Type: research

Pseudomonas orientalis F9 pyoverdine, safracin and phenazine mutants remain effective antagonists against Erwinia amylovora in apple flowers.
Abstract The recently characterized strain Pseudomonas orientalis F9, an isolate from apple flowers in a Swiss orchard, exhibits antagonistic traits against phytopathogens. At high colonisation densities, it exhibits phytotoxicity against apple flowers. P orientalis F9 harbours biosynthesis genes for the siderophore pyoverdine as well as for the antibiotics safracin and phenazine. To elucidate the role of the three compounds in biocontrol we screened a large random knockout library of P. orientalis F9 for lack of pyoverdine production or in vitro antagonism. Transposon mutants that lacked the ability for fluoresce...
Source: Applied and Environmental Microbiology - February 7, 2020 Category: Microbiology Authors: Santos Kron A, Zengerer V, Bieri M, Dreyfuss V, Sostizzo T, Schmid M, Lutz M, Remus-Emsermann MNP, Pelludat C Tags: Appl Environ Microbiol Source Type: research

Characterization of Aspergillus fumigatus mitochondrial acetyl-CoA acetyltransferase as an antifungal target.
In this study, we have characterized recombinant AfERG10A as a functional acetyl-CoA acetyltransferase catalyzing both synthetic and degradative reactions. Unexpectedly, AfERG10A localizes to mitochondria in A. fumigatus as shown by C-terminal GFP-tag fusion. Both knockout and inducible promoter strategies demonstrate that Aferg10A is essential for the survival of A. fumigatus Reduced expression of Aferg10A leads to severe morphological defects and increased susceptibility to oxidative and cell wall stresses. Although the catalytic mechanism of acetyl-CoA acetyltransferase family is highly conserved, the crystal structure ...
Source: Applied and Environmental Microbiology - January 31, 2020 Category: Microbiology Authors: Zhang Y, Wei W, Fan J, Jin C, Lu L, Fang W Tags: Appl Environ Microbiol Source Type: research

Rapid Determination of Viable but Non-culturable Escherichia coli O157:H7 and Salmonella enterica in Fresh Produce by Loop-mediated Isothermal Amplification Coupled with a Propidium Monoazide Treatment.
In this study, we assessed propidium monoazide (PMA)-qPCR assays and novel methods combining PMA and loop-mediated isothermal amplification (LAMP) for the detection and quantification of VBNC E. coli O157:H7 and S. enterica in fresh produce. The performance of PMA-LAMP assays targeting wzy gene of E. coli O157:H7 and agfA gene of S. enterica and PMA-qPCR assays were compared in pure culture and spiked tomato, lettuce and spinach. No cross-reaction was observed in the specificity tests. The limit of detection (LOD) with PMA-LAMP was 9.0 CFU/reaction for E. coli O157:H7 and 4.6 CFU/reaction for S. enterica in pure culture, a...
Source: Applied and Environmental Microbiology - January 31, 2020 Category: Microbiology Authors: Han L, Wang K, Ma L, Delaquis P, Bach S, Feng J, Lu X Tags: Appl Environ Microbiol Source Type: research

Biosynthesis of diverse siderophores in Shewanella oneidensis: a result of promiscuous enzymes.
In this study, we examined a siderophore-overproducing mutant of S. oneidensis, which lacks an AvbA counterpart, and found that it can also produce these three siderophores. We identified both SpeC and SpeF as promiscuous decarboxylases for both lysine and ornithine to synthesize siderophore precursors cadaverine and putrescine respectively. Intriguingly, putrescine is mainly synthesized from arginine through an arginine decarboxylation pathway in a constitutive manner, not liable to the concentrations of iron and siderophores. Our results provide further evidence that the substrate availability plays a determining role in...
Source: Applied and Environmental Microbiology - January 31, 2020 Category: Microbiology Authors: Wang S, Liang H, Liu L, Jiang X, Wu S, Gao H Tags: Appl Environ Microbiol Source Type: research

Sml1 inhibits DNA repair activity of Rev1 in Saccharomyces cerevisiae during oxidative stress.
Abstract In Saccharomyces cerevisiae, Y family DNA polymerase Rev1 is involved in the repair of DNA damage by translesion DNA synthesis (TLS). In the current study, to elucidate the role of Rev1 in oxidative stress-induced DNA damage in S. cerevisiae, REV1 was deleted and overexpressed; transcriptome analysis of these mutants along with the wild-type strain was performed to screen potential genes that could be associated with REV1 during response to DNA damage. Under 2 mM H2O2 treatment, the deletion of REV1 resulted in a 1.5- and 2.8-fold decrease in the survival rate and mutation frequency, respectively, whereas...
Source: Applied and Environmental Microbiology - January 31, 2020 Category: Microbiology Authors: Yao R, Zhou P, Wu C, Liu L, Wu J Tags: Appl Environ Microbiol Source Type: research

The ZKIR Assay, a novel Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples.
This study shows that the ZKIR assay is an accurate, specific and sensitive novel method to detect the presence of Kp in complex matrices, and indicates that Kp isolates from environmental samples differ from clinical isolates.IMPORTANCE The Klebsiella pneumoniae species complex (Kp) includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp ecology and routes o...
Source: Applied and Environmental Microbiology - January 31, 2020 Category: Microbiology Authors: Barbier E, Rodrigues C, Depret G, Passet V, Gal L, Piveteau P, Brisse S Tags: Appl Environ Microbiol Source Type: research

Engineering of cyclodextrin glycosyltransferase reveals pH-regulatory mechanism of enhanced long chain glycosylated sophoricoside specificity.
Abstract Sophoricoside glycosylated derivatives, especially long chain glycosylated sophoricosides (LCGS) have greatly improved water solubility compared with sophoricoside. Here cyclodextrin glycosyltransferase from Paenibacillus macerans (PmCGTase) was employed for sophoricoside glycosylation. Saturation mutagenesis of alanine 156, alanine 166, glycine 173, and leucine 174 were performed due to their non-conservative properties among (α-, β-, and γ-) CGTases with different product specificities. Variants L174P, A156V/L174P, and A156V/L174P/A166Y greatly improved the product specificity for LCGS....
Source: Applied and Environmental Microbiology - January 31, 2020 Category: Microbiology Authors: Han R, Ni J, Zhou J, Dong J, Xu G, Ni Y Tags: Appl Environ Microbiol Source Type: research

The cell wall integrity pathway contributes to the early stages of Aspergillus fumigatus asexual development.
This study points to an essential role for the CWIP during conidiation and provides further insights into the complex regulation of asexual development in filamentous fungi. PMID: 32005734 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - January 31, 2020 Category: Microbiology Authors: Rocha MC, Fabri JHTM, Simões IT, Silva-Rocha R, Hagiwara D, da Cunha AF, Goldman GH, Cánovas D, Malavazi I Tags: Appl Environ Microbiol Source Type: research

Ferrous Iron-Activated Transcriptional Factor AdhR Regulates Redox Homeostasis in Clostridium beijerinckii.
Abstract The AdhR regulatory protein is an activator of σ54-dependent transcription of adhA1 and adhA2 genes, which are required for alcohol synthesis in C. beijerinckii Here, we identified the signal perceived by AdhR and determined the regulatory mechanism of AdhR activity. By assaying the activity of AdhR in N-terminally truncated forms, a negative control mechanism of AdhR activity was identified, in which the central AAA+ domain is subject to repression by the N-terminal GAF and PAS domains. Binding of Fe2+ to the GAF domain was found to relieve intramolecular repression and stimulate the ATPase activit...
Source: Applied and Environmental Microbiology - January 31, 2020 Category: Microbiology Authors: Yang B, Nie X, Xiao Y, Gu Y, Jiang W, Yang C Tags: Appl Environ Microbiol Source Type: research

Deciphering the bifidobacterial population within the canine and feline gut microbiota.
In this study, the taxonomical composition of canine and feline gut microbiota was explored at genus- and bifidobacterial-species levels, allowing classification of these microbial populations into distinct Gut Community State Types at either of the two investigated taxonomic levels. Furthermore, the reconstruction of core gut microbiota coupled with co-variance network analysis based on bifidobacterial ITS profiling revealed differences in the bifidobacterial composition of canine and feline gut microbiota, suggesting that particular bifidobacterial species have developed a selective ability to colonize a specific host. ...
Source: Applied and Environmental Microbiology - January 31, 2020 Category: Microbiology Authors: Alessandri G, Milani C, Mancabelli L, Longhi G, Anzalone R, Lugli GA, Duranti S, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M Tags: Appl Environ Microbiol Source Type: research

Functional Bacillus thuringiensis Cyt1Aa is necessary to synergize Lysinibacillus sphaericus Binary toxin against Bin-resistant and refractory mosquito species.
-Filha MHNL Abstract The Binary (Bin) toxin from Lysinibacillus sphaericus is effective to mosquito larvae but its utilization is threatened by the development of insect resistance. Bin toxin is composed by the BinB subunit required for binding to midgut receptors, and the BinA subunit that causes toxicity after cell internalization, mediated by BinB. Culex quinquefasciatus resistance to this toxin is caused by mutations that prevent expression of Bin toxin-receptors in the midgut. Previously, it was shown that the Cyt1Aa toxin, from Bacillus thuringiensis subsp. israelensis (Bti), restores Bin toxicity to Bin-res...
Source: Applied and Environmental Microbiology - January 31, 2020 Category: Microbiology Authors: do Nascimento NA, Torres-Quintero MC, Molina SL, Pacheco S, Romão TP, Pereira-Neves A, Soberón M, Bravo A, Silva-Filha MHNL Tags: Appl Environ Microbiol Source Type: research

Analogous and diverse functions of APSES-type transcription factors in the morphogenesis of the entomopathogenic fungus, Metarhizium rileyi.
In this study, we characterized two orthologous APSES genes (MrStuA and MrXbp) in the entomopathogenic fungus, Metarhizium rileyi Deletion of either MrStuA or MrXbp impaired dimorphic transition, conidiation, fungal virulence, and microsclerotium formation. Compared with the wild-type strain, ΔMrStuA and ΔMrXbp mutants were hypersensitive to thermal and oxidative stress. Furthermore, RNA-seq analysis revealed that MrStuA and MrXbp independently regulate their own distinctive subsets of signaling pathways during dimorphic transition and microsclerotium formation, but also show overlapping regulation of genes dur...
Source: Applied and Environmental Microbiology - January 31, 2020 Category: Microbiology Authors: Xin C, Zhang J, Nian S, Wang G, Wang Z, Song Z, Ren G Tags: Appl Environ Microbiol Source Type: research

Competitive exclusion is a major bioprotective mechanism of lactobacilli against fungal spoilage in fermented milk products.
In this study, we show that depletion of free manganese is a major bioprotective mechanism of lactobacilli in dairy products. High manganese uptake and intracellular storage provides a link to the distinct non-enzymatic manganese catalyzed oxidative stress defense mechanism, previously described for certain lactobacilli. The evaluation of representative Lactobacillus species in our study identifies multiple relevant species groups for fungal growth inhibition via manganese depletion. Hence, through the natural mechanism of nutrient depletion, the use of dedicated bioprotective lactobacilli constitutes an attractive alterna...
Source: Applied and Environmental Microbiology - January 31, 2020 Category: Microbiology Authors: Siedler S, Rau MH, Bidstrup S, Vento JM, Aunsbjerg SD, Bosma EF, McNair LM, Beisel CL, Neves AR Tags: Appl Environ Microbiol Source Type: research

Lysis of an Lactococcus lactis Di-peptidase Mutant and Rescue by Mutation in the Pleiotropic Regulator CodY.
Abstract Lactococcus lactis subsp. cremoris MG1363 is a model for the lactic acid bacteria (LAB) used in the dairy industry. The proteolytic system, consisting of a proteinase, several peptide- and amino acid uptake systems and a host of intracellular peptidases, plays a vital role in nitrogen metabolism and is of eminent importance for flavor formation in dairy products. The dipeptidase PepV functions in the last stages of proteolysis. A link between nitrogen metabolism and peptidoglycan (PG) biosynthesis was underlined by the finding that deletion of the dipeptidase gene pepV (MGΔpepV) results in a prolong...
Source: Applied and Environmental Microbiology - January 31, 2020 Category: Microbiology Authors: Huang C, Hernandez-Valdes JA, Kuipers OP, Kok J Tags: Appl Environ Microbiol Source Type: research

A Quorum Quenching Bacterial Isolate Contains Multiple Substrate-Inducible Genes Encoding for Degradation of Diffusible Signal Factor.
In this study, we developed an efficient method for screening of highly active DSF-degradation microorganisms. Among them, strain Pseudomonas sp. HS-18 showed a superior DSF degradation activity. Bioinformatics and genetic analyses showed that at least 4 genes, designated as digA-D encoding fatty acyl-CoA ligase homologues, are responsible for DSF signal degradation. Interestingly, all the 4 dig genes were induced by exogenous DSF with digA being the most significantly induced. Expression of the dig genes in Xanthomonas campestris pv. campestris (Xcc) markedly reduced the accumulation of endogenous DSF, decreased productio...
Source: Applied and Environmental Microbiology - January 24, 2020 Category: Microbiology Authors: Wang H, Liao L, Chen S, Zhang LH Tags: Appl Environ Microbiol Source Type: research

In-depth profiling of calcite precipitation by environmental bacteria reveals fundamental mechanistic differences with relevance to application.
This study surveyed environmental bacteria for their ability to precipitate calcium carbonate minerals and investigated both the mechanisms and the resulting crystals. We show that while urease activity leads to the fastest precipitation, it is by no means essential. Importantly, the same quantities of calcium carbonate are produced by non-ureolytic bacteria, and the resulting crystals appear to have larger volumes and more organic components, which is likely beneficial in specific applications. Testing both precipitation mechanisms in a self-healing concrete application showed that non-ureolytic bacteria delivered more ro...
Source: Applied and Environmental Microbiology - January 24, 2020 Category: Microbiology Authors: Reeksting BJ, Hoffmann TD, Tan L, Paine K, Gebhard S Tags: Appl Environ Microbiol Source Type: research

Role of caecal microbiota in the differential resistance of inbred chicken lines to colonization by Campylobacter jejuni.
In this study, we investigated whether heritable differences in colonization of inbred chicken lines by Campylobacter jejuni are associated with differences in caecal microbiota. We performed homologous and heterologous caecal microbiota transplants between line 61 (resistant) and line N (susceptible), by orally administering caecal contents collected from 3-week-old donors to day-of-hatch chicks. Recipient birds were challenged (day 21) with C. jejuni 11168H. In birds given homologous microbiota, the differential resistance of lines to C. jejuni colonization was reproduced. Contrary to our hypothesis, transfer of caecal m...
Source: Applied and Environmental Microbiology - January 24, 2020 Category: Microbiology Authors: Chintoan-Uta C, Wisedchanwet T, Glendinning L, Bremner A, Psifidi A, Vervelde L, Watson K, Watson M, Stevens MP Tags: Appl Environ Microbiol Source Type: research

Nutrient level determines biofilm characteristics and the subsequent impact on microbial corrosion and biocide effectiveness.
Abstract The impact that nutrient level has on biofilm characteristics, biocide effectiveness and the associated risk of microbiologically influenced corrosion (MIC) was assessed using multispecies biofilms from two different oilfield consortia. A range of microbiological, microscopy and corrosion methods demonstrated that the continuous flow of nutrients for the microbial growth resulted in higher activity, thickness and robustness of the biofilms formed on carbon steel, which induced greater localised corrosion compared to biofilms formed under batch, nutrient-depleted conditions. Despite of the differences in b...
Source: Applied and Environmental Microbiology - January 24, 2020 Category: Microbiology Authors: Salgar-Chaparro SJ, Lepkova K, Pojtanabuntoeng T, Darwin A, Machuca LL Tags: Appl Environ Microbiol Source Type: research

Two New Unspecific Peroxygenases from Heterologous Expression of Fungal Genes in Escherichia coli.
iérrez A, Martínez AT Abstract Unspecific peroxygenases (UPOs) constitute a new family of fungal heme-thiolate enzymes with high biotechnological interest. Although several thousand genes encoding hypothetical UPO-type proteins have been identified in sequenced fungal genomes and other databases, only a handful of UPO enzymes have been experimentally characterized to date. Therefore, gene screening and heterologous expression from genetic databases is a priority in the search for ad-hoc UPOs for oxyfunctionalization reactions of interest. Very recently, Escherichia coli production (as a soluble and a...
Source: Applied and Environmental Microbiology - January 24, 2020 Category: Microbiology Authors: Linde D, Olmedo A, González-Benjumea A, Estévez M, Renau-Mínguez C, Carro J, Fernández-Fueyo E, Gutiérrez A, Martínez AT Tags: Appl Environ Microbiol Source Type: research

Thermophilic degradation of hemicellulose, a critical feedstock in the production of bioenergy and other value-added products.
Abstract Renewable fuels have gained importance as the world moves towards diversifying its energy portfolio. A critical step in the biomass to bioenergy initiative is deconstruction of plant cell wall polysaccharides to their unit sugars for subsequent fermentation to fuels. To acquire carbon and energy for their metabolic processes, diverse microorganisms have evolved genes encoding enzymes that depolymerize polysaccharides to their carbon/energy-rich building blocks. The microbial enzymes mostly target the energy present in cellulose, hemicellulose and pectin, three major forms of energy storage in plants. In t...
Source: Applied and Environmental Microbiology - January 24, 2020 Category: Microbiology Authors: Cann I, Pereira GV, Abdel-Hamid AM, Kim H, Wefers D, Kayang BB, Kanai T, Sato T, Bernardi RC, Atomi H, Mackie RI Tags: Appl Environ Microbiol Source Type: research

Correction for Bellenberg et al., "Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms".
Correction for Bellenberg et al., "Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms". Appl Environ Microbiol. 2020 Jan 21;86(3): Authors: Bellenberg S, Buetti-Dinh A, Galli V, Ilie O, Herold M, Christel S, Boretska M, Pivkin IV, Wilmes P, Sand W, Vera M, Dopson M PMID: 31964679 [PubMed - in process] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - January 21, 2020 Category: Microbiology Authors: Bellenberg S, Buetti-Dinh A, Galli V, Ilie O, Herold M, Christel S, Boretska M, Pivkin IV, Wilmes P, Sand W, Vera M, Dopson M Tags: Appl Environ Microbiol Source Type: research

Faster diffusive dynamics of histone-like nucleoid structuring proteins in live bacteria caused by silver ions.
Abstract The antimicrobial activity and mechanism of silver ions (Ag+) have gained broad attention in recent years. However, dynamic studies are rare in this field. Here, we report our measurement of the effects of Ag+ ions on the dynamics of histone-like nucleoid structuring (H-NS) proteins in live bacteria using single-particle tracking photoactivated localization microscopy (sptPALM). It was found that treating the bacteria with Ag+ ions led to faster diffusive dynamics of H-NS proteins. Several techniques were used to understand the mechanism of the observed faster dynamics. Electrophoretic mobility shift assa...
Source: Applied and Environmental Microbiology - January 17, 2020 Category: Microbiology Authors: Sadoon AA, Khadka P, Freeland J, Gundampati RK, Manso R, Ruiz M, Krishnamurthi VR, Thallapuranam SK, Chen J, Wang Y Tags: Appl Environ Microbiol Source Type: research

Respiratory physiology of Lactococcus lactis in chemostat cultures and its effect on cellular robustness in frozen and freeze-dried starter cultures.
This study extends our knowledge on respiratory metabolism in L. lactis and its impact on frozen and freeze-dried starter culture products, and it illustrates the influence of cultivation conditions and microbial physiology on the quality of starter cultures. PMID: 31953330 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - January 17, 2020 Category: Microbiology Authors: Johanson A, Goel A, Olsson L, Franzén CJ Tags: Appl Environ Microbiol Source Type: research

A negative regulator of carotenogenesis in Blakeslea trispora.
In this study, the homologous gene of carotenogenesis regulatory gene (crgA) was cloned from the mating type (-) of B. trispora and the deduced CrgA protein was analyzed for its primary structure and domains. In order to clarify the crgA-mediated regulation in B. trispora, we used the strategies of gene knockout and complementation to investigate the effect of crgA expression on the phenotype of B. trispora In contrast to the wild-type strain, the crgA null mutant was defective in sporulation, but accumulated much more β-carotene (31.2% improvement at the end) accompanied by the enhanced transcription levels of three ...
Source: Applied and Environmental Microbiology - January 17, 2020 Category: Microbiology Authors: Luo W, Gong Z, Li N, Zhao Y, Zhang H, Yang X, Liu Y, Rao Z, Yu X Tags: Appl Environ Microbiol Source Type: research

Potential control of potato soft rot disease by the obligate predators Bdellovibrio and like organisms.
Abstract Bacterial soft rot diseases caused by Pectobacterium spp. and Dickeya spp. affect a wide range of crops including potato, a major food crop. As of today, farmers mostly rely on sanitary practices, water management and plant nutrition for control.We tested the bacterial predators Bdellovibrio and like organisms (BALOs) to control potato soft rot. BALOs are small, motile predatory bacteria found in terrestrial and aquatic environments. They predate on a wide range of Gram-negative bacteria, including animal and plant pathogens. To this end, BALO strains HD100, 109J and ΔmerRNA were shown to efficientl...
Source: Applied and Environmental Microbiology - January 17, 2020 Category: Microbiology Authors: Youdkes D, Helman Y, Burdman S, Matan O, Jurkevitch E Tags: Appl Environ Microbiol Source Type: research

Metagenomic shotgun analyses reveal complex patterns of intra- and interspecific variation in the intestinal microbiomes of codfishes.
tar B Abstract The relative importance of host-specific selection or environmental factors in determining the composition of the intestinal microbiome in wild vertebrates remains poorly understood. Here, we use metagenomic shotgun sequencing of individual specimens to compare the intra- and interspecific variation of intestinal microbiome communities in two ecotypes (NEAC and NCC) of Atlantic cod (Gadus morhua) -that have distinct behavior and habitats- and three Gadidae species that occupy a range of ecological niches. Interestingly, we find significantly diverged microbiomes amongst the two Atlantic cod ecotypes...
Source: Applied and Environmental Microbiology - January 17, 2020 Category: Microbiology Authors: Riiser ES, Haverkamp THA, Varadharajan S, Borgan Ø, Jakobsen KS, Jentoft S, Star B Tags: Appl Environ Microbiol Source Type: research

Dissemination of quinolone resistant Escherichia coli in the Norwegian broiler and pig production chain, and possible persistence in the broiler production environment.
agesen K Abstract In Norway, the use of quinolones in livestock populations is very low, and prophylactic use is prohibited. Despite this, quinolone resistant E. coli (QREC) are present at low levels in several animal species. The source of these QREC is unknown. The aim of this study was to characterize and compare QREC from different animal species to identify putative factors that may promote the occurrence of QREC. A total of 280 QREC isolates, from broilers, pigs, red foxes and wild birds, were whole genome sequenced and analysed. Well-known chromosomal and plasmid-mediated resistance mechanisms were identifi...
Source: Applied and Environmental Microbiology - January 17, 2020 Category: Microbiology Authors: Kaspersen H, Sekse C, Fiskebeck EZ, Slettemeås JS, Simm R, Norström M, Urdahl AM, Lagesen K Tags: Appl Environ Microbiol Source Type: research