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Potential of rice stubble as a reservoir of bradyrhizobial inoculum in rice-legume crop rotation.
This study shows that some rice endophytic bradyrhizobia could perform IAA production, and ACC deaminase activity together with nitrogen fixation ability during symbiosis inside rice tissues. These characteristics may play an important role in rice growth promotion by endophytic bradyrhizobium. However, the NO producing strains should be of concern due to NO possible deleterious effect on rice growth. In addition, this study reports the application of endophytic bradyrhizobia in rice stubbles, and the rice stubbles were used directly as an inoculum for a leguminous plant (mung bean). The degradation of rice stubbles leads ...
Source: Applied and Environmental Microbiology - September 15, 2017 Category: Microbiology Authors: Piromyou P, Greetatorn T, Teamtisong K, Tittabutr P, Boonkerd N, Teaumroong N Tags: Appl Environ Microbiol Source Type: research

Omics analyses of Trichoderma reesei CBS999.97 and QM6a indicate a relevance of female fertility for CAZyme and transporter levels.
hmoll M Abstract The filamentous fungus Trichoderma reesei is predominantly found in the tropics, but also in more temperate regions, such as Europe and is widely known as producer of high amounts of plant cell wall degrading enzymes. We sequenced the genome of the sexually competent isolate CBS999.97, which is phenotypically different from female sterile QM6a, but can cross sexually with QM6a. Transcriptome data for growth on cellulose showed that entire CAZyme families are consistently differentially regulated between these strains. We evaluated backcrossed strains of both mating types, which acquired female fer...
Source: Applied and Environmental Microbiology - September 15, 2017 Category: Microbiology Authors: Tisch D, Pomraning KR, Collett JR, Freitag M, Baker SE, Chen CL, Hsu PW, Chuang YC, Schuster A, Dattenböck C, Stappler E, Sulyok M, Böhmdorfer S, Oberlerchner J, Wang TF, Schmoll M Tags: Appl Environ Microbiol Source Type: research

CmeABC multidrug efflux pump contributes to antibiotic resistance and promotes Campylobacter jejuni survival and multiplication in Acanthamoeba polyphaga.
In this study we found that Campylobacter jejuni was able to survive and multiply inside Acanthamoeba. polyphaga Since these microorganisms can co-exist in the same environment (e.g. in poultry farms), the latter may increase the risk of infection with Campylobacter Our data suggests that, in addition to its role in antibiotic resistance, the CmeABC MDR efflux pump also plays a role in bacterial survival within amoebae. Furthermore, we demonstrated a synergistic effect of the CmeABC MDR efflux pump and TetO on bacterial resistance to tetracycline. Due to its role both in antibiotic resistance and virulence of C. jejuni, th...
Source: Applied and Environmental Microbiology - September 15, 2017 Category: Microbiology Authors: Vieira A, Ramesh A, Seddon AM, Karlyshev AV Tags: Appl Environ Microbiol Source Type: research

Succinate transport is not essential for symbiotic nitrogen fixation by Sinorhizobium meliloti nor Rhizobium leguminosarum.
Abstract Symbiotic nitrogen fixation (SNF) is an energetically expensive process performed by bacteria during endosymbiotic relationships with plants. The bacteria require the plant to provide a carbon source for generation of reductant to power SNF. While C4-dicarboxylates (succinate, fumarate, malate) appear to be the primary, if not sole, carbon source provided to the bacteria, the contribution of each C4-dicarboxylate is not known. We address this issue using a genetic and systems-level analyses. Expression of a malate specific transporter (MaeP) in Sinorhizobium meliloti Rm1021 dct mutants unable to transport...
Source: Applied and Environmental Microbiology - September 15, 2017 Category: Microbiology Authors: Mitsch MJ, diCenzo GC, Cowie A, Finan TM Tags: Appl Environ Microbiol Source Type: research

Inactivation of Human Norovirus GI, GII, and Surrogates by Free Chlorine in Postharvest Leafy Green Wash Water.
This study modeled viral inactivation data and quantified the free chlorine CT values that processing facilities must meet in order to achieve the desired level of hNoV GI and GII reduction. Disinfection experiments were conducted in industrial leafy green wash water collected from a full-scale fresh produce processing facility in the U.S., and hNoV GI and GII results were compared with surrogate molecular and infectivity data. PMID: 28887415 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - September 8, 2017 Category: Microbiology Authors: Dunkin N, Weng SC, Jacangelo JG, Schwab KJ Tags: Appl Environ Microbiol Source Type: research

Identifying the active microbiome associated with roots and rhizosphere soil of oilseed rape.
inlay R Abstract RNA stable isotope probing and high throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing roots and rhizosphere soil of oilseed rape, to identify taxa assimilating plant-derived carbon following (13)CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria and Chloroflexi were the most active bacter...
Source: Applied and Environmental Microbiology - September 8, 2017 Category: Microbiology Authors: Gkarmiri K, Mahmood S, Ekblad A, Alström S, Högberg N, Finlay R Tags: Appl Environ Microbiol Source Type: research

High substrate uptake rates empower Vibrio natriegens as production host for industrial biotechnology.
mbach B Abstract The productivity of industrial fermentation processes is essentially limited by the biomass specific substrate consumption rate (qS) of the applied microbial production system. Since qS depends on the growth rate (μ), we highlight the potential of the fastest growing non-pathogenic bacterium, Vibrio natriegens, as novel candidate for future biotechnological processes. V. natriegens grows rapidly in BHIN complex medium with a μ of up to 4.43 h(-1) (doubling time of 9.4 min) as well as in minimal medium supplemented with various industrially relevant substrates. Bioreactor cultivations in mini...
Source: Applied and Environmental Microbiology - September 8, 2017 Category: Microbiology Authors: Hoffart E, Grenz S, Lange J, Nitschel R, Müller F, Schwentner A, Feith A, Lenfers-Lücker M, Takors R, Blombach B Tags: Appl Environ Microbiol Source Type: research

Expression of chitinases in Listeria monocytogenes is influenced by lmo0327 that encodes an internalin-like protein.
Abstract The chitinolytic system of Listeria monocytogenes thus far comprises two chitinases, ChiA and ChiB, and a lytic polysaccharide monooxygenase, Lmo2467. The role of the system in the bacterium appears to be pleiotropic, as besides mediating hydrolysis of chitin, the second most ubiquitous carbohydrate in nature, the chitinases have been deemed important for colonization of unicellular moulds, as well as mammalian hosts. In order to identify additional components of the chitinolytic system, we screened a transposon mutant library for mutants exhibiting impaired chitin hydrolysis. The screening yielded a muta...
Source: Applied and Environmental Microbiology - September 8, 2017 Category: Microbiology Authors: Paspaliari DK, Kastbjerg VG, Ingmer H, Popowska M, Larsen MH Tags: Appl Environ Microbiol Source Type: research

Oxidative stressors modify the response of Streptococcus mutans to its competence signal peptides.
In this study we used fluorescent reporters to probe the effect of reactive oxygen species on competence signaling at the single cell level. Our data show that different reactive oxygen species have different effects on S. mutans competence, and that some portions of the signaling pathway are more acutely sensitive to oxidative stress than others. PMID: 28887419 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - September 8, 2017 Category: Microbiology Authors: De Furio M, Ahn SJ, Burne RA, Hagen SJ Tags: Appl Environ Microbiol Source Type: research

The Flexibility-Rigidity Coordination of Dense Exopolysaccharide Matrix in Terrestrial Cyanobacteria acclimated to Periodic Desiccation.
Abstract A dense exopolysaccharide (EPS) matrix is crucial for cyanobacterial survival in terrestrial xeric environments, in which cyanobacteria undergo frequent expansion and shrinkage processes during environmental desiccation-rehydration cycles. However, it is unclear how terrestrial cyanobacteria coordinate the structural dynamics of the EPS matrix upon the expansion and shrinkage to avoid potential mechanical stress while benefiting from the matrix. In the present study, we sought to answer this question by investigating the gene expression, protein dynamics, enzymatic characteristics and biological roles of ...
Source: Applied and Environmental Microbiology - September 8, 2017 Category: Microbiology Authors: Liu W, Cui L, Xu H, Zhu Z, Gao X Tags: Appl Environ Microbiol Source Type: research

Impact of "Raised Without Antibiotics" Beef Cattle Production Practices On Occurrences of Antimicrobial Resistance.
Impact of "Raised Without Antibiotics" Beef Cattle Production Practices On Occurrences of Antimicrobial Resistance. Appl Environ Microbiol. 2017 Sep 08;: Authors: Vikram A, Rovira P, Agga GE, Arthur TM, Bosilevac JM, Wheeler TL, Morley PS, Belk KE, Schmidt JW Abstract The specific antimicrobial resistance (AMR) decreases that can be expected from reducing antimicrobial (AM) use in United States (US) beef production have not been defined. To address this data gap, feces were recovered from 36 lots of "raised without antibiotics" (RWA) and 36 lots of "conventional" (CONV) b...
Source: Applied and Environmental Microbiology - September 8, 2017 Category: Microbiology Authors: Vikram A, Rovira P, Agga GE, Arthur TM, Bosilevac JM, Wheeler TL, Morley PS, Belk KE, Schmidt JW Tags: Appl Environ Microbiol Source Type: research

Glycolytic functions are conserved in the genome of the wine yeast Hanseniaspora uvarum and pyruvate kinase limits its capacity for alcoholic fermentation.
Abstract Hanseniaspora uvarum (anamorph Kloeckera apiculata) is a predominant yeast on wine grapes and other fruits and has a strong influence on wine quality, even when Saccharomyces cerevisiae starter cultures are employed. In this work we sequenced and annotated approximately 93% of the H. uvarum genome. Southern and synteny analyses were employed to construct a map of the seven chromosomes present in a type strain. Comparative determinations of specific enzyme activities within the fermentative pathway in H. uvarum and S. cerevisiae indicated that the reduced capacity for ethanol production of the former yeast...
Source: Applied and Environmental Microbiology - September 8, 2017 Category: Microbiology Authors: Langenberg AK, Bink FJ, Wolff L, Walter S, von Wallbrunn C, Grossmann M, Heinisch JJ, Schmitz HP Tags: Appl Environ Microbiol Source Type: research

Forensic human identification using skin microbiomes.
This study used supervised learning to identify individuals with high accuracy and associated stable features from skin microbiomes over a period of up to almost 3 years. These selected features provide a preliminary marker panel for future development of a robust and reproducible method for skin microbiome profiling for forensic human identification.Importance A novel approach is described to attribute skin microbiomes, collected over a period of>2.5 years, to their individual hosts with a high degree of accuracy. Nucleotide diversities of stable clade-specific markers with supervised learning was used to classify skin...
Source: Applied and Environmental Microbiology - September 8, 2017 Category: Microbiology Authors: Schmedes SE, Woerner AE, Budowle B Tags: Appl Environ Microbiol Source Type: research

A survey of putative quorum sensing genes in nitrifying bacteria reveals acyl-homoserine lactone production in ammonia- and nitrite-oxidizing bacteria from the genera Nitrosospira, Nitrobacter, and Nitrospira.
This study characterized putative QS signals produced by different genera and species of nitrifiers. Our work lays the foundation for future experiments investigating communication between nitrifying bacteria, purpose of QS in these microorganisms, and manipulation of QS during nitrification. PMID: 28887424 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - September 8, 2017 Category: Microbiology Authors: Mellbye BL, Spieck E, Bottomley PJ, Sayavedra-Soto LA Tags: Appl Environ Microbiol Source Type: research

CRISPR-Cas9(D10A) Nickase-Assisted Genome Editing in Lactobacillus casei.
Abstract Lactobacillus casei has drawn increasing attention as health-promoting probiotics, while effective genetic manipulation tools are often not available, e.g. the single gene knockout in L. casei still depends on the classic homologous recombination-dependent double crossover strategy that is quite labor intensive and time-requiring. In the present study, a rapid and precise genome editing plasmid pLCNICK was established for L. casei genome engineering based on CRISPR-Cas9(D10A) In addition to the P23-Cas9(D10A) and Pldh-sgRNA (single guide RNA) expression cassettes, pLCNICK includes the homologous arms of t...
Source: Applied and Environmental Microbiology - September 1, 2017 Category: Microbiology Authors: Song X, Huang H, Xiong Z, Ai L, Yang S Tags: Appl Environ Microbiol Source Type: research

Chemical Pretreatment-Independent Saccharifications of Xylan and Cellulose of Rice Straw by Bacterial Weak Lignin-Binding Xylanolytic and Cellulolytic Enzymes.
This study shows that xylan in untreated rice straw was saccharified to xylose in one step without chemical pretreatment, yielding 58.2% of the theoretically maximum value by Paenibacillus curdlanolyticus B-6 PcAxy43A, a weak lignin-binding trifunctional xylanolytic enzyme, endoxylanase/β-xylosidase/arabinoxylan arabinofuranohydrolase. Moreover, xylose yield from untreated rice straw was enhanced to 78.9% by adding endoxylanases, PcXyn10C and PcXyn11A from the same bacterium, resulting in improvement of cellulose accessibility to cellulolytic enzyme. After autoclaving the xylanolytic enzyme-treated rice straw, it was ...
Source: Applied and Environmental Microbiology - September 1, 2017 Category: Microbiology Authors: Teeravivattanakit T, Baramee S, Phitsuwan P, Sornyotha S, Waeonukul R, Pason P, Tachaapaikoon C, Poomputsa K, Kosugi A, Sakka K, Ratanakhanokchai K Tags: Appl Environ Microbiol Source Type: research

Exogenous polyunsaturated fatty acids (PUFAs) impact membrane remodeling and affect virulence phenotypes among pathogenic Vibrio species.
Abstract The pathogenic Vibrio species (cholerae, parahaemolyticus and vulnificus) represent a constant threat to human health, causing food-borne and skin wound infections as a result of ingestion or exposure to contaminated water and seafood. Recent studies have highlighted Vibrio's ability to acquire fatty acids from environmental sources and assimilate them into cell membranes. The possession and conservation of such machinery provokes consideration of fatty acids as important factors in the pathogenic lifestyle of Vibrio species. The findings herein link exogenous fatty acid exposure to changes in bacterial m...
Source: Applied and Environmental Microbiology - September 1, 2017 Category: Microbiology Authors: Moravec AR, Siv AW, Hobby CR, Lindsay EN, Norbash LV, Shults DJ, Symes SJK, Giles DK Tags: Appl Environ Microbiol Source Type: research

Cupriavidus necator H16 uses flavocytochrome c-sulfide dehydrogenase to oxidize self-produced and spiked sulfide.
n L Abstract Heterotrophic bacteria producing sulfide (H2S, HS(-), and S(2-)) during aerobic growth is a common phenomenon. Some with sulfide:quinone oxidoreductase (SQR) and persulfide dioxygenase (PDO) can oxidize self-produced sulfide to sulfite and thiosulfate, but others without these enzymes will release sulfide into the medium, from which H2S can volatilize into the gas phase. Here, we report Cupriavidus necator H16 with the fccAB genes, encoding flavocytochrome c-sulfide dehydrogenases (FCSDs), also oxidized self-produced H2S. The mutant with fccAB being deleted accumulated and released H2S. When fccAB wer...
Source: Applied and Environmental Microbiology - September 1, 2017 Category: Microbiology Authors: Lü C, Xia Y, Liu D, Zhao R, Gao R, Liu H, Xun L Tags: Appl Environ Microbiol Source Type: research

Impacts of Repeated Glyphosate Use on Wheat-Associated Bacteria are Small and Depend on Glyphosate-Use History.
This study provides important information for the future of this important tool for no-till systems and the environmental benefits of reducing soil erosion and fossil fuel inputs. PMID: 28864656 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - September 1, 2017 Category: Microbiology Authors: Schlatter DC, Yin C, Hulbert S, Burke I, Paulitz T Tags: Appl Environ Microbiol Source Type: research

Recovery optimization and survival of human norovirus surrogates, feline calicivirus and murine norovirus on carpet.
Abstract Carpet been attributed to prolonged and reoccurring outbreaks of human noroviruses (HuNoV), the leading cause of acute gastroenteritis worldwide. Viral recovery from environmental surfaces, such as carpet, remains undeveloped. Our aim was to determine survival of HuNoV surrogates on an understudied environmental surface, carpet. First, we measured the zeta potential and absorption capacity of wool and nylon carpet fibers, then developed a mini-spin column elution method (MSC), and lastly characterized the survival of HuNoV surrogates, feline calicivirus (FCV) and murine norovirus (MNV), over 60 days under...
Source: Applied and Environmental Microbiology - September 1, 2017 Category: Microbiology Authors: Buckley D, Fraser A, Huang G, Jiang X Tags: Appl Environ Microbiol Source Type: research

A highly conserved basidiomycete peptide synthetase produces a trimeric hydroxamate siderophore.
Abstract The model white-rot basidiomycete Ceriporiopsis (Gelatoporia) subvermispora B encodes putative natural product biosynthesis genes. Among them is the gene for the seven-domain nonribosomal peptide synthetase CsNPS2. It is a member of the as-yet uncharacterized fungal type VI siderophore synthetase family which is highly conserved and widely distributed among the basidiomycetes. These enzymes include only one adenylation (A) domain, i.e., one complete peptide synthetase module and two thiolation/condensation (T-C) di-domain partial modules which, together, constitute an AT1C1T2C2T3C3 domain setup. The full-...
Source: Applied and Environmental Microbiology - August 25, 2017 Category: Microbiology Authors: Brandenburger E, Gressler M, Leonhardt R, Lackner G, Habel A, Hertweck C, Brock M, Hoffmeister D Tags: Appl Environ Microbiol Source Type: research

Molecular determinants of the matrix thickening of a dual-species Pseudomonas aeruginosa and Enterococcus faecalis biofilm.
In this study, we observed phenotypic changes in a dual-species biofilm of P. aeruginosa and E. faecalis, including a dramatic increase in biofilm matrix thickness. For clear elucidation of the spatial distribution of the dual-species biofilm, P. aeruginosa and E. faecalis were labeled with red and green fluorescence, respectively. E. faecalis was located at the lower part of the dual-species biofilm, while P. aeruginosa developed a structured biofilm on the upper part. Mutants with altered exopolysaccharide (EPS) productions were constructed in order to determine the molecular basis for the synergistic effect of the dual-...
Source: Applied and Environmental Microbiology - August 25, 2017 Category: Microbiology Authors: Lee K, Lee KM, Kim D, Yoon SS Tags: Appl Environ Microbiol Source Type: research

In Bacillus subtilis, the SatA (formerly YyaR) acetyltransferase detoxifies streptothricin via lysine acetylation.
This study focuses on one enzyme that is necessary and sufficient to block the cytotoxic effects of a common soil antibiotic. The alluded enzyme is a member of a family of proteins that is broadly distributed in all domains of life, but poorly studied in B. subtilis and B. anthracis. The initial characterization of the enzyme provides insights into its mechanism of catalysis. PMID: 28842538 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - August 25, 2017 Category: Microbiology Authors: Burckhardt RM, Escalante-Semerena JC Tags: Appl Environ Microbiol Source Type: research

Dietary fibers and protective lactobacilli drive burrata cheese microbiome.
This study aimed at improving the functional attributes and shelf-life of burrata cheese by using protective lactobacilli (Lactobacillus plantarum LPAL and Lactobacillus rhamnosus LRB), fructoligosaccharides and inulin. Six burrata cheeses were made by using: i) the traditional protocol (control); ii) addition of 0.5% fructoligosaccharides and inulin (DF cheese); iii) protective lactobacilli in milk alone (PL cheese); iv) protective lactobacilli in milk and governing liquid (2PL cheese); v) protective lactobacilli in milk and dietary fibers (DF_PL cheese); and vi) protective lactobacilli in milk, governing liquid and dieta...
Source: Applied and Environmental Microbiology - August 25, 2017 Category: Microbiology Authors: Minervini F, Conte A, Del Nobile MA, Gobbetti M, De Angelis M Tags: Appl Environ Microbiol Source Type: research

Critical synergistic concentration of lecithin phospholipids improve the antimicrobial activity of eugenol against Escherichia coli.
In this study, the effect of individual lecithin phospholipids on the antimicrobial properties of eugenol against E. coli C600 was investigated. We tested five major phospholipids common in soy or egg lecithin (DPPC, DSPC, DPPE, DPPA and DPPS) and one synthetic cationic phospholipid (EPC 18:0). Among six phospholipids, DPPC, DSPC, DPPE, DPPA, and the cationic 18:0 EPC showed critical synergistic concentrations that significantly improve the inactivation effect of eugenol against E. coli after 30 min of exposure. At the critical synergistic concentration, an additional ca. 0.4-1.9 log reduction (ca 0.66-2.17 log CFU/mL redu...
Source: Applied and Environmental Microbiology - August 25, 2017 Category: Microbiology Authors: Zhang H, Dudley EG, Harte F Tags: Appl Environ Microbiol Source Type: research

Environmental determinants of Vibrio parahaemolyticus in the Chesapeake Bay.
This study used a unique, large dataset of surface water samples in the Chesapeake Bay (n=1,385) collected from 148 monitoring stations from 2007 to 2010. Water was analyzed for over 20 environmental parameters with additional meteorological and surrounding land use data. V. parahaemolyticus-specific genetic markers thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and tdh-related hemolysin (trh) were assayed using quantitative PCR (qPCR), and interval-censored regression models with non-linear effects were estimated to account for limits of detection and quantitation. tlh was detected in 19.6% of water sa...
Source: Applied and Environmental Microbiology - August 25, 2017 Category: Microbiology Authors: Davis BJK, Jacobs JM, Davis MF, Schwab KJ, DePaola A, Curriero FC Tags: Appl Environ Microbiol Source Type: research

The Limnohabitans genus harbors generalistic and opportunistic subtypes: evidence from spatiotemporal succession in a canyon-shaped reservoir.
V, Šimek K Abstract We studied the diversity of Limnohabitans using Reverse Line Blot Hybridization with Limnohabitans lineage-specific probes in the freshwater canyon-shaped Římov Reservoir (CZ). To examine the succession of distinct lineages we performed two studies: (i) an intensive spring sampling program at the lacustrine part of the Římov Reservoir (from ice melt through a phytoplankton peak to the clear water phase), and (ii) a seasonal study (April to November) when the occurrence of distinct Limnohabitans lineages was related to the inherent longitudinal heterogeneity of the reservo...
Source: Applied and Environmental Microbiology - August 25, 2017 Category: Microbiology Authors: Jezberová J, Jezbera J, Znachor P, Nedoma J, Kasalický V, Šimek K Tags: Appl Environ Microbiol Source Type: research

Lactolisterin BU, a novel Class II broad spectrum bacteriocin from Lactococcus lactis subsp. lactis bv. diacetylactis BGBU1-4.
Abstract Lactococcus lactis subsp. lactis bv. diacetylactis BGBU1-4 produces a novel bacteriocin, lactolisterin BU, with strong antimicrobial activity against many species of Gram-positive bacteria, including important food spoilage and food-borne pathogens such as Listeria monocytogenes, Staphylococcus aureus, Bacillus sp. and streptococci. Lactolisterin BU was extracted from the cell surface of BGBU1-4 by propan-2-ol and purified to homogeneity by C18 solid phase extraction and reversed phase HPLC. The molecular mass of the purified lactolisterin BU was 5160.94 Da and an internal fragment, AVSWAWQH, as determine...
Source: Applied and Environmental Microbiology - August 25, 2017 Category: Microbiology Authors: Lozo J, Mirkovic N, O'Connor PM, Malesevic M, Miljkovic M, Polovic N, Jovcic B, Cotter PD, Kojic M Tags: Appl Environ Microbiol Source Type: research

Probing the genome-scale metabolic landscape of Bordetella pertussis, the causative agent of whooping cough.
This study thus provides novel insights into B. pertussis physiology, and highlights the potential, but also limitations of models solely based on metabolic gene content.IMPORTANCE The metabolic capabilities of Bordetella pertussis - the causative agent of whooping cough - were investigated from a systems-level perspective. We constructed a comprehensive genome-scale metabolic model for B. pertussis, and challenged its predictions experimentally. This systems approach shed light on new potential host-microbe interactions, and allowed to rationally design novel growth media with over two-fold improvements in pertussis toxin...
Source: Applied and Environmental Microbiology - August 25, 2017 Category: Microbiology Authors: Branco Dos Santos F, Olivier BG, Boele J, Smessaert V, De Rop P, Krumpochova P, Klau GW, Giera M, Dehottay P, Teusink B, Goffin P Tags: Appl Environ Microbiol Source Type: research

The oxygen-inducible conversion of lactate to acetate in heterofermentative Lactobacillus brevis ATCC367.
In this study, we reported that both PDH and POX worked in the aerobic conversion of lactate to acetate in L. brevis ATCC367, in dominant and secondary roles, respectively. Our findings will further develop the theory of aerobic metabolism of LAB. PMID: 28842545 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - August 25, 2017 Category: Microbiology Authors: Guo T, Zhang L, Xin Y, Xu Z, He H, Kong J Tags: Appl Environ Microbiol Source Type: research

Mechanism for restoration of fertility in hybrid Zygosaccharomyces rouxii generated by interspecies hybridization.
In this study, we obtained a draft genome sequence of salt-tolerant yeast Zygosaccharomyces rouxii NBRC110957 and revealed that it is a hybrid lineage of Z. rouxii (allodiploid) with two subgenomes equivalent to NBRC1876. Because this allodiploid yeast can mate with other allodiploid strains and form spores, it can be a good model of restoring fertility after interspecies hybridization. We observed that NBRC110957 and NBRC1876 contain six mating type-like (MTL) loci. There are no large deletions or deleterious mutations in MTL loci, except for several base pair deletions in the X region in certain MTL loci. We also assigne...
Source: Applied and Environmental Microbiology - August 25, 2017 Category: Microbiology Authors: Watanabe J, Uehara K, Mogi Y, Tsukioka Y Tags: Appl Environ Microbiol Source Type: research

The arsenic resistance listeria genomic island LGI2 exhibits sequence and integration site diversity and propensity for three Listeria monocytogenes clones with enhanced virulence.
Abstract In the foodborne pathogen Listeria monocytogenes, arsenic resistance is primarily encountered in serotype 4b clones considered to have enhanced virulence, and is associated with an arsenic resistance gene cluster within a 35 kb chromosomal region, Listeria genomic island 2 (LGI2). LGI2 was first identified in strain Scott A and includes genes putatively involved in arsenic and cadmium resistance, DNA integration, conjugation and pathogenicity. However, genomic localization and sequence content of LGI2 remain poorly characterized. Here we investigated 85 arsenic-resistant L. monocytogenes strains, mostly o...
Source: Applied and Environmental Microbiology - August 25, 2017 Category: Microbiology Authors: Lee S, Ward TJ, Jima DD, Parsons C, Kathariou S Tags: Appl Environ Microbiol Source Type: research

Heterologous production of thermophile Thermochromatium tepidum photosynthetic reaction centre and light harvesting 1 complexes in the mesophile Rhodobacter sphaeroides and thermal stabilities of a hybrid core complex.
Abstract The photosynthetic complexes of the thermophile Thermochromatium tepidum are of considerable interest in biohybrid solar cell applications because of the capability of thermophilic proteins to tolerate elevated temperatures. Synthetic operons encoding reaction centre (RC) and light harvesting 1 (LH1) pigment-protein complexes of T. tepidum were expressed in the mesophile Rhodobacter sphaeroides The T. tepidum RC (TRC) was assembled, and functional with the addition of menadione to populate the QA pocket. The production of the T. tepidum LH1 (TLH1) was increased by selection of a phototrophy-capable mutant...
Source: Applied and Environmental Microbiology - August 18, 2017 Category: Microbiology Authors: Jun D, Huang V, Beatty JT Tags: Appl Environ Microbiol Source Type: research

A supervised statistical learning approach for accurate Legionella pneumophila source attribution during outbreaks.
ar TP Abstract Public health agencies are increasingly relying on genomics during Legionnaires' disease investigations. However, the causative bacterium (Legionella pneumophila) has an unusual population structure with extreme temporal and spatial genome sequence conservation. Furthermore, Legionnaires' disease outbreaks can be caused by multiple L. pneumophila genotypes in a single source. These factors can confound cluster identification using standard phylogenomic methods. Here, we show that a statistical learning approach based onL. pneumophila core genome single nucleotide polymorphism (SNP) comparisons elimi...
Source: Applied and Environmental Microbiology - August 18, 2017 Category: Microbiology Authors: Buultjens AH, Chua KYL, Baines SL, Kwong J, Gao W, Cutcher Z, Adcock S, Ballard S, Schultz MB, Tomita T, Subasinghe N, Carter GP, Pidot SJ, Franklin L, Seemann T, Gonçalves Da Silva A, Howden BP, Stinear TP Tags: Appl Environ Microbiol Source Type: research

Cultivation in space flight produces minimal alterations in the susceptibility of Bacillus subtilis cells to 72 different antibiotics and growth-inhibiting compounds.
Abstract Past results have suggested that bacterial antibiotic susceptibility is altered during space flight. To test this notion, Bacillus subtilis cells were cultivated in matched hardware, medium, and environmental conditions either in spaceflight microgravity on the International Space Station, termed Flight (FL) samples, or at Earth-normal gravity, termed Ground Control (GC) samples. Susceptibility of FL and GC samples was compared to 72 antibiotics and growth-inhibitory compounds using the Omnilog Phenotype Microarray (PM) system. Only 9 compounds were identified by PM screening as exhibiting significant differences (P
Source: Applied and Environmental Microbiology - August 18, 2017 Category: Microbiology Authors: Morrison MD, Fajardo-Cavazos P, Nicholson WL Tags: Appl Environ Microbiol Source Type: research

The transcriptional regulator PhlH modulates 2,4-diacetylphloroglucinol biosynthesis in response to the biosynthetic intermediate and end product.
Abstract Certain strains of biocontrol Pseudomonas fluorescens produce the secondary metabolite 2,4-diacetylphloroglucinol (2,4-DAPG) to antagonize the soil-borne phytopathogens in the rhizosphere. The gene cluster responsible for the biosynthesis of 2,4-DAPG is named phlACBDEFGH and it is still unclear how the pathway-specific regulator phlH within this gene cluster regulates the metabolism of 2,4-DAPG. Here, we found that PhlH in Pseudomonas fluorescens strain 2P24 represses the expression of the phlG gene encoding the 2,4-DAPG hydrolase by binding to a sequence motif overlapping with the -35 site recognized by ...
Source: Applied and Environmental Microbiology - August 18, 2017 Category: Microbiology Authors: Yan X, Yang R, Zhao RX, Han JT, Jia WJ, Li DY, Wang Y, Zhang N, Wu Y, Zhang LQ, He YX Tags: Appl Environ Microbiol Source Type: research

Phosphate-Catalyzed Hydrogen Peroxide Formation from Agar, Gellan, and κ-Carrageenan and Recovery of Microorganisms Cultivability by Catalase and Pyruvate.
In this study we investigated the factors affecting H2O2 formation from agar. H2O2 formation is pH-dependent and ammonium ions promote this phosphate-catalyzed H2O2 formation. Amendment of catalase or pyruvate, a well-known H2O2-scavenging agent, effectively eliminated H2O2 Yet results suggest that growth-inhibiting factor(s) that cannot be eliminated by pyruvate (but can be by catalase) are present in PT medium. PMID: 28821549 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - August 18, 2017 Category: Microbiology Authors: Kawasaki K, Kamagata Y Tags: Appl Environ Microbiol Source Type: research

Crystal structure of the TetR family repressor, AlkX, from Dietzia sp. DQ12-45-1b implicated in biodegradation of n-alkanes.
In this study, we determined the crystal structure of AlkX, which implies a distinct DNA/ligand binding mode. Our results shed light upon the regulation mechanism of common alkane degradation process in nature. PMID: 28821550 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - August 18, 2017 Category: Microbiology Authors: Liang JL, Gao Y, He Z, Nie Y, Wang M, JiangYang JH, Zhang XC, Shu WS, Wu XL Tags: Appl Environ Microbiol Source Type: research

Coordinated Regulation of the EII(Man) and fruRKI Operons of Streptococcus mutans by Global and Fructose-Specific Pathways.
Abstract The glucose/mannose-PTS permease EII(Man) encoded by manLMN in the dental caries pathogen Streptococcus mutans has a dominant influence on sugar-specific, CcpA-independent catabolite repression (CR). Mutations in manL affect energy metabolism and virulence-associated traits, including biofilm formation, acid tolerance and competence. Using promoter:reporter fusions, expression of the manLMN and the fruRKI operons, encoding a transcriptional regulator, a fructose-1-P kinase and a fructose-PTS permease EII(Fru), respectively, was monitored in response to carbohydrate source and in mutants lacking CcpA, FruR...
Source: Applied and Environmental Microbiology - August 18, 2017 Category: Microbiology Authors: Zeng L, Chakraborty B, Farivar T, Burne RA Tags: Appl Environ Microbiol Source Type: research

Differences in temperature and water chemistry shape distinct diversity patterns in thermophilic microbial communities.
This study presents the biodiversity and ecology of microbial mats developed in thermal gradients (20-65 °C) in the surroundings of three drillings (CH, CI, MB) tapping a hyperthermal aquifer from Romania. Using a metabarcoding approach, 16S rRNA genes were sequenced from both DNA and RNA transcripts (cDNA) and compared. The relationships between the microbial diversity and the physico-chemical factors were explored. Additionally, the cDNA data was used for in silico functionality predictions, bringing new insights into the functional potential and dynamics of these communities. The results showed that each hot spring ...
Source: Applied and Environmental Microbiology - August 18, 2017 Category: Microbiology Authors: Chiriac CM, Szekeres E, Rudi K, Baricz A, Hegedus A, Dragoş N, Coman C Tags: Appl Environ Microbiol Source Type: research

Erratum for Quir ós et al., "Improving Detection of Shiga Toxin-Producing Escherichia coli by Molecular Methods by Reducing the Interference of Free Shiga Toxin-Encoding Bacteriophages".
Erratum for Quirós et al., "Improving Detection of Shiga Toxin-Producing Escherichia coli by Molecular Methods by Reducing the Interference of Free Shiga Toxin-Encoding Bacteriophages". Appl Environ Microbiol. 2017 Aug 15;83(16): Authors: Quirós P, Martínez-Castillo A, Muniesa M PMID: 28765152 [PubMed - in process] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - August 4, 2017 Category: Microbiology Authors: Quirós P, Martínez-Castillo A, Muniesa M Tags: Appl Environ Microbiol Source Type: research

Erratum for Martinez-Castillo et al., "Shiga Toxin 2-Encoding Bacteriophages in Human Fecal Samples from Healthy Individuals".
Erratum for Martinez-Castillo et al., "Shiga Toxin 2-Encoding Bacteriophages in Human Fecal Samples from Healthy Individuals". Appl Environ Microbiol. 2017 Aug 15;83(16): Authors: Martinez-Castillo A, Quirós P, Navarro F, Miró E, Muniesa M PMID: 28765153 [PubMed - in process] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - August 4, 2017 Category: Microbiology Authors: Martinez-Castillo A, Quirós P, Navarro F, Miró E, Muniesa M Tags: Appl Environ Microbiol Source Type: research

Correction for Brigham et al., "Whole-Genome Microarray and Gene Deletion Studies Reveal Regulation of the Polyhydroxyalkanoate Production Cycle by the Stringent Response in Ralstonia eutropha H16".
Correction for Brigham et al., "Whole-Genome Microarray and Gene Deletion Studies Reveal Regulation of the Polyhydroxyalkanoate Production Cycle by the Stringent Response in Ralstonia eutropha H16". Appl Environ Microbiol. 2017 Aug 01;83(15): Authors: Brigham CJ, Speth DR, Rha C, Sinskey AJ PMID: 28716865 [PubMed - in process] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - July 20, 2017 Category: Microbiology Authors: Brigham CJ, Speth DR, Rha C, Sinskey AJ Tags: Appl Environ Microbiol Source Type: research

Med15B regulates acid stress response and tolerance in Candida glabrata.
This study explored the role of the Mediator tail subunit Med15B in the metabolism of Candida glabrata under acidic conditions. Overexpression of MED15B enhanced yeast tolerance to low pH and improved biomass production, cell viability, and pyruvate yield. Membrane lipid composition data indicated that Med15B might play a critical role in membrane integrity, fluidity, and H(+)-ATPase activity homeostasis at low pH. Thus, controlling membrane composition may serve to increase C. glabrata productivity at low pH. PMID: 28710262 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - July 14, 2017 Category: Microbiology Authors: Qi Y, Liu H, Yu J, Chen X, Liu L Tags: Appl Environ Microbiol Source Type: research

Enzymatic mechanism for arabinan degradation and transport in the thermophilic bacterium Caldanaerobius polysaccharolyticus.
n I Abstract The plant cell wall polysaccharide arabinan is an important supply of arabinose, and unraveling arabinan degrading strategies by microbes is important for understanding its use as a source of energy. Here, we explored the arabinan degrading enzymes in the thermophilic bacterium Caldanaerobius polysaccharolyticus and identified a gene cluster encoding two glycoside hydrolase (GH) family 51 α-L-arabinofuranosidases (CpAbf51A, CpAbf51B), a GH43 endo-arabinanase (CpAbn43A), a GH27 β-L-arabinopyranosidase (CpAbp27A), and two GH127 β-L-arabinofuranosidases (CpAbf127A, CpAbf127B). The genes w...
Source: Applied and Environmental Microbiology - July 14, 2017 Category: Microbiology Authors: Wefers D, Dong J, Abdel-Hamid AM, Müller Paul H, Pereira GV, Han Y, Dodd D, Baskaran R, Mayer B, Mackie RI, Cann I Tags: Appl Environ Microbiol Source Type: research

Two novel dissimilar crystal proteins, Cry5Ca1 and Cry5Da1, synergistically act against Meloidogyne incognita and delay Cry5Ba-based nematode resistance.
Abstract Cry proteins of Bacillus thuringiensis have been successfully used as biopesticides and transgenic crops throughout the world. However, resources against the most serious agricultural pathogens, plant root-knot nematodes, are limited. The genomes of several highly nematicidal virulent Bt strains from our laboratory have been sequenced, facilitating the identification of novel Cry proteins and other virulence factors. We identified two novel Cry proteins, Cry5Ca1 and Cry5Da1, that exhibit high toxicity against Meloidogyne incognita Using the Caenorhabditis elegans model, both Cry5 toxins showed to negative...
Source: Applied and Environmental Microbiology - July 14, 2017 Category: Microbiology Authors: Geng C, Liu Y, Li M, Tang Z, Muhammad S, Zheng J, Wan D, Peng D, Ruan L, Sun M Tags: Appl Environ Microbiol Source Type: research

Francisella like endosymbionts and Rickettsia species in local and imported Hyalomma ticks.
This study was aimed to provide initial characterization of the interaction between Hyalomma and FLE and to determine the prevalence of pathogenic Rickettsia in these ticks. Hyalomma marginatum, H. rufipes, H. dromedarii, H. aegyptium and H. excavatum ticks, identified morphologically and molecularly, were collected from different hosts and locations, representing the genus distribution in Israel, as well as from migratory birds. High prevalence of FLE was found in all Hyalomma species (90.6%), as well as efficient maternal transmission of FLE (91.8%), and the localization of FLE in Malpighian tubules, ovaries and salivary...
Source: Applied and Environmental Microbiology - July 14, 2017 Category: Microbiology Authors: Azagi T, Klement E, Perlman G, Lustig Y, Mumcuoglu KY, Apanaskevich D, Gottlieb Y Tags: Appl Environ Microbiol Source Type: research

Specificity of subtilin-mediated activation of histidine kinase SpaK.
ntian KD Abstract Autoinduction via two-component systems is a widespread regulatory mechanism that senses environmental and metabolic changes. Although the lantibiotics nisin and subtilin are closely related and share the same lanthionine ring structure, they autoinduce their biosynthesis in a highly specific manner. Subtilin can only activate the two-component system SpaRK of Bacillus subtilis, whereas nisin activates solely the two-component system NisRK of Lactococcus lactis To identify components that determine the specificity of subtilin autoinduction, several variants of the respective lantibiotic were anal...
Source: Applied and Environmental Microbiology - July 14, 2017 Category: Microbiology Authors: Geiger C, Spieß T, Korn SM, Kötter P, Entian KD Tags: Appl Environ Microbiol Source Type: research

Increased processivity, misincorporation, and nucleotide incorporation efficiency in Sulfolobus solfataricus Dpo4 thumb domain mutations.
Abstract The present study aimed to increase the processivity of Sulfolobus solfataricus DNA polymerase Dpo4. Protein engineering and bioinformatics were used to compile a library of potential Dpo4 mutation sites. Ten potential mutants were identified and constructed. A primer extension assay was used to evaluate the processivity of Dpo4 mutants. Thumb (A181D) and finger (E63K) domain mutants showed a processivity of 20 and 19 nucleotides (nt), respectively. A little finger domain mutant (I248Y) exhibited a processivity of 17 nt, only 1 nt more than wild-type Dpo4. Furthermore, the A181D mutant showed lower fideli...
Source: Applied and Environmental Microbiology - July 14, 2017 Category: Microbiology Authors: Wang L, Liang C, Wu J, Liu L, Tyo KEJ Tags: Appl Environ Microbiol Source Type: research

Physiological evidence for isopotential tunneling in the electron transport chain of methane-producing archaea.
This study also suggests metabolic efficiency of bacteria and archaea can be improved using exogenously supplied lipophilic electron carriers. Enhancement of methanogen electron transport through methanophenazine has the potential increase renewable methane production at industrial scale. PMID: 28710268 [PubMed - as supplied by publisher] (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - July 14, 2017 Category: Microbiology Authors: Duszenko N, Buan NR Tags: Appl Environ Microbiol Source Type: research