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Sample records for acid bacterium pediococcus

  1. Characterization and Antibacterial Potential of Lactic Acid Bacterium Pediococcus pentosaceus 4I1 Isolated from Freshwater Fish Zacco koreanus

    PubMed Central

    Bajpai, Vivek K.; Han, Jeong-Ho; Rather, Irfan A.; Park, Chanseo; Lim, Jeongheui; Paek, Woon Kee; Lee, Jong Sung; Yoon, Jung-In; Park, Yong-Ha

    2016-01-01

    This study was undertaken to characterize a lactic acid bacterium 4I1, isolated from the freshwater fish, Zacco koreanus. Morphological, biochemical, and molecular characterization of 4I1 revealed it to be Pediococcus pentosaceus 4I1. The cell free supernatant (CFS) of P. pentosaceus 4I1 exhibited significant (p < 0.05) antibacterial effects (inhibition zone diameters: 16.5–20.4 mm) against tested foodborne pathogenic bacteria with MIC and MBC values of 250–500 and 500–1,000 μg/mL, respectively. Further, antibacterial action of CFS of P. pentosaceus 4I1 against two selected bacteria Staphylococcus aureus KCTC-1621 and Escherichia coli O157:H7 was determined in subsequent assays. The CFS of P. pentosaceus 4I1 revealed its antibacterial action against S. aureus KCTC-1621 and E. coli O157:H7 on membrane integrity as confirmed by a reduction in cell viability, increased potassium ion release (900 and 800 mmol/L), reduced absorption at 260-nm (3.99 and 3.77 OD), and increased relative electrical conductivity (9.9 and 9.7%), respectively. Gas chromatography–mass spectrometry (GC–MS) analysis of the CFS of P. pentosaceus 4I1 resulted in the identification of seven major compounds, which included amino acids, fatty acids and organic acids. Scanning electron microscopic-based morphological analysis further confirmed the antibacterial effect of CFS of P. pentosaceus 4I1 against S. aureus KCTC-1621 and E. coli O157:H7. In addition, the CFS of P. Pentosaceus 4I1 displayed potent inhibitory effects on biofilms formation by S. aureus KCTC-1621 and E. coli O157:H7. The study indicates the CFS of P. pentosaceus 4I1 offers an alternative means of controlling foodborne pathogens. PMID:28066360

  2. Metabolism of hydroxycinnamic acids and their tartaric acid esters by Brettanomyces and Pediococcus in red wines.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Caffeic, p-coumaric, and ferulic acids and their corresponding tartaric acid esters (caftaric, coutaric, and fertaric, respectively) are found in wines in varying concentrations. While Brettanomyces and Pediococcus can utilize the free acids, it is not known whether they can metabolize the correspon...

  3. Appraisal of conjugated linoleic acid production by probiotic potential of Pediococcus spp. GS4.

    PubMed

    Dubey, Vinay; Ghosh, Asit Ranjan; Mandal, Badal Kumar

    2012-11-01

    Probiotics with ability to produce conjugated linoleic acid (CLA) is considered as an additive health benefit property for its known role in colon cancer mitigation. The conversion involves the biohydrogenation of the unsaturated fatty acid into conjugated form. Probiotic strain Pediococcus spp. GS4 was efficiently able to biohydrogenate linoleic acid (LA) into its conjugated form within 48 h of incubation. Quantum of CLA produced with a concentration of 121 μg/ml and sustained cell viability of 8.94 log cfu/ml maximally. Moreover, antibacterial effect of LA on the strain ability for biohydrogenation was examined at different concentrations and concluded to have a direct relationship between LA and amount of CLA produced. The efficiency of the strain for CLA production at different pH was also estimated and found maximum at pH 6.0 with 149 μg/ml while this ability was reduced at pH 9.0 to 63 μg/ml. Sesame oil, which is rich in the triacylglycerol form of LA, was also found to act as a substrate for CLA production by Pediococcus spp. GS4 with the aid of lipase-catalyzed triacylglycerol hydrolysis and amount of CLA produced was 31 μg/ml at 0.2 % while 150 μg/ml at 1.0 % of lipolysed oil in skim milk medium. Conjugated form was analyzed using UV scanning, RP-HPLC, and GC-MS. This study also focused on the alternative use of lipolysed sesame oil instead of costly LA for biohydrogenation and could be a potential source for the industrial production of CLA.

  4. Genome sequence of the phage clP1, which infects the beer spoilage bacterium Pediococcus damnosus.

    PubMed

    Kelly, David; O'Sullivan, Orla; Mills, Susan; McAuliffe, Olivia; Ross, R Paul; Neve, Horst; Coffey, Aidan

    2012-08-01

    Pediococcus damnosus (P. damnosus) bacteriophage (phage) clP1 is a novel virulent phage isolated from a municipal sewage sample collected in Southern Ireland. This phage infects the beer spoilage strain P. damnosus P82 which was isolated from German breweries. Sequencing of the phage has revealed a linear double stranded DNA genome of 38,013 base pairs (bp) with an overall GC content of 47.6%. Fifty seven open reading frames (ORFs) were identified of which 30 showed homology to previously sequenced proteins, and as a consequence 20 of these were assigned predicted functions. The majority of genes displayed homology with genes from the Lactobacillus plantarum phage phiJL-1. All genes were located on the same coding strand and in the same orientation. Morphological characterisation placed phage clP1 as a member of the Siphoviridae family with an isometric head (59 nm diameter) and non-contractile tail (length 175 nm; diameter 10nm. Interestingly, the phage clP1 genome was found to share very limited identity with other phage genome sequences in the database, and was hence considered unique. This was highlighted by the genome organisation which differed slightly to the consensus pattern of genomic organisation usually found in Siphoviridae phages. With the genetic machinery present for a lytic lifecycle and the absence of potential endotoxin factors, this phage may have applications in the biocontrol of beer spoilage bacteria. To our knowledge, this study represents the first reported P. damnosus phage genome sequence.

  5. Complete Genome Sequence of Pediococcus pentosaceus Strain wikim 20, Isolated from Korean Kimchi

    PubMed Central

    Lee, Se Hee; Jung, Min Young; Park, Boyeon; Sung-Oh, Sohn; Park, Hae Woong; Choi, Hak-Jong

    2016-01-01

    Pediococcus pentosaceus strain wikim 20 is a lactic acid bacterium that was isolated from kimchi, a representative traditional Korean fermented food. Here, we announce the complete genome sequence of P. pentosaceus strain wikim 20 consisting of a 1,830,629-bp chromosome and provide a description of its annotation. PMID:27834699

  6. Draft Genome Sequence of Pediococcus parvulus 2.6, a Probiotic β-Glucan Producer Strain

    PubMed Central

    Pérez-Ramos, Adrián; Mohedano, M. Luz; Puertas, Ana; Lamontanara, Antonella; Orru, Luigi; Spano, Giuseppe; Capozzi, Vittorio; Dueñas, M. Teresa

    2016-01-01

    We report here the draft genome sequence of the probiotic Pediococcus parvulus 2.6, a lactic acid bacterial strain isolated from ropy cider. The bacterium produces a prebiotic and immunomodulatory exopolysaccharide, and this is the first strain of the P. parvulus species whose genome has been characterized. PMID:27979937

  7. Production of racemic lactic acid in Pediococcus cerevisiae cultures by two lactate dehydrogenases.

    PubMed

    Gordon, G L; Doelle, H W

    1975-02-01

    Nicotinamide adenine dinucleotide (NAD)-dependent d(minus)-and l(plus)-lactate dehydrogenases have been partially purified 89- and 70-fold simultaneously from cell-free extracts of Pediococcus cerevisiae. Native molecular weights, as estimated from molecular sieve chromatography and electrophoresis in nondenaturing polyacrylamide gels, are 71,000 to 73,000 for d(minus)-lactate dehydrogenase and 136,000 to 139,000 for l(plus)-lactate dehydrogenase. Electrophoresis in sodium dodecyl sulfate-containing gels reveals subunits with approximate molecular weights of 37,000 to 39,000 for both enzymes. By lowering the pyruvate concentration from 5.0 to 0.5 mM, the pH optimum for pyruvate reduction by d(minus)-lactate dehydrogenase decreases from pH 8.0 to 3.6. However, l(plus)-lactate dehydrogenase displays an optimum for pyruvate reduction between pH 4.5 and 6.0 regardless of the pyruvate concentration. The enzymes obey Michaelis-Menten kinetics for both pyruvate and reduced NAD at pH 5.4 and 7.4, with increased affinity for both substrates at the acid pH. alpha-Ketobutyrate can be used as a reducible substrate, whereas oxamate has no inhibitory effect on lactate oxidation by either enzyme. Adenosine triphosphate causes inhibition of both enzymes by competition with reduced NAD. Adenosine diphosphate is also inhibitory under the same conditions, whereas NAD acts as a product inhibitor. These results are discussed with relation to the lactate isomer production during the growth cycle of P. cerevisiae.

  8. Biochemical, kinetic, and in silico characterization of DING protein purified from probiotic lactic acid bacteria Pediococcus acidilactici NCDC 252.

    PubMed

    Attri, Pooja; Khaket, Tejinder P; Jodha, Drukshakshi; Singh, Jasbir; Dhanda, Suman

    2015-01-01

    DING proteins are intriguing proteins characterized by conserved N-terminal sequence. In spite of unusually high sequence conservation even between distantly related species, DING proteins exhibit outstanding functional diversity. An extracellular caseinolytic alkaline enzyme was purified to homogeneity from a probiotic lactic acid bacteria Pediococcus acidilactici NCDC 252 using a simple procedure involving ammonium sulphate precipitation and gel filtration chromatography. This was purified 45.72-fold with a yield and specific activity of 43.5 % and 250 U/mg, respectively. The calculated molecular weight was 38.7 and 38.9 kDa by MALDI and SDS-PAGE, respectively, and pI was 7.77. The enzyme exhibited optimal activity at pH 8.0 and 40 °C. It was considerably stable up to pH 12. For casein, the enzyme had K m of 20 μM with V max of 26 U/ml. The enzyme was resistant to organic solvents but sensitive to DTNB and EDTA that confirmed it as thiol protein with involvement of metal ions in catalysis. Its tryptic peptide fragments showed 95 % similarity with eukaryotic DING, i.e., human phosphate binding protein (HPBP). Homology-based structure evaluation using HBPB as template revealed both to be structurally conserved and also possessing conserved phosphate binding motifs.

  9. Catabolism of Serine by Pediococcus acidilactici and Pediococcus pentosaceus

    PubMed Central

    Bavan, Tharmatha; Oberli, Andrea; Roetschi, Alexandra; Badertscher, René; Guggenbühl, Barbara; Berthoud, Hélène

    2013-01-01

    The ability to produce diacetyl from pyruvate and l-serine was studied in various strains of Pediococcus pentosaceus and Pediococcus acidilactici isolated from cheese. After being incubated on both substrates, only P. pentosaceus produced significant amounts of diacetyl. This property correlated with measurable serine dehydratase activity in cell extracts. A gene encoding the serine dehydratase (dsdA) was identified in P. pentosaceus, and strains that showed no serine dehydratase activity carried mutations that rendered the gene product inactive. A functional dsdA was cloned from P. pentosaceus FAM19132 and expressed in Escherichia coli. The purified recombinant enzyme catalyzed the formation of pyruvate from l- and d-serine and was active at low pH and elevated NaCl concentrations, environmental conditions usually present in cheese. Analysis of the amino acid profiles of culture supernatants from dsdA wild-type and dsdA mutant strains of P. pentosaceus did not show differences in serine levels. In contrast, P. acidilactici degraded serine. Moreover, this species also catabolized threonine and produced alanine and α-aminobutyrate. PMID:23241976

  10. Engineering wild-type robust Pediococcus acidilactici strain for high titer L- and D-lactic acid production from corn stover feedstock.

    PubMed

    Yi, Xia; Zhang, Peng; Sun, Jiaoe; Tu, Yi; Gao, Qiuqiang; Zhang, Jian; Bao, Jie

    2016-01-10

    Pediococcus acidilactici TY112 producing L-lactic acid and P. acidilactici ZP26 producing D-lactic acid, were engineered from the wild-type P. acidilactici DQ2 by ldhD or ldh gene disruption, and the robustness of the wild-type strain to the inhibitors derived from lignocellulose pretreatment was maintained well. In simultaneous saccharification and fermentation (SSF), 77.66 g L(-1) of L-lactic acid and 76.76 g L(-1) of D-lactic acid were obtained at 25% (w/w) solids content of dry dilute acid pretreated and biodetoxified corn stover feedstock. L- and D-Lactic acid yield and productivity were highly dependent on the inhibitor removal extent due to the significant down-regulation on the expressions of ldh and ldhD encoding lactate dehydrogenase by inhibitor, especially syringaldehyde and vanillin at the low concentrations. This study provided a prototype of industrial process for high titer L- and D-lactic acid production from lignocellulose feedstock.

  11. Metabolic engineering of Pediococcus acidilactici BD16 for production of vanillin through ferulic acid catabolic pathway and process optimization using response surface methodology.

    PubMed

    Kaur, Baljinder; Chakraborty, Debkumar; Kumar, Balvir

    2014-10-01

    Occurrence of feruloyl-CoA synthetase (fcs) and enoyl-CoA hydratase (ech) genes responsible for the bioconversion of ferulic acid to vanillin have been reported and characterized from Amycolatopsis sp., Streptomyces sp., and Pseudomonas sp. Attempts have been made to express these genes in Escherichia coli DH5α, E. coli JM109, and Pseudomonas fluorescens. However, none of the lactic acid bacteria strain having GRAS status was previously proposed for heterologous expression of fcs and ech genes for production of vanillin through biotechnological process. Present study reports heterologous expression of vanillin synthetic gene cassette bearing fcs and ech genes in a dairy isolate Pediococcus acidilactici BD16. After metabolic engineering, statistical optimization of process parameters that influence ferulic acid to vanillin biotransformation in the recombinant strain was carried out using central composite design of response surface methodology. After scale-up of the process, 3.14 mM vanillin was recovered from 1.08 mM ferulic acid per milligram of recombinant cell biomass within 20 min of biotransformation. From LCMS-ESI spectral analysis, a metabolic pathway of phenolic biotransformations was predicted in the recombinant P. acidilactici BD16 (fcs (+)/ech (+)).

  12. Citrate Metabolism by Pediococcus halophilus

    PubMed Central

    Kanbe, Chiyuki; Uchida, Kinji

    1987-01-01

    Several strains of non-citrate-metabolizing Pediococcus halophilus have previously been isolated from soy sauce mash or moromi. The factors controlling the metabolism of citrate in soy pediococci were studied. All the soy pediococcal strains tested which failed to decompose citrate did not possess citrate lyase [citrate (pro-3S)-lyase; EC 4.1.3.6] activity. In P. halophilus, citrate lyase was an inducible enzyme, and the optimum pH for activity was 7.0. The metabolism of citrate in P. halophilus was different from that observed in lactic streptococci. The main products from citrate were acetate and formate, and this bacterium produced no acetoin or diacetyl. Formate production from citrate was greatly reduced in the presence of glucose. P. halophilus 7117 (Cit+) was proved to contain citrate lyase, pyruvate formate-lyase (EC 2.3.1.54) phosphotransacetylase (phosphate acetyltransferase; EC 2.3.1.8), and acetate kinase (EC 2.7.2.1), i.e., all the enzymes necessary to convert citrate to acetate and formate. PMID:16347358

  13. Evaluation of potential probiotic characteristics and antibacterial effects of strains of Pediococcus species isolated from broiler chickens.

    PubMed

    Noohi, N; Ebrahimipour, G; Rohani, M; Talebi, M; Pourshafie, M R

    2016-06-01

    Pediococcus spp. were isolated from poultry rectum, faeces and food as good probiotic candidates in order to select strains to be used as probiotic in poultry feed. A total of 168 lactic acid bacteria were isolated and 51 isolates including 31 Lactobacillus spp. and 20 Pediococcus spp. were able to survive in low pH and bile salt concentration. The Pediococcus spp. were identified and their ability to form biofilm, adhesion to Caco-2 cells and antimicrobial activities against enteric pathogenic bacteria were determined. The results showed the presence of two strains, Pediococcus acidilactici P17 and P19 in rectal swab samples from 21-d old chickens with significant antibacterial activities against Salmonella enteritidis and Escherichia coli. The results suggest that only a few isolates of Pediococcus with potential probiotic activities are present in the poultry industry.

  14. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    PubMed Central

    Rhee, Mun Su; Moritz, Brélan E.; Xie, Gary; Glavina del Rio, T.; Dalin, E.; Tice, H.; Bruce, D.; Goodwin, L.; Chertkov, O.; Brettin, T.; Han, C.; Detter, C.; Pitluck, S.; Land, Miriam L.; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O.; Shanmugam, K. T.

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 °C and pH 5.0 and ferments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 °C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemicellulose. This bacterium is also considered as a potential probiotic. Complete genome sequence of a representative strain, B. coagulans strain 36D1, is presented and discussed. PMID:22675583

  15. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    SciTech Connect

    Xie, Gary; Dalin, Eileen; Tice, Hope; Chertkov, Olga; Land, Miriam L

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer-ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi-cellulose. This bacterium is also considered as a potential probiotic. Complete genome squence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  16. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    SciTech Connect

    Rhee, Mun Su; Moritz, Brelan E.; Xie, Gary; Glavina Del Rio, Tijana; Dalin, Eileen; Tice, Hope; Bruce, David; Goodwin, Lynne A.; Chertkov, Olga; Brettin, Thomas S; Han, Cliff; Detter, J. Chris; Pitluck, Sam; Land, Miriam L; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O.; Shanmugam, Keelnathan T.

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer- ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this spo- rogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attrac- tive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi- cellulose. This bacterium is also considered as a potential probiotic. Complete genome se- quence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  17. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1.

    PubMed

    Rhee, Mun Su; Moritz, Brélan E; Xie, Gary; Glavina Del Rio, T; Dalin, E; Tice, H; Bruce, D; Goodwin, L; Chertkov, O; Brettin, T; Han, C; Detter, C; Pitluck, S; Land, Miriam L; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O; Shanmugam, K T

    2011-12-31

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 °C and pH 5.0 and ferments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 °C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemicellulose. This bacterium is also considered as a potential probiotic. Complete genome sequence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  18. Endohyphal Bacterium Enhances Production of Indole-3-Acetic Acid by a Foliar Fungal Endophyte

    PubMed Central

    Hoffman, Michele T.; Gunatilaka, Malkanthi K.; Wijeratne, Kithsiri; Gunatilaka, Leslie; Arnold, A. Elizabeth

    2013-01-01

    Numerous plant pathogens, rhizosphere symbionts, and endophytic bacteria and yeasts produce the important phytohormone indole-3-acetic acid (IAA), often with profound effects on host plants. However, to date IAA production has not been documented among foliar endophytes -- the diverse guild of primarily filamentous Ascomycota that live within healthy, above-ground tissues of all plant species studied thus far. Recently bacteria that live within hyphae of endophytes (endohyphal bacteria) have been detected, but their effects have not been studied previously. Here we show not only that IAA is produced in vitro by a foliar endophyte (here identified as Pestalotiopsis aff. neglecta, Xylariales), but that IAA production is enhanced significantly when the endophyte hosts an endohyphal bacterium (here identified as Luteibacter sp., Xanthomonadales). Both the endophyte and the endophyte/bacterium complex appear to rely on an L-tryptophan dependent pathway for IAA synthesis. The bacterium can be isolated from the fungus when the symbiotic complex is cultivated at 36°C. In pure culture the bacterium does not produce IAA. Culture filtrate from the endophyte-bacterium complex significantly enhances growth of tomato in vitro relative to controls and to filtrate from the endophyte alone. Together these results speak to a facultative symbiosis between an endophyte and endohyphal bacterium that strongly influences IAA production, providing a new framework in which to explore endophyte-plant interactions. PMID:24086270

  19. First Insights into the Genome of the Amino Acid-Metabolizing Bacterium Clostridium litorale DSM 5388

    PubMed Central

    Poehlein, Anja; Alghaithi, Hamed S.; Chandran, Lenin; Chibani, Cynthia M.; Davydova, Elena; Dhamotharan, Karthikeyan; Ge, Wanwan; Gutierrez-Gutierrez, David A.; Jagirdar, Advait; Khonsari, Bahar; Nair, Kamal Prakash P. R.

    2014-01-01

    Clostridium litorale is a Gram-positive, rod-shaped, and spore-forming bacterium, which is able to use amino acids such as glycine, sarcosine, proline, and betaine as single carbon and energy sources via Stickland reactions. The genome consists of a circular chromosome (3.41 Mb) and a circular plasmid (27 kb). PMID:25081264

  20. Effect of tannic acid on the transcriptome of the soil bacterium Pseudomonas protegens Pf-5

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tannins are plant-produced organic compounds that are found in soils, are able to sequester iron, and have antimicrobial properties. We studied the effect of tannic acid on the molecular physiology of the soil-inhabiting biocontrol bacterium Pseudomonas protegens Pf-5 (formerly Pseudomonas fluoresce...

  1. Anaerobic Degradation of Cyanuric Acid, Cysteine, and Atrazine by a Facultative Anaerobic Bacterium

    PubMed Central

    Jessee, J. A.; Benoit, R. E.; Hendricks, A. C.; Allen, G. C.; Neal, J. L.

    1983-01-01

    A facultative anaerobic bacterium that rapidly degrades cyanuric acid (CA) was isolated from the sediment of a stream that received industrial wastewater effluent. CA decomposition was measured throughout the growth cycle by using a high-performance liquid chromatography assay, and the concomitant production of ammonia was also measured. The bacterium used CA or cysteine as a major, if not the sole, carbon and energy source under anaerobic, but not aerobic, conditions in a defined medium. The cell yield was greatly enhanced by the simultaneous presence of cysteine and CA in the medium. Cysteine was preferentially used rather than CA early in the growth cycle, but all of the CA was used without an apparent lag after the cysteine was metabolized. Atrazine was also degraded by this bacterium under anaerobic conditions in a defined medium. PMID:16346187

  2. An oleaginous bacterium that intrinsically accumulates long-chain free Fatty acids in its cytoplasm.

    PubMed

    Katayama, Taiki; Kanno, Manabu; Morita, Naoki; Hori, Tomoyuki; Narihiro, Takashi; Mitani, Yasuo; Kamagata, Yoichi

    2014-02-01

    Medium- and long-chain fatty acids are present in organisms in esterified forms that serve as cell membrane constituents and storage compounds. A large number of organisms are known to accumulate lipophilic materials as a source of energy and carbon. We found a bacterium, designated GK12, that intrinsically accumulates free fatty acids (FFAs) as intracellular droplets without exhibiting cytotoxicity. GK12 is an obligatory anaerobic, mesophilic lactic acid bacterium that was isolated from a methanogenic reactor. Phylogenetic analysis based on 16S rRNA gene sequences showed that GK12 is affiliated with the family Erysipelotrichaceae in the phylum Firmicutes but is distantly related to type species in this family (less than 92% similarity in 16S rRNA gene sequence). Saturated fatty acids with carbon chain lengths of 14, 16, 18, and 20 were produced from glucose under stress conditions, including higher-than-optimum temperatures and the presence of organic solvents that affect cell membrane integrity. FFAs were produced at levels corresponding to up to 25% (wt/wt) of the dry cell mass. Our data suggest that FFA accumulation is a result of an imbalance between excess membrane fatty acid biosynthesis due to homeoviscous adaptation and limited β-oxidation activity due to anaerobic growth involving lactic acid fermentation. FFA droplets were not further utilized as an energy and carbon source, even under conditions of starvation. A naturally occurring bacterium that accumulates significant amounts of long-chain FFAs with noncytotoxicity would provide useful strategies for microbial biodiesel production.

  3. Effect of Tannic Acid on the Transcriptome of the Soil Bacterium Pseudomonas protegens Pf-5

    PubMed Central

    Lim, Chee Kent; Penesyan, Anahit; Hassan, Karl A.

    2013-01-01

    Tannins are a diverse group of plant-produced, polyphenolic compounds with metal-chelating and antimicrobial properties that are prevalent in many soils. Using transcriptomics, we determined that tannic acid, a form of hydrolysable tannin, broadly affects the expression of genes involved in iron and zinc homeostases, sulfur metabolism, biofilm formation, motility, and secondary metabolite biosynthesis in the soil- and rhizosphere-inhabiting bacterium Pseudomonas protegens Pf-5. PMID:23435890

  4. Susceptibility of Pediococcus isolates to antimicrobial compounds in relation to hop-resistance and beer-spoilage

    PubMed Central

    2009-01-01

    Background Though important in the context of food microbiology and as potential pathogens in immuno-compromised humans, bacterial isolates belonging to the genus Pediococcus are best known for their association with contamination of ethanol fermentation processes (beer, wine, or fuel ethanol). Use of antimicrobial compounds (e.g., hop-compounds, Penicillin) by some industries to combat Pediococcus contaminants is long-standing, yet knowledge about the resistance of pediococci to antimicrobial agents is minimal. Here we examined Pediococcus isolates to determine whether antibiotic resistance is associated with resistance to hops, presence of genes known to correlate with beer spoilage, or with ability to grow in beer. Results Lactic acid bacteria susceptibility test broth medium (LSM) used in combination with commercially available GPN3F antimicrobial susceptibility plates was an effective method for assessing antimicrobial susceptibility of Pediococcus isolates. We report the finding of Vancomycin-susceptible Pediococcus isolates from four species. Interestingly, we found that hop-resistant, beer-spoilage, and beer-spoilage gene-harbouring isolates had a tendency to be more susceptible, rather than more resistant, to antimicrobial compounds. Conclusion Our findings indicate that the mechanisms involved in conferring hop-resistance or ability to spoil beer by Pediococcus isolates are not associated with resistance to antibiotics commonly used for treatment of human infections. Also, Vancomycin-resistance was found to be isolate-specific and not intrinsic to the genus as previously believed. PMID:19735560

  5. A partial proteome reference map of the wine lactic acid bacterium Oenococcus oeni ATCC BAA-1163.

    PubMed

    Mohedano, María de la Luz; Russo, Pasquale; de Los Ríos, Vivian; Capozzi, Vittorio; Fernández de Palencia, Pilar; Spano, Giuseppe; López, Paloma

    2014-02-26

    Oenococcus oeni is the main lactic acid bacterium that carries out the malolactic fermentation in virtually all red wines and in some white and sparkling wines. Oenococcus oeni possesses an array of metabolic activities that can modify the taste and aromatic properties of wine. There is, therefore, industrial interest in the proteins involved in these metabolic pathways and related transport systems of this bacterium. In this work, we report the characterization of the O. oeni ATCC BAA-1163 proteome. Total and membrane protein preparations from O. oeni were standardized and analysed by two-dimensional gel electrophoresis. Using tandem mass spectrometry, we identified 224 different spots corresponding to 152 unique proteins, which have been classified by their putative function and subjected to bioinformatics analysis.

  6. Biosynthesis of the respiratory toxin bongkrekic acid in the pathogenic bacterium Burkholderia gladioli.

    PubMed

    Moebius, Nadine; Ross, Claudia; Scherlach, Kirstin; Rohm, Barbara; Roth, Martin; Hertweck, Christian

    2012-09-21

    Bongkrekic acid (BA), an infamous respiratory toxin of the pathogenic bacterium Burkholderia gladioli, causes lethal intoxications when tempe bongkrek is produced with contaminated Rhizopus oligosporus cultures. Genome sequencing of B. gladioli pathovar cocovenenans unveiled the genetic basis for BA biosynthesis, and pointed to a homologous bon gene cluster in a B. gladioli strain from an infected rice plant. For functional genetics in B. gladioli λ Red recombination was established. Dissection of the modular type I polyketide synthase (a trans-AT PKS) provided insights into complex polyketide assembly. Isoprenoid-like β-branching events and a six-electron oxidation of a methyl group to a carboxylic acid give rise to the unique branched tricarboxylic fatty acid. The role of the cytochrome P450 monooxygenase, BonL, was proven by structural elucidation of deoxybongkrekic acid from a mutant.

  7. Tolerance of the nanocellulose-producing bacterium Gluconacetobacter xylinus to lignocellulose-derived acids and aldehydes.

    PubMed

    Zhang, Shuo; Winestrand, Sandra; Chen, Lin; Li, Dengxin; Jönsson, Leif J; Hong, Feng

    2014-10-08

    Lignocellulosic biomass serves as a potential alternative feedstock for production of bacterial nanocellulose (BNC), a high-value-added product of bacteria such as Gluconacetobacter xylinus. The tolerance of G. xylinus to lignocellulose-derived inhibitors (formic acid, acetic acid, levulinic acid, furfural, and 5-hydroxymethylfurfural) was investigated. Whereas 100 mM formic acid completely suppressed the metabolism of G. xylinus, 250 mM of either acetic acid or levulinic acid still allowed glucose metabolism and BNC production to occur. Complete suppression of glucose utilization and BNC production was observed after inclusion of 20 and 30 mM furfural and 5-hydroxymethylfurfural, respectively. The bacterium oxidized furfural and 5-hydroxymethylfurfural to furoic acid and 5-hydroxymethyl-2-furoic acid, respectively. The highest yields observed were 88% for furoic acid/furfural and 76% for 5-hydroxymethyl-2-furoic acid/5-hydroxymethylfurfural. These results are the first demonstration of the capability of G. xylinus to tolerate lignocellulose-derived inhibitors and to convert furan aldehydes.

  8. Thermal inactivation of Pediococcus sp. in simulated apple cider during high-temperature short-time pasteurization.

    PubMed

    Piyasena, P; McKellar, R C; Bartlett, F M

    2003-01-26

    Prompted by concerns regarding outbreaks of food-borne illness which have occurred due to the consumption of commercial, nonpasteurized fruit juices contaminated with Escherichia coli O157:H7, the US Food and Drug Administration and Canadian Food Inspection Agency are considering several new safety standards to apply to fresh juices, including mandatory pasteurization of all apple cider. In support of these initiatives, a study was conducted to evaluate the pasteurization of simulated cider using a heat-resistant nonpathogenic test bacterium, Pediococcus sp. NRRL B-2354. Thermal inactivation of the Pediococcus sp. was determined using a pilot scale high-temperature short-time (HTST) pasteurizer with a plate heat exchanger. The cumulative lethal effect, or pasteurization effect (PE), was obtained by converting times at different temperatures in the various sections of the pasteurizer to the equivalent time at the reference temperature (72 degrees C). PE was then related by a simple linear function to the log(10) of the percentage of viable counts with a power transformation of the PE values to improve linear fit. r(2) values for the four Pediococcus sp. trials varied from 0.921 to 0.981. Intertrial variation was incorporated into the model using @RISK simulation software. Output from simulations confirmed that treatment at 71 degrees C for 16 s can ensure a 5-log reduction of Pediococcus sp.

  9. Influence of yeast and lactic acid bacterium on the constituent profile of soy sauce during fermentation.

    PubMed

    Harada, Risa; Yuzuki, Masanobu; Ito, Kotaro; Shiga, Kazuki; Bamba, Takeshi; Fukusaki, Eiichiro

    2017-02-01

    Soy sauce is a Japanese traditional seasoning composed of various constituents that are produced by various microbes during a long-term fermentation process. Due to the complexity of the process, the investigation of the constituent profile during fermentation is difficult. Metabolomics, the comprehensive study of low molecular weight compounds in biological samples, is thought to be a promising strategy for deep understanding of the constituent contribution to food flavor characteristics. Therefore, metabolomics is suitable for the analysis of soy sauce fermentation. Unfortunately, only few and unrefined studies of soy sauce fermentation using metabolomics approach have been reported. Therefore, we investigated changes in low molecular weight hydrophilic and volatile compounds of soy sauce using gas chromatography/mass spectrometry (GC/MS)-based non-targeted metabolic profiling. The data were analyzed by statistical analysis to evaluate influences of yeast and lactic acid bacterium on the constituent profile. Consequently, our results suggested a novel finding that lactic acid bacterium affected the production of several constituents such as cyclotene, furfural, furfuryl alcohol and methional in the soy sauce fermentation process.

  10. Effect of Encapsulation on Viability of Pediococcus pentosaceus OZF During Its Passage Through the Gastrointestinal Tract Model.

    PubMed

    Kiran, Fadime; Mokrani, Mohamed; Osmanagaoglu, Ozlem

    2015-07-01

    The main goal of this study was to develop an improved oral delivery system for Pediococcus pentosaceus OZF, a promising probiotic bacterium, and to assess its viability under simulated gastrointestinal (GI) tract model by comparing the efficiency of microbiological and molecular approaches. Encapsulation was carried out using extrusion method and as a result, encapsulation system including 0.75 % lactulose, 1.8 % sodium alginate, 0.1 M CaCl2, and 5 min gelling time was shown to have a significantly protective effect against pH 2.0 acid stress over 3 h. However, completely loss of viability was exhibited by free OZF cells under similar conditions. To provide an additional barrier for capsules, coating process was investigated using different biopolymers, and the survival rates of free and encapsulated OZF cells upon expose to simulated GI conditions were detected by conventional culture techniques and propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR) method. No significant differences between the biopolymers were detected, except the chitosan which leads totally 85 % protection and extra 25 % improvement in the survival of OZF cells compared to uncoated capsules. In conclusion, our findings indicated that chitosan-coated capsules provided an important protective effect on the viability of OZF cells against the GI system conditions encountered during the transit of food. In addition, this study was found successful in monitoring the viable OZF cells in capsules using PMA-qPCR method.

  11. Eubacterium rangiferina, a novel usnic acid-resistant bacterium from the reindeer rumen

    NASA Astrophysics Data System (ADS)

    Sundset, Monica A.; Kohn, Alexandra; Mathiesen, Svein D.; Præsteng, Kirsti E.

    2008-08-01

    Reindeer are able to eat and utilize lichens as an important source of energy and nutrients. In the current study, the activities of antibiotic secondary metabolites including usnic, antranoric, fumarprotocetraric, and lobaric acid commonly found in lichens were tested against a collection of 26 anaerobic rumen bacterial isolates from reindeer ( Rangifer tarandus tarandus) using the agar diffusion method. The isolates were identified based on their 16S ribosomal ribonucleic acid (rRNA) gene sequences. Usnic acid had a potent antimicrobial effect against 25 of the isolates, belonging to Clostridiales, Enterococci, and Streptococci. Isolates of Clostridia and Streptococci were also susceptible to atranoric and lobaric acid. However, one isolate (R3_91_1) was found to be resistant to usnic, antranoric, fumarprotocetraric, and lobaric acid. R3_91_1 was also seen invading and adhering to lichen particles when grown in a liquid anaerobic culture as demonstrated by transmission electron microscopy. This was a Gram-negative, nonmotile rod (0.2-0.7 × 2.0-3.5 μm) with a deoxyribonucleic acid G + C content of 47.0 mol% and main cellular fatty acids including 15:0 anteiso-dimethyl acetal (DMA), 16:0 iso-fatty acid methyl ester (FAME), 13:0 iso-3OH FAME, and 17:0 anteiso-FAME, not matching any of the presently known profiles in the MIDI database. Combined, the phenotypic and genotypic traits including the 16S rRNA gene sequence show that R3_91_1 is a novel species inside the order Clostridiales within the family Lachnospiraceae, for which we propose the name Eubacterium rangiferina. This is the first record of a rumen bacterium able to tolerate and grow in the presence of usnic acid, indicating that the rumen microorganisms in these animals have adapted mechanisms to deal with lichen secondary metabolites, well known for their antimicrobial and toxic effects.

  12. Eubacterium rangiferina, a novel usnic acid-resistant bacterium from the reindeer rumen.

    PubMed

    Sundset, Monica A; Kohn, Alexandra; Mathiesen, Svein D; Praesteng, Kirsti E

    2008-08-01

    Reindeer are able to eat and utilize lichens as an important source of energy and nutrients. In the current study, the activities of antibiotic secondary metabolites including usnic, antranoric, fumarprotocetraric, and lobaric acid commonly found in lichens were tested against a collection of 26 anaerobic rumen bacterial isolates from reindeer (Rangifer tarandus tarandus) using the agar diffusion method. The isolates were identified based on their 16S ribosomal ribonucleic acid (rRNA) gene sequences. Usnic acid had a potent antimicrobial effect against 25 of the isolates, belonging to Clostridiales, Enterococci, and Streptococci. Isolates of Clostridia and Streptococci were also susceptible to atranoric and lobaric acid. However, one isolate (R3_91_1) was found to be resistant to usnic, antranoric, fumarprotocetraric, and lobaric acid. R3_91_1 was also seen invading and adhering to lichen particles when grown in a liquid anaerobic culture as demonstrated by transmission electron microscopy. This was a Gram-negative, nonmotile rod (0.2-0.7 x 2.0-3.5 microm) with a deoxyribonucleic acid G + C content of 47.0 mol% and main cellular fatty acids including 15:0 anteiso-dimethyl acetal (DMA), 16:0 iso-fatty acid methyl ester (FAME), 13:0 iso-3OH FAME, and 17:0 anteiso-FAME, not matching any of the presently known profiles in the MIDI database. Combined, the phenotypic and genotypic traits including the 16S rRNA gene sequence show that R3_91_1 is a novel species inside the order Clostridiales within the family Lachnospiraceae, for which we propose the name Eubacterium rangiferina. This is the first record of a rumen bacterium able to tolerate and grow in the presence of usnic acid, indicating that the rumen microorganisms in these animals have adapted mechanisms to deal with lichen secondary metabolites, well known for their antimicrobial and toxic effects.

  13. The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403

    PubMed Central

    Bolotin, Alexander; Wincker, Patrick; Mauger, Stéphane; Jaillon, Olivier; Malarme, Karine; Weissenbach, Jean; Ehrlich, S. Dusko; Sorokin, Alexei

    2001-01-01

    Lactococcus lactis is a nonpathogenic AT-rich gram-positive bacterium closely related to the genus Streptococcus and is the most commonly used cheese starter. It is also the best-characterized lactic acid bacterium. We sequenced the genome of the laboratory strain IL1403, using a novel two-step strategy that comprises diagnostic sequencing of the entire genome and a shotgun polishing step. The genome contains 2,365,589 base pairs and encodes 2310 proteins, including 293 protein-coding genes belonging to six prophages and 43 insertion sequence (IS) elements. Nonrandom distribution of IS elements indicates that the chromosome of the sequenced strain may be a product of recent recombination between two closely related genomes. A complete set of late competence genes is present, indicating the ability of L. lactis to undergo DNA transformation. Genomic sequence revealed new possibilities for fermentation pathways and for aerobic respiration. It also indicated a horizontal transfer of genetic information from Lactococcus to gram-negative enteric bacteria of Salmonella-Escherichia group. [The sequence data described in this paper has been submitted to the GenBank data library under accession no. AE005176.] PMID:11337471

  14. Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3

    PubMed Central

    Xiao, Jingfa; Hao, Lirui; Crowley, David E.; Zhang, Zhewen; Yu, Jun; Huang, Ning; Huo, Mingxin; Wu, Jiayan

    2015-01-01

    Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to degrade a variety of aromatic hydrocarbon compounds, although the degradation pathways and substrate versatilities remain largely unknown. Here we studied the bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon source. Genome sequencing of C. gilardii CR3 was carried out to elucidate possible mechanisms for the naphthenic acid biodegradation. The genome of C. gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of respectively 3,539,530 bp and 2,039,213 bp in size. The genome for strain CR3 encoded 4,502 putative protein-coding genes, 59 tRNA genes, and many other non-coding genes. Many genes were associated with xenobiotic biodegradation and metal resistance functions. Pathway prediction for degradation of cyclohexanecarboxylic acid, a representative naphthenic acid, suggested that naphthenic acid undergoes initial ring-cleavage, after which the ring fission products can be degraded via several plausible degradation pathways including a mechanism similar to that used for fatty acid oxidation. The final metabolic products of these pathways are unstable or volatile compounds that were not toxic to CR3. Strain CR3 was also shown to have tolerance to at least 10 heavy metals, which was mainly achieved by self-detoxification through ion efflux, metal-complexation and metal-reduction, and a powerful DNA self-repair mechanism. Our genomic analysis suggests that CR3 is well adapted to survive the harsh environment in natural asphalts containing naphthenic acids and high concentrations of heavy metals. PMID:26301592

  15. Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3.

    PubMed

    Wang, Xiaoyu; Chen, Meili; Xiao, Jingfa; Hao, Lirui; Crowley, David E; Zhang, Zhewen; Yu, Jun; Huang, Ning; Huo, Mingxin; Wu, Jiayan

    2015-01-01

    Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to degrade a variety of aromatic hydrocarbon compounds, although the degradation pathways and substrate versatilities remain largely unknown. Here we studied the bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon source. Genome sequencing of C. gilardii CR3 was carried out to elucidate possible mechanisms for the naphthenic acid biodegradation. The genome of C. gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of respectively 3,539,530 bp and 2,039,213 bp in size. The genome for strain CR3 encoded 4,502 putative protein-coding genes, 59 tRNA genes, and many other non-coding genes. Many genes were associated with xenobiotic biodegradation and metal resistance functions. Pathway prediction for degradation of cyclohexanecarboxylic acid, a representative naphthenic acid, suggested that naphthenic acid undergoes initial ring-cleavage, after which the ring fission products can be degraded via several plausible degradation pathways including a mechanism similar to that used for fatty acid oxidation. The final metabolic products of these pathways are unstable or volatile compounds that were not toxic to CR3. Strain CR3 was also shown to have tolerance to at least 10 heavy metals, which was mainly achieved by self-detoxification through ion efflux, metal-complexation and metal-reduction, and a powerful DNA self-repair mechanism. Our genomic analysis suggests that CR3 is well adapted to survive the harsh environment in natural asphalts containing naphthenic acids and high concentrations of heavy metals.

  16. Quantitative analysis of growth and volatile fatty acid production by the anaerobic ruminal bacterium Megasphaera elsdenii T81

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Megaspheara elsdenii T81 grew on either DL-lactate or D-glucose at similar rates (0.85 per h), but displayed major differences in the fermentation of these substrates. Lactate was fermented at up to 210-mM concentration to yield acetic, propionic, butyric, and valeric acids. The bacterium was able t...

  17. Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis subsp. lactis TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese

    PubMed Central

    Velly, H.; Abraham, A.-L.; Loux, V.; Delacroix-Buchet, A.; Fonseca, F.; Bouix, M.

    2014-01-01

    Lactococcus lactis is a lactic acid bacterium used in the production of many fermented foods, such as dairy products. Here, we report the genome sequence of L. lactis subsp. lactis TOMSC161, isolated from nonscalded curd pressed cheese. This genome sequence provides information in relation to dairy environment adaptation. PMID:25377704

  18. Complete genome sequence of Lactococcus lactis IO-1, a lactic acid bacterium that utilizes xylose and produces high levels of L-lactic acid.

    PubMed

    Kato, Hiroaki; Shiwa, Yuh; Oshima, Kenshiro; Machii, Miki; Araya-Kojima, Tomoko; Zendo, Takeshi; Shimizu-Kadota, Mariko; Hattori, Masahira; Sonomoto, Kenji; Yoshikawa, Hirofumi

    2012-04-01

    We report the complete genome sequence of Lactococcus lactis IO-1 (= JCM7638). It is a nondairy lactic acid bacterium, produces nisin Z, ferments xylose, and produces predominantly L-lactic acid at high xylose concentrations. From ortholog analysis with other five L. lactis strains, IO-1 was identified as L. lactis subsp. lactis.

  19. Lactobacillus formosensis sp. nov., a lactic acid bacterium isolated from fermented soybean meal.

    PubMed

    Chang, Chi-huan; Chen, Yi-sheng; Lee, Tzu-tai; Chang, Yu-chung; Yu, Bi

    2015-01-01

    A Gram-reaction-positive, catalase-negative, facultatively anaerobic, rod-shaped lactic acid bacterium, designated strain S215(T), was isolated from fermented soybean meal. The organism produced d-lactic acid from glucose without gas formation. 16S rRNA gene sequencing results showed that strain S215(T) had 98.74-99.60 % sequence similarity to the type strains of three species of the genus Lactobacillus (Lactobacillus farciminis BCRC 14043(T), Lactobacillus futsaii BCRC 80278(T) and Lactobacillus crustorum JCM 15951(T)). A comparison of two housekeeping genes, rpoA and pheS, revealed that strain S215(T) was well separated from the reference strains of species of the genus Lactobacillus. DNA-DNA hybridization results indicated that strain S215(T) had DNA related to the three type strains of species of the genus Lactobacillus (33-66 % relatedness). The DNA G+C content of strain S215(T) was 36.2 mol%. The cell walls contained peptidoglycan of the d-meso-diaminopimelic acid type and the major fatty acids were C18 : 1ω9c, C16 : 0 and C19 : 0 cyclo ω10c/C19 : 1ω6c. Phenotypic and genotypic features demonstrated that the isolate represents a novel species of the genus Lactobacillus, for which the name Lactobacillus formosensis sp. nov. is proposed. The type strain is S215(T) ( = NBRC 109509(T) = BCRC 80582(T)).

  20. A Highly Stable d-Amino Acid Oxidase of the Thermophilic Bacterium Rubrobacter xylanophilus

    PubMed Central

    Furukawara, Makoto; Omae, Keishi; Tadokoro, Namiho; Saito, Yayoi; Abe, Katsumasa; Kera, Yoshio

    2014-01-01

    d-Amino acid oxidase (DAO) is a biotechnologically attractive enzyme that can be used in a variety of applications, but its utility is limited by its relatively poor stability. A search of a bacterial genome database revealed a gene encoding a protein homologous to DAO in the thermophilic bacterium Rubrobacter xylanophilus (RxDAO). The recombinant protein expressed in Escherichia coli was a monomeric protein containing noncovalently bound flavin adenine dinucleotide as a cofactor. This protein exhibited oxidase activity against neutral and basic d-amino acids and was significantly inhibited by a DAO inhibitor, benzoate, but not by any of the tested d-aspartate oxidase (DDO) inhibitors, thus indicating that the protein is DAO. RxDAO exhibited higher activities and affinities toward branched-chain d-amino acids, with the highest specific activity toward d-valine and catalytic efficiency (kcat/Km) toward d-leucine. Substrate inhibition was observed in the case of d-tyrosine. The enzyme had an optimum pH range and temperature of pH 7.5 to 10 and 65°C, respectively, and was stable between pH 5.0 and pH 8.0, with a T50 (the temperature at which 50% of the initial enzymatic activity is lost) of 64°C. No loss of enzyme activity was observed after a 1-week incubation period at 30°C. This enzyme was markedly inactivated by phenylmethylsulfonyl fluoride but not by thiol-modifying reagents and diethyl pyrocarbonate, which are known to inhibit certain DAOs. These results demonstrated that RxDAO is a highly stable DAO and suggested that this enzyme may be valuable for practical applications, such as the determination and quantification of branched-chain d-amino acids, and as a scaffold to generate a novel DAO via protein engineering. PMID:25217016

  1. Cloning and expression of the malolactic gene of Pediococcus damnosus NCFB1832 in Saccharomyces cerevisiae.

    PubMed

    Bauer, Rolene; Volschenk, Heinrich; Dicks, Leon M T

    2005-09-10

    Wine production is characterized by a primary alcoholic fermentation, conducted by Saccharomyces cerevisiae, followed by a secondary malolactic fermentation (MLF). Although most lactic acid bacteria (LAB) have the ability to metabolize L-malate, only a few species survive the high ethanol and SO2 levels in wine. Wines produced in colder viticultural regions have a lower pH than wines produced in warmer regions. The decarboxylation of L-malate in these wines leads to an increase in pH, more organoleptic complexity and microbiological stability. MLF is, however, difficult to control and problems often occur during filtering of such wines. Pediococcus spp. are known to occur in high pH wines and have strong malolactic activity. However, some pediococci synthesize exocellular polysaccharides, which may lead to abnormal viscosity in wine. In this study, the malolactic gene from Pediococcus damnosus NCFB1832 (mleD) was cloned into S. cerevisiae and co-expressed with the malate permease gene (mae1) of Schizosaccharomyces pombe. Expression of the mleD gene was compared to the expression of two other malolactic genes, mleS from Lactococcus lactis MG1363 and mleA from Oenococcus oeni Lal1. The genetically modified strain of S. cerevisiae decreased the level of L-malate in grape must to less than 0.3 gl(-1) within 3 days. This is the first expression of a malolactic gene from Pediococcus in S. cerevisiae.

  2. Fermentation products of solvent tolerant marine bacterium Moraxella spp. MB1 and its biotechnological applications in salicylic acid bioconversion.

    PubMed

    Wahidullah, Solimabi; Naik, Deepak N; Devi, Prabha

    2013-01-01

    As part of a proactive approach to environmental protection, emerging issues with potential impact on the environment is the subject of ongoing investigation. One emerging area of environmental research concerns pharmaceuticals like salicylic acid, which is the main metabolite of various analgesics including aspirin. It is a common component of sewage effluent and also an intermediate in the degradation pathway of various aromatic compounds which are introduced in the marine environment as pollutants. In this study, biotransformation products of salicylic acid by seaweed, Bryopsis plumosa, associated marine bacterium, Moraxella spp. MB1, have been investigated. Phenol, conjugates of phenol and hydroxy cinnamic acid derivatives (coumaroyl, caffeoyl, feruloyl and trihydroxy cinnamyl) with salicylic acid (3-8) were identified as the bioconversion products by electrospray ionization mass spectrometry. These results show that the microorganism do not degrade phenolic acid but catalyses oxygen dependent transformations without ring cleavage. The degradation of salicylic acid is known to proceed either via gentisic acid pathway or catechol pathway but this is the first report of biotransformation of salicylic acid into cinnamates, without ring cleavage. Besides cinnamic acid derivatives (9-12), metabolites produced by the bacterium include antimicrobial indole (13) and β-carbolines, norharman (14), harman (15) and methyl derivative (16), which are beneficial to the host and the environment.

  3. Generation of Food-Grade Recombinant Lactic Acid Bacterium Strains by Site-Specific Recombination

    PubMed Central

    Martín, M. Cruz; Alonso, Juan C.; Suárez, Juan E.; Alvarez, Miguel A.

    2000-01-01

    The construction of a delivery and clearing system for the generation of food-grade recombinant lactic acid bacterium strains, based on the use of an integrase (Int) and a resolvo-invertase (β-recombinase) and their respective target sites (attP-attB and six, respectively) is reported. The delivery system contains a heterologous replication origin and antibiotic resistance markers surrounded by two directly oriented six sites, a multiple cloning site where passenger DNA could be inserted (e.g., the cI gene of bacteriophage A2), the int gene, and the attP site of phage A2. The clearing system provides a plasmid-borne gene encoding β-recombinase. The nonreplicative vector-borne delivery system was transformed into Lactobacillus casei ATCC 393 and, by site-specific recombination, integrated as a single copy in an orientation- and Int-dependent manner into the attB site present in the genome of the host strain. The transfer of the clearing system into this strain, with the subsequent expression of the β-recombinase, led to site-specific DNA resolution of the non-food-grade DNA. These methods were validated by the construction of a stable food-grade L. casei ATCC 393-derived strain completely immune to phage A2 infection during milk fermentation. PMID:10831443

  4. Rhizobium hidalgonense sp. nov., a nodule endophytic bacterium of Phaseolus vulgaris in acid soil.

    PubMed

    Yan, Jun; Yan, Hui; Liu, Li Xue; Chen, Wen Feng; Zhang, Xiao Xia; Verástegui-Valdés, Myrthala M; Wang, En Tao; Han, Xiao Zeng

    2017-01-01

    One Gram-negative, aerobic, motile, rod-shaped bacterium, designated as FH14(T), was isolated from nodules of Phaseolus vulgaris grown in Hidalgo State of Mexico. Results based upon 16S rRNA gene (≥99.8 % similarities to known species), concatenated sequence (recA, atpD and glnII) analysis of three housekeeping genes (≤93.4 % similarities to known species) and average nucleotide identity (ANI) values of genome sequence (ranged from 87.6 to 90.0 % to related species) indicated the distinct position of strain FH14(T) within the genus Rhizobium. In analyses of symbiotic genes, only nitrogen fixation gene nifH was amplified that had nucleotide sequence identical to those of the bean-nodulating strains in R. phaseoli and R. vallis, while nodulation gene nodC gene was not amplified. The failure of nodulation to its original host P. vulgaris and other legumes evidenced the loss of its nodulation capability. Strain FH14(T) contained summed feature 8 (C18:1 ω6c/C18:1 ω7c, 59.96 %), C16:0 (10.6 %) and summed feature 2 (C12:0 aldehyde/unknown 10.928, 10.24 %) as the major components of cellular fatty acids. Failure to utilize alaninamide, and utilizing L-alanine, L-asparagine and γ-amino butyric acid as carbon source, distinguished the strain FH14(T) from the type strains for the related species. The genome size and DNA G+C content of FH14(T) were 6.94 Mbp and 60.8 mol %, respectively. Based on those results, a novel specie in Rhizobium, named Rhizobium hidalgonense sp. nov., was proposed, with FH14(T) (=HAMBI 3636(T) = LMG 29288(T)) as the type strain.

  5. Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM

    PubMed Central

    Altermann, Eric; Russell, W. Michael; Azcarate-Peril, M. Andrea; Barrangou, Rodolphe; Buck, B. Logan; McAuliffe, Olivia; Souther, Nicole; Dobson, Alleson; Duong, Tri; Callanan, Michael; Lick, Sonja; Hamrick, Alice; Cano, Raul; Klaenhammer, Todd R.

    2005-01-01

    Lactobacillus acidophilus NCFM is a probiotic bacterium that has been produced commercially since 1972. The complete genome is 1,993,564 nt and devoid of plasmids. The average GC content is 34.71% with 1,864 predicted ORFs, of which 72.5% were functionally classified. Nine phage-related integrases were predicted, but no complete prophages were found. However, three unique regions designated as potential autonomous units (PAUs) were identified. These units resemble a unique structure and bear characteristics of both plasmids and phages. Analysis of the three PAUs revealed the presence of two R/M systems and a prophage maintenance system killer protein. A spacers interspersed direct repeat locus containing 32 nearly perfect 29-bp repeats was discovered and may provide a unique molecular signature for this organism. In silico analyses predicted 17 transposase genes and a chromosomal locus for lactacin B, a class II bacteriocin. Several mucus- and fibronectin-binding proteins, implicated in adhesion to human intestinal cells, were also identified. Gene clusters for transport of a diverse group of carbohydrates, including fructooligosaccharides and raffinose, were present and often accompanied by transcriptional regulators of the lacI family. For protein degradation and peptide utilization, the organism encoded 20 putative peptidases, homologs for PrtP and PrtM, and two complete oligopeptide transport systems. Nine two-component regulatory systems were predicted, some associated with determinants implicated in bacteriocin production and acid tolerance. Collectively, these features within the genome sequence of L. acidophilus are likely to contribute to the organisms' gastric survival and promote interactions with the intestinal mucosa and microbiota. PMID:15671160

  6. Recycling of carbon dioxide and acetate as lactic acid by the hydrogen-producing bacterium Thermotoga neapolitana.

    PubMed

    d'Ippolito, Giuliana; Dipasquale, Laura; Fontana, Angelo

    2014-09-01

    The heterotrophic bacterium Thermotoga neapolitana produces hydrogen by fermentation of sugars. Under capnophilic (carbon dioxide requiring) conditions, the process is preferentially associated with the production of lactic acid, which, as shown herein, is synthesized by reductive carboxylation of acetyl coenzyme A. The enzymatic coupling is dependent on the carbon dioxide stimulated activity of heterotetrameric pyruvate:ferredoxin oxidoreductase. Under the same culture conditions, T. neapolitana also operates the unfavorable synthesis of lactic acid from an exogenous acetate supply. This process, which requires carbon dioxide (or carbonate) and an unknown electron donor, allows for the conversion of carbon dioxide into added-value chemicals without biomass deconstruction.

  7. Identification and Characterization of a New 7-Aminocephalosporanic Acid Deacetylase from Thermophilic Bacterium Alicyclobacillus tengchongensis

    PubMed Central

    Ding, Jun-Mei; Yu, Ting-Ting; Han, Nan-Yu; Yu, Jia-Lin; Li, Jun-Jun; Yang, Yun-Juan; Tang, Xiang-Hua; Xu, Bo; Zhou, Jun-Pei

    2015-01-01

    ABSTRACT Deacetylation of 7-aminocephalosporanic acid (7-ACA) at position C-3 provides valuable starting material for producing semisynthetic β-lactam antibiotics. However, few enzymes have been characterized in this process before now. Comparative analysis of the genome of the thermophilic bacterium Alicyclobacillus tengchongensis revealed a hypothetical protein (EstD1) with typical esterase features. The EstD1 protein was functionally cloned, expressed, and purified from Escherichia coli BL21(DE3). It indeed displayed esterase activity, with optimal activity at around 65°C and pH 8.5, with a preference for esters with short-chain acyl esters (C2 to C4). Sequence alignment revealed that EstD1 is an SGNH hydrolase with the putative catalytic triad Ser15, Asp191, and His194, which belongs to carbohydrate esterase family 12. EstD1 can hydrolyze acetate at the C-3 position of 7-aminocephalosporanic acid (7-ACA) to form deacetyl-7-ACA, which is an important starting material for producing semisynthetic β-lactam antibiotics. EstD1 retained more than 50% of its initial activity when incubated at pH values ranging from 4 to 11 at 65°C for 1 h. To the best of our knowledge, this enzyme is a new SGNH hydrolase identified from thermophiles that is able to hydrolyze 7-ACA. IMPORTANCE Deacetyl cephalosporins are highly valuable building blocks for the industrial production of various kinds of semisynthetic β-lactam antibiotics. These compounds are derived mainly from 7-ACA, which is obtained by chemical or enzymatic processes from cephalosporin C. Enzymatic transformation of 7-ACA is the main method because of the adverse effects chemical deacylation brought to the environment. SGNH hydrolases are widely distributed in plants. However, the tools for identifying and characterizing SGNH hydrolases from bacteria, especially from thermophiles, are rather limited. Here, our work demonstrates that EstD1 belongs to the SGNH family and can hydrolyze acetate at the C-3 position of

  8. Influence of Artisan Bakery- or Laboratory-Propagated Sourdoughs on the Diversity of Lactic Acid Bacterium and Yeast Microbiotas

    PubMed Central

    Minervini, Fabio; Lattanzi, Anna; De Angelis, Maria; Gobbetti, Marco

    2012-01-01

    Seven mature type I sourdoughs were comparatively back-slopped (80 days) at artisan bakery and laboratory levels under constant technology parameters. The cell density of presumptive lactic acid bacteria and related biochemical features were not affected by the environment of propagation. On the contrary, the number of yeasts markedly decreased from artisan bakery to laboratory propagation. During late laboratory propagation, denaturing gradient gel electrophoresis (DGGE) showed that the DNA band corresponding to Saccharomyces cerevisiae was no longer detectable in several sourdoughs. Twelve species of lactic acid bacteria were variously identified through a culture-dependent approach. All sourdoughs harbored a certain number of species and strains, which were dominant throughout time and, in several cases, varied depending on the environment of propagation. As shown by statistical permutation analysis, the lactic acid bacterium populations differed among sourdoughs propagated at artisan bakery and laboratory levels. Lactobacillus plantarum, Lactobacillus sakei, and Weissella cibaria dominated in only some sourdoughs back-slopped at artisan bakeries, and Leuconostoc citreum seemed to be more persistent under laboratory conditions. Strains of Lactobacillus sanfranciscensis were indifferently found in some sourdoughs. Together with the other stable species and strains, other lactic acid bacteria temporarily contaminated the sourdoughs and largely differed between artisan bakery and laboratory levels. The environment of propagation has an undoubted influence on the composition of sourdough yeast and lactic acid bacterium microbiotas. PMID:22635989

  9. Enterococcus faecium QU 50: a novel thermophilic lactic acid bacterium for high-yield l-lactic acid production from xylose.

    PubMed

    Abdel-Rahman, Mohamed Ali; Tashiro, Yukihiro; Zendo, Takeshi; Sakai, Kenji; Sonomoto, Kenji

    2015-01-01

    Production of optically pure lactic acid from lignocellulosic material for commercial purposes is hampered by several difficulties, including heterofermentation of pentose sugars and high energy consumption by mesophilic lactic acid bacteria. Here, we report a novel lactic acid bacterium, strain QU 50, that has the potential to produce optically pure l-lactic acid (≥99.2%) in a homofermentative manner from xylose under thermophilic conditions. Strain QU 50 was isolated from Egyptian fertile soil and identified as Enterococcus faecium QU 50 by analyzing its sugar fermentation pattern and 16S rRNA gene sequence. Enterococcus faecium QU 50 fermented xylose efficiently to produce lactic acid over wide pH (6.0-10.0) and temperature ranges (30-52°C), with a pH of 6.5 and temperature of 50°C being optimal. To our knowledge, this is the first report of homofermentative lactic acid production from xylose by a thermophilic lactic acid bacterium.

  10. Fractionation of carbon isotopes in biosynthesis of fatty acids by a piezophilic bacterium Moritella japonica strain DSK1

    NASA Astrophysics Data System (ADS)

    Fang, Jiasong; Uhle, Maria; Billmark, Kaycie; Bartlett, Douglas H.; Kato, Chaki

    2006-04-01

    We examined stable carbon isotope fractionation in biosynthesis of fatty acids of a piezophilic bacterium Moritella japonica strain DSK1. The bacterium was grown to stationary phase at pressures of 0.1, 10, 20, and 50 MPa in media prepared using sterile-filtered natural seawater supplied with glucose as the sole carbon source. Strain DSK1 synthesized typical bacterial fatty acids (C 14-19 saturated, monounsaturated, and cyclopropane fatty acids) as well as long-chain polyunsaturated fatty acids (PUFA) (20:6 ω3). Bacterial cell biomass and individual fatty acids exhibited consistent pressure-dependent carbon isotope fractionations relative to glucose. The observed Δδ FA-glucose (-1.0‰ to -11.9‰) at 0.1 MPa was comparable to or slightly higher than fractionations reported in surface bacteria. However, bulk biomass and fatty acids became more depleted in 13C with pressure. Average carbon isotope fractionation (Δδ FA-glucose) at high pressures was much higher than that for surface bacteria: -15.7‰, -15.3‰, and -18.3‰ at 10, 20, and 50 MPa, respectively. PUFA were more 13C depleted than saturated and monounsaturated fatty acids at all pressures. The observed isotope effects may be ascribed to the kinetics of enzymatic reactions that are affected by hydrostatic pressure and to biosynthetic pathways that are different for short-chain and long-chain fatty acids. A simple quantitative calculation suggests that in situ piezophilic bacterial contribution of polyunsaturated fatty acids to marine sediments is nearly two orders of magnitude higher than that of marine phytoplankton and that the carbon isotope imprint of piezophilic bacteria can override that of surface phytoplankton. Our results have important implications for marine biogeochemistry. Depleted fatty acids reported in marine sediments and the water column may be derived simply from piezophilic bacteria resynthesis of organic matter, not from bacterial utilization of a 13C-depleted carbon source (i

  11. The amino acid sequence of the cytochrome c-554(547) from the chemolithotrophic bacterium Thiobacillus neapolitanus.

    PubMed Central

    Ambler, R P; Meyer, T E; Trudinger, P A; Kamen, M D

    1985-01-01

    An amino acid sequence is proposed for the cytochrome c-554(547) from the bacterium Thiobacillus neapolitanus N.C.I.B. 8539). It consists of a polypeptide chain of 91 residues, with a pair of haem-attachment cysteine residues at positions 15 and 18. There is similarity in sequence with each of the halves of the sequence of the dihaem cytochromes c4 and with a cytochrome c-554(548) from a halophilic strain of Paracoccus. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50127 (11 pages) at the British Library (Lending Division), Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1985) 225, 5. PMID:2988504

  12. Influence of phenolic compounds on the growth and arginine deiminase system in a wine lactic acid bacterium

    PubMed Central

    Alberto, María R.; de Nadra, María C. Manca; Arena, Mario E.

    2012-01-01

    The influence of seven phenolic compounds, normally present in wine, on the growth and arginine deiminase system (ADI) of Lactobacillus hilgardii X1B, a wine lactic acid bacterium, was established. This system provides energy for bacterial growth and produces citrulline that reacts with ethanol forming the carcinogen ethyl carbamate (EC), found in some wines. The influence of phenolic compounds on bacterial growth was compound dependent. Growth and final pH values increased in presence of arginine. Arginine consumption decreased in presence of protocatechuic and gallic acids (31 and 17%, respectively) and increased in presence of quercetin, rutin, catechin and the caffeic and vanillic phenolic acids (between 10 and 13%, respectively). ADI enzyme activities varied in presence of phenolic compounds. Rutin, quercetin and caffeic and vanillic acids stimulated the enzyme arginine deiminase about 37–40%. Amounts of 200 mg/L gallic and protocatechuic acids inhibited the arginine deiminase enzyme between 53 and 100%, respectively. Ornithine transcarbamylase activity was not modified at all concentrations of phenolic compounds. As gallic and protocatechuic acids inhibited the arginine deiminase enzyme that produces citrulline, precursor of EC, these results are important considering the formation of toxic compounds. PMID:24031815

  13. Influence of phenolic compounds on the growth and arginine deiminase system in a wine lactic acid bacterium.

    PubMed

    Alberto, María R; de Nadra, María C Manca; Arena, Mario E

    2012-01-01

    The influence of seven phenolic compounds, normally present in wine, on the growth and arginine deiminase system (ADI) of Lactobacillus hilgardii X1B, a wine lactic acid bacterium, was established. This system provides energy for bacterial growth and produces citrulline that reacts with ethanol forming the carcinogen ethyl carbamate (EC), found in some wines. The influence of phenolic compounds on bacterial growth was compound dependent. Growth and final pH values increased in presence of arginine. Arginine consumption decreased in presence of protocatechuic and gallic acids (31 and 17%, respectively) and increased in presence of quercetin, rutin, catechin and the caffeic and vanillic phenolic acids (between 10 and 13%, respectively). ADI enzyme activities varied in presence of phenolic compounds. Rutin, quercetin and caffeic and vanillic acids stimulated the enzyme arginine deiminase about 37-40%. Amounts of 200 mg/L gallic and protocatechuic acids inhibited the arginine deiminase enzyme between 53 and 100%, respectively. Ornithine transcarbamylase activity was not modified at all concentrations of phenolic compounds. As gallic and protocatechuic acids inhibited the arginine deiminase enzyme that produces citrulline, precursor of EC, these results are important considering the formation of toxic compounds.

  14. Purification, characterization, gene cloning and nucleotide sequencing of D: -stereospecific amino acid amidase from soil bacterium: Delftia acidovorans.

    PubMed

    Hongpattarakere, Tipparat; Komeda, Hidenobu; Asano, Yasuhisa

    2005-12-01

    The D-amino acid amidase-producing bacterium was isolated from soil samples using an enrichment culture technique in medium broth containing D-phenylalanine amide as a sole source of nitrogen. The strain exhibiting the strongest activity was identified as Delftia acidovorans strain 16. This strain produced intracellular D-amino acid amidase constitutively. The enzyme was purified about 380-fold to homogeneity and its molecular mass was estimated to be about 50 kDa, on sodium dodecyl sulfate polyacrylamide gel electrophoresis. The enzyme was active preferentially toward D-amino acid amides rather than their L-counterparts. It exhibited strong amino acid amidase activity toward aromatic amino acid amides including D-phenylalanine amide, D-tryptophan amide and D-tyrosine amide, yet it was not specifically active toward low-molecular-weight D-amino acid amides such as D-alanine amide, L-alanine amide and L-serine amide. Moreover, it was not specifically active toward oligopeptides. The enzyme showed maximum activity at 40 degrees C and pH 8.5 and appeared to be very stable, with 92.5% remaining activity after the reaction was performed at 45 degrees C for 30 min. However, it was mostly inactivated in the presence of phenylmethanesulfonyl fluoride or Cd2+, Ag+, Zn2+, Hg2+ and As3+ . The NH2 terminal and internal amino acid sequences of the enzyme were determined; and the gene was cloned and sequenced. The enzyme gene damA encodes a 466-amino-acid protein (molecular mass 49,860.46 Da); and the deduced amino acid sequence exhibits homology to the D-amino acid amidase from Variovorax paradoxus (67.9% identity), the amidotransferase A subunit from Burkholderia fungorum (50% identity) and other enantioselective amidases.

  15. Unusual fatty acid compositions of the hyperthermophilic archaeon Pyrococcus furiosus and the bacterium Thermotoga maritima.

    PubMed Central

    Carballeira, N M; Reyes, M; Sostre, A; Huang, H; Verhagen, M F; Adams, M W

    1997-01-01

    The fatty acid compositions of the hyperthermophilic microorganisms Thermotoga maritima and Pyrococcus furiosus were studied and compared. A total of 37 different fatty acids were identified in T. maritima, including the novel 13,14-dimethyloctacosanedioic acid. In contrast, a total of 18 different fatty acids were characterized, as minor components, in P. furiosus, and these included saturated, monounsaturated, and dicarboxylic acids. This is the first report of fatty acids from an archaeon. PMID:9098079

  16. Fractionation of Carbon Isotopes in Biosynthesis of Fatty Acids by A Piezophilic Bacterium Moritella Japonica DSK1

    NASA Astrophysics Data System (ADS)

    Fang, J.; Uhle, M.; Bartlett, D.; Kato, C.

    2005-12-01

    We examined stable carbon isotope fractionation in biosynthesis of fatty acids of a piezophilic bacterium Moritella japonica DSK1. DSK1 was grown to stationary phase at pressures of 0.1, 10, 20, and 50 MPa in media prepared using natural seawater supplied with glucose with the sole carbon source. DSk1 synthesized typical bacterial fatty acids (C14-19 saturated, monounsaturated, and cyclopropane fatty acids) as well as long-chain polyunsaturated fatty acids (PUFA) (20:6ω3). Bacterial cell biomass and individual fatty acids exhibited consistent pressure-dependent carbon isotope fractionations relative to glucose. The observed ΔδFA-glucose (-1.0 to -11.9%) at 0.1 MPa was comparable to or slightly higher than fractionations reported on surface bacteria. However, Bulk biomass and fatty acids became more depleted in 13C with pressure. Average carbon isotope fractionation ΔδFA-glucose) at high pressures was much higher than that for surface bacteria: -15.7, -15.3, and -18.3‰ at 10, 20, and 50 MPa, respectively. PUFA were more 13C depleted than saturated and monounsaturated fatty acids at all pressures. The observed isotope effects may be ascribed to the kinetics of enzymatic reactions affected by hydrostatic pressure and to different biosynthetic pathways for short-chain and long-chain fatty acids. Our results have important implications for marine biogeochemistry. The 13C depleted fatty acids in marine sediments and water column may be derived simply from piezophilic bacteria resynthesis of organic matter, not from bacterial utilization of a 13C-depleted carbon source (i.e., methane). The interpretation of carbon isotope signatures of marine lipids must be based on principles derived from piezophilic bacteria.

  17. Dietary supplementation of Pediococcus pentosaceus enhances innate immunity, physiological health and resistance to Vibrio anguillarum in orange-spotted grouper (Epinephelus coioides).

    PubMed

    Huang, Jian-Bin; Wu, Yu-Chi; Chi, Shau-Chi

    2014-08-01

    Groupers (Epinephelus spp.) are economically important fish species in Southeast Asian aquaculture. Vibriosis caused by Vibro spp. is one of the severe bacterial diseases that devastate the grouper aquaculture industry. Probiotics have been reported to show the potential to enhance fish immunity and to antagonize pathogens. In our previous study, a lactic acid bacterium Pediococcus pentosaceus strain 4012 (LAB4012), isolated from cobia intestine, protects cobia from photobacteriosis after a 2-week feeding. In this study, we examined the potential of LAB4012 to be a probiotic for the orange-spotted grouper through feeding, thus to guard against vibriosis. In vitro, LAB4012 culture supernatant with low pH suppressed the growth of Vibrio anguillarum, and lactic acid in the metabolite of LAB4012 appeared to be the major factor to the growth inhibition of V. anguillarum. In vivo, the challenge test showed that the cumulative mortality of the LAB4012-fed groupers was significantly lower than that of the control fish after V. anguillarum infection. Supplementation of LAB4012 in commercial diet not only enhanced the growth rate and erythrocyte numbers of the groupers, but also regulated the gene expression of the pro-/anti-inflammatory cytokines. One day post-infection of V. anguillarum, the leukocyte numbers in the peripheral blood and the phagocytic activity of the head-kidney phagocytes in the LAB4012-fed groupers were found significantly increased, when compared with those without LAB4012-feeding. These results suggested that LAB4012 can be a dietary probiotic for groupers in modulating the immunity and protecting the groupers from V. anguillarum infection.

  18. Identification of an Arachidonic Acid-Producing Bacterium and Description of Kineococcus arachidonicus sp. nov.

    SciTech Connect

    Fliermans, C.B.

    2001-05-15

    The identification of bacterial with the ability to produce polyunsaturated fatty acids as been limited almost exclusively to gram-negative, psychrophilic, marine microorganisms. Here we describe a new gram-type-positive bactgerium, strain SRS30216T, that produces the polyunsaturated fatty acid, arachidonic acid, and is neither psychrophilic nor a marine isolate.

  19. Isolation and characterization of Halomonas sp. strain IMPC, a p-coumaric acid-metabolizing bacterium that decarboxylates other cinnamic acids under hypersaline conditions.

    PubMed

    Abdelkafi, Slim; Labat, Marc; Casalot, Laurence; Chamkha, Mohamed; Sayadi, Sami

    2006-02-01

    A moderately halophilic, mesophilic, Gram-negative, motile, nonsporulating bacterium, designated strain IMPC, was isolated from a table-olive fermentation rich in aromatic compounds, after enrichment on p-coumaric acid under halophilic conditions. Strain IMPC was able to degrade p-coumaric acid. p-hydroxybenzaldehyde and p-hydroxybenzoic acid were detected as breakdown products from p-coumaric acid. Protocatechuic acid was identified as the final aromatic product of p-coumaric acid catabolism before ring fission. Strain IMPC transformed various cinnamic acids with substituent H, OH, CH(3) or OCH(3) in the para- and/or meta-position of the aromatic ring to the corresponding benzoic acids, indicating a specific selection. A beta-oxidation pathway was proposed for these transformations. Phylogenetic analysis of the 16S rRNA gene revealed that this isolate was a member of the genus Halomonas. Strain IMPC was closely related to Halomonas elongata ATCC 33173(T)and Halomonas eurihalina ATCC 49336(T).

  20. A CMP-N-acetylneuraminic acid synthetase purified from a marine bacterium, Photobacterium leiognathi JT-SHIZ-145.

    PubMed

    Kajiwara, Hitomi; Mine, Toshiki; Miyazaki, Tatsuo; Yamamoto, Takeshi

    2011-01-01

    A cytidine 5'-monophospho-N-acetylneuraminic acid (CMP-Neu5Ac) synthetase was found in a crude extract prepared from Photobacterium leiognathi JT-SHIZ-145, a marine bacterium that also produces a β-galactoside α2,6-sialyltransferase. The CMP-Neu5Ac synthetase was purified from the crude extract of the cells by a combination of anion-exchange and gel filtration column chromatography. The purified enzyme migrated as a single band (60 kDa) on sodium dodecylsulfate-polyacrylamide gel electrophoresis. The activity of the enzyme was maximal at 35 °C at pH 9.0, and the synthetase required Mg(2+) for activity. Although these properties are similar to those of other CMP-Neu5Ac synthetases isolated from bacteria, this synthetase produced not only CMP-Neu5Ac from cytidine triphosphate and Neu5Ac, but also CMP-N-glycolylneuraminic acid from cytidine triphosphate and N-glycolylneuraminic acid, unlike CMP-Neu5Ac synthetase purified from Escherichia coli.

  1. Elongation of exogenous fatty acids by the bioluminescent bacterium Vibrio harveyi

    SciTech Connect

    Byers, D.M.

    1989-01-01

    Bioluminescent bacteria require myristic acid (C14:0) to produce the myristaldehyde substrate of the light-emitting luciferase reaction. Since both endogenous and exogenous C14:0 can be used for this purpose, the metabolism of exogenous fatty acids by luminescent bacteria has been investigated. Both Vibrio harveyi and Vibrio fischeri incorporated label from (1-14C)myristic acid (C14:0) into phospholipid acyl chains as well as into CO2. In contrast, Photobacterium phosphoreum did not exhibit phospholipid acylation or beta-oxidation using exogenous fatty acids. Unlike Escherichia coli, the two Vibrio species can directly elongate fatty acids such as octanoic (C8:0), lauric (C12:0), and myristic acid, as demonstrated by radio-gas liquid chromatography. The induction of bioluminescence in late exponential growth had little effect on the ability of V. harveyi to elongate fatty acids, but it did increase the amount of C14:0 relative to C16:0 labeled from (14C)C8:0. This was not observed in a dark mutant of V. harveyi that is incapable of supplying endogenous C14:0 for luminescence. Cerulenin preferentially decreased the labeling of C16:0 and of unsaturated fatty acids from all 14C-labeled fatty acid precursors as well as from (14C)acetate, suggesting that common mechanisms may be involved in elongation of fatty acids from endogenous and exogenous sources. Fatty acylation of the luminescence-related synthetase and reductase enzymes responsible for aldehyde synthesis exhibited a chain-length preference for C14:0, which also was indicated by reverse-phase thin-layer chromatography of the acyl groups attached to these enzymes. The ability of V. harveyi to activate and elongate exogenous fatty acids may be related to an adaptive requirement to metabolize intracellular C14:0 generated by the luciferase reaction during luminescence development.

  2. Development of plasmid vector and electroporation condition for gene transfer in sporogenic lactic acid bacterium, Bacillus coagulans.

    PubMed

    Rhee, Mun Su; Kim, Jin-Woo; Qian, Yilei; Ingram, L O; Shanmugam, K T

    2007-07-01

    Bacillus coagulans is a sporogenic lactic acid bacterium that ferments glucose and xylose, major components of plant biomass, a potential feedstock for cellulosic ethanol. The temperature and pH for optimum rate of growth of B. coagulans (50 to 55 degrees C, pH 5.0) are very similar to that of commercially developed fungal cellulases (50 degrees C; pH 4.8). Due to this match, simultaneous saccharification and fermentation (SSF) of cellulose to products by B. coagulans is expected to require less cellulase than needed if the SSF is conducted at a sub-optimal temperature, such as 30 degrees C, the optimum for yeast, the main biocatalyst used by the ethanol industry. To fully exploit B. coagulans as a platform organism, we have developed an electroporation method to transfer plasmid DNA into this genetically recalcitrant bacterium. We also constructed a B. coagulans/E. coli shuttle vector, plasmid pMSR10 that contains the rep region from a native plasmid (pMSR0) present in B. coagulans strain P4-102B. The native plasmid, pMSR0 (6823bp), has 9 ORFs, and replicates by rolling-circle mode of replication. Plasmid pNW33N, developed for Geobacillus stearothermophilus, was also transformed into this host and stably maintained while several other Bacillus/Escherichia coli shuttle vector plasmids were not transformed into B. coagulans. The transformation efficiency of B. coagulans strain P4-102B using the plasmids pNW33N or pMSR10 was about 1.5x10(16) per mole of DNA. The availability of shuttle vectors and an electroporation method is expected to aid in genetic and metabolic engineering of B. coagulans.

  3. RT-qPCR analysis of putative beer-spoilage gene expression during growth of Lactobacillus brevis BSO 464 and Pediococcus claussenii ATCC BAA-344(T) in beer.

    PubMed

    Bergsveinson, Jordyn; Pittet, Vanessa; Ziola, Barry

    2012-10-01

    Lactic acid bacteria (LAB) contamination of beer presents a continual economic threat to brewers. Interestingly, only certain isolates of LAB can grow in the hostile beer environment (e.g., as studied here, Lactobacillus brevis BSO 464 (Lb464) and a non-ropy isolate of Pediococcus claussenii ATCC BAA-344(T) (Pc344NR)), indicating that significant genetic specialization is required. The genes hitA, horA, horB, horC, and bsrA, which have been proposed to confer beer-spoiling ability to an organism, are suspected of counteracting the antimicrobial effects of hops. However, these genes are not present in the same combination (if at all) across beer-spoiling organisms. As such, we sought to investigate the extent to which these genes participate during Lb464 and Pc344NR mid-logarithmic growth in beer through reverse transcription quantitative PCR analysis. We first determined the optimal reference gene set needed for data normalization and, for each bacterium, established that two genes were needed for accurate assessment of gene expression. Following this, we found that horA expression was induced for Pc344NR, but not for Lb464, during growth in beer. Instead, horC expression was dramatically increased in Lb464 when growing in beer, whereas no change was detected for the other putative beer-spoilage-related genes. This indicates that HorC may be one of the principle mediators enabling growth of Lb464 in beer, whereas in Pc344NR, this may be attributable to HorA. These findings not only reveal that Lb464 and Pc344NR are unique in their beer-specific genetic expression profile but also indicate that a range of genetic specialization exists among beer-spoilage bacteria.

  4. Bile acids are new products of a marine bacterium, Myroides sp. strain SM1.

    PubMed

    Maneerat, Suppasil; Nitoda, Teruhiko; Kanzaki, Hiroshi; Kawai, Fusako

    2005-06-01

    Strain SM1 was isolated as a biosurfactant-producing microorganism from seawater and presumptively identified as Myroides sp., based on morphology, biochemical characteristics and 16S rDNA sequence. The strain produced surface-active compounds in marine broth, which were purified, using emulsification activity for n-hexadecane as an indicator. The purified compounds were identified by thin-layer chromatography, (1)H- and (13)C-NMR spectra and fast atom bombardment mass spectrometry as cholic acid, deoxycholic acid and their glycine conjugates. Type strains of the genus Myroides, M. odoratus JCM7458 and M. odoramitimus JCM7460, also produced these compounds. Myroides sp. strain SM1 possessed a biosynthetic route to cholic acid from cholesterol. Thus, bile acids were found as new products of prokaryotic cells, genus Myroides.

  5. Complete genome sequence of Enterococcus mundtii QU 25, an efficient L-(+)-lactic acid-producing bacterium.

    PubMed

    Shiwa, Yuh; Yanase, Hiroaki; Hirose, Yuu; Satomi, Shohei; Araya-Kojima, Tomoko; Watanabe, Satoru; Zendo, Takeshi; Chibazakura, Taku; Shimizu-Kadota, Mariko; Yoshikawa, Hirofumi; Sonomoto, Kenji

    2014-08-01

    Enterococcus mundtii QU 25, a non-dairy bacterial strain of ovine faecal origin, can ferment both cellobiose and xylose to produce l-lactic acid. The use of this strain is highly desirable for economical l-lactate production from renewable biomass substrates. Genome sequence determination is necessary for the genetic improvement of this strain. We report the complete genome sequence of strain QU 25, primarily determined using Pacific Biosciences sequencing technology. The E. mundtii QU 25 genome comprises a 3 022 186-bp single circular chromosome (GC content, 38.6%) and five circular plasmids: pQY182, pQY082, pQY039, pQY024, and pQY003. In all, 2900 protein-coding sequences, 63 tRNA genes, and 6 rRNA operons were predicted in the QU 25 chromosome. Plasmid pQY024 harbours genes for mundticin production. We found that strain QU 25 produces a bacteriocin, suggesting that mundticin-encoded genes on plasmid pQY024 were functional. For lactic acid fermentation, two gene clusters were identified-one involved in the initial metabolism of xylose and uptake of pentose and the second containing genes for the pentose phosphate pathway and uptake of related sugars. This is the first complete genome sequence of an E. mundtii strain. The data provide insights into lactate production in this bacterium and its evolution among enterococci.

  6. Characterization of a nitroreductase with selective nitroreduction properties in the food and intestinal lactic acid bacterium Lactobacillus plantarum WCFS1.

    PubMed

    Guillén, Hugo; Curiel, Jose Antonio; Landete, José María; Muñoz, Rosario; Herraiz, Tomás

    2009-11-11

    Nitroreductases reduce nitroaromatic compounds and other oxidants in living organisms, having interesting implications in environmental and human health. A putative nitrobenzoate reductase encoding gene (lp_0050) was recently annotated in the completed DNA sequence of lactic acid bacterium Lactobacillus plantarum WCFS1 strain. In this research, this L. plantarum gene was cloned and expressed, and the corresponding protein (PnbA) was biochemically characterized. This L. plantarum PnbA reductase is a 216 amino acid residue FMN-flavoprotein, which exhibits 23% identity with Pseudomonas putida and Ralstonia eutropha nitroreductases and <11% identity with those from enterobacteria such as E. cloacae . This reductase also showed 32-43% identity (65-72% similarity) to predicted PnbA proteins from other lactic acid bacteria. It utilized a wide range of electron acceptors including dichlorophenolindophenol (DCPIP), nitroblue tetrazolium (NBT), ferricyanide, and quinones (menadione, benzoquinone), but not pyridinium cations (paraquat and N-methyl-beta-carbolines), and it was inhibited by dicoumarol and diphenyliodonium. HPLC-MS and spectroscopic data showed that it specifically catalyzed the reduction of the 4-nitroaromatic group to the corresponding hydroxylamine in the presence of NAD(P)H. Kinetics parameters (V(max) and K(m)) showed a higher efficiency for the reduction of 2,4-dinitrobenzoate than for the reduction of 4-nitrobenzoate. It was chemoselective for the reduction of 4-nitrobenzoates, being unable to reduce other nitroaromatics. Then, L. plantarum PnbA reductase might be more specific than other microbial nitroreductases that reduce a wider range of nitroaromatic compounds. The physiological and functional role of nitroreductases remain unknown; however, their presence in lactic acid bacteria widely occurring in foods and the human intestinal tract should be of further interest.

  7. Gluconic acid production and phosphate solubilization by the plant growth-promoting bacterium Azospirillum spp.

    NASA Astrophysics Data System (ADS)

    Rodriguez, Hilda; Gonzalez, Tania; Goire, Isabel; Bashan, Yoav

    2004-11-01

    In vitro gluconic acid formation and phosphate solubilization from sparingly soluble phosphorus sources by two strains of the plant growth-promoting bacteria A. brasilense (Cd and 8-I) and one strain of A. lipoferum JA4 were studied. Strains of A. brasilense were capable of producing gluconic acid when grown in sparingly soluble calcium phosphate medium when their usual fructose carbon source is amended with glucose. At the same time, there is a reduction in pH of the medium and release of soluble phosphate. To a greater extent, gluconic acid production and pH reduction were observed for A. lipoferum JA4. For the three strains, clearing halos were detected on solid medium plates with calcium phosphate. This is the first report of in vitro gluconic acid production and direct phosphate solubilization by A. brasilense and the first report of P solubilization by A. lipoferum. This adds to the very broad spectrum of plant growth-promoting abilities of this genus.

  8. Gluconacetobacter kakiaceti sp. nov., an acetic acid bacterium isolated from a traditional Japanese fruit vinegar.

    PubMed

    Iino, Takao; Suzuki, Rei; Tanaka, Naoto; Kosako, Yoshimasa; Ohkuma, Moriya; Komagata, Kazuo; Uchimura, Tai

    2012-07-01

    Two novel acetic acid bacteria, strains G5-1(T) and I5-1, were isolated from traditional kaki vinegar (produced from fruits of kaki, Diospyros kaki Thunb.), collected in Kumamoto Prefecture, Japan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains G5-1(T) and I5-1 formed a distinct subline in the genus Gluconacetobacter and were closely related to Gluconacetobacter swingsii DST GL01(T) (99.3% 16S rRNA gene sequence similarity). The isolates showed 96-100% DNA-DNA relatedness with each other, but <53% DNA-DNA relatedness with closely related members of the genus Gluconacetobacter. The isolates could be distinguished from closely related members of the genus Gluconacetobacter by not producing 2- and 5-ketogluconic acids from glucose, producing cellulose, growing without acetic acid and with 30% (w/v) d-glucose, and producing acid from sugars and alcohols. Furthermore, the genomic DNA G+C contents of strains G5-1(T) and I5-1 were a little higher than those of their closest phylogenetic neighbours. On the basis of the phenotypic characteristics and phylogenetic position, strains G5-1(T) and I5-1 are assigned to a novel species, for which the name Gluconacetobacter kakiaceti sp. nov. is proposed; the type strain is G5-1(T) (=JCM 25156(T)=NRIC 0798(T)=LMG 26206(T)).

  9. Gluconacetobacter maltaceti sp. nov., a novel vinegar producing acetic acid bacterium.

    PubMed

    Slapšak, Nina; Cleenwerck, Ilse; De Vos, Paul; Trček, Janja

    2013-02-01

    Comparison of HaeIII- and HpaII-restriction profiles of PCR-amplified 16S-23S rDNA ITS regions of Gluconacetobacter sp. LMG 1529(T) and SKU 1109 with restriction profiles of reference strains of acetic acid bacteria described by Trček and Teuber [34] revealed the same but unique restriction profiles for LMG 1529(T) and SKU 1109. Further analyses of nearly complete 16S rRNA gene sequences, nearly complete 16S-23S rDNA ITS sequences, as well as concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, allocated both strains to a single phylogenetic cluster well separated from the other species of the genus Gluconacetobacter. DNA-DNA hybridizations confirmed their novel species identity by 73% DNA-DNA relatedness between both strains, and values below the species level (<70%) between SKU 1109 and the type strains of the closest phylogenetic neighbors. The classification of strains LMG 1529(T) and SKU 1109 into a single novel species was confirmed also by AFLP and (GTG)(5)-PCR DNA fingerprinting data, as well as by phenotypic data. Strains LMG 1529(T) and SKU 1109 can be differentiated from their closely related Gluconacetobacter species, Gluconacetobacter entanii and Gluconacetobacter hansenii, by their ability to form 2-keto-d-gluconic acid from d-glucose, their ability to use d-mannitol, d-gluconate and glycerol as carbon source and form acid from d-fructose, and their ability to grow without acetic acid. The major fatty acid of LMG 1529(T) and SKU 1109 is C(18:1ω7c) (60.2-64.8%). The DNA G+C content of LMG 1529(T) and SKU 1109 is 62.5 and 63.3mol% respectively. The name Gluconacetobacter maltaceti sp. nov. is proposed. The type strain is LMG 1529(T) (=NBRC 14815(T)=NCIMB 8752(T)).

  10. Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop.

    PubMed

    Li, Leilei; Praet, Jessy; Borremans, Wim; Nunes, Olga C; Manaia, Célia M; Cleenwerck, Ilse; Meeus, Ivan; Smagghe, Guy; De Vuyst, Luc; Vandamme, Peter

    2015-01-01

    In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as Asaia astilbis or as 'Commensalibacter intestini', except for two isolates (R-52486 and LMG 28161(T)) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161(T) was determined and showed the highest pairwise similarity to Saccharibacter floricola S-877(T) (96.5%), which corresponded with genus level divergence in the family Acetobacteraceae. Isolate LMG 28161(T) was subjected to whole-genome shotgun sequencing; a 16S-23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family Acetobacteraceae. The DNA G+C content of strain LMG 28161(T) was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161(T) were similar to those of established AAB species [with C18:1ω7c (43.1%) as the major component], but the amounts of fatty acids such as C19:0 cyclo ω8c, C14:0 and C14:0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161(T) ( =DSM 28636(T) =R-52487(T)) as the type strain of the type species.

  11. Oxidation of nitrapyrin to 6-chloropicolinic acid by the ammonia-oxidizing bacterium nitrosomonas europaea

    SciTech Connect

    Vannelli, T.; Hooper, A.B.

    1992-07-01

    Suspensions of Nitrosomonas europaea catalyzed the oxidation of the commercial nitrification inhibitor nitrapyrin (2-chloro-6-(trichloromethyl)-pyridine). Rapid oxidation of nitrapyrin (at a concentration of 10 microM) required the concomitant oxidation of ammonia, hydroxylamine, or hydrazine. The turnover rate was highest in the presence of 10 mM ammonia (0.8 nmol of nitrapyrin per min/mg of protein). The product of the reaction was 6-chloropicolinic acid. By the use of (18)O2, it was shown that one of the oxygens in 6-chloropicolinic acid came from diatomic oxygen and that the other came from water. Approximately 13% of the radioactivity of (2,6-(14)C) nitrapyrin was shown to bind to cells. Most (94%) of the latter was bound indiscriminately to membrane proteins. The nitrapyrin bound to membrane proteins may account for the observed inactivation of ammonia oxidation. (Copyright (c) 1992, American Society for Microbiology.)

  12. Biodegradation of Picolinic Acid by a Newly Isolated Bacterium Alcaligenes faecalis Strain JQ135.

    PubMed

    Qiu, Jiguo; Zhang, Junjie; Zhang, Yanting; Wang, Yuhong; Tong, Lu; Hong, Qing; He, Jian

    2017-04-01

    We isolated a bacterial strain JQ135 from municipal wastewater, which was capable of efficiently degrading picolinic acid (PA). Based on the physico-biochemical characteristics and 16S rDNA analysis, strain JQ135 was identified as Alcaligenes faecalis. In addition, strain JQ135 produced an orange pigment when cultured in the Luria-Bertani medium, which is different from the previously reported strains of A. faecalis. During the degradation of PA by the resting strain JQ135 cells, only one intermediate, 6-hydroxypicolinic acid (6HPA), was detected by ultraviolet spectrophotometry, high-pressure liquid chromatography, and liquid chromatography-mass spectrometry. A random transposon mutagenesis library of strain JQ135 was constructed. One mutant, Mut-G31, could convert PA into 6HPA without further degradation. The disrupted gene (orf2) was amplified from Mut-G31, and its product showed 32% identity to the 3-deoxy-D-manno-octulosonic acid kinase (KdkA) from Haemophilus influenzae. Results from complementation analysis confirmed that GTG was the initiation codon of the kdkA-like orf2, and that it was essential for PA biodegradation by strain JQ135. This study provides the first genetic evidence for the bacterial degradation of PA.

  13. Lactococcus piscium: a psychrotrophic lactic acid bacterium with bioprotective or spoilage activity in food-a review.

    PubMed

    Saraoui, T; Leroi, F; Björkroth, J; Pilet, M F

    2016-10-01

    The genus Lactococcus comprises 12 species, some known for decades and others more recently described. Lactococcus piscium, isolated in 1990 from rainbow trout, is a psychrotrophic lactic acid bacterium, probably disregarded because most of the strains are unable to grow at 30°C. During the last 10 years, this species has been isolated from a large variety of food: meat, seafood and vegetables, mostly packed under vacuum (VP) or modified atmosphere (MAP) and stored at chilled temperature. Recently, culture-independent techniques used for characterization of microbial ecosystems have highlighted the importance of Lc. piscium in food. Its role in food spoilage varies according to the strain and the food matrix. However, most studies have indicated that Lc. piscium spoils meat, whereas it does not degrade the sensory properties of seafood. Lactococcus piscium strains have a large antimicrobial spectrum, including Gram-positive and negative bacteria. In various seafoods, some strains have a protective effect against spoilage and can extend the sensory shelf-life of the products. They can also inhibit the growth of Listeria monocytogenes, by a cell-to-cell contact-dependent. This article reviews the physiological and genomic characteristics of Lc. piscium and discusses its spoilage or protective activities in food.

  14. Reduction of Cr(VI) under acidic conditions by the facultative Fe(III)-reducing bacterium Acidiphilium cryptum

    SciTech Connect

    David E. Cummings; Scott Fendorf; Rajesh K. Sani; Brent M. Peyton; Timothy S. Magnuson

    2007-01-01

    The potential for biological reduction of Cr(VI) under acidic conditions was evaluated with the acidophilic, facultatively metal-reducing bacterium Acidiphilium cryptum strain JF-5 to explore the role of acidophilic microorganisms in the Cr cycle in low-pH environments. An anaerobic suspension of washed A. cryptum cells rapidly reduced 50 M Cr(VI) at pH 3.2; biological reduction was detected from pH 1.7-4.7. The reduction product, confirmed by XANES analysis, was entirely Cr(III) that was associated predominantly with the cell biomass (70-80%) with the residual residing in the aqueous phase. Reduction of Cr(VI) showed a pH optimum similar to that for growth and was inhibited by 5 mM HgCl2, suggesting that the reaction was enzyme-mediated. Introduction of O2 into the reaction medium slowed the reduction rate only slightly, whereas soluble Fe(III) (as ferric sulfate) increased the rate dramatically, presumably by the shuttling of electrons from bioreduced Fe(II) to Cr(VI) in a coupled biotic-abiotic cycle. Starved cells could not reduce Cr(VI) when provided as sole electron acceptor, indicating that Cr(VI) reduction is not an energy-conserving process in A. cryptum. We speculate, rather, that Cr(VI) reduction is used here as a detoxification mechanism.

  15. Distribution and Functions of Phosphotransferase System Genes in the Genome of the Lactic Acid Bacterium Oenococcus oeni

    PubMed Central

    Jamal, Zohra; Miot-Sertier, Cécile; Thibau, François; Dutilh, Lucie; Lonvaud-Funel, Aline; Ballestra, Patricia; Le Marrec, Claire

    2013-01-01

    Oenococcus oeni, the lactic acid bacterium primarily responsible for malolactic fermentation in wine, is able to grow on a large variety of carbohydrates, but the pathways by which substrates are transported and phosphorylated in this species have been poorly studied. We show that the genes encoding the general phosphotransferase proteins, enzyme I (EI) and histidine protein (HPr), as well as 21 permease genes (3 isolated ones and 18 clustered into 6 distinct loci), are highly conserved among the strains studied and may form part of the O. oeni core genome. Additional permease genes differentiate the strains and may have been acquired or lost by horizontal gene transfer events. The core pts genes are expressed, and permease gene expression is modulated by the nature of the bacterial growth substrate. Decryptified O. oeni cells are able to phosphorylate glucose, cellobiose, trehalose, and mannose at the expense of phosphoenolpyruvate. These substrates are present at low concentrations in wine at the end of alcoholic fermentation. The phosphotransferase system (PTS) may contribute to the perfect adaptation of O. oeni to its singular ecological niche. PMID:23524676

  16. The effect of humic acid on uptake/adsorption of copper by a marine bacterium and two marine ciliates.

    PubMed

    Lores, E M; Snyder, R A; Pennock, J R

    1999-01-01

    The effect of humic acid (HA) on Cu uptake by a bacterium and two bacterivorus ciliates was investigated. The presence of HA resulted in a statistically significant (p<0.001) decrease in Cu associated with bacteria that were exposed to 67 microg Cu L(-1). Complexation of Cu appears to lower the availability of Cu with respect to bacterial cell surface binding and uptake. For ciliates, 10 mg HA L(-1) significantly reduced uptake of Cu by Uronema, but did not reduce uptake of Cu by Pleuronema. Uronema exposed to 67 microg Cu L(-1) accumulated 54% less Cu when 10 mg HA L(-1) was present (0.50 pg ciliate(-1) vs 0.23 pg ciliate(-1)). Uronema feeding on V. natriegens, took up less than half as much Cu as unfed Uronema when exposed to Cu without HA (0.41 pg Cu fed ciliate(-1) vs 0.86 pg Cu unfed ciliate(-1), but only 40% less when exposed to Cu and HA (0.31 pg Cu fed ciliate(-1) vs 0.51 pg Cu unfed ciliate(-1)). The lower % reduction attributable to fed ciliates in the presence of HA suggests that some of the Cu associated with HA is available through trophic processes.

  17. Microbacter margulisiae gen. nov., sp. nov., a propionigenic bacterium isolated from sediments of an acid rock drainage pond.

    PubMed

    Sánchez-Andrea, Irene; Sanz, Jose Luis; Stams, Alfons J M

    2014-12-01

    A novel anaerobic propionigenic bacterium, strain ADRI(T), was isolated from sediment of an acid rock drainage environment (Tinto River, Spain). Cells were small (0.4-0.6×1-1.7 µm), non-motile and non-spore-forming rods. Cells possessed a Gram-negative cell-wall structure and were vancomycin-resistant. Strain ADRI(T) utilized yeast extract and various sugars as substrates and formed propionate, lactate and acetate as major fermentation products. The optimum growth temperature was 30 °C and the optimum pH for growth was pH 6.5, but strain ADRI(T) was able to grow at a pH as low as 3.0. Oxidase, indole formation, and urease and catalase activities were negative. Aesculin and gelatin were hydrolysed. The predominant cellular fatty acids of strain ADRI(T) were anteiso-C15 : 0 (30.3 %), iso-C15 : 0 (29.2 %) and iso-C17 : 0 3-OH (14.9 %). Major menaquinones were MK-8 (52 %) and MK-9 (48 %). The genomic DNA G+C content was 39.9 mol%. Phylogenetically, strain ADRI(T) was affiliated to the family Porphyromonadaceae of the phylum Bacteroidetes. The most closely related cultured species were Paludibacter propionicigenes with 16S rRNA gene sequence similarity of 87.5 % and several species of the genus Dysgonomonas (similarities of 83.5-85.4 % to the type strains). Based on the distinctive ecological, phenotypic and phylogenetic characteristics of strain ADRI(T), a novel genus and species, Microbacter margulisiae gen. nov., sp. nov., is proposed. The type strain is ADRI(T) ( = JCM 19374(T) = DSM 27471(T)).

  18. Application of ethylene diamine tetra acetic acid degrading bacterium Burkholderia cepacia on biotreatment process.

    PubMed

    Chen, Wei-Ting; Shen, Shu-Min; Shu, Chi-Min

    2015-10-01

    Ethylene diamine tetra acetic acid (EDTA), the effluent of secondary biotreatment units, can be properly biodegraded by Burkholderia cepacia. Through batch degradation of EDTA, the raw wastewater of EDTA was controlled at 50 mg/L, and then nutrients was added in diluted wastewater to cultivate activated sludge, which the ratio of composition is depicted as "COD:N:P:Fe = 100:5:1:0.5". After 27 days, the removal efficiency of Fe-EDTA and COD was 100% and 92.0%, correspondingly. At the continuous process, the raw wastewater of EDTA was dictated at 166 mg/L before adding nutrients to cultivate activated sludge, in which the ratio of composition did also follow with batch process. After 22 days, the removal efficiency of Fe-EDTA and COD for experimental group was 71.46% and 62.58%, correspondingly. The results showed that the batch process was more suited for EDTA biodegradation.

  19. Iron sources used by the nonpathogenic lactic acid bacterium Lactobacillus sakei as revealed by electron energy loss spectroscopy and secondary-ion mass spectrometry.

    PubMed

    Duhutrel, Philippe; Bordat, Christian; Wu, Ting-Di; Zagorec, Monique; Guerquin-Kern, Jean-Luc; Champomier-Vergès, Marie-Christine

    2010-01-01

    Lactobacillus sakei is a lactic acid bacterium naturally found on meat. Although it is generally acknowledged that lactic acid bacteria are rare species in the microbial world which do not have iron requirements, the genome sequence of L. sakei 23K has revealed quite complete genetic equipment dedicated to transport and use of this metal. Here, we aimed to investigate which iron sources could be used by this species as well as their role in the bacterium's physiology. Therefore, we developed a microscopy approach based on electron energy loss spectroscopy (EELS) analysis and nano-scale secondary-ion mass spectrometry (SIMS) in order to analyze the iron content of L. sakei cells. This revealed that L. sakei can use iron sources found in its natural ecosystem, myoglobin, hemoglobin, hematin, and transferrin, to ensure long-term survival during stationary phase. This study reveals that analytical image methods (EELS and SIMS) are powerful complementary tools for investigation of metal utilization by bacteria.

  20. Production of L-lactic Acid from Biomass Wastes Using Scallop Crude Enzymes and Novel Lactic Acid Bacterium

    NASA Astrophysics Data System (ADS)

    Yanagisawa, Mitsunori; Nakamura, Kanami; Nakasaki, Kiyohiko

    In the present study, biomass waste raw materials including paper mill sludge, bamboo, sea lettuce, and shochu residue (from a distiller) and crude enzymes derived from inedible and discarded scallop parts were used to produce L-lactic acid for the raw material of biodegradable plastic poly-lactic acid. The activities of cellulase and amylase in the crude enzymes were 22 and 170units/L, respectively, and L-lactic acid was produced from every of the above mentioned biomass wastes, by the method of liquid-state simultaneous saccharification and fermentation (SSF) . The L-lactic acid concentrations produced from sea lettuce and shochu residue, which contain high concentration of starch were 3.6 and 9.3g/L, respectively, and corresponded to greater than 25% of the conversion of glucans contained in these biomass wastes. Furthermore, using the solid state SSF method, concentrations as high as 13g/L of L-lactic acid were obtained from sea lettuce and 26g/L were obtained from shochu residue.

  1. Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field.

    PubMed

    Honda, Takuya; Fujita, Takashi; Tonouchi, Akio

    2013-10-01

    A novel anaerobic bacterium that could ferment amino acids and organic acids was isolated from an anaerobic, propionate-oxidizing enrichment culture originating from soil of a rice field in Japan. Cells of the isolate, designated strain 4F6E(T), were Gram-staining-negative, oxidase- and catalase-negative, non-spore-forming, vibrio-shaped, motile rods (0.8×2.0-2.5 µm) with two or three lateral flagella. Growth occurred at 20-42 °C (optimum at 37-40 °C), at pH 6.4-8.4 (optimum at pH 7.3) and at 0-1.5 % (w/v) NaCl (optimum at 0-0.5 %). Good growth occurred on glycine, serine, cysteine, pyruvate and citrate, whereas poor growth was observed on threonine, glutamine, L-malate, α-ketoglutarate, peptone and Casamino acids. In co-culture with the hydrogen-utilizing methanogen Methanobacterium formicicum JCM 10132(T), strain 4F6E(T) oxidized alanine, valine, leucine, isoleucine, methionine, aspartate, glutamate, histidine, asparagine and fumarate. Yeast extract was required for growth. The G+C content of genomic DNA was 61.9 mol%. A phylogenetic analysis based on comparison of the 16S rRNA gene sequence showed that the type strains of Fretibacterium fastidiosum, Aminobacterium colombiense and Aminobacterium mobile, members of the family Synergistaceae, were the closest relatives of strain 4F6E(T), with low sequence similarities (89.3, 89.5 and 86.2 %, respectively). Strain 4F6E(T) contained iso-C13 : 0 (24.43 %), iso-C15 : 0 (16.47 %) and C19 : 1ω11c/C19 : 1ω9c (16.32 %) as the major fatty acids, which differed from those of F. fastidiosum, Aminobacterium colombiense and Aminobacterium mobile. On the basis of phenotypic, chemotaxonomic and phylogenetic differences between strain 4F6E(T) and the type strains of F. fastidiosum and Aminobacterium species, we propose that strain 4F6E(T) represents a novel genus and species, Aminivibrio pyruvatiphilus gen. nov., sp. nov. The type strain of Aminivibrio pyruvatiphilus is strain 4F6E(T) (

  2. Enterococcus bulliens sp. nov., a novel lactic acid bacterium isolated from camel milk.

    PubMed

    Kadri, Zaina; Spitaels, Freek; Cnockaert, Margo; Praet, Jessy; El Farricha, Omar; Swings, Jean; Vandamme, Peter

    2015-11-01

    Four lactic acid bacteria isolates obtained from fresh dromedary camel milk produced in Dakhla, a city in southern Morocco, were characterised in order to determine their taxonomic position. The four isolates had highly similar MALDI-TOF MS and RAPD fingerprints and identical 16S rRNA gene sequences. Comparative sequence analysis revealed that the 16S rRNA gene sequence of the four isolates was most similar to that of Enterococcus sulfureus ATCC 49903(T) and Enterococcus italicus DSM 15952(T) (99.33 and 98.59% similarity, respectively). However, sequence analysis of the phenylalanyl-tRNA synthase (pheS), RNA polymerase (rpoA) and ATP synthase (atpA) genes revealed that the taxon represented by strain LMG 28766(T) was well separated from E. sulfureus LMG 13084(T) and E. italicus LMG 22039(T), which was further confirmed by DNA-DNA hybridization values that were clearly below the species demarcation threshold. The novel taxon was easily differentiated from its nearest neighbour species through sequence analysis of protein encoding genes, MALDI-TOF mass spectrometry and multiple biochemical tests, but had a similar percentage G+C content of about 39%. We therefore propose to formally classify these isolates as Enterococcus bulliens sp. nov., with LMG 28766(T) (=CCMM B1177(T)) as the type strain.

  3. Complete Genome Sequence of the Prototype Lactic Acid Bacterium Lactococcus lactis subsp. cremoris MG1363▿

    PubMed Central

    Wegmann, Udo; O'Connell-Motherway, Mary; Zomer, Aldert; Buist, Girbe; Shearman, Claire; Canchaya, Carlos; Ventura, Marco; Goesmann, Alexander; Gasson, Michael J.; Kuipers, Oscar P.; van Sinderen, Douwe; Kok, Jan

    2007-01-01

    Lactococcus lactis is of great importance for the nutrition of hundreds of millions of people worldwide. This paper describes the genome sequence of Lactococcus lactis subsp. cremoris MG1363, the lactococcal strain most intensively studied throughout the world. The 2,529,478-bp genome contains 81 pseudogenes and encodes 2,436 proteins. Of the 530 unique proteins, 47 belong to the COG (clusters of orthologous groups) functional category “carbohydrate metabolism and transport,” by far the largest category of novel proteins in comparison with L. lactis subsp. lactis IL1403. Nearly one-fifth of the 71 insertion elements are concentrated in a specific 56-kb region. This integration hot-spot region carries genes that are typically associated with lactococcal plasmids and a repeat sequence specifically found on plasmids and in the “lateral gene transfer hot spot” in the genome of Streptococcus thermophilus. Although the parent of L. lactis MG1363 was used to demonstrate lysogeny in Lactococcus, L. lactis MG1363 carries four remnant/satellite phages and two apparently complete prophages. The availability of the L. lactis MG1363 genome sequence will reinforce its status as the prototype among lactic acid bacteria through facilitation of further applied and fundamental research. PMID:17307855

  4. Asaia krungthepensis sp. nov., an acetic acid bacterium in the alpha-Proteobacteria.

    PubMed

    Yukphan, Pattaraporn; Potacharoen, Wanchern; Tanasupawat, Somboon; Tanticharoen, Morakot; Yamada, Yuzo

    2004-03-01

    Three bacterial strains were isolated from flowers collected in Bangkok, Thailand, by an enrichment-culture approach for acetic acid bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates were located in the lineage of the genus Asaia but constituted a cluster separate from the type strains of Asaia bogorensis and Asaia siamensis. The DNA base composition of the isolates was 60.2-60.5 mol% G+C, with a range of 0.3 mol%. The isolates constituted a taxon separate from Asaia bogorensis and Asaia siamensis on the basis of DNA-DNA relatedness. The isolates had morphological, physiological, biochemical and chemotaxonomic characteristics similar to those of the type strains of Asaia bogorensis and Asaia siamensis, but the isolates grew on maltose. The major ubiquinone was Q(10). On the basis of the results obtained, the name Asaia krungthepensis sp. nov. is proposed for the isolates. The type strain is isolate AA08(T) (=BCC 12978(T)=TISTR 1524(T)=NBRC 100057(T)=NRIC 0535(T)), which had a DNA G+C content of 60.3 mol% and was isolated from a heliconia flower ('paksaasawan' in Thai; Heliconia sp.) collected in Bangkok, Thailand.

  5. Isolation and characterisation of lactic acid bacterium for effective fermentation of cellobiose into optically pure homo L-(+)-lactic acid.

    PubMed

    Abdel-Rahman, Mohamed Ali; Tashiro, Yukihiro; Zendo, Takeshi; Shibata, Keisuke; Sonomoto, Kenji

    2011-02-01

    Effective utilisation of cellulosic biomasses for economical lactic acid production requires a microorganism with potential ability to utilise efficiently its major components, glucose and cellobiose. Amongst 631 strains isolated from different environmental samples, strain QU 25 produced high yields of l-(+)-lactic acid of high optical purity from cellobiose. The QU 25 strain was identified as Enterococcus mundtii based on its sugar fermentation pattern and 16S rDNA sequence. The production of lactate by fermentation was optimised for the E. mundtii QU25 strain. The optimal pH and temperature for batch culturing were found to be 7.0°C and 43°C, respectively. E. mundtii QU 25 was able to metabolise a mixture of glucose and cellobiose simultaneously without apparent carbon catabolite repression. Moreover, under the optimised culture conditions, production of optically pure l-lactic acid (99.9%) increased with increasing cellobiose concentrations. This indicates that E. mundtii QU 25 is a potential candidate for effective lactic acid production from cellulosic hydrolysate materials.

  6. Soil acidity determines the effectiveness of an organic amendment and a native bacterium for increasing soil stabilisation in semiarid mine tailings.

    PubMed

    Carrasco, L; Caravaca, F; Azcón, R; Roldán, A

    2009-01-01

    Unstable mine tailings are vulnerable to water and air erosion, so it is important to promote their surface stabilisation in order to avoid the spread of heavy metals. In a greenhouse experiment, we assessed the effect of the addition of Aspergillus niger-treated sugar beet waste and inoculation with a native bacterium, Bacillus cereus, on the stabilisation of soil aggregates of two acidic, semiarid mine tailings, with different acidity degree, during watering and drying periods. Organic amendment raised the pH of both the moderately and highly acidic tailings, whereas the bacterial inoculation increased this parameter in the former. Only the amendment addition increased soil water-soluble carbon in both tailings compared with their controls, under either watering or drying conditions. Both the amendment and B. cereus enhanced water-soluble carbohydrates. Both treatments increased dehydrogenase activity and aggregate stability, particularly in the moderately acidic tailing under drying conditions. After soil drying, aggregate stability was increased by the amendment (about 66% higher than the control soil) and by the bacterium (about 45% higher than the control soil) in the moderately acidic tailing. The effectiveness of these treatments as structure-stabilisation methods for degraded, semiarid mine ecosystems appears to be restricted to tailings of moderate acidity.

  7. Isolation, characterization, and amino acid sequences of auracyanins, blue copper proteins from the green photosynthetic bacterium Chloroflexus aurantiacus

    NASA Technical Reports Server (NTRS)

    McManus, J. D.; Brune, D. C.; Han, J.; Sanders-Loehr, J.; Meyer, T. E.; Cusanovich, M. A.; Tollin, G.; Blankenship, R. E.

    1992-01-01

    Three small blue copper proteins designated auracyanin A, auracyanin B-1, and auracyanin B-2 have been isolated from the thermophilic green gliding photosynthetic bacterium Chloroflexus aurantiacus. All three auracyanins are peripheral membrane proteins. Auracyanin A was described previously (Trost, J. T., McManus, J. D., Freeman, J. C., Ramakrishna, B. L., and Blankenship, R. E. (1988) Biochemistry 27, 7858-7863) and is not glycosylated. The two B forms are glycoproteins and have almost identical properties to each other, but are distinct from the A form. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis apparent monomer molecular masses are 14 (A), 18 (B-2), and 22 (B-1) kDa. The amino acid sequences of the B forms are presented. All three proteins have similar absorbance, circular dichroism, and resonance Raman spectra, but the electron spin resonance signals are quite different. Laser flash photolysis kinetic analysis of the reactions of the three forms of auracyanin with lumiflavin and flavin mononucleotide semiquinones indicates that the site of electron transfer is negatively charged and has an accessibility similar to that found in other blue copper proteins. Copper analysis indicates that all three proteins contain 1 mol of copper per mol of protein. All three auracyanins exhibit a midpoint redox potential of +240 mV. Light-induced absorbance changes and electron spin resonance signals suggest that auracyanin A may play a role in photosynthetic electron transfer. Kinetic data indicate that all three proteins can donate electrons to cytochrome c-554, the electron donor to the photosynthetic reaction center.

  8. Genome Sequence and Transcriptome Analysis of Meat-Spoilage-Associated Lactic Acid Bacterium Lactococcus piscium MKFS47

    PubMed Central

    Johansson, Per; Laine, Pia; Smolander, Olli-Pekka; Sonck, Matti; Rahkila, Riitta; Jääskeläinen, Elina; Paulin, Lars; Auvinen, Petri; Björkroth, Johanna

    2015-01-01

    Lactococcus piscium is a psychrotrophic lactic acid bacterium and is known to be one of the predominant species within spoilage microbial communities in cold-stored packaged foods, particularly in meat products. Its presence in such products has been associated with the formation of buttery and sour off-odors. Nevertheless, the spoilage potential of L. piscium varies dramatically depending on the strain and growth conditions. Additional knowledge about the genome is required to explain such variation, understand its phylogeny, and study gene functions. Here, we present the complete and annotated genomic sequence of L. piscium MKFS47, combined with a time course analysis of the glucose catabolism-based transcriptome. In addition, a comparative analysis of gene contents was done for L. piscium MKFS47 and 29 other lactococci, revealing three distinct clades within the genus. The genome of L. piscium MKFS47 consists of one chromosome, carrying 2,289 genes, and two plasmids. A wide range of carbohydrates was predicted to be fermented, and growth on glycerol was observed. Both carbohydrate and glycerol catabolic pathways were significantly upregulated in the course of time as a result of glucose exhaustion. At the same time, differential expression of the pyruvate utilization pathways, implicated in the formation of spoilage substances, switched the metabolism toward a heterofermentative mode. In agreement with data from previous inoculation studies, L. piscium MKFS47 was identified as an efficient producer of buttery-odor compounds under aerobic conditions. Finally, genes and pathways that may contribute to increased survival in meat environments were considered. PMID:25819958

  9. Isolation and characterization of Pediococcus halophilus from salted anchovies (Engraulis anchoita).

    PubMed Central

    Villar, M; de Ruiz Holgado, A P; Sanchez, J J; Trucco, R E; Oliver, G

    1985-01-01

    The presence of bacteria in salted anchovies during and at the end of the curing process was investigated. Attempts to isolate bacteria under aerobic or anaerobic conditions led to the isolation of only bacteria of the genus Pediococcus which were identified as Pediococcus halophilus. The isolates correspond to a rather heterogeneous group in which some of the members differ in some biochemical tests from the types described in the literature. PMID:3994370

  10. Purification and partial characterization of a tripeptidase from Pediococcus pentosaceus K9.2.

    PubMed

    Simitsopoulou, M; Vafopoulou, A; Choli-Papadopoulou, T; Alichanidis, E

    1997-12-01

    A tripeptidase was purified from the cytoplasm of Pediococcus pentosaceus K9.2 by anion-exchange chromatography, gel filtration chromatography, and high-performance liquid chromatography. The molecular mass of the enzyme was estimated by gel filtration at 100,000 Da. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified peptidase showed one protein band of 45,000 Da. Optimal enzyme activity was obtained at pH 7.0 and at 50 degrees C. The peptidase hydrolyzed all tripeptides tested. Cleavage was not observed with dipeptides, oligopeptides, or amino acid-p-nitroanilide derivatives. Strong inhibition of activity was caused by EDTA, 1,10-phenanthroline, dithiothreitol, and beta-mercaptoethanol, whereas phenylmethylsulfonyl fluoride and sulfur-reactive reagents had no effect on peptidase activity. Mg2+, Mn2+, and Ca2+ stimulated the hydrolyzing activity of the enzyme. The 20 N-terminal amino acids of the tripeptidase from P. pentosaceus had 84% identity with those from the corresponding N-terminal region of the tripeptidase from Lactococcus lactis subsp. cremoris Wg2.

  11. Agrowaste to vanillin conversion by a natural Pediococcus acidilactici strain BD16.

    PubMed

    Chakraborty, Debkumar; Kaur, Baljinder; Obulisamy, Karthikeyan; Selvam, Ammaiyappan; Wong, Jonathan W C

    2016-10-13

    Owing to its flavoring, antimicrobial, antioxidant and anticarcinogenic nature, vanillin is widely used in foods, beverages, perfumes and pharmaceutical products. Ferulic acid (FA) is an important precursor of vanillin which is abundant in cereals like maize, rice and wheat and sugar beet. A major drawback of microbial vanillin production from FA is the degradation and biotransformation of toxic vanillin to other phenolic derivatives. The present study is undertaken to explore microbial vanillin production from FA precursor rice bran by employing vanillin-resistant Pediococcus acidilactici BD16, a natural lactic acid bacteria isolate. Extracellular, intracellular and cellular vanillin dehydrogenase activity was found least, which was minimized vanillin degradation, and the strain resists more than 5 g L(-1) vanillin in the medium. A metabolomics approach was followed for the detection of FA, vanillin and other metabolites generated during fermentation of rice bran medium. A metabolic pathway was also predicted for vanillin biosynthesis. Approximately 1.06 g L(-1) of crude vanillin was recovered from rice-bran-containing medium and this further offers scope for the industrial utilization of the organism and its genetic manipulation to enhance production of biovanillin.

  12. Evaluation of beneficial attributes for phytate-degrading Pediococcus pentosaceus CFR R123.

    PubMed

    Raghavendra, P; Rao, T S C; Halami, P M

    2010-09-01

    In this study we have screened and selected potent phytate-degrading lactic acid bacteria (LAB), and evaluated their beneficial attributes. Around 60 LAB strains were isolated from several cereal- and pulse-based conventional fermented preparations. They were screened for their ability to degrade myo-inositol hexakisphosphate (IP6) by cobalt chloride qualitative staining method (plate assay). One of the cultures, Pediococcus pentosaceus CFR R123, was capable of degrading both calcium and sodium salts of phytic acid. Additionally, we have carried out an in vitro evaluation for the beneficial attributes of phytate degrading CFR R123. P. pentosaceus CFR R123 showed 53% survivability at pH 2 and 62% at pH 2.5, whereas cultures of Lactobacillus rhamnosus GG showed a survivability of 55% and 82%, respectively. CFR R123 could also withstand 0.3% ox-bile, whereas no growth was observed for GG. The strain CFR R123 exhibited 62.8% hydrophobicity to xylene whereas 59% was found for GG. Both the tested strains showed a good spectrum of antibacterial activity against food-borne pathogens like Escherichia coli, Listeria monocytogenes Scott A, etc. P. pentosaceus CFR R123 possessed β-galactosidase activity and cholesterol reduction ability. In conclusion, LAB with phytate degrading ability and several beneficial attributes could potentially be used as a starter culture to improve the nutritional security of functional food.

  13. Thermosyntropha lipolytica gen. nov., sp. nov., a lipolytic, anaerobic, alkalitolerant, thermophilic bacterium utilizing short- and long-chain fatty acids in syntrophic coculture with a methanogenic archaeum

    SciTech Connect

    Svetlitshnyi, V.; Wiegel, J.; Rainey, F.

    1996-10-01

    Three strains of an anaerobic thermophilic organoheterotrophic lipolytic alkalitolerant bacterium, Thermosyntropha lipolytica gen. nov., sp. nov. (type strain JW/VS-264{sup T}; DSM 11003) were isolated from alkaline hot springs of Lake Bogoria (Kenya). The cells were nonmotile, non-spore forming, straight or slightly curved rods. At 60{degrees}C, the pH range for growth determined at 25{degrees}C [pH{sup 25{degrees}C}] was 7.15 to 9.5, with an optimum between 8.1 and 8.9 (pH{sup 60{degrees}C} of 7.6 and 8.1). At a pH{sup 25{degrees}C} of 8.5 temperature range for growth was from 52 to 70{degrees}C, with an optimum between 60 and 66{degrees}C. The shortest doubling time was around 1 h. In pure culture the bacterium grew in a mineral base medium supplemented with yeast extract, tryptone, Casamino Acids, betaine, and crotonate as carbon sources, producing acetate as a major product and constitutively a lipase. During growth in the presence of olive oil, free long-chain fatty acids were accumulated in the medium but the pure culture syntrophic coculture (Methanobacterium strain JW/VS-M29) the lipolytic bacteria grew on triacylglycerols and linear saturated and unsaturated fatty acids with 4 to 18 carbon atoms, but glycerol was not utilized. Fatty acids with even numbers of carbon atoms were degraded to acetate and methane, while from odd-numbered fatty acids 1 mol of propionate per mol of fatty acid was additionally formed. 16S rDNA sequence analysis identified Syntrophospora and Syntrophomonas spp. as closest phylogenetic neighbors.

  14. Pediococcus cerevisiae mutant with altered transport of folates.

    PubMed

    Mandelbaum-Shavit, F; Grossowicz, N

    1975-08-01

    A Pediococcus cerevisiae mutant that actively accumulated folate (PteGlu), in contrast to the wild-type, was also found to exhibit changes in the pattern of uptake of 5-methyl-tetrahydrofolate (5-CH3-H4PteGlu) and amethopterin. Most of the 5-CH3-H4PteGlue accumulated through a glucose- and temperature-dependent process, and a concentrative uptake was also found in gluocse-starved cells and in cells incubated at OC. About 75% of the accumulated 5-CH3-H4PteGlu exchanged with amethopterin. In contrast to the wild type, the mutant accumulated both diastereoisomers of 5-CH3-H4PteGlue by glucose-dependent and glucose-independent processes. Amethopterin and PteGlue competitively inhibited the uptake in both processes, with an apparent lower affinity of the carrier for PteGlu than for the analogue. p-Chloromercuribenzoate strongly inhibited the uptake (75%). The p-chloromercuribenzoate-nonsusceptible and temperature-independent uptake was also competed by amethopterin. Metabolic poisons like sodium azide, potassium fluoride, iodoacetate, and 2,4-dimitrophenol inhibited the glucose-dependent process. Uptake, in the absence of glucose, was enhanced by sodium azide and potassium fluoride.

  15. Fed-batch pediocin production by Pediococcus acidilactici NRRL B-5627 on whey.

    PubMed

    Pérez Guerra, Nelson; Bernárdez, Paula Fajardo; Agrasar, Ana Torrado; López Macías, Cristina; Castro, Lorenzo Pastrana

    2005-08-01

    Cell growth and pediocin production by Pediococcus acidilactici NRRL B-5627 on whey were compared by using batch fermentation and re-alkalized fed-batch fermentation. The batch fermentations were performed on DWG [DW (diluted whey) supplemented with 1% (w/v) glucose], DWYE [DW supplemented with 2% (w/v) yeast extract] and DWGYE (DW supplemented with 1% glucose plus 2% yeast extract) media. The fed-batch culture on DWYE medium was fed with a mixture of concentrated whey (48 g of total sugars/l) supplemented with 2% yeast extract and 400 g/l concentrated glucose. The re-alkalized fed-batch culture was characterized by higher biomass (6.57 g/l) and pediocin [517.6 BU (bacteriocin activity units)/ml] concentrations compared with the batch processes on MRS (de Man, Rogosa and Sharpe) broth (1.76 g/l and 493.2 BU/ml), DW (0.17 g/l and 57.7 BU/ml), DWG (0.14 g/l and 53.6 BU/ml), DWYE (1.43 g/l and 187.6 BU/ml) and DWGYE (1.28 g/l and 167.3 BU/ml) media. A mixed acid fermentation was observed during the growth of P. acidilactici NRRL B-5627 in the fed-batch culture on DWYE medium, and other products (acetic acid and ethanol) in addition to lactic acid accumulated in the medium. Mathematical models were set up to describe fed-batch production of biomass and pediocin by P. acidilactici. The models developed offer a better fit and a more realistic description of the experimental biomass and pediocin production data when compared with the logistic and Luedeking and Piret model.

  16. The Culture of Pediococcus pentosaceus T1 Inhibits 
Listeria Proliferation in Salmon Fillets and Controls Maturation of Kimchi.

    PubMed

    Jang, Seongho; Lee, Dongyun; Jang, Il Sang; Choi, Hyeon-Son; Suh, Hyung Joo

    2015-03-01

    The objective of this study is to evaluate the antilisterial effect of Pediococcus pentosaceus T1, which was isolated from kimchi, and to assess its potential for extending the shelf life of salmon and kimchi. Pediococcus pentosaceus T1 culture effectively inhibited proliferation of Listeria monocytogenes in a dose-dependent manner in a salmon-based medium. Antilisterial effect of the culture was stronger than that of nisin, an antibacterial peptide, as evidenced by lower minimum inhibitory concentration value (20 mg/mL) compared to nisin (over 20 mg/mL). P. pentosaceus T1 culture also effectively inhibited the growth of Listeria in salmon fillet. In particular, the culture (6 g per 100 mL) showed a stronger inhibitory effect than sodium hypochlorite (0.2 mg/mL), a disinfectant used in food processing. In kimchi fermentation, the treatment with P. pentosaceus T1 culture suppressed changes of acidity and pH during maturation. The inhibitory effect of the culture on kimchi lactic acid bacteria, which include Leuconostoc mesenteroides and Lactobacillus sakei, led to a drastic decrease in maturation rates of kimchi. Moreover, sensory test on kimchi treated with P. pentosaceus T1 showed that the culture improved overall acceptability of kimchi, which can be observed in higher scores of sourness, texture, off-flavour and mouthfeel compared with untreated kimchi. The results of this study suggest that kimchi-derived P. pentosaceus T1 could be a potential antilisterial agent in fish products as well as a starter to control overmaturation of kimchi.

  17. The Culture of Pediococcus pentosaceus T1 Inhibits 
Listeria Proliferation in Salmon Fillets and Controls Maturation of Kimchi

    PubMed Central

    Jang, Seongho; Lee, Dongyun; Jang, Il Sang; Choi, Hyeon-Son

    2015-01-01

    Summary The objective of this study is to evaluate the antilisterial effect of Pediococcus pentosaceus T1, which was isolated from kimchi, and to assess its potential for extending the shelf life of salmon and kimchi. Pediococcus pentosaceus T1 culture effectively inhibited proliferation of Listeria monocytogenes in a dose-dependent manner in a salmon-based medium. Antilisterial effect of the culture was stronger than that of nisin, an antibacterial peptide, as evidenced by lower minimum inhibitory concentration value (20 mg/mL) compared to nisin (over 20 mg/mL). P. pentosaceus T1 culture also effectively inhibited the growth of Listeria in salmon fillet. In particular, the culture (6 g per 100 mL) showed a stronger inhibitory effect than sodium hypochlorite (0.2 mg/mL), a disinfectant used in food processing. In kimchi fermentation, the treatment with P. pentosaceus T1 culture suppressed changes of acidity and pH during maturation. The inhibitory effect of the culture on kimchi lactic acid bacteria, which include Leuconostoc mesenteroides and Lactobacillus sakei, led to a drastic decrease in maturation rates of kimchi. Moreover, sensory test on kimchi treated with P. pentosaceus T1 showed that the culture improved overall acceptability of kimchi, which can be observed in higher scores of sourness, texture, off-flavour and mouthfeel compared with untreated kimchi. The results of this study suggest that kimchi-derived P. pentosaceus T1 could be a potential antilisterial agent in fish products as well as a starter to control overmaturation of kimchi. PMID:27904329

  18. Structure and regulation of the omega-3 polyunsaturated fatty acid synthase genes from the deep-sea bacterium Photobacterium profundum strain SS9.

    PubMed

    Allen, Eric E; Bartlett, Douglas H

    2002-06-01

    Omega-3 polyunsaturated fatty acids (PUFAs) such as eicosapentaenoic acid (20:5n-3; EPA) and docosahexaenoic acid (22:6n-3; DHA) have been shown to be of major importance in the promotion of cardiovascular health, proper human development and the prevention of some cancers. A high proportion of bacterial isolates from low-temperature and high-pressure marine environments produce EPA or DHA. This paper presents the sequence of a 33 kbp locus from the deep-sea bacterium Photobacterium profundum strain SS9 which includes four of the five genes required for EPA biosynthesis. As with other bacterial pfa (polyunsaturated fatty acid) genes, the deduced amino acid sequences encoded by the SS9 genes reveal large multidomain proteins that are likely to catalyse EPA biosynthesis by a novel polyketide synthesis mechanism. RNase protection experiments separated the SS9 pfa genes into two transcriptional units, pfaA-C and pfaD. The pfaA transcriptional start site was identified. Cultivation at elevated hydrostatic pressure or reduced temperature did not increase pfa gene expression despite the resulting increase in percentage composition of EPA under these conditions. However, a regulatory mutant was characterized which showed both increased expression of pfaA-D and elevated EPA percentage composition. This result suggests that a regulatory factor exists which coordinates pfaA-D transcription. Additional consideration regarding the activities required for PUFA synthesis is provided together with comparative analyses of bacterial pfa genes and gene products.

  19. A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti.

    PubMed

    Draghi, W O; Del Papa, M F; Hellweg, C; Watt, S A; Watt, T F; Barsch, A; Lozano, M J; Lagares, A; Salas, M E; López, J L; Albicoro, F J; Nilsson, J F; Torres Tejerizo, G A; Luna, M F; Pistorio, M; Boiardi, J L; Pühler, A; Weidner, S; Niehaus, K; Lagares, A

    2016-07-11

    Abiotic stresses in general and extracellular acidity in particular disturb and limit nitrogen-fixing symbioses between rhizobia and their host legumes. Except for valuable molecular-biological studies on different rhizobia, no consolidated models have been formulated to describe the central physiologic changes that occur in acid-stressed bacteria. We present here an integrated analysis entailing the main cultural, metabolic, and molecular responses of the model bacterium Sinorhizobium meliloti growing under controlled acid stress in a chemostat. A stepwise extracellular acidification of the culture medium had indicated that S. meliloti stopped growing at ca. pH 6.0-6.1. Under such stress the rhizobia increased the O2 consumption per cell by more than 5-fold. This phenotype, together with an increase in the transcripts for several membrane cytochromes, entails a higher aerobic-respiration rate in the acid-stressed rhizobia. Multivariate analysis of global metabolome data served to unequivocally correlate specific-metabolite profiles with the extracellular pH, showing that at low pH the pentose-phosphate pathway exhibited increases in several transcripts, enzymes, and metabolites. Further analyses should be focused on the time course of the observed changes, its associated intracellular signaling, and on the comparison with the changes that operate during the sub lethal acid-adaptive response (ATR) in rhizobia.

  20. A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti

    PubMed Central

    Draghi, W. O.; Del Papa, M. F.; Hellweg, C.; Watt, S. A.; Watt, T. F.; Barsch, A.; Lozano, M. J.; Lagares, A.; Salas, M. E.; López, J. L.; Albicoro, F. J.; Nilsson, J. F.; Torres Tejerizo, G. A.; Luna, M. F.; Pistorio, M.; Boiardi, J. L.; Pühler, A.; Weidner, S.; Niehaus, K.; Lagares, A.

    2016-01-01

    Abiotic stresses in general and extracellular acidity in particular disturb and limit nitrogen-fixing symbioses between rhizobia and their host legumes. Except for valuable molecular-biological studies on different rhizobia, no consolidated models have been formulated to describe the central physiologic changes that occur in acid-stressed bacteria. We present here an integrated analysis entailing the main cultural, metabolic, and molecular responses of the model bacterium Sinorhizobium meliloti growing under controlled acid stress in a chemostat. A stepwise extracellular acidification of the culture medium had indicated that S. meliloti stopped growing at ca. pH 6.0–6.1. Under such stress the rhizobia increased the O2 consumption per cell by more than 5-fold. This phenotype, together with an increase in the transcripts for several membrane cytochromes, entails a higher aerobic-respiration rate in the acid-stressed rhizobia. Multivariate analysis of global metabolome data served to unequivocally correlate specific-metabolite profiles with the extracellular pH, showing that at low pH the pentose-phosphate pathway exhibited increases in several transcripts, enzymes, and metabolites. Further analyses should be focused on the time course of the observed changes, its associated intracellular signaling, and on the comparison with the changes that operate during the sub lethal acid-adaptive response (ATR) in rhizobia. PMID:27404346

  1. Detection of Pediococcus spp. in brewing yeast by a rapid immunoassay.

    PubMed

    Whiting, M; Crichlow, M; Ingledew, W M; Ziola, B

    1992-02-01

    A membrane immunofluorescent-antibody test was developed to detect diacetyl-producing Pediococcus contaminants in brewery pitching yeast (yeast [Saccharomyces cerevisiae] slurry collected for reinoculation). Centrifugations at 11 and 5,100 x g separate yeast cells from bacteria and concentrate the bacteria, respectively. Pelleted bacteria resuspended and trapped on a black membrane filter are reacted with monoclonal antibodies specific for cell surface antigens and then with fluorescein-conjugated indicator antibodies. Whether pitching yeast is contaminated with pediococci at 0.001% is determined in less than 4 h. The sensitivity of the assay is 2 orders of magnitude below the Pediococcus detection limit of direct microscopy.

  2. Cloacibacillus evryensis gen. nov., sp. nov., a novel asaccharolytic, mesophilic, amino-acid-degrading bacterium within the phylum 'Synergistetes', isolated from an anaerobic sludge digester.

    PubMed

    Ganesan, Akila; Chaussonnerie, Sébastien; Tarrade, Anne; Dauga, Catherine; Bouchez, Théodore; Pelletier, Eric; Le Paslier, Denis; Sghir, Abdelghani

    2008-09-01

    A novel anaerobic, mesophilic, amino-acid-utilizing bacterium, strain 158T, was isolated from an anaerobic digester of a wastewater treatment plant. Cells of strain 158T were non-motile, rod-shaped (2.0-3.0 x 0.8-1.0 microm) and stained Gram-negative. Optimal growth occurred at 37 degrees C and pH 7.0 in an anaerobic basal medium containing 1 % Casamino acids. Strain 158T fermented arginine, histidine, lysine and serine and showed growth on yeast extract, brain-heart infusion (BHI) medium and tryptone, but not on carbohydrates, organic acids or alcohols. The end products of degradation were: acetate, butyrate, H2 and CO2 from arginine; acetate, propionate, butyrate, H2 and CO2 from lysine; and acetate, propionate, butyrate, valerate, H2 and CO2 from histidine, serine, BHI medium, Casamino acids and tryptone. The DNA G+C content was 55.8 mol%. The 16S rRNA gene sequence of strain 158T showed only 92.6 % sequence similarity with that of Synergistes jonesii, the only described species of the 'Synergistes' group. The major cellular fatty acids were iso-C(15:0) (16.63 %), iso-C(15:0) 3-OH (12.41 %) and C(17:1)omega6c (9.46 %) and the polar fatty acids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylamine; these fatty acid profiles did not resemble those of any recognized bacterial species. Due to the considerable differences in genotypic, phenotypic and phylogenetic characteristics between strain 158T and those of its nearest relative, it is proposed that strain 158T represents a novel species in a new genus, Cloacibacillus evryensis gen. nov., sp. nov., in the phylum 'Synergistetes'. The type strain is 158T (=DSM 19522T=JCM 14828T).

  3. Microbial β-Galactosidase of Pediococcus pentosaceus ID-7: Isolation, Cloning, and Molecular Characterization.

    PubMed

    Lee, Ji-Yeong; Kwak, Mi-Sun; Roh, Jong-Bok; Kim, Kwang; Sung, Moon-Hee

    2017-03-28

    Pediococcus pentosaceus ID-7 was isolated from kimchi, a Korean fermented food, and it showed high activity for lactose hydrolysis. The β-galactosidase of P. pentosaceus ID-7 belongs to the GH2 group, which is composed of two distinct proteins. The heterodimeric LacLM type of β-galactosidase found in P. pentosaceus ID-7 consists of two genes partially overlapped, lacL and lacM encoding LacL (72.2 kDa) and LacM (35.4 kDa). In this study, Escherichia coli MM294 was used for the production of LacL, LacM, and LacLM. These three types of recombinant proteins were expressed, purified, and characterized. The specific activities of LacLM and LacL were 339 and 31 U/mg, respectively. However, activity was not detected with LacM alone. The optimal pH of LacLM and LacL was pH 7.5 and pH 7.0, and the optimal temperature of LacLM and LacL was 40°C and 50°C, respectively. The optimal temperature changes indicate that LacLM is able to achieve higher activity at a relatively lower temperature. LacLM was strongly activated by Mg(2+), Mn(2+), and Zn(2+), which was not true for LacL. Consistent with this, EDTA strongly inactivated LacLM and LacL, but the presence of reducing agents did not dramatically alter the activity. Taken together, multiple alignment of amino acid sequences and phylogenetic analysis results of LacL and LacM of P. pentosaceus ID-7 suggest the evolution of LacL into LacLM and that the use of divalent metal ions results in higher activity.

  4. Environmental factors influencing growth of and exopolysaccharide formation by Pediococcus parvulus 2.6.

    PubMed

    Velasco, S; Arsköld, E; Paese, M; Grage, H; Irastorza, A; Rådström, P; van Niel, E W J

    2006-10-01

    Natural exopolysaccharides (EPSs) from food-grade lactic acid bacteria have potential for development and exploitation as food additives and functional food ingredients with both health and economic benefits. In this study, we have examined the physiological capacity of EPS production in Pediococcus parvulus 2.6. EPS formation by P. parvulus 2.6 was found to be linked to biomass yields, provided that glucose was not limiting. Higher biomass yields and EPS productions were obtained when cultures were pH-controlled at pH 5.2. Various compounds have been tested for their influence on growth rate and EPS formation. Of those, only glucose (up to 75 g l(-1)), ethanol (up to 4.9%, w/v) and glycerol (up to 6.6%, w/v) had positive effects on EPS production. EPS production was not directly linked to growth, because its production continued in the stationary phase provided that glucose was present. According to an empirical model, the growth of P. parvulus 2.6 was completely inhibited by 58.9+/-18.1 g l(-1) lactate. Lactate, the sole fermentation product, was suggested to affect growth by chelation of manganese. The organism grew in an apparent linear fashion due to this imposed manganese limitation. This could be overcome by increasing the manganese concentration to at least 2 mg l(-1) in the medium. The excretion of Mn(2+) upon depletion of glucose indicated that maintenance of the high Mn(2+) gradient over the cell membrane is an energy requiring process. EPS production was increased from 0.12 g l(-1) to 4.10 g l(-1) in an improved medium that is based on the results from this study.

  5. Characterization of two distinct glycosyl hydrolase family 78 alpha-L-rhamnosidases from Pediococcus acidilactici.

    PubMed

    Michlmayr, Herbert; Brandes, Walter; Eder, Reinhard; Schümann, Christina; del Hierro, Andrés M; Kulbe, Klaus D

    2011-09-01

    α-L-Rhamnosidases play an important role in the hydrolysis of glycosylated aroma compounds (especially terpenes) from wine. Although several authors have demonstrated the enological importance of fungal rhamnosidases, the information on bacterial enzymes in this context is still limited. In order to fill this important gap, two putative rhamnosidase genes (ram and ram2) from Pediococcus acidilactici DSM 20284 were heterologously expressed, and the respective gene products were characterized. In combination with a bacterial β-glucosidase, both enzymes released the monoterpenes linalool and cis-linalool oxide from a muscat wine extract under ideal conditions. Additionally, Ram could release significant amounts of geraniol and citronellol/nerol. Nevertheless, the potential enological value of these enzymes is limited by the strong negative effects of acidity and ethanol on the activities of Ram and Ram2. Therefore, a direct application in winemaking seems unlikely. Although both enzymes are members of the same glycosyl hydrolase family (GH 78), our results clearly suggest the distinct functionalities of Ram and Ram2, probably representing two subclasses within GH 78: Ram could efficiently hydrolyze only the synthetic substrate p-nitrophenyl-α-L-rhamnopyranoside (V(max) = 243 U mg(-1)). In contrast, Ram2 displayed considerable specificity toward hesperidin (V(max) = 34 U mg(-1)) and, especially, rutinose (V(max) = 1,200 U mg(-1)), a disaccharide composed of glucose and rhamnose. Both enzymes were unable to hydrolyze the flavanone glycoside naringin. Interestingly, both enzymes displayed indications of positive substrate cooperativity. This study presents detailed kinetic data on two novel rhamnosidases, which could be relevant for the further study of bacterial glycosidases.

  6. Complete Genome Sequence of the Beer Spoilage Organism Pediococcus claussenii ATCC BAA-344T

    PubMed Central

    Pittet, Vanessa; Abegunde, Teju; Marfleet, Travis; Haakensen, Monique; Morrow, Kendra; Jayaprakash, Teenus; Schroeder, Kristen; Trost, Brett; Byrns, Sydney; Bergsveinson, Jordyn; Kusalik, Anthony

    2012-01-01

    Pediococcus claussenii is a common brewery contaminant. We have sequenced the chromosome and plasmids of the type strain P. claussenii ATCC BAA-344. A ropy variant was chosen for sequencing to obtain genetic information related to growth in beer, as well as exopolysaccharide and possibly biofilm formation by this organism. PMID:22328764

  7. Complete genome sequence of the beer spoilage organism Pediococcus claussenii ATCC BAA-344T.

    PubMed

    Pittet, Vanessa; Abegunde, Teju; Marfleet, Travis; Haakensen, Monique; Morrow, Kendra; Jayaprakash, Teenus; Schroeder, Kristen; Trost, Brett; Byrns, Sydney; Bergsveinson, Jordyn; Kusalik, Anthony; Ziola, Barry

    2012-03-01

    Pediococcus claussenii is a common brewery contaminant. We have sequenced the chromosome and plasmids of the type strain P. claussenii ATCC BAA-344. A ropy variant was chosen for sequencing to obtain genetic information related to growth in beer, as well as exopolysaccharide and possibly biofilm formation by this organism.

  8. Effects of hydrostatic pressure and temperature on the uptake and respiration of amino acids by a facultatively psychrophilic marine bacterium.

    NASA Technical Reports Server (NTRS)

    Paul, K. L.; Morita, R. Y.

    1971-01-01

    Studies of pressure and temperature effects on glutamic acid transport and utilization indicated that hydrostatic pressure and low temperature inhibit glutamate transport more than glutamate respiration. The effects of pressure on transport were reduced at temperatures near the optimum. Similar results were obtained for glycine, phenylalanine, and proline. Pressure effects on the transport systems of all four amino acids were reversible to some degree. Both proline and glutamic acid were able to protect their transport proteins against pressure damage. The data presented indicate that the uptake of amino acids by cells under pressure is inhibited, which is the cause of their inability to grow under pressure.

  9. Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms

    NASA Technical Reports Server (NTRS)

    Jackson, B. E.; Bhupathiraju, V. K.; Tanner, R. S.; Woese, C. R.; McInerney, M. J.

    1999-01-01

    Strain SBT is a new, strictly anaerobic, gram-negative, nonmotile, non-sporeforming, rod-shaped bacterium that degrades benzoate and certain fatty acids in syntrophic association with hydrogen/formate-using microorganisms. Strain SBT produced approximately 3 mol of acetate and 0.6 mol of methane per mol of benzoate in coculture with Methanospirillum hungatei strain JF1. Saturated fatty acids, some unsaturated fatty acids, and methyl esters of butyrate and hexanoate also supported growth of strain SBT in coculture with Desulfovibrio strain G11. Strain SBT grew in pure culture with crotonate, producing acetate, butyrate, caproate, and hydrogen. The molar growth yield was 17 +/- 1 g cell dry mass per mol of crotonate. Strain SBT did not grow with fumarate, iron(III), polysulfide, or oxyanions of sulfur or nitrogen as electron acceptors with benzoate as the electron donor. The DNA base composition of strain SBT was 43.1 mol% G+C. Analysis of the 16 S rRNA gene sequence placed strain SBT in the delta-subdivision of the Proteobacteria, with sulfate-reducing bacteria. Strain SBT was most closely related to members of the genus Syntrophus. The clear phenotypic and genotypic differences between strain SBT and the two described species in the genus Syntrophus justify the formation of a new species, Syntrophus aciditrophicus.

  10. Effects of orally administered probiotic Pediococcus acidilactici on the small and large intestine of weaning piglets. A qualitative and quantitative micro-anatomical study.

    PubMed

    Di Giancamillo, A; Vitari, F; Savoini, G; Bontempo, V; Bersani, C; Dell'Orto, V; Domeneghini, C

    2008-06-01

    Probiotic research has been approached, above all in recent years, by widely differing points of view, both for human and animal uses. Lactic acid bacteria release bacteriocins, and some of them may function as probiotic. The aim of the present study was to investigate the effects of dietary supplementation with the probiotic Pediococcus acidilactici on the piglet intestine, on circulating lymphocytes, and on aspects of piglet performance during the first 42 days after weaning. Sixteen female piglets were at weaning assigned to two dietary groups: Control (Ctr, 8 animals) and Pediococcus acidilactici supplemented (Pa, 8 animals). Piglets' growth was monitored from weaning to the end of the trial. On day 42 post-weaning, the piglets were slaughtered and small specimens from both ileum and cecum were examined with haematoxylin/eosin staining to ascertain structural details. Histometry was performed by villi and crypts measurements, as well as GALT measurements. Histochemical analyses were performed to investigate the intestinal mucins. Immunohistochemical analyses were used to visualize proliferating as well as apoptotic mucosal cells, and to identify mucosal macrophages and IgA producing cells. Intra-epithelial CD8+ T lymphocytes were identified and counted. Subsets of circulating T lymphocytes were analyzed by flow cytometry. Pediococcus acidilactici supplementation positively influenced weight and post-weaning average daily gain of treated piglets. Histometry showed an increase in villi height and crypts depth in Pa animals in comparison with controls. Treated piglets showed a larger number of proliferating enterocytes than controls. Intra-epithelial CD8+ T lymphocytes were scarcer in treated than in control piglets, likely in relation with catarrhal enteritis shown in the latter. We conclude that the studied supplementation was possibly able to protect the piglet small intestinal mucosa, improving local resistance to infections in the stressful weaning period.

  11. Oral Administration of Live Exopolysaccharide-Producing Pediococcus parvulus, but Not Purified Exopolysaccharide, Suppressed Enterobacteriaceae without Affecting Bacterial Diversity in Ceca of Mice

    PubMed Central

    Xu, Jie; Öste, Rickard; Holst, Olle; Molin, Göran

    2013-01-01

    Growing evidence indicates that the gut microbiota could have an important role in the development of diet- and lifestyle-induced diseases. It has been shown that modulation of the gut microbiota by means of probiotics and prebiotics could improve host health. An oat-based product fermented by the exopolysaccharide (EPS)-producing organism Pediococcus parvulus 2.6 has been reported to have a bifidogenic effect. To find out whether the effect could be attributed to the EPS or the bacterium, mice were fed a diet supplemented with 2% purified EPS or 108 CFU/g of live P. parvulus 2.6 for 6 weeks. Both supplementations altered the gut microbiota composition but in different directions. Purified EPS not only significantly lowered the microbial diversity (P < 0.001) but decreased the bifidobacterial population (P = 0.01). In contrast, the live EPS-producing bacterium P. parvulus 2.6 antagonized Enterobacteriaceae without disturbing the homeostasis of the cecal microbiota. PMID:23770909

  12. Growth and gas formation by Lactobacillus wasatchensis, a novel obligatory heterofermentative nonstarter lactic acid bacterium, in Cheddar-style cheese made using a Streptococcus thermophilus starter.

    PubMed

    Ortakci, Fatih; Broadbent, Jeffery R; Oberg, Craig J; McMahon, Donald J

    2015-11-01

    A novel slow-growing, obligatory heterofermentative, nonstarter lactic acid bacterium (NSLAB), Lactobacillus wasatchensis WDC04, was studied for growth and gas production in Cheddar-style cheese made using Streptococcus thermophilus as the starter culture. Cheesemaking trials were conducted using S. thermophilus alone or in combination with Lb. wasatchensis deliberately added to cheese milk at a level of ~10(4) cfu/mL. Resulting cheeses were ripened at 6 or 12°C. At d 1, starter streptococcal numbers were similar in both cheeses (~10(9) cfu/g) and fast-growing NSLAB lactobacilli counts were below detectable levels (<10(2) cfu/g). As expected, Lactobacillus wasatchensis counts were 3×10(5) cfu/g in cheeses inoculated with this bacterium and below enumeration limits in the control cheese. Starter streptococci decreased over time at both storage temperatures but declined more rapidly at 12°C, especially in cheese also containing Lb. wasatchensis. Populations of fast-growing NSLAB and the slow-growing Lb. wasatchensis reached 5×10(7) and 2×10(8) cfu/g, respectively, after 16 wk of storage at 12°C. Growth of NSLAB coincided with a reduction in galactose concentration in the cheese from 0.6 to 0.1%. Levels of galactose at 6°C had similar decrease. Gas formation and textural defects were only observed in cheese with added Lb. wasatchensis ripened at 12°C. Use of S. thermophilus as starter culture resulted in galactose accumulation that Lb. wasatchensis can use to produce CO2, which contributes to late gas blowing in Cheddar-style cheeses, especially when the cheese is ripened at elevated temperature.

  13. Lysinibacillus endophyticus sp. nov., an indole-3-acetic acid producing endophytic bacterium isolated from corn root (Zea mays cv. Xinken-5).

    PubMed

    Yu, Jiang; Guan, Xuejiao; Liu, Chongxi; Xiang, Wensheng; Yu, Zhenhua; Liu, Xiaobing; Wang, Guanghua

    2016-10-01

    A Gram-positive, aerobic, motile, rod-shaped bacterium, designated strain C9(T), was isolated from surface sterilised corn roots (Zea mays cv. Xinken-5) and found to be able to produce indole-3-acetic acid. A polyphasic taxonomic study was carried out to determine the status of strain C9(T). The major cellular fatty acids were found to contain iso-C15:0, anteiso-C15:0 and anteiso-C17:0, and the only menaquinone was identified as MK-7. The polar lipid profile was found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and an unidentified lipid. The cell wall peptidoglycan was found to be of the A4α L-Lys-D-Asp type and the whole cell sugar was found to be glucose. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain C9(T) belongs to the genus Lysinibacillus and is closely related to Lysinibacillus chungkukjangi NBRC 108948(T) (98.1 % similarity) and Lysinibacillus sinduriensis DSM 27595(T) (98.0 %). However, the low levels of DNA-DNA relatedness and some differential phenotypic characteristics allowed the strain to be distinguished from its close relatives. Therefore, it is concluded that strain C9(T) represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus endophyticus sp. nov. is proposed. The type strain is C9(T) (=DSM 100506(T) = CGMCC 1.15291(T)).

  14. Favourable effects of eicosapentaenoic acid on the late step of the cell division in a piezophilic bacterium, Shewanella violacea DSS12, at high-hydrostatic pressures.

    PubMed

    Kawamoto, Jun; Sato, Takako; Nakasone, Kaoru; Kato, Chiaki; Mihara, Hisaaki; Esaki, Nobuyoshi; Kurihara, Tatsuo

    2011-08-01

    Shewanella violacea DSS12, a deep-sea bacterium, produces eicosapentaenoic acid (EPA) as a component of membrane phospholipids. Although various isolates from the deep sea, such as Photobacterium profundum SS9, Colwellia psychrerythraea 34H and various Shewanella strains, produce EPA- or docosahexaenoic acid-containing phospholipids, the physiological role of these polyunsaturated fatty acids remains unclear. In this article, we illustrate the physiological importance of EPA for high-pressure adaptation in strain DSS12 with the help of an EPA-deficient mutant (DSS12(pfaA)). DSS12(pfaA) showed significant growth retardation at 30 MPa, but not at 0.1 MPa. We also found that DSS12(pfaA) grown at 30 MPa forms filamentous cells. When an EPA-containing phospholipid (sn-1-oleoly-sn-2-eicosapentaenoyl phosphatidylethanolamine) was supplemented, the growth retardation and the morphological defect of DSS12(pfaA) were suppressed, indicating that the externally added EPA-containing phospholipid compensated for the loss of endogenous EPA. In contrast, the addition of an oleic acid-containing phospholipid (sn-1,2-dioleoyl phosphatidylethanolamine) did not affect the growth and the morphology of the cells. Immunofluorescent microscopic analysis with anti-FtsZ antibody revealed a number of Z-rings and separated nucleoids in DSS12(pfaA) grown at 30 MPa. These results demonstrate the physiological importance of EPA for the later step of Z-ring formation of S. violacea DSS12 under high-pressure conditions.

  15. Nucleotide and deduced amino acid sequences of a subtilisin-like serine protease from a deep-sea bacterium, Alkalimonas collagenimarina AC40(T).

    PubMed

    Kurata, Atsushi; Uchimura, Kohsuke; Shimamura, Shigeru; Kobayashi, Tohru; Horikoshi, Koki

    2007-11-01

    The acpI gene encoding an alkaline protease (AcpI) from a deep-sea bacterium, Alkalimonas collagenimarina AC40(T), was shotgun-cloned and sequenced. It had a 1,617-bp open reading frame encoding a protein of 538 amino acids. Based on analysis of the deduced amino acid sequence, AcpI is a subtilisin-like serine protease belonging to subtilase family A. It consists of a prepropeptide, a catalytic domain, and a prepeptidase C-terminal domain like other serine proteases from the genera Pseudomonas, Shewanella, Alteromonas, and Xanthomonas. Heterologous expression of the acpI gene in Escherichia coli cells yielded a 28-kDa recombinant AcpI (rAcpI), suggesting that both the prepropeptide and prepeptidase C-terminal domains were cleaved off to give the mature form. Analysis of N-terminal and C-terminal amino acid sequences of purified rAcpI showed that the mature enzyme would be composed of 273 amino acids. The optimal pH and temperature for the caseinolytic activity of the purified rAcpI were 9.0-9.5 and 45 degrees C in 100 mM glycine-NaOH buffer. Calcium ions slightly enhanced the enzyme activity and stability. The enzyme favorably hydrolyzed gelatin, collagen, and casein. AcpI from A. collagenimarina AC40(T) was also purified from culture broth, and its molecular mass was around 28 kDa, indicating that the cleavage manner of the enzyme is similar to that in E. coli cells.

  16. Isolation and characterization of pediocin L50, a new bacteriocin from Pediococcus acidilactici with a broad inhibitory spectrum.

    PubMed

    Cintas, L M; Rodriguez, J M; Fernandez, M F; Sletten, K; Nes, I F; Hernandez, P E; Holo, H

    1995-07-01

    Lactic acid bacteria were isolated from Spanish dry-fermented sausages and screened for bacteriocin production. About 10% of the isolates produced antimicrobial substances when grown on solid media, but only 2% produced detectable activity in liquid media. Strain L50, identified as Pediococcus acidilactici, showed the strongest inhibitory activity and was active against members of all of the gram-positive genera tested. The strain produced a heat-stable bacteriocin when grown at 8 to 32 degrees C but not at 45 degrees C. The bacteriocin was purified to homogeneity. Its mass was determined to be 5,250.11 +/- 0.30 by electrospray mass spectrometry. The N terminus of the bacteriocin was blocked for sequencing by Edman degradation, but a partial sequence of 42 amino acids was obtained after cleavage of the peptide by cyanogen bromide. The sequence showed no similarity to those of other bacteriocins. Pediocin L50 appears to contain modified amino acids but not lanthionine or methyl-lanthionine.

  17. Diet supplementation of Pediococcus pentosaceus in cobia (Rachycentron canadum) enhances growth rate, respiratory burst and resistance against photobacteriosis.

    PubMed

    Xing, Chen-Fu; Hu, Hung-Hsi; Huang, Jian-Bin; Fang, Han-Chun; Kai, Yu-Hsuan; Wu, Yu-Chi; Chi, Shau-Chi

    2013-10-01

    Cobia (Rachycentron canadum) is an economically important fish species for aquaculture in tropical and sub-tropical areas. Cobia aquaculture industry has severely damaged due to photobacteriosis caused by Photobacterium damselae subsp. piscicida (Pdp), especially in Taiwan. Antibiotics and vaccines have been applied to control Pdp infection, but the efficacy has been inconsistent. One species of lactic acid bacteria, Pediococcus pentosaceus strain 4012 (LAB 4012), was isolated from the intestine of adult cobia, and its culture supernatant can effectively inhibit Pdp growth in vitro. The acidic pH derived from metabolic acids in LAB culture supernatant was demonstrated to be an important factor for the suppression. After a 2-week feeding of LAB 4012, the growth rate of the fed cobia was 12% higher than that of the non-fed group, and the relative percentage of survival (RPS) of the fed cobia was found to be 74.4 in Pdp immersion challenge. In addition, the respiratory burst (RB) of peripheral blood leukocytes (PBL) in the LAB 4012-fed group was significantly higher than that of the non-fed group. Although feeding LAB 4012 did not improve specific antibody response in cobia after immunization with Pdp vaccine, it still significantly raised the survival rate by 22% over that of the non-fed group after Pdp immersion challenge. Judging by the quick induction of high protection against Pdp infection and promotion of growth in larvae, LAB 4012 was considered to be a viable probiotic for cobia aquaculture.

  18. Fatty acids in bacterium Dietzia sp. grown on simple and complex hydrocarbons determined as FAME by GC-MS.

    PubMed

    Hvidsten, Ina; Mjøs, Svein Are; Bødtker, Gunhild; Barth, Tanja

    2015-09-01

    The influence of growth substrates on the fatty acids produced by Dietzia sp. A14101 has been studied to investigate how qualitative and semi-quantitative information on fatty acids correlates with the ability of this strain to access and utilize a wide range of water-immiscible HC-substrates by modifying the FA content and thus also the properties of the cellular membrane. After incubation on different substrates and media, the profiles of fatty acids (FA) were analyzed by gas chromatography and mass spectrometry (GC-MS). The equivalent chain length (ECL) index calibration system was employed to identify FA. The effect of each substrate on the cell surface charge and on the hydrophobicity of the cellular membrane was also investigated. The results indicate that the variation of the content of saturated fatty acids (SAT-FA) versus mono-unsaturated fatty acids (MUFA) was found to be the most pronounced while branched FA exhibited much less variation in spite of different substrate regimes. The regulation of the ratio of SAT-FA and MUFA seems to be coupled with the regulation of the charge and hydrophobicity of the outer cellular surface. The exposure to a water immiscible substrate led to the development of the negative cellular surface charge, production of carotenoid-type pigments and increased hydrophobicity of the cellular surface. The specific aspects of the adaptation mechanism could have implications for bioremediation and/or (M)EOR applications.

  19. Biological degradation of 4-chlorobenzoic acid by a PCB-metabolizing bacterium through a pathway not involving (chloro)catechol.

    PubMed

    Adebusoye, Sunday A

    2017-02-01

    Cupriavidus sp. strain SK-3, previously isolated on polychlorinated biphenyl mixtures, was found to aerobically utilize a wide spectrum of substituted aromatic compounds including 4-fluoro-, 4-chloro- and 4-bromobenzoic acids as a sole carbon and energy source. Other chlorobenzoic acid (CBA) congeners such as 2-, 3-, 2,3-, 2,5-, 3,4- and 3,5-CBA were all rapidly transformed to respective chlorocatechols (CCs). Under aerobic conditions, strain SK-3 grew readily on 4-CBA to a maximum concentration of 5 mM above which growth became impaired and yielded no biomass. Growth lagged significantly at concentrations above 3 mM, however chloride elimination was stoichiometric and generally mirrored growth and substrate consumption in all incubations. Experiments with resting cells, cell-free extracts and analysis of metabolite pools suggest that 4-CBA was metabolized in a reaction exclusively involving an initial hydrolytic dehalogenation yielding 4-hydroxybenzoic acid, which was then hydroxylated to protocatechuic acid (PCA) and subsequently metabolized via the β-ketoadipate pathway. When strain SK-3 was grown on 4-CBA, there was gratuitous induction of the catechol-1,2-dioxygenase and gentisate-1,2-dioxygenase pathways, even if both were not involved in the metabolism of the acid. While activities of the modified ortho- and meta-cleavage pathways were not detectable in all extracts, activity of PCA-3,4-dioxygenase was over ten-times higher than those of catechol-1,2- and gentisate-1,2-dioxygenases. Therefore, the only reason other congeners were not utilized for growth was the accumulation of CCs, suggesting a narrow spectrum of the activity of enzymes downstream of benzoate-1,2-dioxygenase, which exhibited affinity for a number of substituted analogs, and that the metabolic bottlenecks are either CCs or catabolites of the modified ortho-cleavage metabolic route.

  20. Diversity of the Lactic Acid Bacterium and Yeast Microbiota in the Switch from Firm- to Liquid-Sourdough Fermentation

    PubMed Central

    Di Cagno, Raffaella; Pontonio, Erica; Buchin, Solange; De Angelis, Maria; Lattanzi, Anna; Valerio, Francesca; Calasso, Maria

    2014-01-01

    Four traditional type I sourdoughs were comparatively propagated (28 days) under firm (dough yield, 160) and liquid (dough yield, 280) conditions to mimic the alternative technology options frequently used for making baked goods. After 28 days of propagation, liquid sourdoughs had the lowest pH and total titratable acidity (TTA), the lowest concentrations of lactic and acetic acids and free amino acids, and the most stable density of presumptive lactic acid bacteria. The cell density of yeasts was the highest in liquid sourdoughs. Liquid sourdoughs showed simplified microbial diversity and harbored a low number of strains, which were persistent. Lactobacillus plantarum dominated firm sourdoughs over time. Leuconostoc lactis and Lactobacillus brevis dominated only some firm sourdoughs, and Lactobacillus sanfranciscensis persisted for some time only in some firm sourdoughs. Leuconostoc citreum persisted in all firm and liquid sourdoughs, and it was the only species detected in liquid sourdoughs at all times; it was flanked by Leuconostoc mesenteroides in some sourdoughs. Saccharomyces cerevisiae, Candida humilis, Saccharomyces servazzii, Saccharomyces bayanus-Kazachstania sp., and Torulaspora delbrueckii were variously identified in firm and liquid sourdoughs. A total of 197 volatile components were identified through purge and trap–/solid-phase microextraction–gas chromatography-mass spectrometry (PT–/SPME–GC-MS). Aldehydes, several alcohols, and some esters were at the highest levels in liquid sourdoughs. Firm sourdoughs mainly contained ethyl acetate, acetic acid, some sulfur compounds, and terpenes. The use of liquid fermentation would change the main microbial and biochemical features of traditional baked goods, which have been manufactured under firm conditions for a long time. PMID:24632249

  1. Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella species in human feces by using group-specific PCR primers and denaturing gradient gel electrophoresis.

    PubMed

    Walter, J; Hertel, C; Tannock, G W; Lis, C M; Munro, K; Hammes, W P

    2001-06-01

    Denaturing gradient gel electrophoresis (DGGE) of DNA fragments generated by PCR with 16S ribosomal DNA-targeted group-specific primers was used to detect lactic acid bacteria (LAB) of the genera Lactobacillus, Pediococcus, Leuconostoc, and Weissella in human feces. Analysis of fecal samples of four subjects revealed individual profiles of DNA fragments originating not only from species that have been described as intestinal inhabitants but also from characteristically food-associated bacteria such as Lactobacillus sakei, Lactobacillus curvatus, Leuconostoc mesenteroides, and Pediococcus pentosaceus. Comparison of PCR-DGGE results with those of bacteriological culture showed that the food-associated species could not be cultured from the fecal samples by plating on Rogosa agar. On the other hand, all of the LAB species cultured from feces were detected in the DGGE profile. We also detected changes in the types of LAB present in human feces during consumption of a milk product containing the probiotic strain Lactobacillus rhamnosus DR20. The analysis of fecal samples from two subjects taken before, during, and after administration of the probiotic revealed that L. rhamnosus was detectable by PCR-DGGE during the test period in the feces of both subjects, whereas it was detectable by culture in only one of the subjects.

  2. The Antisense RNA Approach: a New Application for In Vivo Investigation of the Stress Response of Oenococcus oeni, a Wine-Associated Lactic Acid Bacterium

    PubMed Central

    Darsonval, Maud; Msadek, Tarek; Alexandre, Hervé

    2015-01-01

    Oenococcus oeni is a wine-associated lactic acid bacterium mostly responsible for malolactic fermentation in wine. In wine, O. oeni grows in an environment hostile to bacterial growth (low pH, low temperature, and ethanol) that induces stress response mechanisms. To survive, O. oeni is known to set up transitional stress response mechanisms through the synthesis of heat stress proteins (HSPs) encoded by the hsp genes, notably a unique small HSP named Lo18. Despite the availability of the genome sequence, characterization of O. oeni genes is limited, and little is known about the in vivo role of Lo18. Due to the lack of genetic tools for O. oeni, an efficient expression vector in O. oeni is still lacking, and deletion or inactivation of the hsp18 gene is not presently practicable. As an alternative approach, with the goal of understanding the biological function of the O. oeni hsp18 gene in vivo, we have developed an expression vector to produce antisense RNA targeting of hsp18 mRNA. Recombinant strains were exposed to multiple stresses inducing hsp18 gene expression: heat shock and acid shock. We showed that antisense attenuation of hsp18 affects O. oeni survival under stress conditions. These results confirm the involvement of Lo18 in heat and acid tolerance of O. oeni. Results of anisotropy experiments also confirm a membrane-protective role for Lo18, as previous observations had already suggested. This study describes a new, efficient tool to demonstrate the use of antisense technology for modulating gene expression in O. oeni. PMID:26452552

  3. The amino acid sequence of the zinc-requiring beta-lactamase II from the bacterium Bacillus cereus 569.

    PubMed

    Ambler, R P; Daniel, M; Fleming, J; Hermoso, J M; Pang, C; Waley, S G

    1985-09-23

    The amino acid sequence of the zinc-requiring beta-lactamase II from Bacillus cereus strain 569 has been determined. It consists of a single polypeptide chain of 227 residues. It is the only example so far fully characterized of a class B beta-lactamase, and is structurally and mechanistically distinct from both the widely distributed class A beta-lactamases (such as the Escherichia coli RTEM enzyme) and from the chromosomally encoded class C enzymes from Gram-negative bacteria.

  4. Aminiphilus circumscriptus gen. nov., sp. nov., an anaerobic amino-acid-degrading bacterium from an upflow anaerobic sludge reactor.

    PubMed

    Díaz, C; Baena, S; Fardeau, M-L; Patel, B K C

    2007-08-01

    Strain ILE-2(T) was isolated from an upflow anaerobic sludge bed reactor treating brewery wastewater. The motile, non-sporulating, slightly curved cells (2-4 x 0.1 microm) stained Gram-negative and grew optimally at 42 degrees C and pH 7.1 with 0.5 % NaCl. The strain required yeast extract for growth and fermented Casamino acids, peptone, isoleucine, arginine, lysine, alanine, valine, glutamate, histidine, glutamine, methionine, malate, fumarate, glycerol and pyruvate to acetate, propionate and minor amounts of branched-chain fatty acids. Carbohydrates, formate, acetate, propionate, butyrate, isovalerate, methanol, ethanol, 1-propanol, butanol, lactate, succinate, starch, casein, gelatin, xylan and a number of other amino acids were not utilized. The DNA G+C content of strain ILE-2(T) was 52.7 mol%. 16S rRNA gene sequence analysis revealed that ILE-2(T) was distantly related to members of the genera Aminobacterium (83 % similarity) and Aminomonas (85 % similarity) in the family Syntrophomonadaceae, order Clostridiales, phylum Firmicutes. On the basis of the results of our polyphasic analysis, strain ILE-2(T) represents a novel species and genus within the family Syntrophomonadaceae, for which the name Aminiphilus circumscriptus gen. nov., sp. nov. is proposed. The type strain of Aminiphilus circumscriptus is ILE-2(T) (=DSM 16581(T) =JCM 14039(T)).

  5. High genetic diversity among strains of the unindustrialized lactic acid bacterium Carnobacterium maltaromaticum in dairy products as revealed by multilocus sequence typing.

    PubMed

    Rahman, Abdur; Cailliez-Grimal, Catherine; Bontemps, Cyril; Payot, Sophie; Chaillou, Stéphane; Revol-Junelles, Anne-Marie; Borges, Frédéric

    2014-07-01

    Dairy products are colonized with three main classes of lactic acid bacteria (LAB): opportunistic bacteria, traditional starters, and industrial starters. Most of the population structure studies were previously performed with LAB species belonging to these three classes and give interesting knowledge about the population structure of LAB at the stage where they are already industrialized. However, these studies give little information about the population structure of LAB prior their use as an industrial starter. Carnobacterium maltaromaticum is a LAB colonizing diverse environments, including dairy products. Since this bacterium was discovered relatively recently, it is not yet commercialized as an industrial starter, which makes C. maltaromaticum an interesting model for the study of unindustrialized LAB population structure in dairy products. A multilocus sequence typing scheme based on an analysis of fragments of the genes dapE, ddlA, glpQ, ilvE, pyc, pyrE, and leuS was applied to a collection of 47 strains, including 28 strains isolated from dairy products. The scheme allowed detecting 36 sequence types with a discriminatory index of 0.98. The whole population was clustered in four deeply branched lineages, in which the dairy strains were spread. Moreover, the dairy strains could exhibit a high diversity within these lineages, leading to an overall dairy population with a diversity level as high as that of the nondairy population. These results are in agreement with the hypothesis according to which the industrialization of LAB leads to a diversity reduction in dairy products.

  6. Identification of a 4-deoxy-L-erythro-5-hexoseulose uronic acid reductase, FlRed, in an alginolytic bacterium Flavobacterium sp. strain UMI-01.

    PubMed

    Inoue, Akira; Nishiyama, Ryuji; Mochizuki, Shogo; Ojima, Takao

    2015-01-16

    In alginate-assimilating bacteria, alginate is depolymerized to unsaturated monosaccharide by the actions of endolytic and exolytic alginate lyases (EC 4.2.2.3 and EC 4.2.2.11). The monosaccharide is non-enzymatically converted to 4-deoxy-L-ery thro-5-hexoseulose uronic acid (DEH), then reduced to 2-keto-3-deoxy-D-gluconate (KDG) by a specific reductase, and metabolized through the Entner-Doudoroff pathway. Recently, the NADPH-dependent reductase A1-R that belongs to short-chain dehydrogenases/reductases (SDR) superfamily was identified as the DEH-reductase in Sphingomonas sp. A1. We have subsequently noticed that an SDR-like enzyme gene, flred, occurred in the genome of an alginolytic bacterium Flavobacterium sp. strain UMI-01. In the present study, we report on the deduced amino-acid sequence of flred and DEH-reducing activity of recombinant FlRed. The deduced amino-acid sequence of flred comprised 254 residues and showed 34% amino-acid identities to that of A1-R from Sphingomonas sp. A1 and 80%-88% to those of SDR-like enzymes from several alginolytic bacteria. Common sequence motifs of SDR-superfamily enzymes, e.g., the catalytic tetrad Asn-Lys-Tyr-Ser and the cofactor-binding sequence Thr-Gly-x-x-x-Gly-x-Gly in Rossmann fold, were completely conserved in FlRed. On the other hand, an Arg residue that determined the NADPH-specificity of Sphingomonas A1-R was replaced by Glu in FlRed. Thus, we investigated cofactor-preference of FlRed using a recombinant enzyme. As a result, the recombinant FlRed (recFlRed) was found to show high specificity to NADH. recFlRed exhibited practically no activity toward variety of aldehyde, ketone, keto ester, keto acid and aldose substrates except for DEH. On the basis of these results, we conclude that FlRed is the NADH-dependent DEH-specific SDR of Flavobacterium sp. strain UMI-01.

  7. Characterization of lactose utilization and β-galactosidase in Lactobacillus brevis KB290, the hetero-fermentative lactic acid bacterium.

    PubMed

    Honda, Hiroyuki; Yajima, Nobuhiro; Saito, Tadao

    2012-12-01

    Unlike dairy lactic acid bacteria, Lactobacillus brevis cannot ferment milk. We characterized the lactose utilization by L. brevis KB290. In a carbohydrate fermentation assay using API 50 CHL, we showed during 7 days L. brevis did not ferment lactose. L. brevis grew to the stationary phase in 2 weeks in MRS broth containing lactose as the carbon source. L. brevis slowly consumed the lactose in the medium. L. brevis hydrolyzed lactose and a lactose analog, o-nitrophenyl-β-D-galactopyranoside (ONPGal). This β-galactosidase activity for ONPGal was not repressed by glucose, galactose, fructose, xylose, or maltose showing the microorganism may not have carbon catabolite repression. We purified the L. brevis β-galactosidase using ammonium sulfate precipitation and several chromatographies. The enzyme's molecular weight is estimated at 72 and 37 kDa using SDS-PAGE analysis. The N-terminal amino acid sequence of the larger protein was 90 % similar to the sequence of the putative β-galactosidase (YP_796339) and the smaller protein was identical to the sequence of the putative β-galactosidase (YP_796338) in L. brevis ATCC367. This suggests the enzyme is a heterodimeric β-galactosidase. The specific activity of the purified enzyme for lactose is 55 U/mg. We speculate inhibition of lactose transport delays the lactose utilization in L. brevis KB290.

  8. Aureispira marina gen. nov., sp. nov., a gliding, arachidonic acid-containing bacterium isolated from the southern coastline of Thailand.

    PubMed

    Hosoya, Shoichi; Arunpairojana, Vullapa; Suwannachart, Chatrudee; Kanjana-Opas, Akkharawit; Yokota, Akira

    2006-12-01

    Three strains of gliding bacteria, 24(T), 62 and 71, isolated from a marine sponge and algae from the southern coastline of Thailand, were studied using a polyphasic approach to clarify their taxonomic positions. A phylogenetic analysis based on 16S rRNA gene sequences showed that the three isolates formed a distinct lineage within the family 'Saprospiraceae' of the phylum Bacteroidetes and were related to members of the genus Saprospira. The G+C contents of the isolates were in the range 38-39 mol%. The major respiratory quinone was MK-7. The predominant cellular fatty acids were 20 : 4omega6c (arachidonic acid), 16 : 0 and iso-17 : 0. On the basis of morphological, physiological and chemotaxonomic characteristics, together with DNA-DNA hybridization data and 16S rRNA gene sequences, the isolates represent a novel species of a novel genus, for which the name Aureispira marina gen. nov., sp. nov. is proposed. The type strain of Aureispira marina is 24(T) (=IAM 15389(T)=TISTR 1719(T)).

  9. Draft Genome Sequence of the Pediocin-Encoding Biopreservative and Biocontrol Strain Pediococcus acidilactici D3

    PubMed Central

    Rajendran, Mahitha; Altermann, Eric

    2013-01-01

    We describe a draft genome sequence for Pediococcus acidilactici strain D3, a component of multistrain commercial cultures with biopreservative and biocontrol properties in food-based applications. Strain D3 encodes at least one antimicrobial peptide, pediocin AMPd3. The AMPd3-encoding operon exhibits high sequence similarity to the archetype pediocin, PA-1, encoded by P. acidilactici PAC 1.0. PMID:23788534

  10. Deduced amino acid sequence, functional expression, and unique enzymatic properties of the form I and form II ribulose bisphosphate carboxylase/oxygenase from the chemoautotrophic bacterium Thiobacillus denitrificans.

    PubMed

    Hernandez, J M; Baker, S H; Lorbach, S C; Shively, J M; Tabita, F R

    1996-01-01

    The cbbL cbbS and cbbM genes of Thiobacillus denitrificans, encoding form I and form II ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), respectively, were found to complement a RubisCO-negative mutant of Rhodobacter sphaeroides to autotrophic growth. Endogenous T. denitrificans promoters were shown to function in R. sphaeroides, resulting in high levels of cbbL cbbS and cbbM expression in the R. sphaeroides host. This expression system provided high levels of both T. denitrificans enzymes, each of which was highly purified. The deduced amino acid sequence of the form I enzyme indicated that the large subunit was closely homologous to previously sequenced form I RubisCO enzymes from sulfur-oxidizing bacteria. The form I T. denitrificans enzyme possessed a very low substrate specificity factor and did not exhibit fallover, and yet this enzyme showed a poor ability to recover from incubation with ribulose 1,5-bisphosphate. The deduced amino acid sequence of the form II T. denitrificans enzyme resembled those of other form II RubisCO enzymes. The substrate specificity factor was characteristically low, and the lack of fallover and the inhibition by ribulose 1,5-bisphosphate were similar to those of form II RubisCO obtained from nonsulfur purple bacteria. Both form I and form II RubisCO from T. denitrificans possessed high KCO2 values, suggesting that this organism might suffer in environments containing low levels of dissolved CO2. These studies present the initial description of the kinetic properties of form I and form II RubisCO from a chemoautotrophic bacterium that synthesizes both types of enzyme.

  11. Influence of nitrogen substrates and substrate C:N ratios on the nitrogen isotopic composition of amino acids from the marine bacterium Vibrio harveyi

    NASA Astrophysics Data System (ADS)

    Maki, K.; Ohkouchi, N.; Chikaraishi, Y.; Fukuda, H.; Miyajima, T.; Nagata, T.

    2014-09-01

    Nitrogen (N) isotopic compositions of individual hydrolysable amino acids (δ15NAAs) in N pools have been increasingly used for trophic position assessment and evaluation of sources and transformation processes of organic matter in marine environments. However, there are limited data about variability in δ15NAAs patterns and how this variability influences marine bacteria, an important mediator of trophic transfer and organic matter transformation. We explored whether marine bacterial δ15NAAs profiles change depending on the type and C:N ratio of the substrate. The δ15NAAs profile of a marine bacterium, Vibrio harveyi, was examined using medium containing either glutamate, alanine or ammonium as the N source [substrate C:N ratios (range, 3 to 20) were adjusted with glucose]. The data were interpreted as a reflection of isotope fractionations associated with de novo synthesis of amino acids by bacteria. Principal component analysis (PCA) using the δ15N offset values normalized to glutamate + glutamine δ15N revealed that δ15NAAs profiles differed depending on the N source and C:N ratio of the substrate. High variability in the δ15N offset of alanine and valine largely explained this bacterial δ15NAAs profile variability. PCA was also conducted using bacterial and phytoplankton (cyanobacteria and eukaryotic algae) δ15NAAs profile data reported previously. The results revealed that bacterial δ15NAAs patterns were distinct from those of phytoplankton. Therefore, the δ15NAAs profile is a useful indicator of biochemical responses of bacteria to changes in substrate conditions, serving as a potentially useful method for identifying organic matter sources in marine environments.

  12. Marinilactibacillus piezotolerans sp. nov., a novel marine lactic acid bacterium isolated from deep sub-seafloor sediment of the Nankai Trough.

    PubMed

    Toffin, Laurent; Zink, Klaus; Kato, Chiaki; Pignet, Patricia; Bidault, Adeline; Bienvenu, Nadège; Birrien, Jean-Louis; Prieur, Daniel

    2005-01-01

    A piezotolerant, mesophilic, marine lactic acid bacterium (strain LT20T) was isolated from a deep sub-seafloor sediment core collected at Nankai Trough, off the coast of Japan. Cells were Gram-positive, rod-shaped, non-sporulating and non-motile. The NaCl concentration range for growth was 0-120 g l(-1), with the optimum at 10-20 g l(-1). The temperature range for growth at pH 7.0 was 4-50 degrees C, with the optimum at 37-40 degrees C. The optimum pH for growth was 7.0-8.0. The optimum pressure for growth was 0.1 MPa with tolerance up to 30 MPa. The main cellular phospholipids were phosphatidylglycerols (25 %), diphosphatidylglycerols (34 %) and a group of compounds tentatively identified as ammonium-containing phosphatidylserines (32 %); phosphatidylethanolamines (9 %) were minor components. The fatty acid composition was dominated by side chains of 16 : 0, 14 : 0 and 16 : 1. The G+C content of the genomic DNA was 42 mol%. On the basis of 16S rRNA gene sequence analysis and the secondary structure of the V6 region, this organism was found to belong to the genus Marinilactibacillus and was closely related to Marinilactibacillus psychrotolerans M13-2(T) (99 %), Marinilactibacillus sp. strain MJYP.25.24 (99 %) and Alkalibacterium olivapovliticus strain ww2-SN4C (97 %). Despite the high similarity between their 16S rRNA gene sequences (99 %), the DNA-DNA hybridization levels were less than 20 %. On the basis of physiological and genetic characteristics, it is proposed that this organism be classified as a novel species, Marinilactibacillus piezotolerans sp. nov. The type strain is LT20T (=DSM 16108T=JCM 12337T).

  13. Deduced amino acid sequence, functional expression, and unique enzymatic properties of the form I and form II ribulose bisphosphate carboxylase/oxygenase from the chemoautotrophic bacterium Thiobacillus denitrificans.

    PubMed Central

    Hernandez, J M; Baker, S H; Lorbach, S C; Shively, J M; Tabita, F R

    1996-01-01

    The cbbL cbbS and cbbM genes of Thiobacillus denitrificans, encoding form I and form II ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), respectively, were found to complement a RubisCO-negative mutant of Rhodobacter sphaeroides to autotrophic growth. Endogenous T. denitrificans promoters were shown to function in R. sphaeroides, resulting in high levels of cbbL cbbS and cbbM expression in the R. sphaeroides host. This expression system provided high levels of both T. denitrificans enzymes, each of which was highly purified. The deduced amino acid sequence of the form I enzyme indicated that the large subunit was closely homologous to previously sequenced form I RubisCO enzymes from sulfur-oxidizing bacteria. The form I T. denitrificans enzyme possessed a very low substrate specificity factor and did not exhibit fallover, and yet this enzyme showed a poor ability to recover from incubation with ribulose 1,5-bisphosphate. The deduced amino acid sequence of the form II T. denitrificans enzyme resembled those of other form II RubisCO enzymes. The substrate specificity factor was characteristically low, and the lack of fallover and the inhibition by ribulose 1,5-bisphosphate were similar to those of form II RubisCO obtained from nonsulfur purple bacteria. Both form I and form II RubisCO from T. denitrificans possessed high KCO2 values, suggesting that this organism might suffer in environments containing low levels of dissolved CO2. These studies present the initial description of the kinetic properties of form I and form II RubisCO from a chemoautotrophic bacterium that synthesizes both types of enzyme. PMID:8550452

  14. Aminobacterium thunnarium sp. nov., a mesophilic, amino acid-degrading bacterium isolated from an anaerobic sludge digester, pertaining to the phylum Synergistetes.

    PubMed

    Hamdi, Olfa; Ben Hania, Wajdi; Postec, Anne; Bouallagui, Hassib; Hamdi, Moktar; Bonin, Patricia; Ollivier, Bernard; Fardeau, Marie-Laure

    2015-02-01

    A new Gram-staining-positive, non-sporulating, mesophilic, amino acid-degrading anaerobic bacterium, designated strain OTA 102(T), was isolated from an anaerobic sequencing batch reactor treating wastewater from cooking tuna. The cells were curved rods (0.6-2.5×0.5 µm) and occurred singly or in pairs. The strain was motile by means of one lateral flagellum. Strain OTA 102(T) grew at temperatures between 30 and 45 °C (optimum 40 °C), between pH 6.0 and 8.4 (optimum pH 7.2) and NaCl concentrations between 1 and 5 % (optimum 2 %, w/v). Strain OTA 102(T) required yeast extract for growth. Serine, threonine, glycine, cysteine, citrate, fumarate, α-ketoglutarate and pyruvate were fermented. When co-cultured with Methanobacterium formicicum as the hydrogen scavenger, strain OTA 102(T) oxidized alanine, valine, leucine, isoleucine, aspartate, tyrosine, methionine, histidine and asparagine. The genomic DNA G+C content of strain OTA 102(T) was 41.7 mol%. The main fatty acid was iso-C15 : 0. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain OTA 102(T) was related to Aminobacterium colombiense and Aminobacterium mobile (95.5 and 95.2 % similarity, respectively), of the phylum Synergistetes. On the basis of phylogenetic, genetic and physiological characteristics, strain OTA 102(T) is proposed to represent a novel species of the genus Aminobacterium, Aminobacterium thunnarium sp. nov. The type strain is OTA 102(T) ( = DSM 27500(T) = JCM 19320(T)).

  15. Effects of phenazine-1-carboxylic acid on the biology of the plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae.

    PubMed

    Xu, Shu; Pan, Xiayan; Luo, Jianying; Wu, Jian; Zhou, Zehua; Liang, Xiaoyu; He, Yawen; Zhou, Mingguo

    2015-01-01

    Xanthomonas oryzae pv. oryzae (Xoo) is the casual agent of bacterial blight, which is one of the most serious diseases of rice. The antibiotic phenazine-1-carboxylic acid (PCA), which is primarily produced by Pseudomonas spp., was found and previously reported very effective against Xoo. However, the biological effects of PCA on Xoo remain unclear. In this study, we found that PCA increased the accumulation of reactive oxygen species (ROS) and reduced the activities of catalase (CAT) and superoxide dismutase (SOD) in Xoo. Xoo was more sensitive to H2O2 than Xanthomonas oryzae pv. oryzicola (Xoc), and had a much lower expression of CAT genes. In addition, proteomic analysis indicated that PCA inhibited carbohydrate metabolism and nutrient uptake in Xoo, and analysis of carbon source utilization further confirmed that carbohydrate metabolism in Xoo was repressed by PCA. In conclusion, PCA acted as a redox-cycling agent that disturbed the redox balance in Xoo and reduced CAT and SOD activities, resulting in higher accumulation of ROS, altered carbohydrate metabolism, and lower energy production and nutrient uptake. Moreover, a deficient antioxidant system in Xoo made it very sensitive to PCA.

  16. Hematite Reduction Buffers Acid Generation and Enhances Nutrient Uptake by a Fermentative Iron Reducing Bacterium, Orenia metallireducens Strain Z6.

    PubMed

    Dong, Yiran; Sanford, Robert A; Chang, Yun-Juan; McInerney, Michael J; Fouke, Bruce W

    2017-01-03

    Fermentative iron-reducing organisms have been identified in a variety of environments. Instead of coupling iron reduction to respiration, they have been consistently observed to use ferric iron minerals as an electron sink for fermentation. In the present study, a fermentative iron reducer, Orenia metallireducens strain Z6, was shown to use iron reduction to enhance fermentation not only by consuming electron equivalents, but also by generating alkalinity that effectively buffers the pH. Fermentation of glucose by this organism in the presence of a ferric oxide mineral, hematite (Fe2O3), resulted in enhanced glucose decomposition compared with fermentation in the absence of an iron source. Parallel evidence (i.e., genomic reconstruction, metabolomics, thermodynamic analyses, and calculation of electron transfer) suggested hematite reduction as a proton-consuming reaction effectively consumed acid produced by fermentation. The buffering effect of hematite was further supported by a greater extent of glucose utilization by strain Z6 in media with increasing buffer capacity. Such maintenance of a stable pH through hematite reduction for enhanced glucose fermentation complements the thermodynamic interpretation of interactions between microbial iron reduction and other biogeochemical processes. This newly discovered feature of iron reducer metabolism also has significant implications for groundwater management and contaminant remediation by providing microbially mediated buffering systems for the associated microbial and/or chemical reactions.

  17. Carboxydothermus pertinax sp. nov., a thermophilic, hydrogenogenic, Fe(III)-reducing, sulfur-reducing carboxydotrophic bacterium from an acidic hot spring.

    PubMed

    Yoneda, Yasuko; Yoshida, Takashi; Kawaichi, Satoshi; Daifuku, Takashi; Takabe, Keiji; Sako, Yoshihiko

    2012-07-01

    A novel anaerobic, Fe(III)-reducing, hydrogenogenic, carboxydotrophic bacterium, designated strain Ug1(T), was isolated from a volcanic acidic hot spring in southern Kyushu Island, Japan. Cells of the isolate were rod-shaped (1.0-3.0 µm long) and motile due to peritrichous flagella. Strain Ug1(T) grew chemolithoautotrophically on CO (100% in the gas phase) with reduction of ferric citrate, amorphous iron (III) oxide, 9,10-anthraquinone 2,6-disulfonate, thiosulfate or elemental sulfur. No carboxydotrophic growth occurred with sulfate, sulfite, nitrate or fumarate as electron acceptor. During growth on CO, H(2) and CO(2) were produced. Growth occurred on molecular hydrogen as an energy source and carbon dioxide as a sole carbon source. Growth was observed on various organic compounds under an N(2) atmosphere with the reduction of ferric iron. The temperature range for carboxydotrophic growth was 50-70 °C, with an optimum at 65 °C. The pH(25 °C) range for growth was 4.6-8.6, with an optimum between 6.0 and 6.5. The doubling time under optimum conditions using CO with ferric citrate was 1.5 h. The DNA G+C content was 42.2 mol%. Analysis of 16S rRNA gene sequences demonstrated that this strain belongs to the thermophilic carboxydotrophic bacterial genus Carboxydothermus, with sequence similarities of 94.1-96.6% to members of this genus. The isolate can be distinguished from other members of the genus Carboxydothermus by its ability to grow with elemental sulfur or thiosulfate coupled to CO oxidation. On the basis of phylogenetic analysis and unique physiological features, the isolate represents a novel species of the genus Carboxydothermus for which the name Carboxydothermus pertinax sp. nov. is proposed; the type strain of the novel species is Ug1(T) (=DSM 23698(T)=NBRC 107576(T)).

  18. Genomic features of Lactococcus lactis IO-1, a lactic acid bacterium that utilizes xylose and produces high levels of L-lactic acid.

    PubMed

    Shimizu-Kadota, Mariko; Kato, Hiroaki; Shiwa, Yuh; Oshima, Kenshiro; Machii, Miki; Araya-Kojima, Tomoko; Zendo, Takeshi; Hattori, Masahira; Sonomoto, Kenji; Yoshikawa, Hirofumi

    2013-01-01

    Lactococcus lactis IO-1 (JCM7638) produces L-lactic acid predominantly when grown at high xylose concentrations, and its utilization is highly desired in the green plastics industry. Therefore it is worthwhile studying its genomic traits. In this study, we focused on (i) genes of possible horizontal transfer derivation (prophages, the nisin-sucrose transposon, and several restriction-modification systems), and (ii) genes for the synthetic pathways of amino acids and vitamins in the IO-1 genome. In view of the results of this analysis, we consider their meanings in strain IO-1.

  19. Effect of the oral intake of probiotic Pediococcus acidilactici BA28 on Helicobacter pylori causing peptic ulcer in C57BL/6 mice models.

    PubMed

    Kaur, Baljinder; Garg, Neena; Sachdev, Atul; Kumar, Balvir

    2014-01-01

    Probiotic lactic acid bacteria are being proposed to cure peptic ulcers by reducing colonization of Helicobacter pylori within the stomach mucosa and by eradicating already established infection. In lieu of that, in vitro inhibitory activity of pediocin-producing probiotic Pediococcus acidilactici BA28 was evaluated against H. pylori by growth inhibition assays. Further, chronic gastritis was first induced in two groups of C57BL/6 mice by orogastric inoculation with H. pylori with polyethylene catheter, and probiotic P. acidilactici BA28 was orally administered to study the eradication and cure of peptic ulcer disease. H. pylori and P. acidilactici BA28 were detected in gastric biopsy and fecal samples of mice, respectively. A probiotic treatment with P. acidilactici BA28, which is able to eliminate H. pylori infection and could reverse peptic ulcer disease, is being suggested as a co-adjustment with conventional antibiotic treatment. The study provided an evidence of controlling peptic ulcer disease, by diet mod

  20. The Use of Tomato Powder Fermented with Pediococcus pentosaceus and Lactobacillus sakei for the Ready-to-Cook Minced Meat Quality Improvement

    PubMed Central

    Juodeikiene, Grazina; Zadeike, Daiva; Viskelis, Pranas; Urbonaviciene, Dalia

    2015-01-01

    Summary In this study, the influence of lactic acid fermentation on the quality of tomato powder was evaluated. The effect of adding fermented tomato powder to ready-to-cook minced pork meat to improve its nutritional value and sensory characteristics was also analysed. The cell growth of Lactobacillus sakei (7.53 log CFU/g) was more intense in the medium containing tomato powder, compared to the growth of Pediococcus pentosaceus (6.35 log CFU/g) during 24 h of fermentation; however, higher acidity (pH=4.1) was observed in the tomato powder samples fermented with Pediococcus pentosaceus. The spontaneous fermentation of tomato powder reduced cell growth by 38% and pH values slightly increased to 4.17, compared to the fermentation with pure LAB. The lactofermentation of tomato powder increased the average β-carotene and lycopene mass fractions by 43.9 and 50.2%, respectively, compared with the nonfermented samples. Lycopene and β-carotene contents in the ready-to-cook minced pork meat were proportional to the added tomato powder (10 and 30%). After cooking, β-carotene and lycopene contents decreased, on average, by 24.2 and 41.2%, respectively. The highest loss (up to 49.2%) of carotenoids was found in samples with 30% nonfermented tomato powder. Tomato powder fermented with 10% Lactobacillus sakei KTU05-6 can be recommended as both a colouring agent and a source of lycopene in the preparation of ready-to-cook minced pork meat. PMID:27904345

  1. Pediococcus parvulus gtf gene encoding the GTF glycosyltransferase and its application for specific PCR detection of beta-D-glucan-producing bacteria in foods and beverages.

    PubMed

    Werning, Maria Laura; Ibarburu, Idoia; Dueñas, Maria Teresa; Irastorza, Ana; Navas, Jesús; López, Paloma

    2006-01-01

    Exopolysaccharide production by lactic acid bacteria is beneficial in the dairy and oat-based food industries and is used to improve the texture of the fermented products. However, beta-D-glucan-producing bacteria are considered spoilage microorganisms in alcoholic beverages because their secreted exopolysaccharides alter the viscosity of cider, wine, and beer, rendering them unpalatable. The plasmidic glycosyltransferase (gtf) gene of the Pediococcus parvulus 2.6 strain isolated from ropy cider has been cloned and sequenced, and its GTF product was functionally expressed in Streptococcus pneumoniae. The GTF protein, which has glycosyltransferase activity, belongs to the COG1215 membrane-bound glycosyltransferase family, and agglutination tests revealed that the enzyme enables S. pneumoniae to synthesize beta-D-glucan. PCR amplification and Southern blot hybridization showed that the gtf gene is also present at different genomic locations in the beta-D-glucan producers Lactobacillus diolivorans G77 and Oenococcus oeni I4 strains, also isolated from ropy cider. A PCR assay has been developed for the detection of exopolysaccharide-producing bacteria. Forward and reverse primers, included respectively in the coding sequences of the putative glycosyltransferase domain and the fifth trans-membrane segment of the GTF, were designed. Analysis of 76 ropy and nonropy lactic acid bacteria validated the method for specific detection of beta-D-glucan homopolysaccharide producer Pediococcus, Lactobacillus, and Oenococcus strains. The limit of the assay in cider was 3 X 10(2) CFU/ml. This molecular method can be useful for the detection of ropy bacteria in cider before spoilage occurs, as well as for isolation of new exopolysaccharide-producing strains of industrial interest.

  2. Effects of the organic acids produced by a lactic acid bacterium in Apis mellifera colony development, Nosema ceranae control and fumagillin efficiency.

    PubMed

    Maggi, Matías; Negri, Pedro; Plischuk, Santiago; Szawarski, Nicolás; De Piano, Fiorella; De Feudis, Leonardo; Eguaras, Martín; Audisio, Carina

    2013-12-27

    The European honey bee Apis mellifera is known to be affected by many parasites and pathogens that have great impact over the insect development. Among parasites affecting bee health, Nosema ceranae is one of the main biotic factors affecting colony populations. As honey bee populations decline, interest in pathogenic and mutualistic relationships between bees and microorganisms has increased. The main goal of the current study was to assess the effect of the oral administration of the metabolites produced by Lactobacillus johnsonii CRL1647 (mainly organic acids) supplemented in syrup, on: (I) N. ceranae sporulation dynamics before and after fumagillin application, and (II) performance of A. mellifera colonies. Different experiments were conducted to evaluate the effects of these bacterial metabolites on bees: in vitro administration revealed no toxic effects against bees. Colonies fed with the lactic acids incremented their beehive population and also the amount of fat bodies per bee. Finally, the organic acids reduced the intensity of the pathogen after the second application of treatment as well as enhanced the fumagillin efficiency. This study provides important information for the development of new control substances against nosemosis.

  3. Antifungal and sprout regulatory bioactivities of phenylacetic acid, indole-3-acetic acid, and tyrosol isolated from the potato dry rot suppressive bacterium Enterobacter cloacae S11:T:07.

    PubMed

    Slininger, P J; Burkhead, K D; Schisler, D A

    2004-12-01

    Enterobacter cloacae S11: T:07 (NRRL B-21050) is a promising biological control agent that has significantly reduced both fungal dry rot disease and sprouting in laboratory and pilot potato storages. The metabolites phenylacetic acid (PAA), indole-3-acetic acid (IAA), and tyrosol (TSL) were isolated from S11:T:07 liquid cultures provided with three different growth media. The bioactivities of these metabolites were investigated via thin-layer chromatography bioautography of antifungal activity, wounded potato assays of dry rot suppressiveness, and cored potato eye assays of sprout inhibition. Relative accumulations of PAA, IAA, and TSL in cultures were nutrient dependent. For the first time, IAA, TSL, and PAA were shown to have antifungal activity against the dry rot causative pathogen Gibberella pulicaris, and to suppress dry rot infection of wounded potatoes. Disease suppression was optimal when all three metabolites were applied in combination. Dosages of IAA that resulted in disease suppression also resulted in sprout inhibition. These results suggest the potential for designing culture production and formulation conditions to achieve a dual purpose biological control agent able to suppress both dry rot and sprouting of stored potatoes.

  4. Evaluation of lactic acid bacterium fermentation products and food-grade chemicals to control Listeria monocytogenes in blue crab (Callinectes sapidus) meat.

    PubMed Central

    Degnan, A J; Kaspar, C W; Otwell, W S; Tamplin, M L; Luchansky, J B

    1994-01-01

    Fresh blue crab (Callinectes sapidus) meat was obtained from retail markets in Florida and sampled for viable Listeria monocytogenes. The pathogen was found in crabmeat in three of four different lots tested by enrichment and at levels of 75 CFU/g in one of the same four lots by direct plating. Next, crabmeat was steam sterilized, inoculated with a three-strain mixture of L. monocytogenes (ca. 5.5 log10 CFU/g), washed with various lactic acid bacterium fermentation products (2,000 to 20,000 arbitrary units [AU]/ml of wash) or food-grade chemicals (0.25 to 4 M), and stored at 4 degrees C. Counts of the pathogen remained relatively constant in control samples during storage for 6 days, whereas in crabmeat washed with Perlac 1911 or MicroGard (10,000 to 20,000 AU), numbers initially decreased (0.5 to 1.0 log10 unit/g) but recovered to original levels within 6 days. Numbers of L. monocytogenes cells decreased 1.5 to 2.7 log10 units/g of crabmeat within 0.04 day when washed with 10,000 to 20,000 AU of Alta 2341, enterocin 1083, or Nisin per ml. Thereafter, counts increased 0.5 to 1.6 log10 units within 6 days. After washing with food-grade chemicals, modest reductions (0.4 to 0.8 log10 unit/g) were observed with sodium acetate (4 M), sodium diacetate (0.5 or 1 M), sodium lactate (1 M), or sodium nitrite (1.5 M). However, Listeria counts in crabmeat washed with 2 M sodium diacetate decreased 2.6 log10 units/g within 6 days. In addition, trisodium phosphate reduced L. monocytogenes counts from 1.7 (0.25 M) to > 4.6 (1 M) log10 units/g within 6 days.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7944362

  5. Phenotypic and Genotypic Characterization of Pediococcus Strains Isolated from Human Clinical Sources

    PubMed Central

    Barros, Rosana R.; Carvalho, Maria Da Glória S.; Peralta, José Mauro; Facklam, Richard R.; Teixeira, Lúcia M.

    2001-01-01

    Seventy-two strains of pediococci isolated from human clinical sources were characterized by conventional physiological tests, chromogenic enzymatic tests, analysis of whole-cell protein profiles (WCPP) by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and analysis of chromosomal DNA restriction profiles by pulsed-field gel electrophoresis (PFGE). Conventional tests allowed identification of 67 isolates: 52 strains were identified as Pediococcus acidilactici, 15 strains were identified as Pediococcus pentosaceus, and 5 strains were not identified because of atypical reactions. Analysis of WCPP identified all isolates since each species had a unique WCPP. By the WCPP method, the atypical strains were identified as P. acidilactici (two strains) and P. pentosaceus (three strains). The chromogenic substrate test with o-nitrophenyl-β-d-glucopyranoside differentiated all 54 strains of P. acidilactici (negative reactions) and 13 (72%) of 18 strains of P. pentosaceus (positive reactions). Isolates of both species were shown to be nonclonal as revealed by the genetic diversity when chromosomal DNA was analyzed by PFGE. Using WCPP as the definitive identification procedure, P. acidilactici (28 of 54 strains; 51.8%) was more likely than P. pentosaceus (4 of 18 strains; 22.3%) to be isolated from blood cultures. PMID:11283035

  6. Characterization of Two Distinct Glycosyl Hydrolase Family 78 α-l-Rhamnosidases from Pediococcus acidilactici▿†

    PubMed Central

    Michlmayr, Herbert; Brandes, Walter; Eder, Reinhard; Schümann, Christina; del Hierro, Andrés M.; Kulbe, Klaus D.

    2011-01-01

    α-l-Rhamnosidases play an important role in the hydrolysis of glycosylated aroma compounds (especially terpenes) from wine. Although several authors have demonstrated the enological importance of fungal rhamnosidases, the information on bacterial enzymes in this context is still limited. In order to fill this important gap, two putative rhamnosidase genes (ram and ram2) from Pediococcus acidilactici DSM 20284 were heterologously expressed, and the respective gene products were characterized. In combination with a bacterial β-glucosidase, both enzymes released the monoterpenes linalool and cis-linalool oxide from a muscat wine extract under ideal conditions. Additionally, Ram could release significant amounts of geraniol and citronellol/nerol. Nevertheless, the potential enological value of these enzymes is limited by the strong negative effects of acidity and ethanol on the activities of Ram and Ram2. Therefore, a direct application in winemaking seems unlikely. Although both enzymes are members of the same glycosyl hydrolase family (GH 78), our results clearly suggest the distinct functionalities of Ram and Ram2, probably representing two subclasses within GH 78: Ram could efficiently hydrolyze only the synthetic substrate p-nitrophenyl-α-l-rhamnopyranoside (Vmax = 243 U mg−1). In contrast, Ram2 displayed considerable specificity toward hesperidin (Vmax = 34 U mg−1) and, especially, rutinose (Vmax = 1,200 U mg−1), a disaccharide composed of glucose and rhamnose. Both enzymes were unable to hydrolyze the flavanone glycoside naringin. Interestingly, both enzymes displayed indications of positive substrate cooperativity. This study presents detailed kinetic data on two novel rhamnosidases, which could be relevant for the further study of bacterial glycosidases. PMID:21784921

  7. Characterization of Pediococcus acidilactici strains isolated from rainbow trout (Oncorhynchus mykiss) feed and larvae: safety, DNA fingerprinting, and bacteriocinogenicity.

    PubMed

    Araújo, Carlos; Muñoz-Atienza, Estefanía; Poeta, Patrícia; Igrejas, Gilberto; Hernández, Pablo E; Herranz, Carmen; Cintas, Luis M

    2016-05-03

    The use of lactic acid bacteria (LAB) as probiotics constitutes an alternative or complementary strategy to chemotherapy and vaccination for disease control in aquaculture. The objectives of this work were (1) the in vitro safety assessment of 8 Pediococcus acidilactici strains isolated from rainbow trout (Oncorhynchus mykiss, Walbaum) feed and larvae; (2) the evaluation of their genetic relatedness; (3) the study of their antimicrobial/bacteriocin activity against fish pathogens; and (4) the biochemical and genetic characterization of the bacteriocin produced by the strain displaying the greatest antimicrobial activity. Concerning the safety assessment, none of the pediococci showed antibiotic resistance nor produced hemolysin or gelatinase, degraded gastric mucin, or deconjugated bile salts. Four strains (50%) produced tyramine or putrescine, but the corresponding genes were not amplified by PCR. Enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) fingerprinting allowed clustering of the pediococci into 2 well-defined groups (68% similarity). From the 8 pediococci displaying direct antimicrobial activity against at least 3 out of 9 fish pathogens, 6 strains (75%) were identified as bacteriocin producers. The bacteriocin produced by P. acidilactici L-14 was purified, and mass spectrometry and DNA sequencing revealed its identity to pediocin PA-1 (PedPA-1). Altogether, our results allowed the identification of 4 (50%) putatively safe pediococci, including 2 bacteriocinogenic strains. ERIC-PCR fingerprinting was a valuable tool for genetic profiling of P. acidilactici strains. This work reports for the first time the characterization of a PedPA-1-producing P. acidilactici strain isolated from an aquatic environment (rainbow trout larvae), which shows interesting properties related to its potential use as a probiotic in aquaculture.

  8. Chemical and rheological properties of the beta-glucan produced by Pediococcus parvulus 2.6.

    PubMed

    Velasco, Susana E; Areizaga, Javier; Irastorza, Ana; Dueñas, Maria T; Santamaria, Antxon; Muñoz, María E

    2009-03-11

    Some physicochemical and rheological properties of the exopolysaccharide (EPS) produced by Pediococcus parvulus 2.6 were examined. Structural characterization by NMR ((1)H and 2D-COSY) showed that the same EPS, a 2-substituted (1,3)-beta-D-glucan, was synthesized irrespective of sugar source used for growth (glucose, fructose, or maltose). The molecular masses of these beta-glucans were always very high (>10(6) Da) and influenced by the culture medium or sugar source. The steady shear rheological experiments showed that all concentrations of the beta-glucan aqueous solutions exhibited a pseudoplastic behavior at high shear rates. Viscoelastic behavior of beta-glucan solutions was determined by dynamic oscillatory analysis. A critical concentration of 0.35% associated with the appearance of entanglements was calculated. The beta-glucan adopts an ordered hydrogen bond dependent helical conformation in neutral and slightly alkaline aqueous solutions, which was partly denatured under more alkaline conditions.

  9. Isolation of Pediococcus acidilactici Kp10 with ability to secrete bacteriocin-like inhibitory substance from milk products for applications in food industry

    PubMed Central

    2012-01-01

    Background Lactic acid bacteria (LAB) can be isolated from traditional milk products. LAB that secrete substances that inhibit pathogenic bacteria and are resistant to acid, bile, and pepsin but not vancomycin may have potential in food applications. Results LAB isolated from a range of traditional fermented products were screened for the production of bacteriocin-like inhibitory substances. A total of 222 LAB strains were isolated from fermented milk products in the form of fresh curds, dried curds, and ghara (a traditional flavor enhancer prepared from whey), and fermented cocoa bean. Eleven LAB isolates that produced antimicrobial substances were identified as Lactococcus lactis, Lactobacillus plantarum, and Pediococcus acidilactici strains by biochemical methods and 16S rDNA gene sequencing. Of these, the cell-free supernatant of Kp10 (P. acidilactici) most strongly inhibited Listeria monocytogenes. Further analysis identified the antimicrobial substance produced by Kp10 as proteinaceous in nature and active over a wide pH range. Kp10 (P. acidilactici) was found to be catalase-negative, able to produce β-galactosidase, resistant to bile salts (0.3%) and acidic conditions (pH 3), and susceptible to most antibiotics. Conclusion Traditionally prepared fermented milk products are good sources of LAB with characteristics suitable for industrial applications. The isolate Kp10 (P. acidilactici) shows potential for the production of probiotic and functional foods. PMID:23153191

  10. Effect of ethanol and low pH on citrulline and ornithine excretion and arc gene expression by strains of Lactobacillus brevis and Pediococcus pentosaceus.

    PubMed

    Araque, Isabel; Bordons, Albert; Reguant, Cristina

    2013-02-01

    The accumulation of citrulline and ornithine in wine or beer as a result of the arginine catabolism of some lactic acid bacteria (LAB) species increases the risk of ethyl carbamate and putrescine formation, respectively. Several LAB species, which are found as spoilage bacteria in alcoholic beverages, have been reported to be arginine degrading. This study evaluates the effect of ethanol content and low pH on the excretion of citrulline and ornithine by two strains belonging to the potential contaminant species Lactobacillus brevis and Pediococcus pentosaceus. In the conditions that most affected cell viability, arginine consumption per cell increased noticeably, indicating that arginine utilization may be a stress responsive mechanism. L. brevis showed a higher accumulation of ornithine in the media than P. pentosaceus. In the presence of ethanol, a higher expression of the arcC gene was found in P. pentosaceus, which resulted in a lower excretion of citrulline and ornithine than in L. brevis. This suggests that L. brevis is more likely to produce these amino acids, which are precursors of ethyl carbamate and putrescine.

  11. Lactobacillus plantarum and Pediococcus pentosaceus starter cultures as a tool for microflora management in malting and for enhancement of malt processability.

    PubMed

    Laitila, Arja; Sweins, Hannele; Vilpola, Arvi; Kotaviita, Erja; Olkku, Juhani; Home, Silja; Haikara, Auli

    2006-05-31

    Lactobacillus plantarum VTT E-78076 (E76) and Pediococcus pentosaceus VTT E-90390 (E390) starter cultures were added to the steeping water of normal malting barley in order to balance the microbial community and to enhance malt processability. In this study, we also investigated the effects of lactic acid-acidified MRS-spent medium (MRS-LA) on malting performance. Malting trials with five different two-row barley varieties were carried out in 25 kg pilot scale. The starter cultures promoted yeast growth during malting and restricted the growth of harmful bacteria and Fusarium fungi. Furthermore, they had positive effects on malt characteristics. Reduction in wort viscosity and beta-glucan content and enhanced xylanase and microbial beta-glucanase activities were observed. Starter cultures notably improved lautering performance. Some of the beneficial effects were due to the lactic acid and low pH, as similar effects were obtained with MRS-LA. Starter cultures offer a tool for tailoring of malt properties.

  12. Broth and agar hop-gradient plates used to evaluate the beer-spoilage potential of Lactobacillus and Pediococcus isolates.

    PubMed

    Haakensen, M; Schubert, A; Ziola, B

    2009-03-15

    Identification of the beer-spoilage Lactobacillus and Pediococcus bacteria has largely taken two approaches; identification of spoilage-associated genes or identification of specific species of bacteria regardless of ability to grow in beer. The problem with these two approaches is that they are either overly inclusive (i.e., detect all bacteria of a given species regardless of spoilage potential) or overly selective (i.e., rely upon individual, putative spoilage-associated genes). Our goal was to design a method to assess the ability of Lactobacillus and Pediococcus to spoil beer that is independent of speciation or genetic background. In searching for a method by which to differentiate between beer-spoilage bacteria and bacteria that cannot grow in beer, we explored the ability of lactobacilli and pediococci isolates to grow in the presence of varying concentrations of hop-compounds and ethanol in broth medium versus on agar medium. The best method for differentiating between bacteria that can grow in beer and bacteria that do not pose a threat as beer-spoilage organisms was found to be a hop-gradient agar plate containing ethanol. This hop-gradient agar plate technique provides a rapid and simple solution to the dilemma of assessing the ability of Lactobacillus and Pediococcus isolates to grow in beer, and provides new insights into the different strategies used by these bacteria to survive under the stringent conditions of beer.

  13. Cloning, expression, and nucleotide sequence of genes involved in production of pediocin PA-1, and bacteriocin from Pediococcus acidilactici PAC1.0.

    PubMed Central

    Marugg, J D; Gonzalez, C F; Kunka, B S; Ledeboer, A M; Pucci, M J; Toonen, M Y; Walker, S A; Zoetmulder, L C; Vandenbergh, P A

    1992-01-01

    The production of pediocin PA-1, a small heat-stable bacteriocin, is associated with the presence of the 9.4-kbp plasmid pSRQ11 in Pediococcus acidilactici PAC1.0. It was shown by subcloning of pSRQ11 in Escherichia coli cloning vectors that pediocin PA-1 is produced and, most probably, secreted by E. coli cells. Deletion analysis showed that a 5.6-kbp SalI-EcoRI fragment derived from pSRQ11 is required for pediocin PA-1 production. Nucleotide sequence analysis of this 5.6-kbp fragment indicated the presence of four clustered open reading frames (pedA, pedB, pedC, and pedD). The pedA gene encodes a 62-amino-acid precursor of pediocin PA-1, as the predicted amino acid residues 19 to 62 correspond entirely to the amino acid sequence of the purified pediocin PA-1. Introduction of a mutation in pedA resulted in a complete loss of pediocin production. The pedB and pedC genes, encoding proteins of 112 and 174 amino acid residues, respectively, are located directly downstream of the pediocin structural gene. Functions could not be assigned to their gene products; mutation analysis showed that the PedB protein is not involved in pediocin PA-1 production. The mutation analysis further revealed that the fourth gene, pedD, specifying a relatively large protein of 724 amino acids, is required for pediocin PA-1 production in E. coli. The predicted pedD protein shows strong similarities to several ATP-dependent transport proteins, including the E. coli hemolysin secretion protein HlyB and the ComA protein, which is required for competence induction for genetic transformation in Streptococcus pneumoniae.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1514784

  14. Putrescine production from different amino acid precursors by lactic acid bacteria from wine and cider.

    PubMed

    Costantini, Antonella; Pietroniro, Roberta; Doria, Francesca; Pessione, Enrica; Garcia-Moruno, Emilia

    2013-07-01

    The aim of this work was to study the production of biogenic amines and particularly putrescine in lactic acid bacteria (LAB) related to wine and cider. We applied an analytical protocol that involves the use of PCR and TLC techniques to determine the production of putrescine from different precursors. Moreover, we also studied the ability of the Lactobacillus and Pediococcus tested to produce histamine and tyramine. The results showed that the majority of the Lactobacillus brevis analyzed harbour both AgDI and tdc genes and are tyramine and putrescine producers. Conversely, among the other LAB tested, only one Lactobacillus hilgardii and one Pediococcus pentosaceus produced putrescine. The AgDI gene was also detected in two other LAB (Lactobacillus mali and Pediococcus parvulus), but no putrescine production was observed. Finally, hdc gene and histamine production were found in strains (L. hilgardii 5211, isolated from wine, and Lactobacillus casei 18, isolated from cider) that were not putrescine producers.

  15. 3-mercaptopropionate dioxygenase, a cysteine dioxygenase homologue, catalyzes the initial step of 3-mercaptopropionate catabolism in the 3,3-thiodipropionic acid-degrading bacterium variovorax paradoxus.

    PubMed

    Bruland, Nadine; Wübbeler, Jan Hendrik; Steinbüchel, Alexander

    2009-01-02

    The thioether 3,3-thiodipropionic acid can be used as precursor substrate for biotechnological synthesis of 3-mercaptopropionic acid-containing polythioesters. Therefore, the hitherto unknown catabolism of this compound was elucidated to engineer novel and improved polythioester biosynthesis pathways in the future. Bacteria capable of using 3,3-thiodipropionic acid as the sole source of carbon and energy for growth were enriched from the environment. From eleven isolates, TBEA3, TBEA6, and SFWT were morphologically and physiologically characterized. Their 16 S rDNAs and other features affiliated these isolates to the beta-subgroup of the proteobacteria. Tn5::mob mutagenesis of isolate Variovorax paradoxus TBEA6 yielded ten mutants fully or partially impaired in growth on 3,3-thiodipropionic acid. Genotypic characterization of two 3,3-thiodipropionic acid-negative mutants demonstrated the involvement of a bacterial cysteine dioxygenase (EC 1.13.11.22) homologue in the further catabolism of the 3,3-thiodipropionic acid cleavage product 3-mercaptopropionic acid. Detection of 3-sulfinopropionate in the supernatant of one of these mutants during cultivation on 3,3-thiodipropionic acid as well as in vivo and in vitro enzyme assays using purified protein demonstrated oxygenation of 3-mercaptopropionic acid to 3-sulfinopropionate by this enzyme; cysteine and cysteamine were not used as substrate. Beside cysteine dioxygenase and cysteamine dioxygenase, this 3-mercaptopropionic acid dioxygenase is the third example for a thiol dioxygenase and the first report about the microbial catabolism of 3-mercaptopropionic acid. Insertion of Tn5::mob in a gene putatively coding for a family III acyl-CoA-transferase resulted in the accumulation of 3-sulfinopropionate during cultivation on 3,3-thiodipropionic acid, indicating that this compound is further metabolized to 3-sulfinopropionyl-CoA and subsequently to propionyl-CoA.

  16. Antimicrobial susceptibility of vancomycin-resistant Leuconostoc, Pediococcus, and Lactobacillus species.

    PubMed Central

    Swenson, J M; Facklam, R R; Thornsberry, C

    1990-01-01

    Eighty-five strains of vancomycin-resistant gram-positive bacteria from three genera, Leuconostoc, Pediococcus, and Lactobacillus, were tested to determine susceptibility to 24 antimicrobial agents by broth microdilution and to 10 agents by disk diffusion. The MICs of vancomycin and teicoplanin ranged from 64 to greater than 512 micrograms/ml; however, the MICs of daptomycin, a new lipopeptide, were all less than or equal to 0.25 micrograms/ml. None of the organisms were resistant to imipenem, minocycline, chloramphenicol, gentamicin, or daptomycin. The MICs of penicillin were in the moderately susceptible range for all but three strains. Susceptibility to the other agents varied by genus and, in some cases, by species. When disk diffusion results were compared with MICs for drugs recommended for streptococci by the National Committee for Clinical Laboratory Standards, Villanova, Pa., few very major or major errors were obtained, but the number of minor errors was 19.3%. Therefore, we recommended that MIC testing be used instead of disk diffusion testing for these organisms. PMID:2344161

  17. Carrier-mediated transport of folate in a mutant of Pediococcus cerevisiae.

    PubMed

    Mandelbaum-Shavit, F; Grossowicz, N

    1973-05-01

    A mutant strain of Pediococcus cerevisiae (P. cerevisiae/PteGlu) was isolated which grows on low-folate (PteGlu) concentrations (200 pg/ml). The growth response of the parent and mutant strains to folinate (5-CHO-H(4)PteGlu) was the same. The transport of (14)C-PteGlu by P. cerevisiae/PteGlu was temperature-dependent (Q(10) between 27 C and 37 C was about 2), energy-dependent, and pH-dependent and was inhibited by iodoacetate, 2,4-dinitrophenol, potassium fluoride, and sodium azide. The uptake obeyed saturation kinetics with an apparent K(m) of 6.6 x 10(-6) M and V(max) of 4.0 x 10(-10) mol per min per mg (dry weight). At the steady state the intracellular concentration of PteGlu was 120-fold higher from that of the medium. Reduced folates like 5-CHO-H(4)PteGlu and methyl-tetrahydrofolate (5-CH(3)-H(4)PteGlu) as well as 2,4-diaminoanalogues (amethopterin and aminopterin) were shown to compete for the PteGlue-carrier.

  18. Effect of high pressure on growth and bacteriocin production of Pediococcus acidilactici HA-6111-2

    NASA Astrophysics Data System (ADS)

    Castro, S. M.; Kolomeytseva, M.; Casquete, R.; Silva, J.; Saraiva, J. A.; Teixeira, P.

    2015-10-01

    This study was aimed to investigate the effect of high pressure processing (HPP, 200-600 MPa) on the (i) survival of Listeria innocua and Pediococcus acidilactici HA-6111-2; (ii) production of bacteriocin bacHA-6111-2 and (iii) activity of bacteriocin against untreated and pressure-treated L. innocua cells. Inactivation of P. acidilactici was observed for pressures of >300 MPa. However, at this pressure level, L. innocua was more sensitive. Bacteriocin crude extract was pressure stable, with a decrease for pressures of ≥400 MPa. Pressures of ≤200 MPa did not affect bacteriocin production when compared with non-pressure-treated cells, whereas higher pressures caused a 2- to 4-fold decrease on the maximum level of bacteriocin production. Growth curves of P. acidilactici were fitted with the modified Gompertz model. The lag phase period depended on the magnitude of the pressure applied: there was a delay in the exponential phase as pressure increased and, as a consequence, in the beginning of bacteriocin production. Since P. acidilactici HA-6111-2 and its bacteriocin have shown resistance to pressures up to 300-400 MPa, they could be used in combination with HPP in order to improve food safety.

  19. Probiotic properties of Pediococcus strains isolated from jeotgals, salted and fermented Korean sea-food.

    PubMed

    Lee, Kang Wook; Park, Ji Yeong; Sa, Hyun Deok; Jeong, Ji Hee; Jin, Dong Eun; Heo, Ho Jin; Kim, Jeong Hwan

    2014-08-01

    Three Pediococcus pentosaceus strains were isolated from jeotgals, salted and fermented Korean sea-foods, and their probiotic potentials were examined. After 2 h exposure to pH 3.0, P. pentosaceus F66 survived with the survival ratio of 32.6% followed by P. pentosaceus D56 (17.2%) and P. pentosaceus A24 (7.5%). P. pentosaceus F66 also survived better (26.6%) than P. pentosaceus A24 (13.7%) and P. pentosaceus D56 (5.8%) after 2 h exposure to 0.3% bile salts. Three strains grew slowly on MRS broth with 15% NaCl (w/v), reaching the OD600 values of 0.4-0.8 in 36 h. They adhered to Caco-2 cells (10.9-13.9 CFU/cell) with similar degree of adherence of a positive control, Lactobacillus rhamnosus GG (12.8 ± 0.5 CFU/cell). Three strains possess some desirable enzyme activities such as β-galactosidase, α-glucosidase, β-glucosidase, and N-acetyl-β-glucosidase. From these results, P. pentosaceus F66 seems qualified as a probiotic and can be utilized for fermented foods including jeotgals.

  20. Safety Evaluation of Multiple Strains of Lactobacillus plantarum and Pediococcus pentosaceus in Wistar Rats Based on the Ames Test and a 28-Day Feeding Study

    PubMed Central

    Leu, Sew-Fen; Huang, Quan-Rong; Chou, Lan-Chun; Huang, Chun-Chih

    2014-01-01

    Three lactic acid bacterial strains, Lactobacillus plantarum, HK006, and HK109, and Pediococcus pentosaceus PP31 exhibit probiotic potential as antiallergy agents, both in vitro and in vivo. However, the safety of these new strains requires evaluation when isolated from infant faeces or pickled cabbage. Multiple strains (HK006, HK109, and PP31) were subject to a bacterial reverse mutation assay and a short-term oral toxicity study. The powder product exhibited mutagenic potential in Salmonella Typhimurium strains TA98 and TA1535 (with or without metabolic activation). In the short-term oral toxicity study, rats received a normal dosage of 390 mg/kg/d (approximately 9 × 109 CFU/kg/d) or a high dosage of 1950 mg/kg/d (approximately 4.5 × 1010 CFU/kg/d) for 28 d. No adverse effects were observed regarding the general condition, behaviour, growth, feed and water consumption, haematology, clinical chemistry indices, organ weights, or histopathologic analysis of the rats. These studies have demonstrated that the consumption of multiple bacterial strains is not associated with any signs of mutagenicity of S. Typhimurium or toxicity in Wistar rats, even after consuming large quantities of bacteria. PMID:25379552

  1. Whole-Genome Sequence Analysis of Bombella intestini LMG 28161T, a Novel Acetic Acid Bacterium Isolated from the Crop of a Red-Tailed Bumble Bee, Bombus lapidarius

    PubMed Central

    Li, Leilei; Illeghems, Koen; Van Kerrebroeck, Simon; Borremans, Wim; Cleenwerck, Ilse; Smagghe, Guy; De Vuyst, Luc

    2016-01-01

    The whole-genome sequence of Bombella intestini LMG 28161T, an endosymbiotic acetic acid bacterium (AAB) occurring in bumble bees, was determined to investigate the molecular mechanisms underlying its metabolic capabilities. The draft genome sequence of B. intestini LMG 28161T was 2.02 Mb. Metabolic carbohydrate pathways were in agreement with the metabolite analyses of fermentation experiments and revealed its oxidative capacity towards sucrose, D-glucose, D-fructose and D-mannitol, but not ethanol and glycerol. The results of the fermentation experiments also demonstrated that the lack of effective aeration in small-scale carbohydrate consumption experiments may be responsible for the lack of reproducibility of such results in taxonomic studies of AAB. Finally, compared to the genome sequences of its nearest phylogenetic neighbor and of three other insect associated AAB strains, the B. intestini LMG 28161T genome lost 69 orthologs and included 89 unique genes. Although many of the latter were hypothetical they also included several type IV secretion system proteins, amino acid transporter/permeases and membrane proteins which might play a role in the interaction with the bumble bee host. PMID:27851750

  2. Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers

    PubMed Central

    2013-01-01

    Background Trypanosomatids of the genera Angomonas and Strigomonas live in a mutualistic association characterized by extensive metabolic cooperation with obligate endosymbiotic Betaproteobacteria. However, the role played by the symbiont has been more guessed by indirect means than evidenced. Symbiont-harboring trypanosomatids, in contrast to their counterparts lacking symbionts, exhibit lower nutritional requirements and are autotrophic for essential amino acids. To evidence the symbiont’s contributions to this autotrophy, entire genomes of symbionts and trypanosomatids with and without symbionts were sequenced here. Results Analyses of the essential amino acid pathways revealed that most biosynthetic routes are in the symbiont genome. By contrast, the host trypanosomatid genome contains fewer genes, about half of which originated from different bacterial groups, perhaps only one of which (ornithine cyclodeaminase, EC:4.3.1.12) derived from the symbiont. Nutritional, enzymatic, and genomic data were jointly analyzed to construct an integrated view of essential amino acid metabolism in symbiont-harboring trypanosomatids. This comprehensive analysis showed perfect concordance among all these data, and revealed that the symbiont contains genes for enzymes that complete essential biosynthetic routes for the host amino acid production, thus explaining the low requirement for these elements in symbiont-harboring trypanosomatids. Phylogenetic analyses show that the cooperation between symbionts and their hosts is complemented by multiple horizontal gene transfers, from bacterial lineages to trypanosomatids, that occurred several times in the course of their evolution. Transfers occur preferentially in parts of the pathways that are missing from other eukaryotes. Conclusion We have herein uncovered the genetic and evolutionary bases of essential amino acid biosynthesis in several trypanosomatids with and without endosymbionts, explaining and complementing decades of

  3. Influence of triethyl phosphate on phosphatase activity in shooting range soil: Isolation of a zinc-resistant bacterium with an acid phosphatase.

    PubMed

    Story, Sandra; Brigmon, Robin L

    2017-03-01

    Phosphatase-mediated hydrolysis of organic phosphate may be a viable means of stabilizing heavy metals via precipitation as a metal phosphate in bioremediation applications. We investigated the effect of triethyl phosphate (TEP) on soil microbial-phosphatase activity in a heavy-metal contaminated soil. Gaseous TEP has been used at subsurface sites for bioremediation of organic contaminants but not applied in heavy-metal contaminated areas. Little is known about how TEP affects microbial activity in soils and it is postulated that TEP can serve as a phosphate source in nutrient-poor groundwater and soil/sediments. Over a 3-week period, TEP amendment to microcosms containing heavy-metal contaminated soil resulted in increased activity of soil acid-phosphatase and repression of alkaline phosphatase, indicating a stimulatory effect on the microbial population. A soil-free enrichment of microorganisms adapted to heavy-metal and acidic conditions was derived from the TEP-amended soil microcosms using TEP as the sole phosphate source and the selected microbial consortium maintained a high acid-phosphatase activity with repression of alkaline phosphatase. Addition of 5mM zinc to soil-free microcosms had little effect on acid phosphatase but inhibited alkaline phosphatase. One bacterial member from the consortium, identified as Burkholderia cepacia sp., expressed an acid-phosphatase activity uninhibited by high concentrations of zinc and produced a soluble, indigo pigment under phosphate limitation. The pigment was produced in a phosphate-free medium and was not produced in the presence of TEP or phosphate ion, indicative of purple acid-phosphatase types that are pressed by bioavailable phosphate. These results demonstrate that TEP amendment was bioavailable and increased overall phosphatase activity in both soil and soil-free microcosms supporting the possibility of positive outcomes in bioremediation applications.

  4. Draft genome sequence of Sporolactobacillus inulinus strain CASD, an efficient D-lactic acid-producing bacterium with high-concentration lactate tolerance capability.

    PubMed

    Yu, Bo; Su, Fei; Wang, Limin; Xu, Ke; Zhao, Bo; Xu, Ping

    2011-10-01

    Sporolactobacillus inulinus CASD is an efficient D-lactic acid producer with high optical purity. Here we report for the first time the draft genome sequence of S. inulinus (2,930,096 bp). The large number of annotated two-component system genes makes it possible to explore the mechanism of extraordinary lactate tolerance of S. inulinus CASD.

  5. Different Flour Microbial Communities Drive to Sourdoughs Characterized by Diverse Bacterial Strains and Free Amino Acid Profiles

    PubMed Central

    Celano, Giuseppe; De Angelis, Maria; Minervini, Fabio; Gobbetti, Marco

    2016-01-01

    This work aimed to investigate whether different microbial assemblies in flour may influence the microbiological and biochemical characteristics of traditional sourdough. To reach this purpose, members of lactic acid bacteria, enterobacteria, and yeasts were isolated from durum wheat flour. Secondly, the isolated microorganisms (Pediococcus pentosaceus, Saccharomyces cerevisiae, Pantoea agglomerans, and Escherichia hermannii) were inoculated in doughs prepared with irradiated flour (gamma rays at 10 kGy), so that eight different microbial assemblies were obtained. Two non-inoculated controls were prepared, one of which (C-IF) using irradiated flour and the other (C) using non-irradiated flour. As shown by plate counts, irradiation of flour caused total inactivation of yeasts and a decrease of all the other microbial populations. However, acidification occurred also in the dough C-IF, due to metabolic activity of P. pentosaceus that had survived irradiation. After six fermentations, P. pentosaceus was the dominant lactic acid bacterium species in all the sourdoughs produced with irradiated flour (IF). Yet, IF-based sourdoughs broadly differed from each other in terms of strains of P. pentosaceus, probably due to the different microorganisms initially inoculated. Quantitative and qualitative differences of free amino acids concentration were found among the sourdoughs, possibly because of different microbial communities. In addition, as shown by culture-independent analysis (16S metagenetics), irradiation of flour lowered and modified microbial diversity of sourdough ecosystem. PMID:27877165

  6. Role of two amino acid residues' insertion on thermal stability of thermophilic α-amylase AMY121 from a deep sea bacterium Bacillus sp. SCSIO 15121.

    PubMed

    Li, Lizhen; Yang, Jian; Li, Jie; Long, Lijuan; Xiao, Yunzhu; Tian, Xinpeng; Wang, Fazuo; Zhang, Si

    2015-05-01

    α-Amylases from Bacillus licheniformis (BLA) and Bacillus amyloliquefaciens (BAA) are both important industrial enzymes with high similarity in structure but significant differences in thermostability. The mechanisms underlying this discrepancy are still poorly understood. Here, we investigated the role of two amino acids' insertion on the thermostability of these two group amylases. A newly obtained thermophilic amylase AMY121 was found much closer to BLA in both primary structure and enzymological properties. Two amino acids' insertion widespread among BAA group α-amylases was identified as one of the key factors leading to the thermostability differences, since thermostability of insertion mutants (AMY121-EG and AMY121-AA) from AMY121 significantly decreased, while that of deletion mutant from BAA increased. Moreover, we proposed that conformational disturbance caused by insertion mutation might weaken the calcium-binding affinity and consequently decrease the enzyme thermostability.

  7. Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

    SciTech Connect

    Dees, C.; Ringleberg, D.; Scott, T.C.; Phelps, T.

    1994-06-01

    The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescens with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.

  8. Dethiosulfatibacter aminovorans gen. nov., sp. nov., a novel thiosulfate-reducing bacterium isolated from coastal marine sediment via sulfate-reducing enrichment with Casamino acids.

    PubMed

    Takii, Susumu; Hanada, Satoshi; Tamaki, Hideyuki; Ueno, Yutaka; Sekiguchi, Yuji; Ibe, Akihiro; Matsuura, Katsumi

    2007-10-01

    A sulfate-reducing enrichment culture originating from coastal marine sediment of the eutrophic Tokyo Bay, Japan, was successfully established with Casamino acids as a substrate. A thiosulfate reducer, strain C/G2(T), was isolated from the enrichment culture after further enrichment with glutamate. Cells of strain C/G2(T) were non-motile rods (0.6-0.8 microm x 2.2-4.8 microm) and were found singly or in pairs and sometimes in short chains. Spores were not formed. Cells of strain C/G2(T) stained Gram-negatively, despite possessing Gram-positive cell walls. The optimum temperature for growth was 28-30 degrees C, the optimum pH was around 7.8 and the optimum salt concentration was 20-30 g l(-1). Lactate, pyruvate, serine, cysteine, threonine, glutamate, histidine, lysine, arginine, Casamino acids, peptone and yeast extract were fermented as single substrates and no sugar was used as a fermentative substrate. A Stickland reaction was observed with some pairs of amino acids. Fumarate, alanine, proline, phenylalanine, tryptophan, glutamine and aspartate were utilized only in the presence of thiosulfate. Strain C/G2(T) fermented glutamate to H2, CO2, acetate and propionate. Thiosulfate and elemental sulfur were reduced to sulfide. Sulfate, sulfite and nitrate were not utilized as electron acceptors. The growth of strain C/G2(T) on Casamino acids or glutamate was enhanced by co-culturing with Desulfovibrio sp. isolated from the original mixed culture enriched with Casamino acids. The DNA G+C content of strain C/G2(T) was 41.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain C/G2(T) formed a distinct cluster with species of the genus Sedimentibacter. The closest relative was Sedimentibacter hydroxybenzoicus (with a gene sequence similarity of 91 %). On the basis of its phylogenetic and phenotypic properties, strain C/G2(T) (=JCM 13356(T)=NBRC 101112(T)=DSM 17477(T)) is proposed as representing a new genus and novel species, Dethiosulfatibacter

  9. Falcatimonas natans gen. nov., sp. nov., a strictly anaerobic, amino-acid-decomposing bacterium isolated from a methanogenic reactor of cattle waste.

    PubMed

    Watanabe, Misa; Kaku, Nobuo; Ueki, Katsuji; Ueki, Atsuko

    2016-11-01

    A strictly anaerobic bacterial strain (WN011T) was isolated from a methanogenic reactor treating waste from cattle farms. Cells of the strain were Gram-stain-negative curved rods with a polar flagellum. Spores were not produced. The optimum temperature for growth was 35-37 °C and the optimum pH was 6.7. The strain did not utilize carbohydrates as growth substrates. The strain grew in PY medium and produced acetate, butyrate, isovalerate and H2 as well as propionate and isobutyrate as minor products. Amino acids (l-isoleucine, l-leucine, l-lysine, l-serine, l-threonine and l-valine) added to PY medium enhanced growth of the strain and increased the amounts of fermentation products. Oxidase, catalase and nitrate-reducing activities were negative. Hydrogen sulfide was produced. The genomic DNA G+C content was 38.8 mol%. Compounds related to iso-C15 : 0 (fatty acid, dimethylacetal and aldehyde) were detected as predominant components by the cellular fatty acids analysis. The diagnostic diamino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid. On the basis of 16S rRNA gene sequences, three clones from wastewater were very closely related to strain WN011T (up to 99.9 % sequence similarity). The most closely related described species were those in cluster XIVa of the class Clostridia such as Ruminococcus gauvreauii (93.8 % 16S rRNA gene sequence similarity), Clostridium fimetarium (93.5 %) and Clostridium bolteae(93.5 %). Based on the distinct differences in phylogenetic and phenotypic characteristics of strain WN011T from those of related species, it is concluded that strain WN011T represents a novel species of a new genus in the family Lachnospiraceae, for which the name Falcatimonas natans gen. nov., sp. nov. is proposed. The type strain of the type species is WN011T (=JCM 16476T=DSM 22923T).

  10. Transcriptome sequence and plasmid copy number analysis of the brewery isolate Pediococcus claussenii ATCC BAA-344 T during growth in beer.

    PubMed

    Pittet, Vanessa; Phister, Trevor G; Ziola, Barry

    2013-01-01

    Growth of specific lactic acid bacteria in beer leads to spoiled product and economic loss for the brewing industry. Microbial growth is typically inhibited by the combined stresses found in beer (e.g., ethanol, hops, low pH, minimal nutrients); however, certain bacteria have adapted to grow in this harsh environment. Considering little is known about the mechanisms used by bacteria to grow in and spoil beer, transcriptome sequencing was performed on a variant of the beer-spoilage organism Pediococcus claussenii ATCC BAA-344(T) (Pc344-358). Illumina sequencing was used to compare the transcript levels in Pc344-358 growing mid-exponentially in beer to those in nutrient-rich MRS broth. Various operons demonstrated high gene expression in beer, several of which are involved in nutrient acquisition and overcoming the inhibitory effects of hop compounds. As well, genes functioning in cell membrane modification and biosynthesis demonstrated significantly higher transcript levels in Pc344-358 growing in beer. Three plasmids had the majority of their genes showing increased transcript levels in beer, whereas the two cryptic plasmids showed slightly decreased gene expression. Follow-up analysis of plasmid copy number in both growth environments revealed similar trends, where more copies of the three non-cryptic plasmids were found in Pc344-358 growing in beer. Transcriptome sequencing also enabled the addition of several genes to the P. claussenii ATCC BAA-344(T) genome annotation, some of which are putatively transcribed as non-coding RNAs. The sequencing results not only provide the first transcriptome description of a beer-spoilage organism while growing in beer, but they also highlight several targets for future exploration, including genes that may have a role in the general stress response of lactic acid bacteria.

  11. Caproiciproducens galactitolivorans gen. nov., sp. nov., a bacterium capable of producing caproic acid from galactitol, isolated from a wastewater treatment plant.

    PubMed

    Kim, Byung-Chun; Seung Jeon, Byoung; Kim, Seil; Kim, Hyunook; Um, Youngsoon; Sang, Byoung-In

    2015-12-01

    A strictly anaerobic, Gram-stain-positive, non-spore-forming, rod-shaped bacterial strain, designated BS-1T, was isolated from an anaerobic digestion reactor during a study of bacteria utilizing galactitol as the carbon source. Its cells were 0.3-0.5 μm × 2-4 μm, and they grew at 35-45 °C and at pH 6.0-8.0. Strain BS-1T produced H2, CO2, ethanol, acetic acid, butyric acid and caproic acid as metabolic end products of anaerobic fermentation. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that strain BS-1T represented a novel bacterial genus within the family Ruminococcaceae, Clostridium Cluster IV. The type strains that were most closely related to strain BS-1T were Clostridium sporosphaeroides KCTC 5598T (94.5 %), Clostridium leptum KCTC 5155T (94.3 %), Ruminococcus bromii ATCC 27255T (92.1 %) and Ethanoligenens harbinense YUAN-3T (91.9 %). Strain BS-1T had 17.6 % and 20.9 % DNA-DNA relatedness values with C. sporosphaeroides DSM 1294T and C. leptum DSM 753T, respectively. The major components of the cellular fatty acids were C16 : 0 dimethyl aldehyde (DMA) (22.1 %), C16 : 0 aldehyde (14.1 %) and summed feature 11 (iso-C17 : 0 3-OH and/or C18 : 2 DMA; 10.0 %). The genomic DNA G+C content was 50.0 mol%. Phenotypic and phylogenetic characteristics allowed strain BS-1T to be clearly distinguished from other taxa of the genus Clostridium Cluster IV. On the basis of these data, the isolate is considered to represent a novel genus and novel species within Clostridium Cluster IV, for which the name Caproiciproducens galactitolivorans gen. nov., sp. nov. is proposed. The type species is BS-1T ( = JCM 30532T and KCCM 43048T).

  12. Methylocystis bryophila sp. nov., a facultatively methanotrophic bacterium from acidic Sphagnum peat, and emended description of the genus Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993.

    PubMed

    Belova, Svetlana E; Kulichevskaya, Irina S; Bodelier, Paul L E; Dedysh, Svetlana N

    2013-03-01

    A novel species is proposed for two facultatively methanotrophic representatives of the genus Methylocystis, strains H2s(T) and S284, which were isolated from an acidic (pH 4.3) Sphagnum peat-bog lake (Teufelssee, Germany) and an acidic (pH 3.8) peat bog (European North Russia), respectively. Cells of strains H2s(T) and S284 are aerobic, Gram-negative, non-motile, curved coccoids or short rods that contain an intracytoplasmic membrane system typical of type-II methanotrophs. They possess both a soluble and a particulate methane monooxygenase (MMO); the latter is represented by two isozymes, pMMO1 and pMMO2. The preferred growth substrates are methane and methanol. In the absence of C1 substrates, however, these methanotrophs are capable of slow growth on acetate. Atmospheric nitrogen is fixed by means of an aerotolerant nitrogenase. Strains H2s(T) and S284 grow between pH 4.2 and 7.6 (optimum pH 6.0-6.5) and at 8-37 °C (optimum 25-30 °C). The major fatty acids are C18 : 1ω8c, C18 : 1ω7c and C16 : 1ω7c; the major quinone is Q-8. The DNA G+C content is 62.0-62.3 mol%. Strains H2s(T) and S284 share identical 16S rRNA gene sequences, which displayed 96.6-97.3 % similarity to sequences of other taxonomically characterized members of the genus Methylocystis. Therefore, strains H2s(T) and S284 are classified as members of a novel species, for which the name Methylocystis bryophila sp. nov. is proposed; strain H2s(T) ( = DSM 21852(T)  = VKM B-2545(T)) is the type strain.

  13. Modeling the acid-base properties of bacterial surfaces: A combined spectroscopic and potentiometric study of the gram-positive bacterium Bacillus subtilis.

    PubMed

    Leone, Laura; Ferri, Diego; Manfredi, Carla; Persson, Per; Shchukarev, Andrei; Sjöberg, Staffan; Loring, John

    2007-09-15

    In this study, macroscopic and spectroscopic data were combined to develop a surface complexation model that describes the acid-base properties of Bacillus subtilis. The bacteria were freeze-dried and then resuspended in 0.1 M NaCl ionic medium. Macroscopic measurements included potentiometric acid-base titrations and electrophoretic mobility measurements. In addition, ATR-FTIR spectra of wet pastes from suspensions of Bacillus subtilis at different pH values were collected. The least-squares program MAGPIE was used to generate a surface complexation model that takes into account the presence of three acid-base sites on the surface: tripple bond COOH, tripple bond NH+, and tripple bond PO-, which were identified previously by XPS measurements. Both potentiometric titration data and ATR-FTIR spectra were used quantitatively, and electrostatic effects at the charged bacterial surface were accounted for using the constant capacitance model. The model was calculated using two different approaches: in the first one XPS data were used to constrain the ratio of the total concentrations of all three surface sites. The capacitance of the double layer, the total buffer capacity, and the deprotonation constants of the tripple bond NH+, tripple bond POH, and tripple bond COOH species were determined in the fit. A second approach is presented in which the ratio determined by XPS of the total concentrations of tripple bond NH+ to tripple bond PO- sites is relaxed. The total concentration of tripple bond PO- sites was determined in the fit, while the deprotonation constant for tripple bond POH was manually varied until the minimization led to a model which predicted an isoelectric point that resulted in consistency with electrophoretic mobility data. The model explains well the buffering capacity of Bacillus subtilis suspensions in a wide pH range (between pH=3 and pH=9) which is of considerable environmental interest. In particular, a similar quantitative use of the IR data

  14. Necrotizing cellulitis of the abdominal wall, caused by Pediococcus sp., due to rupture of a retroperitoneal stromal cell tumor

    PubMed Central

    Michalopoulos, Nick; Arampatzi, Stergiani; Papavramidis, Theodossis S.; Kotidis, Efstathios; Laskou, Styliani; Papavramidis, Spiros T.

    2013-01-01

    INTRODUCTION Soft tissue necrotizing infections are a significant cause of morbidity and mortality. The aim of this study is to present a patient with necrotizing infection of abdominal wall resulting from the rupture of a retroperitoneal stromal tumor. PRESENTATION OF CASE We present a 60-year-old Caucasian male patient with necrotizing infection of abdominal wall secondary to the rupture of a retroperitoneal stromal tumor. The patient was initially treated with debridement and fasciotomy of the anterior abdominal wall. Laparotomy revealed purulent peritonitis caused by infiltration and rupture of the splenic flexure by the tumor. Despite prompt intervention the patient died 19 days later. The isolated microorganism causing the infection was the rarely identified as cause of infections in humans Pediococcus sp., a gram-positive, catalase-negative coccus. DISCUSSION Necrotizing infections of abdominal wall are usually secondary either to perineal or to intra-abdominal infections. Gastrointestinal stromal cell tumors could be rarely complicated with perforation and abscess formation. In our case, the infiltrated by the extra-gastrointestinal stromal cell tumor ruptured colon was the source of the infection. The pediococci are rarely isolated as the cause of severe septicemia. CONCLUSION Ruptured retroperitoneal stromal cell tumors are extremely rare cause of necrotizing fasciitis, and before this case, Pediococcus sp. has never been isolated as the responsible agent. PMID:23357010

  15. Antifungal and Zearalenone Inhibitory Activity of Pediococcus pentosaceus Isolated from Dairy Products on Fusarium graminearum.

    PubMed

    Sellamani, Muthulakshmi; Kalagatur, Naveen K; Siddaiah, Chandranayaka; Mudili, Venkataramana; Krishna, Kadirvelu; Natarajan, Gopalan; Rao Putcha, Venkata L

    2016-01-01

    The present study was aimed to evaluate the bio-control efficacy of Pediococcus pentosaceus isolated from traditional fermented dairy products originated from India, against the growth and zearalenone (ZEA) production of Fusarium graminearum. The cell-free supernatants of P. pentosaceus (PPCS) were prepared and chemical profiling was carried out by GC-MS and MALDI-TOF analysis. Chemical profiling of PPCS evidenced that, the presence of phenolic antioxidants, which are responsible for the antifungal activity. Another hand, MALDI-TOF analysis also indicated the presence of antimicrobial peptides. To know the antioxidant potential of PPCS, DPPH free radical scavenging assay was carried out and IC50 value was determined as 32 ± 1.89 μL/mL. The antifungal activity of P. pentosaceus was determined by dual culture overlay technique and zone of inhibition was recorded as 47 ± 2.81%, and antifungal activity of PPCS on F. graminearum was determined by micro-well dilution and scanning electron microscopic techniques. The minimum inhibitory concentration (MIC) of PPCS was determined as 66 ± 2.18 μL/mL in the present study. Also a clear variation in the micromorphology of mycelia treated with MIC value of PPCS compared to untreated control was documented. Further, the mechanism of growth inhibition was revealed by ergosterol analysis and determination of reactive oxygen species (ROS) in PPCS treated samples. The effects of PPCS on mycelial biomass and ZEA production were observed in a dose-dependent manner. The mechanism behind the suppression of ZEA production was studied by reverse transcriptase qPCR analysis of ZEA metabolic pathway genes (PKS4 and PKS13), and results showed that there is a dose dependent down-regulation of target gene expression in PPCS treated samples. The results of the present study were collectively proved that, the antifungal and ZEA inhibitory activity of PPCS against F. graminearum and it may find a potential application in agriculture and food

  16. Antifungal and Zearalenone Inhibitory Activity of Pediococcus pentosaceus Isolated from Dairy Products on Fusarium graminearum

    PubMed Central

    Sellamani, Muthulakshmi; Kalagatur, Naveen K.; Siddaiah, Chandranayaka; Mudili, Venkataramana; Krishna, Kadirvelu; Natarajan, Gopalan; Rao Putcha, Venkata L.

    2016-01-01

    The present study was aimed to evaluate the bio-control efficacy of Pediococcus pentosaceus isolated from traditional fermented dairy products originated from India, against the growth and zearalenone (ZEA) production of Fusarium graminearum. The cell-free supernatants of P. pentosaceus (PPCS) were prepared and chemical profiling was carried out by GC-MS and MALDI-TOF analysis. Chemical profiling of PPCS evidenced that, the presence of phenolic antioxidants, which are responsible for the antifungal activity. Another hand, MALDI-TOF analysis also indicated the presence of antimicrobial peptides. To know the antioxidant potential of PPCS, DPPH free radical scavenging assay was carried out and IC50 value was determined as 32 ± 1.89 μL/mL. The antifungal activity of P. pentosaceus was determined by dual culture overlay technique and zone of inhibition was recorded as 47 ± 2.81%, and antifungal activity of PPCS on F. graminearum was determined by micro-well dilution and scanning electron microscopic techniques. The minimum inhibitory concentration (MIC) of PPCS was determined as 66 ± 2.18 μL/mL in the present study. Also a clear variation in the micromorphology of mycelia treated with MIC value of PPCS compared to untreated control was documented. Further, the mechanism of growth inhibition was revealed by ergosterol analysis and determination of reactive oxygen species (ROS) in PPCS treated samples. The effects of PPCS on mycelial biomass and ZEA production were observed in a dose-dependent manner. The mechanism behind the suppression of ZEA production was studied by reverse transcriptase qPCR analysis of ZEA metabolic pathway genes (PKS4 and PKS13), and results showed that there is a dose dependent down-regulation of target gene expression in PPCS treated samples. The results of the present study were collectively proved that, the antifungal and ZEA inhibitory activity of PPCS against F. graminearum and it may find a potential application in agriculture and food

  17. Characterization of the multiple molecular mechanisms underlying RsaL control of phenazine-1-carboxylic acid biosynthesis in the rhizosphere bacterium Pseudomonas aeruginosa PA1201.

    PubMed

    Sun, Shuang; Chen, Bo; Jin, Zi-Jing; Zhou, Lian; Fang, Yun-Ling; Thawai, Chitti; Rampioni, Giordano; He, Ya-Wen

    2017-03-18

    Phenazines are important secondary metabolites that have been found to affect a broad spectrum of organisms. Two almost identical gene clusters phz1 and phz2 are responsible for phenazines biosynthesis in the rhizobacterium Pseudomonas aeruginosa PA1201. Here, we show that the transcriptional regulator RsaL is a potent repressor of phenazine-1-carboxylic acid (PCA) biosynthesis. RsaL negatively regulates phz1 expression and positively regulates phz2 expression via multiple mechanisms. First, RsaL binds to a 25-bp DNA region within the phz1 promoter to directly repress phz1 expression. Second, RsaL indirectly regulates the expression of both phz clusters by decreasing the activity of the las and pqs quorum sensing (QS) systems, and by promoting the rhl QS system. Finally, RsaL represses phz1 expression through the downstream transcriptional regulator CdpR. RsaL directly binds to the promoter region of cdpR to positively regulate its expression, and subsequently CdpR regulates phz1 expression in a negative manner. We also show that RsaL represents a new mechanism for the turnover of the QS signal molecule N-3-oxododecanoyl-homoserine lactone (3-oxo-C12-HSL). Overall, this study elucidates RsaL control of phenazines biosynthesis and indicates that a PA1201 strain harboring deletions in both the rsaL and cdpR genes could be used to improve the industrial production of PCA.

  18. Growth of Leuconostoc mesenteroides NRRL-B523 in an alkaline medium: suboptimal pH growth inhibition of a lactic acid bacterium.

    PubMed

    Wolf, Barry F; Fogler, H Scott

    2005-01-05

    Bacterial profile modification (BPM), a form of tertiary oil recovery, diverts water from the water-flooded high-permeability zone into the oil-bearing low-permeability zone. During field use, exopolymer-producing bacteria plug the high-permeability zone only in the immediate vicinity of the injection point (the near-well bore region). For effective BPM the plug must penetrate far into the formation. Slowing the specific growth rate, lengthening the lag phase, and slowing the polymerization rate are techniques that can prolong the onset of biopolymer gelation and extend the depth of the biological plug. In batch experiments, the growth of Leuconostoc mesenteroides NRRL-B523 was inhibited by the synergistic effects of high substrate loading and an alkaline pH. Exponential growth was delayed up to 190 h. It was observed that cell division was significantly retarded until the medium pH, reduced by the acid byproducts of fermentation, reached a critical value of 6.79 +/- 0.06. A mathematical model was developed to describe the relationship between specific growth rate, lag time, and medium pH.

  19. Pediocin production in milk by Pediococcus acidilactici in co-culture with Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus.

    PubMed

    Somkuti, George A; Steinberg, Dennis H

    2010-01-01

    The production of pediocin in milk by Pediococcus acidilactici was evaluated in co-culture with the dairy fermentation cultures Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus. The cultures were tested singly and in different combinations in milk (0 or 2% fat content) during incubation at 40 degrees C for up to 10 h. Cell-free milk samples taken every 60 min were tested for bacteriocin activity against Listeria monocytogenes. Pediocin activity was not detectable when P. acidilactici was inoculated into milk as a monoculture. When P. acidilactici was grown in combination with the yogurt starter cultures S. thermophilus and Lb. delbrueckii ssp. bulgaricus, pediocin concentration reached 3,200-6,400 units ml(-1) after 8 h of incubation. The results showed that pediocin producing pediococci may be useful adjunct components in mixed cultures of S. thermophilus and Lb. delbrueckii ssp. bulgaricus to amplify the bioprotective properties of fermented dairy foods against Listeria contamination.

  20. Genomic Diversity within the Genus Pediococcus as Revealed by Randomly Amplified Polymorphic DNA PCR and Pulsed-Field Gel Electrophoresis

    PubMed Central

    Simpson, P. J.; Stanton, C.; Fitzgerald, G. F.; Ross, R. P.

    2002-01-01

    The genomic diversity of 33 previously assigned strains from six species within the genus Pediococcus was assessed by randomly amplified polymorphic DNA (RAPD) PCR and pulsed-field-gel electrophoresis (PFGE). The RAPD PCR patterns produced by two separate random primers, termed P1 (ACGCGCCCT) and P2 (ATGTAACGCC), were compared by the Pearson correlation coefficient and the unweighted pair group method with arithmetic averages clustering algorithm. Pattern variations between repeat samples set a strain discrimination threshold of less than 70% similarity. P1 and P2 primers alone and in combination produced 14, 21, and 28 distinct patterns, respectively. When each strain was assigned with a type strain with which it shared the highest level of similarity, both primers grouped 17 of the 27 strains to their proposed species. PFGE following genomic digestion with the restriction enzymes ApaI, NotI, and AscI produced 30, 32, and 28 distinct macrorestriction patterns, respectively. Specific DNA fragments within the NotI and AscI macrorestriction patterns for each strain were observed that allowed 27 of the 33 strains to be assigned to their proposed species. For example, following digestion with AscI, all Pediococcus parvulus strains were characterized by two DNA fragments, one of approximately 220 kb and another between 700 and 800 kb. The exceptions correlated with those observed with both RAPD PCR primers and included three P. damnosus and two P. pentosaceus strains that grew at temperatures regarded as nonpermissive for their proposed species but not for those with which they grouped. PMID:11823217

  1. Single Bacterium Detection Using Sers

    NASA Astrophysics Data System (ADS)

    Gonchukov, S. A.; Baikova, T. V.; Alushin, M. V.; Svistunova, T. S.; Minaeva, S. A.; Ionin, A. A.; Kudryashov, S. I.; Saraeva, I. N.; Zayarny, D. A.

    2016-02-01

    This work is devoted to the study of a single Staphylococcus aureus bacterium detection using surface-enhanced Raman spectroscopy (SERS) and resonant Raman spectroscopy (RS). It was shown that SERS allows increasing sensitivity of predominantly low frequency lines connected with the vibrations of Amide, Proteins and DNA. At the same time the lines of carotenoids inherent to this kind of bacterium are well-detected due to the resonance Raman scattering mechanism. The reproducibility and stability of Raman spectra strongly depend on the characteristics of nanostructured substrate, and molecular structure and size of the tested biological object.

  2. Multiple Genome Sequences of Important Beer-Spoiling Lactic Acid Bacteria

    PubMed Central

    Geissler, Andreas J.; Vogel, Rudi F.

    2016-01-01

    Seven strains of important beer-spoiling lactic acid bacteria were sequenced using single-molecule real-time sequencing. Complete genomes were obtained for strains of Lactobacillus paracollinoides, Lactobacillus lindneri, and Pediococcus claussenii. The analysis of these genomes emphasizes the role of plasmids as the genomic foundation of beer-spoiling ability. PMID:27795248

  3. Survival and growth of probiotic lactic acid bacteria in refrigerated pickle products

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We examined 10 lactic acid bacteria that have been previously characterized for commercial use as probiotic cultures, mostly for dairy products, including 1 Pediococcus and 9 Lactobacilli. Our objectives were to develop a rapid procedure for determining the long-term survivability of these cultures ...

  4. The effects of feeding with synbiotic (Pediococcus acidilactici and fructooligosaccharide) enriched adult Artemia on skin mucus immune responses, stress resistance, intestinal microbiota and performance of angelfish (Pterophyllum scalare).

    PubMed

    Azimirad, Mahmood; Meshkini, Saeed; Ahmadifard, Nasrollah; Hoseinifar, Seyed Hossein

    2016-07-01

    The aim of this study was to evaluate the effects of feeding on synbiotic (Pediococcus acidilactici and fructooligosaccharide) enriched adult Artemia franciscana on skin mucus immune responses, stress resistance, intestinal microbiota and growth performance of angelfish (Pterophyllum scalare). Three hundred and sixty fish with initial weight 3.2 ± 0.13 g were randomly divided into twelve aquaria (50 L) assigned to four groups in triplicates. Fish were fed for 7 weeks with dietary treatments, including treatment 1: feeding adult Artemia without enrichment (control group), treatment 2: feeding adult Artemia enriched with lyophilised probiotic P. acidilactici (700 mg L(-1)), 3: feeding adult Artemia enriched with prebiotic fructooligosaccharide (FOS) (100 mg L(-1)), group 4: feeding adult Artemia enriched with synbiotic (P. acidilactici (700 mg L(-1)) + FOS (100 mg L(-1))). Skin mucus immune responses (lysozyme activity, total Immunoglobulin and protease), stress resistance against environmental stress (acute decrease of temperature and increase salinity), intestinal microbiota as well as growth indices were measured at the end of feeding trial. Artemia enriched with synbiotic significantly improved growth performance compared to other treatments (P < 0.05). The highest weight gain and specific growth rate (SGR) was observed in synbiotic fed fish (P < 0.05). Compared to the other treatments, the population of lactic acid bacteria was significantly higher in the intestinal microbiota of fish fed synbiotic supplemented diet (P < 0.05). In the environmental stress challenge test, the maximum resistance to abrupt decrease of temperature (17 °C) or elevation of salinity (12 g per liter) was observed in the synbiotic treatment. Also, the total immunoglobulin and lysozyme activity level of skin mucus was significantly elevated in fish fed Artemia enriched with synbiotic (P < 0.05). These results revealed that feeding angelfish with synbiotic

  5. Analysis of cell growth dynamics of Pediococcus acidilactici in the presence of inulin in an optimized microenvironment.

    PubMed

    Samanta Koruri, Sharmistha; Chowdhury, Ranjana; Bhattacharya, Pinaki

    2015-09-01

    The present investigation deals with the optimization of cell growth rate of the candidate probiotic Pediococcus acidilactici in the presence of the specific prebiotic inulin. Three independent variables viz. concentration of inulin, concentration of glucose and pH have been selected for optimization study using response surface methodology. Theoretical analysis indicates that the maximum cell growth rate occurs at pH 7, 20 g/dm(3) concentration of inulin and 20 g/dm(3) concentration of glucose. Validation of these values has been done through a set of programmed experiments. Studies on cell dynamics in the presence of different concentrations of inulin have also been carried out to identify any limitation on the initial inulin concentration. Results clearly indicate that cell growth is enhanced with the increase in inulin concentration. However, there is a critical value of the prebiotic concentration (20 g/dm(3) inulin) beyond which the cell growth is inhibited. A summative type growth model has been proposed to explain the growth behaviour of P. acidilactici in the presence of the dual substrate, i.e. glucose and inulin. While growth on glucose follows Monod model, Haldane-type substrate-inhibited growth model holds good for growth on inulin. Intrinsic kinetic parameters for all the model equations have been determined experimentally.

  6. Aqueous two-phase flotation for primary recovery of bacteriocin-like inhibitory substance (BLIS) from Pediococcus acidilactici Kp10.

    PubMed

    Md Sidek, Nurul Lyana; Tan, Joo Shun; Abbasiliasi, Sahar; Wong, Fadzlie Wong Faizal; Mustafa, Shuhaimi; Ariff, Arbakariya B

    2016-08-01

    An aqueous two-phase flotation (ATPF) system based on polyethylene glycol (PEG) and sodium citrate (NaNO3C6H5O7·2H2O) was considered for primary recovery of bacteriocin-like inhibitory substance (BLIS) from Pediococcus acidilactici Kp10. The effects of ATPF parameters namely phase composition, tie-line length (TLL), volume ratio between the two phases (VR), amount of crude load (CL), pH, nitrogen gas flow rate (FR) and flotation time (FT) on the performance of recovery were evaluated. BLIS was mainly concentrated into the upper PEG-rich phase in all systems tested so far. The optimum conditions for BLIS purification, which composed of PEG 8000/sodium citrate, were: TLL of 42.6, VR of 0.4, CL of 22% (w/w), pH 7, average FT of 30min and FR of 20mL/min. BLIS was partially purified up to 5.9-fold with a separation efficiency of 99% under this optimal conditions. A maximum yield of BLIS activity of about 70.3% was recovered in the PEG phase. The BLIS from the top phase was successfully recovered with a single band in SDS-gel with molecular weight of about 10-15kDa. ATPF was found to be an effective technique for the recovery of BLIS from the fermentation broth of P. acidilactici Kp10.

  7. The rapid identification of lactic acid bacteria present in Chilean winemaking processes using culture-independent analysis.

    PubMed

    Ilabaca, Carolina; Jara, Carla; Romero, Jaime

    2014-01-01

    A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of 16S ribosomal RNA (rRNA) genes was developed to identify lactic acid bacteria (LAB) that are commonly present in winemaking processes (Oenococcus, Pediococcus, Lactobacillus, and Leuconostoc). This culture-independent approach revealed the presence of Oenococcus in the spontaneous malolactic fermentation in industrial Chilean wines.

  8. Statistical media and process optimization for biotransformation of rice bran to vanillin using Pediococcus acidilactici.

    PubMed

    Kaur, Baljinder; Chakraborty, Debkumar

    2013-11-01

    An isolate of P. acidilactici capable of producing vanillin from rice bran was isolated from a milk product. Response Surface Methodology was employed for statistical media and process optimization for production of biovanillin. Statistical medium optimization was done in two steps involving Placket Burman Design and Central Composite Response Designs. The RSM optimized vanillin production medium consisted of 15% (w/v) rice bran, 0.5% (w/v) peptone, 0.1% (w/v) ammonium nitrate, 0.005% (w/v) ferulic acid, 0.005% (w/v) magnesium sulphate, and 0.1% (v/v) tween-80, pH 5.6, at a temperature of 37 degrees C under shaking conditions at 180 rpm. 1.269 g/L vanillin was obtained within 24 h of incubation in optimized culture medium. This is the first report indicating such a high vanillin yield obtained during biotransformation of ferulic acid to vanillin using a Pediococcal isolate.

  9. Simple and rapid purification of pediocin PA-1 from Pediococcus pentosaceous NCDC 273 suitable for industrial application.

    PubMed

    Vijay Simha, B; Sood, S K; Kumariya, Rashmi; Garsa, Anita Kumari

    2012-10-12

    The use of pediocins as food additives or drugs requires a simple and rapid method by which large quantities of homogeneous pediocin are produced at industrial level. Two centrifugation steps required during initial stages of purification i.e. separation of cells from fermentation broth and collection of precipitates after ammonium sulphate precipitation are the major bottlenecks for their large scale purification. In the present work, pediocin production by a new a dairy strain, Pediococcus pentosaceous NCDC 273 (identical to pediocin PA-1 at nucleotide sequence level), was found to be optimum at initial pH of 6.0 and 7.0 of basal MRS supplemented with 20 g/l of glucose or lactose at 20 and 24 h, respectively. Immobilization of cells through entrapment in alginate-xanthan gum gel beads with chitosan coating resulted in negligible cell release during fermentation. Thus, the cell free extract was directly collected through decantation, avoiding the need of centrifugation step at this stage. Subsequent ammonium sulphate precipitation at isoelectric point of pediocin PA-1 (8.85), using magnetic stirrer at high speed (approx. 1200 rpm), resulted in forceful deposition of precipitates on the wall of precipitation beaker allowing their collection using a spatula, avoiding centrifugation step at this stage also. Further purification using cation-exchange chromatography resulted in yield of 134.4% with more than 320 fold purification with the specific activity of 19×10⁵ AU/mg. The collection of single peak of pediocin at 41.9min in RP-HPLC, overlapping with standard pediocin PA-1, resulted in yield of 1.15 μg from 20 μl of sample applied. The overlapping of RP-HPLC peak and SDS-PAGE band corresponding to 4.6 kDa, confirmed the purity and identity of pediocin 273 as pediocin PA-1.

  10. Whole-genome sequence assembly of Pediococcus pentosaceus LI05 (CGMCC 7049) from the human gastrointestinal tract and comparative analysis with representative sequences from three food-borne strains

    PubMed Central

    2014-01-01

    Background Strains of Pediococcus pentosaceus from food and the human gastrointestinal tract have been widely identified, and some have been reported to reduce inflammation, encephalopathy, obesity and fatty liver in animals. In this study, we sequenced the whole genome of P. pentosaceus LI05 (CGMCC 7049), which was isolated from the fecal samples of healthy volunteers, and determined its ability to reduce acute liver injury. No other genomic information for gut-borne P. pentosaceus is currently available in the public domain. Results We obtained the draft genome of P. pentosaceus LI05, which was 1,751,578 bp in size and possessed a mean G + C content of 37.3%. This genome encoded an abundance of proteins that were protective against acids, bile salts, heat, oxidative stresses, enterocin A, arsenate and universal stresses. Important adhesion proteins were also encoded by the genome. Additionally, P. pentosaceus LI05 genes encoded proteins associated with the biosynthesis of not only three antimicrobials, including prebacteriocin, lysin and colicin V, but also vitamins and functional amino acids, such as riboflavin, folate, biotin, thiamine and gamma-aminobutyrate. A comparison of P. pentosaceus LI05 with all known genomes of food-borne P. pentosaceus strains (ATCC 25745, SL4 and IE-3) revealed that it possessed four novel exopolysaccharide biosynthesis proteins, additional putative environmental stress tolerance proteins and phage-related proteins. Conclusions This work demonstrated the probiotic properties of P. pentosaceus LI05 from the gut and the three other food-borne P. pentosaceus strains through genomic analyses. We have revealed the major genomic differences between these strains, providing a framework for understanding the probiotic effects of strain LI05, which exhibits unique physiological and metabolic properties. PMID:25349631

  11. A "MICROTUBULE" IN A BACTERIUM

    PubMed Central

    van Iterson, Woutera; Hoeniger, Judith F. M.; van Zanten, Eva Nijman

    1967-01-01

    A study of the anchorage of the flagella in swarmers of Proteus mirabilis led to the incidental observation of microtubules. These microtubules were found in thin sections and in whole mount preparations of cells from which most of the content had been released by osmotic shock before staining negatively with potassium phosphotungstate (PTA). The microtubules are in negatively stained preparations about 200 A wide, i.e. somewhat thicker than the flagella (approximately 130 A). They are thus somewhat thinner than most microtubules recorded for other cells. They are referred to as microtubules because of their smooth cylindrical wall, or cortex, surrounding a hollow core which is readily filled with PTA when stained negatively. Since this is probably the first time that such a structure is described inside a bacterium, we do not know for certain whether it represents a normal cell constituent or an abnormality, for instance of the type of "polysheaths" (16). PMID:10976198

  12. The lipopolysaccharide of a chloridazon-degrading bacterium.

    PubMed

    Weisshaar, R; Lingens, F

    1983-12-01

    Lipopolysaccharide of a chloridazon-degrading bacterium was obtained by a two-stage extraction procedure with phenol/EDTA in a yield of 0.3% of dried bacteria. The carbohydrate moiety consisted of heptose, 3-deoxyoctulosonic acid and D-glucose in a molar ratio of 1:2:2 X 3. Lipid A was composed of 1 mol 2,3-diamino-2,3-dideoxy-D-glucose, 2 mol amide-bound and 2.6 mol ester-bound fatty acids/mol. Amide-bound fatty acids were 3-hydroxydodecanoic acid and 3-hydroxyhexadecanoic acid; dodecanoic acid and R-(-)-3-hydroxydodec-5-cis-enoic acid were found to be present in ester linkage. Under conditions of acidic hydrolysis, the latter was converted into the cis and trans isomers of 5-hexyltetrahydrofuran-2-acetic acid. Dodecanoic acid was demonstrated to be linked with the hydroxy groups of the amide-bound fatty acids. The taxonomic significance of these results, especially the demonstration of 2,3-diamino-2, 3-dideoxy-D-glucose, is discussed.

  13. Cloacibacillus porcorum sp. nov., a mucin-degrading bacterium from the swine intestinal tract and emended description of the genus Cloacibacillus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A novel anaerobic, mesophilic, amino-acid-fermenting bacterium, designated strain CL-84T, was isolated from the swine intestinal tract on mucin-based media. The bacterium had curved-rod cells (0.8-1.2 µm x 3.5-5.0 µm), stained Gram negative, and was non-motile with no evidence of spores. CL-84T pro...

  14. A PCR assay for detection of acetic acid-tolerant lactic acid bacteria in acidic food products.

    PubMed

    Nakano, Shigeru; Matsumura, Atsushi; Yamada, Toshihiro

    2004-03-01

    A PCR assay for the detection of acetic acid-tolerant lactic acid bacteria in the genera of Lactobacillus and Pediococcus was developed in this study. Primers targeting the bacterial 16S rRNA gene were newly designed and used in this PCR assay. To determine the specificity of the assay, 56 different bacterial strains (of 33 genera), 2 fungi, 3 animals, and 4 plants were tested. Results were positive for most tested bacterial members of 16S rRNA gene-based phylogenetic groups (classified in the Lactobacillus casei and Pediococcus group), including Lactobacillus fructivorans, Lactobacillus brevis, Lactobacillus buchneri, Lactobacillus plantarum, and Lactobacillus paracasei. For all other bacterial strains and eukaryote tested, results were negative. Bacterial DNA for PCR was prepared with a simple procedure with the use of Chelex 100 resin from culture after growth in deMan Rogosa Sharpe broth (pH 6.0). To test this PCR assay for the monitoring of the acetic acid-tolerant lactic acid bacteria, L. fructivorans was inoculated into several acidic food as an indicator. Before the PCR, the inoculation of 10 to 50 CFU of bacteria per g of food was followed by a 28-h enrichment culture step, and the PCR assay allowed the detection of bacterial cells. Including the enrichment culture step, the entire PCR detection process can be completed within 30 h.

  15. Complete genome sequence of the bioleaching bacterium Leptospirillum sp. group II strain CF-1.

    PubMed

    Ferrer, Alonso; Bunk, Boyke; Spröer, Cathrin; Biedendieck, Rebekka; Valdés, Natalia; Jahn, Martina; Jahn, Dieter; Orellana, Omar; Levicán, Gloria

    2016-03-20

    We describe the complete genome sequence of Leptospirillum sp. group II strain CF-1, an acidophilic bioleaching bacterium isolated from an acid mine drainage (AMD). This work provides data to gain insights about adaptive response of Leptospirillum spp. to the extreme conditions of bioleaching environments.

  16. Genome Sequence of the Butyrate-Producing Anaerobic Bacterium Anaerostipes hadrus PEL 85.

    PubMed

    Kant, Ravi; Rasinkangas, Pia; Satokari, Reetta; Pietilä, Taija E; Palva, Airi

    2015-04-02

    Anaerostipes hadrus PEL 85, which was isolated from human feces, is a Gram-positive rod-shaped bacterium. The species may play an important role in gut health, as it was previously reported to produce butyric acid. Here, we present the genome assembly of PEL 85, a novel strain of A. hadrus.

  17. Molecular characterization of lactic acid populations associated with wine spoilage.

    PubMed

    Beneduce, L; Spano, G; Vernile, A; Tarantino, D; Massa, S

    2004-01-01

    We have investigated the prevalence of spoilage lactic acid bacteria (LAB) in table wines produced in the Apulia region. The occurrence of LAB was evaluated in wines produced with low sulphur dioxide doses and not supplemented with selected malolactic starters such as Oenococcus oeni. About 150 strains were isolated from wine must and a molecular characterization was performed using PCR-based techniques. Most of the strains analysed belonged to Lactobacillus plantarum species. However, some of the strains were identified as Pediococcus damnosus and Leuconostoc sp. The amplified fragments of Pediococcus damnosus were cloned and sequenced. The coding sequence was highly homologous to that of the ropy plasmid confirming that the isolated strain was a ropy(+) Pediococcus damnosus. In all the samples analysed, the final must pH value reached was relatively high (from 3.78 to 3.90). The high pH values had probably negatively influenced (counteracted) the activity of sulphur dioxide added, allowing proliferation of spoilage wine microorganisms.

  18. Lactic acid bacteria in dried vegetables and spices.

    PubMed

    Säde, Elina; Lassila, Elisa; Björkroth, Johanna

    2016-02-01

    Spices and dried vegetable seasonings are potential sources of bacterial contamination for foods. However, little is known about lactic acid bacteria (LAB) in spices and dried vegetables, even though certain LAB may cause food spoilage. In this study, we enumerated LAB in 104 spices and dried vegetables products aimed for the food manufacturing industry. The products were obtained from a spice wholesaler operating in Finland, and were sampled during a one-year period. We picked isolates (n = 343) for species identification based on numerical analysis of their ribotyping patterns and comparing them with the corresponding patterns of LAB type strains. We found LAB at levels >2 log CFU/g in 68 (65%) of the samples, with the highest counts detected from dried onion products and garlic powder with counts ranging from 4.24 to 6.64 log CFU/g. The LAB identified were predominantly Weissella spp. (61%) and Pediococcus spp. (15%) with Weissella confusa, Weissella cibaria, Weissella paramesenteroides, Pediococcus acidilactici and Pediococcus pentosaceus being the species identified. Other species identified belonged to the genera of Enterococcus spp. (8%), Leuconostoc spp. (6%) and Lactobacillus spp. (2%). Among the LAB identified, Leuconostoc citreum, Leuconostoc mesenteroides and W. confusa have been associated with food spoilage. Our findings suggest that spices and dried vegetables are potential sources of LAB contamination in the food industry.

  19. A bacterium that degrades and assimilates poly(ethylene terephthalate).

    PubMed

    Yoshida, Shosuke; Hiraga, Kazumi; Takehana, Toshihiko; Taniguchi, Ikuo; Yamaji, Hironao; Maeda, Yasuhito; Toyohara, Kiyotsuna; Miyamoto, Kenji; Kimura, Yoshiharu; Oda, Kohei

    2016-03-11

    Poly(ethylene terephthalate) (PET) is used extensively worldwide in plastic products, and its accumulation in the environment has become a global concern. Because the ability to enzymatically degrade PET has been thought to be limited to a few fungal species, biodegradation is not yet a viable remediation or recycling strategy. By screening natural microbial communities exposed to PET in the environment, we isolated a novel bacterium, Ideonella sakaiensis 201-F6, that is able to use PET as its major energy and carbon source. When grown on PET, this strain produces two enzymes capable of hydrolyzing PET and the reaction intermediate, mono(2-hydroxyethyl) terephthalic acid. Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol.

  20. The domestication of the probiotic bacterium Lactobacillus acidophilus.

    PubMed

    Bull, Matthew J; Jolley, Keith A; Bray, James E; Aerts, Maarten; Vandamme, Peter; Maiden, Martin C J; Marchesi, Julian R; Mahenthiralingam, Eshwar

    2014-11-26

    Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. acidophilus has been designated as safe for human consumption, increasing commercial regulation and clinical demands for probiotic validation has resulted in a need to understand its genetic diversity. By drawing on large, well-characterised collections of lactic acid bacteria, we examined L. acidophilus isolates spanning 92 years and including multiple strains in current commercial use. Analysis of the whole genome sequence data set (34 isolate genomes) demonstrated L. acidophilus was a low diversity, monophyletic species with commercial isolates essentially identical at the sequence level. Our results indicate that commercial use has domesticated L. acidophilus with genetically stable, invariant strains being consumed globally by the human population.

  1. High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater

    SciTech Connect

    Ramsay, Bradley D.; Hwang, Chiachi; Woo, Hannah L.; Carroll, Sue L.; Lucas, Susan; Han, James; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Samuel; Peters, Lin; Chertkov, Olga; Held, Brittany; Detter, John C.; Han, Cliff S.; Tapia, Roxanne; Land, Miriam L.; Hauser, Loren J.; Kyrpides, Nikos C.; Ivanova, Natalia N.; Mikhailova, Natalia; Pagani, Loanna; Woyke, Tanja; Arkin, Adam P.; Dehal, Paramvir; Chivian, Dylan; Criddle, Craig S.; Wu, Weimin; Chakraborty, Romy; Hazen, Terry C.; Fields, Matthew W.

    2015-03-12

    Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction.

  2. Genome Sequence of Klebsiella pneumoniae YZUSK-4, a Bacterium Proposed as a Starter Culture for Fermented Meat Products.

    PubMed

    Yu, Hai; Yin, Yongqi; Xu, Lin; Yan, Ming; Fang, Weiming; Ge, Qingfeng

    2015-07-23

    Klebsiella pneumoniae strain YZUSK-4, isolated from Chinese RuGao ham, is an efficient branched-chain aminotransferase-producing bacterium that can be used widely in fermented meat products to enhance flavor. The draft genome sequence of strain YZUSK-4 may provide useful genetic information on branched-chain amino acid aminotransferase production and branched-chain amino acid metabolism.

  3. Genome Sequence of Klebsiella pneumoniae YZUSK-4, a Bacterium Proposed as a Starter Culture for Fermented Meat Products

    PubMed Central

    Yu, Hai; Yin, Yongqi; Yan, Ming; Fang, Weiming; Ge, Qingfeng

    2015-01-01

    Klebsiella pneumoniae strain YZUSK-4, isolated from Chinese RuGao ham, is an efficient branched-chain aminotransferase-producing bacterium that can be used widely in fermented meat products to enhance flavor. The draft genome sequence of strain YZUSK-4 may provide useful genetic information on branched-chain amino acid aminotransferase production and branched-chain amino acid metabolism. PMID:26205853

  4. Chitin utilization by the insect-transmitted bacterium Xylella fastidiosa.

    PubMed

    Killiny, Nabil; Prado, Simone S; Almeida, Rodrigo P P

    2010-09-01

    Xylella fastidiosa is an insect-borne bacterium that colonizes xylem vessels of a large number of host plants, including several crops of economic importance. Chitin is a polysaccharide present in the cuticle of leafhopper vectors of X. fastidiosa and may serve as a carbon source for this bacterium. Biological assays showed that X. fastidiosa reached larger populations in the presence of chitin. Additionally, chitin induced phenotypic changes in this bacterium, notably increasing adhesiveness. Quantitative PCR assays indicated transcriptional changes in the presence of chitin, and an enzymatic assay demonstrated chitinolytic activity by X. fastidiosa. An ortholog of the chitinase A gene (chiA) was identified in the X. fastidiosa genome. The in silico analysis revealed that the open reading frame of chiA encodes a protein of 351 amino acids with an estimated molecular mass of 40 kDa. chiA is in a locus that consists of genes implicated in polysaccharide degradation. Moreover, this locus was also found in the genomes of closely related bacteria in the genus Xanthomonas, which are plant but not insect associated. X. fastidiosa degraded chitin when grown on a solid chitin-yeast extract-agar medium and grew in liquid medium with chitin as the sole carbon source; ChiA was also determined to be secreted. The gene encoding ChiA was cloned into Escherichia coli, and endochitinase activity was detected in the transformant, showing that the gene is functional and involved in chitin degradation. The results suggest that X. fastidiosa may use its vectors' foregut surface as a carbon source. In addition, chitin may trigger X. fastidiosa's gene regulation and biofilm formation within vectors. Further work is necessary to characterize the role of chitin and its utilization in X. fastidiosa.

  5. A plant growth-promoting bacterium that decreases nickel toxicity in seedlings

    SciTech Connect

    Burd, G.I.; Dixon, D.G.; Glick, B.R.

    1998-10-01

    A plant growth-promoting bacterium, Kluyvera ascorbata SUD165, that contained high levels of heavy metals was isolated from soil collected near Sudbury, Ontario, Canada. The bacterium was resistant to the toxic effects of Ni{sup 2+}, Pb{sup 2+}, Zn{sup 2+}, and CrO{sub 4}{sup {minus}}, produced a siderophore(s), and displayed 1-aminocyclopropane-1-carboxylic acid deaminase activity. Canola seeds inoculated with this bacterium and then grown under gnotobiotic conditions in the presence of high concentrations of nickel chloride were partially protected against nickel toxicity. In addition, protection by the bacterium against nickel toxicity was evident in pot experiments with canola and tomato seeds. The presence of K. ascorbata SUD165 had no measurable influence on the amount of nickel accumulated per milligram (dry weight) of either roots or shoots of canola plants. Therefore, the bacterial plant growth-promoting effect in the presence of nickel was probably not attributable to the reduction of nickel uptake by seedlings. Rather, it may reflect the ability of the bacterium to lower the level of stress ethylene induced by the nickel.

  6. Effects of rheological change by addition of carboxymethylcellulose in culture media of an air-lift fermentor on poly-D-3-hydroxybutyric acid productivity in autotrophic culture of hydrogen-oxidizing bacterium, Alcaligenes eutrophus.

    PubMed

    Taga, N; Tanaka, K; Ishizaki, A

    1997-03-05

    The effects of rheological change by addition of sodium carboxymethylcellulose (CMC) to culture medium in an air-lift-type fermentor on autotrophic production of poly-(D-3-hydroxybutyric acid) [P(3HB)] by two-stage culture of Alcaligenes eutrophus is investigated. Addition of 0.05% CMC increased P(3HB) production rate during the P(3HB) accumulation phase to twice that of the control culture. It was thought that addition of a small amount of CMC was beneficial for production of P(3HB) employing the air-lift fermentor under safe autotrophic culture conditions in wich oxygen concentration was maintained below 6.9% (v/v). the volumetric mass transfer coefficient (K(L)a) observed in the presence of CMC is shown to correlated with the P(3HB) production rate obtained. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 53: 529-533, 1997.

  7. Antimicrobial activity, antibiotic susceptibility and virulence factors of Lactic Acid Bacteria of aquatic origin intended for use as probiotics in aquaculture

    PubMed Central

    2013-01-01

    Background The microorganisms intended for use as probiotics in aquaculture should exert antimicrobial activity and be regarded as safe not only for the aquatic hosts but also for their surrounding environments and humans. The objective of this work was to investigate the antimicrobial/bacteriocin activity against fish pathogens, the antibiotic susceptibility, and the prevalence of virulence factors and detrimental enzymatic activities in 99 Lactic Acid Bacteria (LAB) (59 enterococci and 40 non-enterococci) isolated from aquatic animals regarded as human food. Results These LAB displayed a broad antimicrobial/bacteriocin activity against the main Gram-positive and Gram-negative fish pathogens. However, particular safety concerns based on antibiotic resistance and virulence factors were identified in the genus Enterococcus (86%) (Enterococcus faecalis, 100%; E. faecium, 79%). Antibiotic resistance was also found in the genera Weissella (60%), Pediococcus (44%), Lactobacillus (33%), but not in leuconostocs and lactococci. Antibiotic resistance genes were found in 7.5% of the non-enterococci, including the genera Pediococcus (12.5%) and Weissella (6.7%). One strain of both Pediococcus pentosaceus and Weissella cibaria carried the erythromycin resistance gene mef(A/E), and another two P. pentosaceus strains harboured lnu(A) conferring resistance to lincosamides. Gelatinase activity was found in E. faecalis and E. faecium (71 and 11%, respectively), while a low number of E. faecalis (5%) and none E. faecium exerted hemolytic activity. None enterococci and non-enterococci showed bile deconjugation and mucin degradation abilities, or other detrimental enzymatic activities. Conclusions To our knowledge, this is the first description of mef(A/E) in the genera Pediococcus and Weissella, and lnu(A) in the genus Pediococcus. The in vitro subtractive screening presented in this work constitutes a valuable strategy for the large-scale preliminary selection of putatively safe LAB

  8. Assessment of probiotic properties in lactic acid bacteria isolated from wine.

    PubMed

    García-Ruiz, Almudena; González de Llano, Dolores; Esteban-Fernández, Adelaida; Requena, Teresa; Bartolomé, Begoña; Moreno-Arribas, M Victoria

    2014-12-01

    Probiotic properties are highly strain-dependent but rarely studied in enological lactic acid bacteria (LAB). In this study, the probiotic features of 11 strains of Lactobacillus spp., Pediococcus spp., and Oenococcus oeni, including saliva and acid resistance, bile tolerance and exopolysaccharides' production, were investigated. The assays included two probiotic reference strains (Lactobacillus plantarum CLC 17 and Lactobacillus fermentum CECT5716). The Lactobacillus and Pediococcus strains showed high resistance to lysozyme (>80% resistance to 100 mg/L of lysozyme under conditions simulating the in vivo dilution by saliva) and were capable of surviving at low pH values (pH 1.8) and bile salts, suggesting good adaptation of the wine strains to gastrointestinal conditions. The ability of the strains to adhere to the intestinal mucosa and the inhibition of the adhesion of Escherichia coli to human intestinal cells were also evaluated. Adhesion levels of enological LAB to Caco-2 cells varied from 0.37% to 12.2%, depending on the strain. In particular, Pediococcus pentosaceus CIAL-86 showed a high percentage of adhesion to intestinal cells (>12%), even higher than that shown by the probiotic reference strains, and a high anti-adhesion activity against E. coli CIAL-153 (>30%), all of which support this wine LAB strain as a potential probiotic.

  9. Phenotypic and Genotypic Characterization of Some Lactic Acid Bacteria Isolated from Bee Pollen: A Preliminary Study

    PubMed Central

    BELHADJ, Hani; HARZALLAH, Daoud; BOUAMRA, Dalila; KHENNOUF, Seddik; Dahamna, Saliha; GHADBANE, Mouloud

    2014-01-01

    In the present work, five hundred and sixty-seven isolates of lactic acid bacteria were recovered from raw bee pollen grains. All isolates were screened for their antagonistic activity against both Gram-positive and Gram-negative pathogenic bacteria. Neutralized supernatants of 54 lactic acid bacteria (LAB) cultures from 216 active isolates inhibited the growth of indicator bacteria. They were phenotypically characterized, based on the fermentation of 39 carbohydrates. Using the simple matching coefficient and unweighted pair group algorithm with arithmetic averages (UPGMA), seven clusters with other two members were defined at the 79% similarity level. The following species were characterized: Lactobacillus plantarum, Lactobacillus fermentum, Lactococcus lactis, Pediococcus acidilactici, Pediococcus pentosaceus, and unidentified lactobacilli. Phenotypic characteristics of major and minor clusters were also identified. Partial sequencing of the 16S rRNA gene of representative isolates from each cluster was performed, and ten strains were assigned to seven species: Lactobacillus plantarum, Lactobacillus fermentum, Lactococcus lactis, Lactobacillus ingluviei, Pediococcus pentosaceus, Lactobacillus acidipiscis and Weissella cibaria. The molecular method used failed to determine the exact taxonomic status of BH0900 and AH3133. PMID:24936378

  10. Novel Waddlia Intracellular Bacterium in Artibeus intermedius Fruit Bats, Mexico

    PubMed Central

    Pierlé, Sebastián Aguilar; Morales, Cirani Obregón; Martínez, Leonardo Perea; Ceballos, Nidia Aréchiga; Rivero, Juan José Pérez; Díaz, Osvaldo López; Brayton, Kelly A.

    2015-01-01

    An intracellular bacterium was isolated from fruit bats (Artibeus intermedius) in Cocoyoc, Mexico. The bacterium caused severe lesions in the lungs and spleens of bats and intracytoplasmic vacuoles in cell cultures. Sequence analyses showed it is related to Waddlia spp. (order Chlamydiales). We propose to call this bacterium Waddlia cocoyoc. PMID:26583968

  11. Antagonistic Activity and Mode of Action of Phenazine-1-Carboxylic Acid, Produced by Marine Bacterium Pseudomonas aeruginosa PA31x, Against Vibrio anguillarum In vitro and in a Zebrafish In vivo Model.

    PubMed

    Zhang, Linlin; Tian, Xueying; Kuang, Shan; Liu, Ge; Zhang, Chengsheng; Sun, Chaomin

    2017-01-01

    Phenazine and its derivatives are very important secondary metabolites produced from Pseudomonas spp. and have exhibited broad-spectrum antifungal and antibacterial activities. However, till date, there are few reports about marine derived Pseudomonas and its production of phenazine metabolites. In this study, we isolated a marine Pseudomonas aeruginosa strain PA31x which produced natural product inhibiting the growth of Vibrio anguillarum C312, one of the most serious bacterial pathogens in marine aquaculture. Combining high-resolution electro-spray-ionization mass spectroscopy and nuclear magnetic resonance spectroscopy analyses, the functional compound against V. anguillarum was demonstrated to be phenazine-1-carboxylic acid (PCA), an important phenazine derivative. Molecular studies indicated that the production of PCA by P. aeruginosa PA31x was determined by gene clusters phz1 and phz2 in its genome. Electron microscopic results showed that treatment of V. anguillarum with PCA developed complete lysis of bacterial cells with fragmented cytoplasm being released to the surrounding environment. Additional evidence indicated that reactive oxygen species generation preceded PCA-induced microbe and cancer cell death. Notably, treatment with PCA gave highly significant protective activities against the development of V. anguillarum C312 on zebrafish. Additionally, the marine derived PCA was further found to effectively inhibit the growth of agricultural pathogens, Acidovorax citrulli NP1 and Phytophthora nicotianae JM1. Taken together, this study reveals that marine Pseudomonas derived PCA carries antagonistic activities against both aquacultural and agricultural pathogens, which broadens the application fields of PCA.

  12. Antagonistic Activity and Mode of Action of Phenazine-1-Carboxylic Acid, Produced by Marine Bacterium Pseudomonas aeruginosa PA31x, Against Vibrio anguillarum In vitro and in a Zebrafish In vivo Model

    PubMed Central

    Zhang, Linlin; Tian, Xueying; Kuang, Shan; Liu, Ge; Zhang, Chengsheng; Sun, Chaomin

    2017-01-01

    Phenazine and its derivatives are very important secondary metabolites produced from Pseudomonas spp. and have exhibited broad-spectrum antifungal and antibacterial activities. However, till date, there are few reports about marine derived Pseudomonas and its production of phenazine metabolites. In this study, we isolated a marine Pseudomonas aeruginosa strain PA31x which produced natural product inhibiting the growth of Vibrio anguillarum C312, one of the most serious bacterial pathogens in marine aquaculture. Combining high-resolution electro-spray-ionization mass spectroscopy and nuclear magnetic resonance spectroscopy analyses, the functional compound against V. anguillarum was demonstrated to be phenazine-1-carboxylic acid (PCA), an important phenazine derivative. Molecular studies indicated that the production of PCA by P. aeruginosa PA31x was determined by gene clusters phz1 and phz2 in its genome. Electron microscopic results showed that treatment of V. anguillarum with PCA developed complete lysis of bacterial cells with fragmented cytoplasm being released to the surrounding environment. Additional evidence indicated that reactive oxygen species generation preceded PCA-induced microbe and cancer cell death. Notably, treatment with PCA gave highly significant protective activities against the development of V. anguillarum C312 on zebrafish. Additionally, the marine derived PCA was further found to effectively inhibit the growth of agricultural pathogens, Acidovorax citrulli NP1 and Phytophthora nicotianae JM1. Taken together, this study reveals that marine Pseudomonas derived PCA carries antagonistic activities against both aquacultural and agricultural pathogens, which broadens the application fields of PCA. PMID:28289406

  13. Effect of bioaugmented inoculation on microbiota dynamics during solid-state fermentation of Daqu starter using autochthonous of Bacillus, Pediococcus, Wickerhamomyces and Saccharomycopsis.

    PubMed

    Li, Pan; Lin, Weifeng; Liu, Xiong; Wang, Xiaowen; Gan, Xing; Luo, Lixin; Lin, Wei-Tie

    2017-02-01

    Daqu, a traditional fermentation starter that is used for Chinese liquor and vinegar production, is still manufactured through a traditional spontaneous solid-state fermentation process with no selected microorganisms are intentionally inoculated. The aim of this work was to analyze the microbiota dynamics during the solid-state fermentation process of Daqu using a traditional and bioaugmented inoculation with autochthonous of Bacillus, Pediococcus, Saccharomycopsis and Wickerhamomyces at an industrial scale. Highly similar dynamics of physicochemical parameters, enzymatic activities and microbial communities were observed during the traditional and bioaugmented solid-state fermentation processes. Both in the two cases, groups of Streptophyta, Rickettsiales and Xanthomonadales only dominated the first two days, but Bacillales and Eurotiales became predominant members after 2 and 10 days fermentation, respectively. Phylotypes of Enterobacteriales, Lactobacillales, Saccharomycetales and Mucorales dominated the whole fermentation process. No significant difference (P > 0.05) in microbial structure was observed between the traditional and bioaugmented fermentation processes. However, slightly higher microbial richness was found during the bioaugmented fermentation process after 10 days fermentation. Our results reinforced the microbiota dynamic stability during the solid-state fermentation process of Daqu, and might aid in controlling the traditional Daqu manufacturing process.

  14. Correlation between depression of catabolite control of xylose metabolism and a defect in the phosphoenolpyruvate:mannose phosphotransferase system in Pediococcus halophilus.

    PubMed Central

    Abe, K; Uchida, K

    1989-01-01

    Pediococcus halophilus X-160 which lacks catabolite control by glucose was isolated from nature (soy moromi mash). Wild-type strains, in xylose-glucose medium, utilized glucose preferentially over xylose and showed diauxic growth. With wild-type strain I-13, xylose isomerase activity was not induced until glucose was consumed from the medium. Strain X-160, however, utilized xylose concurrently with glucose and did not show diauxic growth. In this strain, xylose isomerase was induced even in the presence of glucose. Glucose transport activity in intact cells of strain X-160 was less than 10% of that assayed in strain I-13. Determinations of glycolytic enzymes did not show any difference responsible for the unique behavior of strain X-160, but the rate of glucose-6-phosphate formation with phosphoenolpyruvate (PEP) as a phosphoryl donor in permeabilized cells was less than 10% of that observed in the wild type. Starved P. halophilus I-13 cells contained the glycolytic intermediates 3-phosphoglycerate, 2-phosphoglycerate, and PEP (PEP pool). These were consumed concomitantly with glucose or 2-deoxyglucose uptake but were not consumed with xylose uptake. The glucose transport system in P. halophilus was identified as a PEP:mannose phosphotransferase system on the basis of the substrate specificity of PEP pool-starved cells. It is concluded that, in P. halophilus, this system is functional as a main glucose transport system and that defects in this system may be responsible for the depression of glucose-mediated catabolite control. Images PMID:2703460

  15. Evaluating Pediococcus acidilactici and Enterococcus faecium NRRL B-2354 as Thermal Surrogate Microorganisms for Salmonella for In-Plant Validation Studies of Low-Moisture Pet Food Products.

    PubMed

    Ceylan, Erdogan; Bautista, Derrick A

    2015-05-01

    Pediococcus acidilactici ATCC 8042 and Enterococcus faecium NRRL B-2354 were investigated as potential surrogates for Salmonella serovars using thermal death time kinetics in products such as dry pet foods. The D-values of P. acidilactici ATCC 8042, E. faecium NRRL B-2354, and a cocktail of seven Salmonella serovars associated with low-moisture products were determined in a preservative-free dry pet food product at moisture levels of 9.1, 17.9, and 27.0% and heated between 76.7 and 87.8°C. The D-values were calculated by least squares linear regression. The D-values of P. acidilactici ATCC 8042 were higher than those for the Salmonella serovar cocktail but lower than those for E. faecium NRRL 2354. At 9.1% moisture, D-values of 6.54, 11.51, and 11.66 min at 76.7°C, 2.66, 3.22, and 4.08 min at 82.2°C, and 1.07, 1.29, and 1.69 min at 87.8°C were calculated for Salmonella serovars, P. acidilactici ATCC 8042, and E. faecium NRRL B-2354, respectively. The data suggest that the thermal inactivation characteristics of P. acidilactici ATCC 8042 can be utilized as a surrogate to predict the response of Salmonella in dry pet food products that are thermally processed at <90°C.

  16. The Identification of Novel Diagnostic Marker Genes for the Detection of Beer Spoiling Pediococcus damnosus Strains Using the BlAst Diagnostic Gene findEr

    PubMed Central

    Schmid, Jonas; Zehe, Anja; Vogel, Rudi F.

    2016-01-01

    As the number of bacterial genomes increases dramatically, the demand for easy to use tools with transparent functionality and comprehensible output for applied comparative genomics grows as well. We present BlAst Diagnostic Gene findEr (BADGE), a tool for the rapid prediction of diagnostic marker genes (DMGs) for the differentiation of bacterial groups (e.g. pathogenic / nonpathogenic). DMG identification settings can be modified easily and installing and running BADGE does not require specific bioinformatics skills. During the BADGE run the user is informed step by step about the DMG finding process, thus making it easy to evaluate the impact of chosen settings and options. On the basis of an example with relevance for beer brewing, being one of the oldest biotechnological processes known, we show a straightforward procedure, from phenotyping, genome sequencing, assembly and annotation, up to a discriminant marker gene PCR assay, making comparative genomics a means to an end. The value and the functionality of BADGE were thoroughly examined, resulting in the successful identification and validation of an outstanding novel DMG (fabZ) for the discrimination of harmless and harmful contaminations of Pediococcus damnosus, which can be applied for spoilage risk determination in breweries. Concomitantly, we present and compare five complete P. damnosus genomes sequenced in this study, finding that the ability to produce the unwanted, spoilage associated off-flavor diacetyl is a plasmid encoded trait in this important beer spoiling species. PMID:27028007

  17. Paradigms: examples from the bacterium Xylella fastidiosa.

    PubMed

    Purcell, Alexander

    2013-01-01

    The history of advances in research on Xylella fastidiosa provides excellent examples of how paradigms both advance and limit our scientific understanding of plant pathogens and the plant diseases they cause. I describe this from a personal perspective, having been directly involved with many persons who made paradigm-changing discoveries, beginning with the discovery that a bacterium, not a virus, causes Pierce's disease of grape and other plant diseases in numerous plant species, including important crop and forest species.

  18. Pneumonia caused by a previously undescribed bacterium.

    PubMed Central

    Hopfer, R L; Mills, K; Fainstein, V; Fischer, H E; Luna, M P

    1982-01-01

    A new and as yet unidentified bacterium was isolated from the lung tissue of a cancer patient with bilateral pneumonia. Clinically, the pneumonia was consistent with legionellosis; the organism cultured from the lung grew only on the charcoal-yeast extract agar routinely used for Legionella isolation. Subsequent testing, however, showed the organism to be quite distinct from the known Legionella species in its biochemical, antigenic, and growth characteristics. Images PMID:7130363

  19. Characterization of a novel extremely alkalophilic bacterium

    NASA Technical Reports Server (NTRS)

    Souza, K. A.; Deal, P. H.

    1977-01-01

    A new alkalophilic bacterium, isolated from a natural spring of high pH is characterized. It is a Gram-positive, non-sporulating, motile rod requiring aerobic and alkaline conditions for growth. The characteristics of this organism resemble those of the coryneform group of bacteria; however, there are no accepted genera within this group with which this organism can be closely matched. Therefore, a new genus may be warranted.

  20. Coprisamides A and B, new branched cyclic peptides from a gut bacterium of the dung beetle Copris tripartitus.

    PubMed

    Um, Soohyun; Park, So Hyun; Kim, Jihye; Park, Hyen Joo; Ko, Keebeom; Bang, Hea-Son; Lee, Sang Kook; Shin, Jongheon; Oh, Dong-Chan

    2015-03-06

    Coprisamides A and B (1 and 2) were isolated from a bacterium in the gut of the dung beetle Copris tripartitus. Spectroscopic analysis revealed that the planar structures of 1 and 2 are novel cyclic heptapeptides bearing unusual units, such as β-methylaspartic acid and 2,3-diaminopropanoic acid branched to valine and 2-heptatrienyl cinnamic acid. Absolute configurations were established by chemical derivatization and chiroptical spectroscopy. The coprisamides displayed significant activity for induction of quinone reductase.

  1. Halobacterium saccharovorum sp. nov., a carbohydrate-metabolizing, extremely halophilic bacterium

    NASA Technical Reports Server (NTRS)

    Tomlinson, G. A.; Hochstein, L. I.

    1976-01-01

    The previously described extremely halophilic bacterium, strain M6, metabolizes a variety of carbohydrates with the production of acid. In addition, the organism produces nitrite (but no gas) from nitrate, is motile, and grows most rapidly at about 50 C. These characteristics distinguish it from all previously described halophilic bacteria in the genus Halobacterium. It is suggested that it be designated as a new species, Halobacterium saccharovorum.

  2. Influence of supplemented diet with Pediococcus acidilactici on non-specific immunity and stress indicators in green terror (Aequidens rivulatus) during hypoxia.

    PubMed

    Neissi, Alireza; Rafiee, Gholamreza; Nematollahi, Mohammadali; Razavi, Seyed Hadi; Maniei, Fatemeh

    2015-07-01

    Green terror fish were fed for two months with three types of feed including: control diet (C), diet containing 2% fish oil (O) and diet containing fish oil supplemented with 0.1% Pediococcus acidilactici bacteria (PA). At the end of the feeding period, 50 fish of different groups (n = 3) with an average weight of 4.28 g were transferred to 9 tank. Hypoxia tests were set out by sampling at three times including before hypoxia (BH) initiation, hypoxia stress spot (H) and starting mortality (SM). In fish submitted to the diet containing P. acidilactici bacteria, the immune indices of lysozyme activity (4.08, 4.19 and 4.85 μg/ml)], complement activity (2.65, 2.77 and 2.1 U/ml) and total immunoglobulin (10.05, 10.25 and 9.9 μg/ml) improved in all stages of sampling (BH, H and SM), respectively (p < 0.05). The positive effects of the bacteria application also extends for the stress indicators including: cortisol (0.175, 0.3 and 0.335 μM/ml), glucose (0.9, 1.25 and 0.6 μg/ml) and lactate (2.7, 3 and 3.35) μg/ml and plasma electrolytes consisting of Na(+) (178.5, 175.43 and 175.8 mmol/l) and Cl(-)(123.85, 119.30 and 118.43 mmol/l) in all sampling stages (BH, H and SM), respectively (p < 0.05). Put it all together, P. acidilactici, acting as a probiotic, helps reducing stress symptoms in green terror fish.

  3. The effect of Pediococcus acidilactici bacteria used as probiotic supplement on the growth and non-specific immune responses of green terror, Aequidens rivulatus.

    PubMed

    Neissi, Alireza; Rafiee, Gholamreza; Nematollahi, Mohammadali; Safari, Omid

    2013-12-01

    A 56-day feeding trial was conducted on a species of ornamental fish called green terror (Aequidens rivulatus) (0.388 ± 0.0021 g) to assess the effect of probiotic bacteria, Pediococcus acidilactici on the growth indices and innate immune response. The fish were randomly allocated into 9 oval tanks (120 l) at a density of 60 fish per tank. The experimental diets were comprised of the control (C), C complemented with fish oil (O) and the probiotic and fish oil (PA) and fed ad lib twice a day. The growth indices (specific growth rate (SGR), feed conversion ratio (FCR) and immunological indices of fish fed the diets including lysozyme activity, total immunoglobulin and alternative complement activity were measured. The Fish fed with the diet containing P. acidilactici (PA) displayed significantly (P < 0.05) higher final weight (3.25 ± 0.065 g), weight gain (830.94 ± 9.46%), SGR (3.53 ± 0.02%/day) and lower FCR (1.45 ± 0.011) compared to those of other experimental diets. Total immunoglobulin (10.05 ± 0.12 μg/ml), lysozyme activity (4.08 ± 0.85 μg/ml) and alternative complement activity (2.65 ± 0.12 U/ml) in the serum of PA fed fish showed significant compared to other treatments (P < 0.05). The results showed positive effects of P. acidilactici as a potent probiotic on growth indices and non-specific immune system of green terror.

  4. Carbohydrates act as receptors for the periodontitis-associated bacterium Porphyromonas gingivalis: a study of bacterial binding to glycolipids.

    PubMed

    Hellström, Ulrika; Hallberg, Eva C; Sandros, Jens; Rydberg, Lennart; Bäcker, Annika E

    2004-06-01

    In this study we show for the first time the use of carbohydrate chains on glycolipids as receptors for the periodontitis-associated bacterium Porphyromonas gingivalis. Previous studies have shown that this bacterium has the ability to adhere to and invade the epithelial lining of the dental pocket. Which receptor(s) the adhesin of P. gingivalis exploit in the adhesion to epithelial cells has not been shown. Therefore, the binding preferences of this specific bacterium to structures of carbohydrate origin from more than 120 different acid and nonacid glycolipid fractions were studied. The bacteria were labeled externally with (35)S and used in a chromatogram binding assay. To enable detection of carbohydrate receptor structures for P. gingivalis, the bacterium was exposed to a large number of purified total glycolipid fractions from a variety of organs from different species and different histo-blood groups. P. gingivalis showed a preference for fractions of human and pig origin for adhesion. Both nonacid and acid glycolipids were used by the bacterium, and a preference for shorter sugar chains was noticed. Bacterial binding to human acid glycolipid fractions was mainly obtained in the region of the chromatograms where sulfated carbohydrate chains usually are found. However, the binding pattern to nonacid glycolipid fractions suggests a core chain of lactose bound to the ceramide part as a tentative receptor structure. The carbohydrate binding of the bacterium might act as a first step in the bacterial invasion process of the dental pocket epithelium, subsequently leading to damage to periodontal tissue and tooth loss.

  5. Detection of Salmonella bacterium in drinking water using microring resonator.

    PubMed

    Bahadoran, Mahdi; Noorden, Ahmad Fakhrurrazi Ahmad; Mohajer, Faeze Sadat; Abd Mubin, Mohamad Helmi; Chaudhary, Kashif; Jalil, Muhammad Arif; Ali, Jalil; Yupapin, Preecha

    2016-01-01

    A new microring resonator system is proposed for the detection of the Salmonella bacterium in drinking water, which is made up of SiO2-TiO2 waveguide embedded inside thin film layer of the flagellin. The change in refractive index due to the binding of the Salmonella bacterium with flagellin layer causes a shift in the output signal wavelength and the variation in through and drop port's intensities, which leads to the detection of Salmonella bacterium in drinking water. The sensitivity of proposed sensor for detecting of Salmonella bacterium in water solution is 149 nm/RIU and the limit of detection is 7 × 10(-4)RIU.

  6. A bacterium that can grow by using arsenic instead of phosphorus

    USGS Publications Warehouse

    Wolfe-Simon, Felisa; Blum, J.S.; Kulp, T.R.; Gordon, G.W.; Hoeft, S.E.; Pett-Ridge, J.; Stolz, J.F.; Webb, S.M.; Weber, P.K.; Davies, P.C.W.; Anbar, A.D.; Oremland, R.S.

    2011-01-01

    Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

  7. A bacterium that can grow by using arsenic instead of phosphorus.

    PubMed

    Wolfe-Simon, Felisa; Switzer Blum, Jodi; Kulp, Thomas R; Gordon, Gwyneth W; Hoeft, Shelley E; Pett-Ridge, Jennifer; Stolz, John F; Webb, Samuel M; Weber, Peter K; Davies, Paul C W; Anbar, Ariel D; Oremland, Ronald S

    2011-06-03

    Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

  8. A bacterium that can grow by using arsenic instead of phosphorus

    SciTech Connect

    Wolfe-Simon, F; Blum, J S; Kulp, T R; Gordon, G W; Hoeft, S E; Pett-Ridge, J; Stolz, J F; Webb, S M; Weber, P K; Davies, P W; Anbar, A D; Oremland, R S

    2010-11-01

    Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus. Although these six elements make up nucleic acids, proteins and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, CA, which substitutes arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical significance.

  9. Importance of tetrahydroiso alpha-acids to the microbiological stability of beer.

    PubMed

    Caballero, Isabel; Agut, Montserrat; Armentia, Alicia; Blanco, Carlos A

    2009-01-01

    While beer provides a very stable microbiological environment, a few niche microorganisms are capable of growth in malt, wort, and beer. The production of off-flavors and development of turbidity in the packaged product are due to the growth and metabolic activity of wild yeast, certain lactic acid bacteria (LAB) and anaerobic Gram-negative bacteria. Beer also contains bitter hop compounds, which are toxic to Gram-positive and Gram-negative bacteria, and contribute to preventing the spoilage of this beverage. In the boiling process, the hop alpha-acids (humulones) are isomerized into iso alpha-acids. These products are responsible for the bitter taste of beer, but they also play an essential role in enhancing foam stability. Antibacterial activity of iso alpha-acids and their hydrogenated derivates (rhoiso alpha-acids and tetrahydroiso alpha-acids) in MRS broth and beer have been evaluated against different LAB (Lactobacillus and Pediococcus) for the determination of their beer-stabilizing capabilities. Besides this, we have determined the minimum inhibitory concentration and the bacteriostatic effect of each compound against Pediococcus. We found that tetrahydroiso alpha-acids (added directly to beer during production processes) are the compounds that present the greatest antibacterial activity against the main agents implicated in beer spoilage.

  10. Microbial metabolism of polycyclic aromatic hydrocarbons: isolation and characterization of a pyrene-degrading bacterium.

    PubMed Central

    Heitkamp, M A; Franklin, W; Cerniglia, C E

    1988-01-01

    Microbiological analyses of sediments located near a point source for petrogenic chemicals resulted in the isolation of a pyrene-mineralizing bacterium. This isolate was identified as a Mycobacterium sp. on the basis of its cellular and colony morphology, gram-positive and strong acid-fast reactions, diagnostic biochemical tests, 66.6% G + C content of the DNA, and high-molecular-weight mycolic acids (C58 to C64). The mycobacterium mineralized pyrene when grown in a mineral salts medium supplemented with nutrients but was unable to utilize pyrene as a sole source of carbon and energy. The mycobacterium grew well at 24 and 30 degrees C and minimally at 35 degrees C. No growth was observed at 5 or 42 degrees C. The mycobacterium grew well at salt concentrations up to 4%. Pyrene-induced Mycobacterium cultures mineralized 5% of the pyrene after 6 h and reached a maximum of 48% mineralization within 72 h. Treatment of induced and noninduced cultures with chloramphenicol showed that pyrene-degrading enzymes were inducible in this Mycobacterium sp. This bacterium could also mineralize other polycyclic aromatic hydrocarbons and alkyl- and nitro-substituted polycyclic aromatic hydrocarbons including naphthalene, phenanthrene, fluoranthene, 3-methylcholanthrene, 1-nitropyrene, and 6-nitrochrysene. This is the first report of a bacterium able to extensively mineralize pyrene and other polycyclic aromatic hydrocarbons containing four aromatic rings. Images PMID:3202633

  11. Isolation and identification of berberine and berberrubine metabolites by berberine-utilizing bacterium Rhodococcus sp. strain BD7100.

    PubMed

    Ishikawa, Kazuki; Takeda, Hisashi; Wakana, Daigo; Sato, Fumihiko; Hosoe, Tomoo

    2016-05-01

    Based on the finding of a novel berberine (BBR)-utilizing bacterium, Rhodococcus sp. strain BD7100, we investigated the degradation of BBR and its analog berberrubine (BRU). Resting cells of BD7100 demethylenated BBR and BRU, yielding benzeneacetic acid analogs. Isolation of benzeneacetic acid analogs suggested that BD7100 degraded the isoquinoline ring of the protoberberine skeleton. This work represents the first report of cleavage of protoberberine skeleton by a microorganism.

  12. Utilization of Phenylpropanoids by Newly Isolated Bacterium Pseudomonas sp. TRMK1.

    PubMed

    T R, Monisha; I, Mukram; B, Kirankumar; Reddy, Pooja V; Nayak, Anand S; Karegoudar, T B

    2017-01-25

    A bacterium Pseudomonas sp. TRMK1 capable of utilizing various phenylpropanoids was isolated from agro-industrial waste by enrichment culture technique. It is gram-negative, motile, aerobic, and able to utilize three different phenolic acids such as p-coumaric, ferulic, and caffeic acids at concentrations of 5, 10, and 15 mM in 18 h of incubation. The residual concentration of phenolic acids was analyzed by HPLC. The catabolic pathway of p-coumaric, ferulic, and caffeic acids is suggested based on the characterization of metabolic intermediates by GC, GC-HRMS, and different enzymatic assays. Further, Pseudomonas sp. TRMK1 utilizes a wide range of mixture of phenolic acids present in the synthetic effluent.

  13. Copper-binding characteristics of exopolymers from a freshwater-sediment bacterium

    SciTech Connect

    Mittelman, M.W.; Geesey, G.G.

    1985-04-01

    Copper-binding activity by exopolymers from adherent cells of freshwater-sediment bacterium was demonstrated by a combination of equilibrium dialysis and flameless atomic absorption spectrometry. Crude, cell-free exopolymer preparations containing protein and polysaccharide components bound up to 37 nmol of Cu per mg (dry weight). A highly purified exopolysaccharide preparation bound up to 253 nmol of Cu per mg of carbohydrate. The conditional stability constant for the crude exopolymer-Cu complex was 7.3 x 10/sup 8/. This value was similar to those obtained for Cu complexes formed with humic acids and xanthan, an exopolysaccharide produced by Xanthomonas campestris. Studies conducted at copper concentrations, pHs, and temperatures found in sediments from which the bacterium was isolated indicated that the exopolymers were capable of binding copper under natural conditions.

  14. Draft Genome Sequence of the Suttonella ornithocola Bacterium

    PubMed Central

    Waldman Ben-Asher, Hiba; Yerushalmi, Rebecca; Wachtel, Chaim; Barbiro-Michaely, Efrat

    2017-01-01

    ABSTRACT   We report here the draft genome sequence of the Suttonella ornithocola bacterium. To date, this bacterium, found in birds, passed only phylogenetic and phenotypic analyses. To our knowledge, this is the first publication of the Suttonella ornithocola genome sequence. The genetic profile provides a basis for further analysis of its infection pathways. PMID:28209820

  15. Agrobacterium tumefaciens is a diazotrophic bacterium

    SciTech Connect

    Kanvinde, L.; Sastry, G.R.K. )

    1990-07-01

    This is the first report that Agrobacterium tumefaciens can fix nitrogen in a free-living condition as shown by its abilities to grown on nitrogen-free medium, reduce acetylene to ethylene, and incorporate {sup 15}N supplied as {sup 15}N{sub 2}. As with most other well-characterized diazotrophic bacteria, the presence of NH{sub 4}{sup +} in the medium and aerobic conditions repress nitrogen fixation by A. tumefaciens. The system requires molybdenum. No evidence for nodulation was found with pea, peanut, or soybean plants. Further understanding of the nitrogen-fixing ability of this bacterium, which has always been considered a pathogen, should cast new light on the evolution of a pathogenic versus symbiotic relationship.

  16. Preliminary probiotic and technological characterization of Pediococcus pentosaceus strain KID7 and in vivo assessment of its cholesterol-lowering activity

    PubMed Central

    Damodharan, Karthiyaini; Lee, Young Sil; Palaniyandi, Sasikumar A.; Yang, Seung Hwan; Suh, Joo-Won

    2015-01-01

    The study was aimed to characterize the probiotic properties of a Pediococcus pentosaceus strain, KID7, by in vitro and in vivo studies. The strain possessed tolerance to oro-gastrointestinal transit, adherence to the Caco-2 cell line, and antimicrobial activity. KID7 exhibited bile salt hydrolase activity and cholesterol-lowering activity, in vitro. In vivo cholesterol-lowering activity of KID7 was studied using atherogenic diet-fed hypercholesterolemic mice. The experimental animals (C57BL/6J mice) were divided into 4 groups viz., normal diet-fed group (NCD), atherogenic diet-fed group (HCD), atherogenic diet- and KID7-fed group (HCD-KID7), and atherogenic diet- and Lactobacillus acidophilus ATCC 43121-fed group (HCD-L.ac) as positive control. Serum total cholesterol (T-CHO) level was significantly decreased by 19.8% in the HCD-KID7 group (P < 0.05), but not in the HCD-L.ac group compared with the HCD group. LDL cholesterol levels in both HCD-KID7 and HCD-L.ac groups were decreased by 35.5 and 38.7%, respectively, compared with HCD group (both, P < 0.05). Glutamyl pyruvic transaminase (GPT) level was significantly lower in the HCD-KID7 and HCD-L.ac groups compared to HCD group and was equivalent to that of the NCD group. Liver T-CHO levels in the HCD-KID7 group were reduced significantly compared with the HCD group (P < 0.05) but not in the HCD-L.ac group. Analysis of expression of genes associated with lipid metabolism in liver showed that low-density lipoprotein receptor (LDLR), cholesterol-7α-hydroxylase (CYP7A1) and apolipoprotein E (APOE) mRNA expression was significantly increase in the HCD-KID7 group compared to the HCD group. Furthermore, KID7 exhibited desired viability under freeze-drying and subsequent storage conditions with a combination of skim milk and galactomannan. P. pentosaceus KID7 could be a potential probiotic strain, which can be used to develop cholesterol-lowering functional food after appropriate human clinical trials. PMID:26300852

  17. Evolution of a biomass-fermenting bacterium to resist lignin phenolics.

    PubMed

    Cerisy, Tristan; Souterre, Tiffany; Torres-Romero, Ismael; Boutard, Magali; Dubois, Ivan; Patrouix, Julien; Labadie, Karine; Berrabah, Wahiba; Salanoubat, Marcel; Doring, Volker; Tolonen, Andrew

    2017-03-31

    Increasing the resistance of plant-fermenting bacteria to lignocellulosic inhibitors is useful to understand microbial adaptation and to develop candidate strains for consolidated bioprocessing. Here we study and improve inhibitor resistance in Clostridium phytofermentans (also called Lachnoclostridium phytofermentans), a model anaerobe that ferments lignocellulosic biomass. We survey the resistance of this bacterium to a panel of biomass inhibitors, and then evolve strains that grow in increasing concentrations of the lignin phenolic, ferulic acid, by automated, long-term growth selection in an anaerobic GM3 automat. Ultimately, strains resist multiple inhibitors and grow robustly at the solubility limit of ferulate while retaining the ability to ferment cellulose. We analyze genome-wide transcription patterns during ferulate stress and genomic variants that arose along the ferulate growth selection, revealing how cells adapt to inhibitors by changes in gene dosage and regulation, membrane fatty acid structure, and the surface layer. Collectively, this study demonstrates an automated framework for evolution of anaerobes and gives insight into the genetic mechanisms by which bacteria survive exposure to chemical inhibitors.Importance Fermentation of plant biomass is a key part of carbon cycling in diverse ecosystems. Further, industrial biomass fermentation could provide a renewable alternative to fossil fuels. Plants are primarily composed of lignocellulose, a matrix of polysaccharides and polyphenolic lignin. Thus, when microorganisms degrade lignocellulose to access sugars, they also release phenolic and acidic inhibitors. Here, we study how the plant-fermenting bacterium Clostridium phytofermentans resists plant inhibitors using the lignin phenolic, ferulic acid. We examine how the cell responds to abrupt ferulate stress by measuring changes in gene expression. We evolve increasingly resistant strains by automated, long-term cultivation at progressively higher

  18. Molecular screening of wine lactic acid bacteria degrading hydroxycinnamic acids.

    PubMed

    de las Rivas, Blanca; Rodríguez, Héctor; Curiel, José Antonio; Landete, José María; Muñoz, Rosario

    2009-01-28

    The potential to produce volatile phenols from hydroxycinnamic acids was investigated for lactic acid bacteria (LAB) isolated from Spanish grape must and wine. A PCR assay was developed for the detection of LAB that potentially produce volatile phenols. Synthetic degenerate oligonucleotides for the specific detection of the pdc gene encoding a phenolic acid decarboxylase were designed. The pdc PCR assay amplifies a 321 bp DNA fragment from phenolic acid decarboxylase. The pdc PCR method was applied to 85 strains belonging to the 6 main wine LAB species. Lactobacillus plantarum, Lactobacillus brevis, and Pediococcus pentosaceus strains produce a positive response in the pdc PCR assay, whereas Oenococcus oeni, Lactobacillus hilgardii, and Leuconostoc mesenteroides strains did not produce the expected PCR product. The production of vinyl and ethyl derivatives from hydroxycinnamic acids in culture media was determined by high-performance liquid chromatography. A relationship was found between pdc PCR amplification and volatile phenol production, so that the LAB strains that gave a positive pdc PCR response produce volatile phenols, whereas strains that did not produce a PCR amplicon did not produce volatile phenols. The proposed method could be useful for a preliminary identification of LAB strains able to produce volatile phenols in wine.

  19. Yersinia ruckeri sp. nov., the redmouth (RM) bacterium

    USGS Publications Warehouse

    Ewing, W.H.; Ross, A.J.; Brenner, Don J.; Fanning, G. R.

    1978-01-01

    Cultures of the redmouth (RM) bacterium, one of the etiological agents of redmouth disease in rainbow trout (Salmo gairdneri) and certain other fishes, were characterized by means of their biochemical reactions, by deoxyribonucleic acid (DNA) hybridization, and by determination of guanine-plus-cytosine (G+C) ratios in DNA. The DNA relatedness studies confirmed the fact that the RM bacteria are members of the family Enterobacteriaceae and that they comprise a single species that is not closely related to any other species of Enterobacteriaceae. They are about 30% related to species of both Serratia and Yersinia. A comparison of the biochemical reactions of RM bacteria and serratiae indicated that there are many differences between these organisms and that biochemically the RM bacteria are most closely related to yersiniae. The G+C ratios of RM bacteria were approximated to be between 47.5 and 48.5% These values are similar to those of yersiniae but markedly different from those of serratiae. On the basis of their biochemical reactions and their G+C ratios, the RM bacteria are considered to be a new species of Yersinia, for which the name Yersinia ruckeri is proposed. Strain 2396-61 (= ATCC 29473) is designated the type strain of the species.

  20. Thiosulphate oxidation in the phototrophic sulphur bacterium Allochromatium vinosum.

    PubMed

    Hensen, Daniela; Sperling, Detlef; Trüper, Hans G; Brune, Daniel C; Dahl, Christiane

    2006-11-01

    Two different pathways for thiosulphate oxidation are present in the purple sulphur bacterium Allochromatium vinosum: oxidation to tetrathionate and complete oxidation to sulphate with obligatory formation of sulphur globules as intermediates. The tetrathionate:sulphate ratio is strongly pH-dependent with tetrathionate formation being preferred under acidic conditions. Thiosulphate dehydrogenase, a constitutively expressed monomeric 30 kDa c-type cytochrome with a pH optimum at pH 4.2 catalyses tetrathionate formation. A periplasmic thiosulphate-oxidizing multienzyme complex (Sox) has been described to be responsible for formation of sulphate from thiosulphate in chemotrophic and phototrophic sulphur oxidizers that do not form sulphur deposits. In the sulphur-storing A. vinosum we identified five sox genes in two independent loci (soxBXA and soxYZ). For SoxA a thiosulphate-dependent induction of expression, above a low constitutive level, was observed. Three sox-encoded proteins were purified: the heterodimeric c-type cytochrome SoxXA, the monomeric SoxB and the heterodimeric SoxYZ. Gene inactivation and complementation experiments proved these proteins to be indispensable for thiosulphate oxidation to sulphate. The intermediary formation of sulphur globules in A. vinosum appears to be related to the lack of soxCD genes, the products of which are proposed to oxidize SoxY-bound sulphane sulphur. In their absence the latter is instead transferred to growing sulphur globules.

  1. Metabolic Evolution of a Deep-Branching Hyperthermophilic Chemoautotrophic Bacterium

    PubMed Central

    Braakman, Rogier; Smith, Eric

    2014-01-01

    Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA) cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere. PMID:24516572

  2. Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium.

    PubMed

    Braakman, Rogier; Smith, Eric

    2014-01-01

    Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA) cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere.

  3. Isolation and molecular identification of lactic acid bacteria and Bifidobacterium spp. from faeces of the blue-fronted Amazon parrot in Brazil.

    PubMed

    Allegretti, L; Revolledo, L; Astolfi-Ferreira, C S; Chacón, J L; Martins, L M; Seixas, G H F; Ferreira, A J P

    2014-12-01

    In Brazil, the blue-fronted Amazon parrot (Amazona aestiva) is a common pet. The faecal microbiota of these birds include a wide variety of bacterial species, the majority of which belong to the Gram-positive lactic acid bacteria (LAB) clade. The aim of this study was to investigate differences in the diversity and abundance of LAB and Bifidobacterium spp. in the cloacae between wild and captive birds and to select, identify and characterise LAB for consideration as a parrot probiotic. Cloacal swabs were collected from 26 wild and 26 captive birds. Bacterial DNA was extracted, and the 16S rRNA genes were amplified. The numbers of PCR-positive Enterococcus, Pediococcus, and Lactobacillus species isolated from wild and captive birds were significantly different (P<0.05). Enterococcus was the most frequently isolated genus, followed by Pediococcus, Lactobacillus, Lactococcus and Bifidobacterium. Enterococcus faecium, Pediococcus pentosaceus, Lactococcus lactis, Lactobacillus coryniformis, Lactobacillus sanfranciscensis and Bifidobacterium bifidum were the most frequently isolated species from all birds. This study increases our understanding of the faecal microbiota, and may help to improve the nutrition and habitat management of captive and wild parrots. The bacterial population identified in the faecal microbiota of clinically healthy wild and captive parrots can serve as a database to analyse variations in the gut microbiota of pathogen-infected parrots and to develop probiotics specific to these genera.

  4. Phenolic acid degradation potential and growth behavior of lactic acid bacteria in sunflower substrates.

    PubMed

    Fritsch, Caroline; Heinrich, Veronika; Vogel, Rudi F; Toelstede, Simone

    2016-08-01

    Sunflower flour provides a high content of protein with a well-balanced amino acid composition and is therefore regarded as an attractive source for protein. The use for human nutrition is hindered by phenolic compounds, mainly chlorogenic acid, which can lead under specific circumstances to undesirable discolorations. In this study, growth behavior and degradation ability of chlorogenic acid of four lactic acid bacteria were explored. Data suggested that significant higher fermentation performances on sunflower flour as compared to sunflower protein concentrate were reached by Lactobacillus plantarum, Pediococcus pentosaceus, Lactobacillus gasseri and Bifidobacterium animalis subsp. lactis. In fermentation with the latter two strains reduced amounts of chlorogenic acid were observed in sunflower flour (-11.4% and -19.8%, respectively), which were more pronounced in the protein concentrate (-50.7% and -95.6%, respectively). High tolerances against chlorogenic acid and the cleavage product quinic acid with a minimum inhibitory concentration (MIC) of ≥20.48 mg/ml after 48 h were recorded for all strains except Bifidobacterium animalis subsp. lactis, which was more sensitive. The second cleavage compound, caffeic acid revealed a higher antimicrobial potential with MIC values of 0.64-5.12 mg/ml. In this proof of concept study, degradation versus inhibitory effect suggest the existence of basic mechanisms of interaction between phenolic acids in sunflower and lactic acid bacteria and a feasible way to reduce the chlorogenic acid content, which may help to avoid undesired color changes.

  5. Characterizations of intracellular arsenic in a bacterium

    NASA Astrophysics Data System (ADS)

    Wolfe-Simon, F.; Yannone, S. M.; Tainer, J. A.

    2011-12-01

    Life requires a key set of chemical elements to sustain growth. Yet, a growing body of literature suggests that microbes can alter their nutritional requirements based on the availability of these chemical elements. Under limiting conditions for one element microbes have been shown to utilize a variety of other elements to serve similar functions often (but not always) in similar molecular structures. Well-characterized elemental exchanges include manganese for iron, tungsten for molybdenum and sulfur for phosphorus or oxygen. These exchanges can be found in a wide variety of biomolecules ranging from protein to lipids and DNA. Recent evidence suggested that arsenic, as arsenate or As(V), was taken up and incorporated into the cellular material of the bacterium GFAJ-1. The evidence was interpreted to support As(V) acting in an analogous role to phosphate. We will therefore discuss our ongoing efforts to characterize intracellular arsenate and how it may partition among the cellular fractions of the microbial isolate GFAJ-1 when exposed to As(V) in the presence of various levels of phosphate. Under high As(V) conditions, cells express a dramatically different proteome than when grown given only phosphate. Ongoing studies on the diversity and potential role of proteins and metabolites produced in the presence of As(V) will be reported. These investigations promise to inform the role and additional metabolic potential for As in biology. Arsenic assimilation into biomolecules contributes to the expanding set of chemical elements utilized by microbes in unusual environmental niches.

  6. Cloning and characterization of nif structural and regulatory genes in the purple sulfur bacterium, Halorhodospira halophila.

    PubMed

    Tsuihiji, Hisayoshi; Yamazaki, Yoichi; Kamikubo, Hironari; Imamoto, Yasushi; Kataoka, Mikio

    2006-03-01

    Halorhodospira halophila is a halophilic photosynthetic bacterium classified as a purple sulfur bacterium. We found that H. halophila generates hydrogen gas during photoautotrophic growth as a byproduct of a nitrogenase reaction. In order to consider the applied possibilities of this photobiological hydrogen generation, we cloned and characterized the structural and regulatory genes encoding the nitrogenase, nifH, nifD and nifA, from H. halophila. This is the first description of the nif genes for a purple sulfur bacterium. The amino-acid sequences of NifH and NifD indicated that these proteins are an Fe protein and a part of a MoFe protein, respectively. The important residues are conserved completely. The sequence upstream from the nifH region and sequence similarities of nifH and nifD with those of the other organisms suggest that the regulatory system might be a NifL-NifA system; however, H. halophila lacks nifL. The amino-acid sequence of H. halophila NifA is closer to that of the NifA of the NifL-NifA system than to that of NifA without NifL. H. halophila NifA does not conserve either the residue that interacts with NifL or the important residues involved in NifL-independent regulation. These results suggest the existence of yet another regulatory system, and that the development of functional systems and their molecular counterparts are not necessarily correlated throughout evolution. All of these Nif proteins of H. halophila possess an excess of acidic residues, which acts as a salt-resistant mechanism.

  7. Cytoplasmic and Periplasmic Proteomic Signatures of Exponentially Growing Cells of the Psychrophilic Bacterium Pseudoalteromonas haloplanktis TAC125 ▿ †

    PubMed Central

    Wilmes, Boris; Kock, Holger; Glagla, Susanne; Albrecht, Dirk; Voigt, Birgit; Markert, Stephanie; Gardebrecht, Antje; Bode, Rüdiger; Danchin, Antoine; Feller, Georges; Hecker, Michael; Schweder, Thomas

    2011-01-01

    The psychrophilic model bacterium Pseudoalteromonas haloplanktis is characterized by remarkably fast growth rates under low-temperature conditions in a range from 5°C to 20°C. In this study the proteome of cellular compartments, the cytoplasm and periplasm, of P. haloplanktis strain TAC125 was analyzed under exponential growth conditions at a permissive temperature of 16°C. By means of two-dimensional protein gel electrophoresis and mass spectrometry, a first inventory of the most abundant cytoplasmic and periplasmic proteins expressed in a peptone-supplemented minimal medium was established. By this approach major enzymes of the amino acid catabolism of this marine bacterium could be functionally deduced. The cytoplasmic proteome showed a predominance of amino acid degradation pathways and tricarboxylic acid (TCA) cycle enzymes but also the protein synthesis machinery. Furthermore, high levels of cold acclimation and oxidative stress proteins could be detected at this moderate growth temperature. The periplasmic proteome was characterized by a significant abundance of transporters, especially of highly expressed putative TonB-dependent receptors. This high capacity for protein synthesis, efficient amino acid utilization, and substrate transport may contribute to the fast growth rates of the copiotrophic bacterium P. haloplanktis in its natural environments. PMID:21183643

  8. Isolation of lactic acid-forming bacteria from biogas plants.

    PubMed

    Bohn, Jelena; Yüksel-Dadak, Aytül; Dröge, Stefan; König, Helmut

    2017-02-20

    Direct molecular approaches provide hints that lactic acid bacteria play an important role in the degradation process of organic material to methanogenetic substrates in biogas plants. However, their diversity in biogas fermenter samples has not been analyzed in detail yet. For that reason, five different biogas fermenters, which were fed mainly with maize silage and manure from cattle or pigs, were examined for the occurrence of lactic acid-forming bacteria. A total of 197 lactic acid-forming bacterial strains were isolated, which we assigned to 21 species, belonging to the genera Bacillus, Clostridium, Lactobacillus, Pediococcus, Streptococcus and Pseudoramibacter-related. A qualitative multiplex system and a real-time quantitative PCR could be developed for most isolates, realized by the selection of specific primers. Their role in biogas plants was discussed on the basis of the quantitative results and on physiological data of the isolates.

  9. Structure of the O-specific polysaccharide of the bacterium Proteus vulgaris O23.

    PubMed

    Perepelov, A V; Shashkov, A S; Babichka, D; Senchenkova, S N; Bartodziejska, B; Rozalski, A; Knirel, Y A

    2000-09-01

    An acidic O-specific polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of the bacterium Proteus vulgaris O23 (strain PrK 44/57) and found to contain 2-acetamido-2-deoxy-D-galactose, 2-acetamido-2-deoxy-D-glucose, and D-galacturonic acid. Based on 1H- and 13C-NMR spectroscopic studies, including two-dimensional correlation spectroscopy (COSY), total correlation spectroscopy (TOCSY), nuclear Overhauser effect spectroscopy (NOESY), and 1H,13C heteronuclear multiple-quantum coherence (HMQC) experiments, the following structure of the branched tetrasaccharide repeating unit of the polysaccharide was established: [figure], where the degree of O-acetylation of the terminal GalA residue at position 4 is about 80%. A structural similarity of the O-specific polysaccharides of P. vulgaris O23 and P. mirabilis O23 is discussed.

  10. Pangenome Evolution in the Marine Bacterium Alteromonas

    PubMed Central

    López-Pérez, Mario; Rodriguez-Valera, Francisco

    2016-01-01

    We have examined a collection of the free-living marine bacterium Alteromonas genomes with cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., from microbes that can be considered members of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4 Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37.7–83.7% of all nucleotide polymorphisms) but they decreased sharply between species (18.9–5.1%). Regarding the flexible genome, its main expansion occurred within the boundaries of the species, i.e., strains of the same species already have a large and diverse flexible genome. Flexible regions occupy mostly fixed genomic locations. Four large genomic islands are involved in the synthesis of strain-specific glycosydic receptors that we have called glycotypes. These genomic regions are exchanged by homologous recombination within and between species and there is evidence for their import from distant taxonomic units (other genera within the family). In addition, several hotspots for integration of gene cassettes by illegitimate recombination are distributed throughout the genome. They code for features that give each clone specific properties to interact with their ecological niche and must flow fast throughout the whole genus as they are found, with nearly identical sequences, in different species. Models for the generation of this genomic diversity involving phage predation are discussed. PMID:27189983

  11. Overproduction of Hydrogen From an Anaerobic Bacterium

    DTIC Science & Technology

    2008-12-01

    ADM002187. Proceedings of the Army Science Conference (26th) Held in Orlando, Florida on 1-4 December 2008, The original document contains color images...0.02 mg/L folic acid, 0.1 mg/L pyridoxine-HCl, 0.05 mg/L thiamine-HCl, 0.05 mg/L riboflavin , 0.05 mg/L nicotinic acid, 0.05 mg/L calcium

  12. Biochemical characterization of cellulose-binding proteins (CBPA and CBPB) from the rumen cellulolytic bacterium Eubacterium cellulosolvens 5.

    PubMed

    Yoshimatsu, Miho; Toyoda, Atsushi; Onizawa, Naoki; Nakamura, Yutaka; Minato, Hajime

    2007-10-01

    The cellulose-binding proteins, CBPA and CBPB, of rumen cellulolytic bacterium Eubacterium cellulosolvens 5 were biochemically characterized, and their properties were compared. Recombinant CBPA and CBPB were a typical 1,4-beta-endoglucanase. Both proteins bound to insoluble polysaccharides such as Avicel cellulose, acid swollen cellulose, lichenan, chitin, and oat spelt xylan. On the other hand, only recombinant CBPB bound to agarose and starch.

  13. Phenotypic Variation in the Plant Pathogenic Bacterium Acidovorax citrulli

    PubMed Central

    Shrestha, Ram Kumar; Rosenberg, Tally; Makarovsky, Daria; Eckshtain-Levi, Noam; Zelinger, Einat; Kopelowitz, June; Sikorski, Johannes; Burdman, Saul

    2013-01-01

    Acidovorax citrulli causes bacterial fruit blotch (BFB) of cucurbits, a disease that threatens the cucurbit industry worldwide. Despite the economic importance of BFB, little is known about pathogenicity and fitness strategies of the bacterium. We have observed the phenomenon of phenotypic variation in A. citrulli. Here we report the characterization of phenotypic variants (PVs) of two strains, M6 and 7a1, isolated from melon and watermelon, respectively. Phenotypic variation was observed following growth in rich medium, as well as upon isolation of bacteria from inoculated plants or exposure to several stresses, including heat, salt and acidic conditions. When grown on nutrient agar, all PV colonies possessed a translucent appearance, in contrast to parental strain colonies that were opaque. After 72 h, PV colonies were bigger than parental colonies, and had a fuzzy appearance relative to parental strain colonies that are relatively smooth. A. citrulli colonies are generally surrounded by haloes detectable by the naked eye. These haloes are formed by type IV pilus (T4P)-mediated twitching motility that occurs at the edge of the colony. No twitching haloes could be detected around colonies of both M6 and 7a1 PVs, and microscopy observations confirmed that indeed the PVs did not perform twitching motility. In agreement with these results, transmission electron microscopy revealed that M6 and 7a1 PVs do not produce T4P under tested conditions. PVs also differed from their parental strain in swimming motility and biofilm formation, and interestingly, all assessed variants were less virulent than their corresponding parental strains in seed transmission assays. Slight alterations could be detected in some DNA fingerprinting profiles of 7a1 variants relative to the parental strain, while no differences at all could be seen among M6 variants and parental strain, suggesting that, at least in the latter, phenotypic variation is mediated by slight genetic and/or epigenetic

  14. Evidence for distinct L-methionine catabolic pathways in the yeast Geotrichum candidum and the bacterium Brevibacterium linens.

    PubMed

    Arfi, Kenza; Landaud, Sophie; Bonnarme, Pascal

    2006-03-01

    Tracing experiments were carried out to identify volatile and nonvolatile L-methionine degradation intermediates and end products in the yeast Geotrichum candidum and in the bacterium Brevibacterium linens, both of which are present in the surface flora of certain soft cheeses and contribute to the ripening reactions. Since the acid-sensitive bacterium B. linens is known to produce larger amounts and a greater variety of volatile sulfur compounds (VSCs) than the yeast G. candidum produces, we examined whether the L-methionine degradation routes of these microorganisms differ. In both microorganisms, methanethiol and alpha-ketobutyrate are generated; the former compound is the precursor of other VSCs, and the latter is subsequently degraded to 2,3-pentanedione, which has not been described previously as an end product of L-methionine catabolism. However, the L-methionine degradation pathways differ in the first steps of L-methionine degradation. L-Methionine degradation is initiated by a one-step degradation process in the bacterium B. linens, whereas a two-step degradation pathway with 4-methylthio-2-oxobutyric acid (MOBA) and 4-methylthio-2-hydroxybutyric acid (MHBA) as intermediates is used in the yeast G. candidum. Since G. candidum develops earlier than B. linens during the ripening process, MOBA and MHBA generated by G.candidum could also be used as precursors for VSC production by B. linens.

  15. Haloanaerobium salsugo sp. nov., a moderately halophilic, anaerobic bacterium from a subterranean brine

    SciTech Connect

    Bhupathiraju, V.K.; Sharma, P.K.; Tanner, R.S.; McInerney, M.J.; Oren, A.; Woese, C.R.

    1994-07-01

    A strictly anaerobic, moderately halophilic, gram-negative bacterium was isolated from a highly saline oil field brine. The bacterium was a non-spore-forming, nonmotile rod, appearing singly, in pairs, or occasionally as long chains, and measured 0.3 to 0.4 by 2.6 to 4 {micro}m. The bacterium had a specific requirement for NaCl and grew at NaCl concentrations of between 6 and 24%, with optimal growth at 9% NaCl. The isolate grew at temperatures of between 22 and 51 C and pH values of between 5.6 and 8.0. The doubling time in a complex medium containing 10% NaCl was 9 h. Growth was inhibited by chloramphenicol, tetracycline, and penicillin but not by cycloheximide or azide. Fermentable substrates were predominantly carbohydrates. The end products of glucose fermentation were acetate, ethanol, CO{sub 2}, and H{sub 2}. The major components of the cellular fatty acids were C{sub 14:0}, C{sub 16:0}, C{sub 16:1}, and C{sub 17:0 cyc} acids. The DNA base composition of the isolate was 34 mol% G+C. Oligonucleotide catalog and sequence analyses of the 16S rRNA showed that strain VS-752{sup T} was most closely related to Haloanaerobium praevalens GSL{sup T} (ATCC 33744), the sole member of the genus Haloanaerobium. The authors propose that strain VS-752 (ATCC 51327) by established as the type strain of a new species, Haloanaerobium salsugo, in the genus Haloanaerobium. 40 refs., 3 figs, 5 tabs.

  16. Expression of a Clostridium perfringens genome-encoded putative N-acetylmuramoyl-L-alanine amidase as a potential antimicrobial to control the bacterium

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Clostridium perfringens is a Gram-positive, spore-forming anaerobic bacterium that plays a substantial role in non-foodborne human, animal and avian diseases as well as human foodborne disease. Previously discovered C. perfringens bacteriophage lytic enzyme amino acid sequences were utilized to iden...

  17. Degradation of phenolic compounds by the lignocellulose deconstructing thermoacidophilic bacterium Alicyclobacillus Acidocaldarius

    DOE PAGES

    Aston, John E.; Apel, William A.; Lee, Brady D.; ...

    2015-11-05

    Alicyclobacillus acidocaldarius, a thermoacidophilic bacterium, has a repertoire of thermo- and acid-stable enzymes that deconstruct lignocellulosic compounds. The work presented here describes the ability of A. acidocaldarius to reduce the concentration of the phenolic compounds: phenol, ferulic acid, ρ-coumaric acid and sinapinic acid during growth conditions. The extent and rate of the removal of these compounds were significantly increased by the presence of micro-molar copper concentrations, suggesting activity by copper oxidases that have been identified in the genome of A. acidocaldarius. Substrate removal kinetics was first order for phenol, ferulic acid, ρ-coumaric acid and sinapinic acid in the presence ofmore » 50 μM copper sulfate. In addition, laccase enzyme assays of cellular protein fractions suggested significant activity on a lignin analog between the temperatures of 45 and 90 °C. As a result, this work shows the potential for A. acidocaldarius to degrade phenolic compounds, demonstrating potential relevance to biofuel production and other industrial processes.« less

  18. Degradation of phenolic compounds by the lignocellulose deconstructing thermoacidophilic bacterium Alicyclobacillus Acidocaldarius

    SciTech Connect

    Aston, John E.; Apel, William A.; Lee, Brady D.; Thompson, David N.; Lacey, Jeffrey A.; Newby, Deborah T.; Reed, David. W.; Thompson, Vicki S.

    2015-11-05

    Alicyclobacillus acidocaldarius, a thermoacidophilic bacterium, has a repertoire of thermo- and acid-stable enzymes that deconstruct lignocellulosic compounds. The work presented here describes the ability of A. acidocaldarius to reduce the concentration of the phenolic compounds: phenol, ferulic acid, ρ-coumaric acid and sinapinic acid during growth conditions. The extent and rate of the removal of these compounds were significantly increased by the presence of micro-molar copper concentrations, suggesting activity by copper oxidases that have been identified in the genome of A. acidocaldarius. Substrate removal kinetics was first order for phenol, ferulic acid, ρ-coumaric acid and sinapinic acid in the presence of 50 μM copper sulfate. In addition, laccase enzyme assays of cellular protein fractions suggested significant activity on a lignin analog between the temperatures of 45 and 90 °C. As a result, this work shows the potential for A. acidocaldarius to degrade phenolic compounds, demonstrating potential relevance to biofuel production and other industrial processes.

  19. Alicyclobacillus vulcanalis sp. nov., a thermophilic, acidophilic bacterium isolated from Coso Hot Springs, California, USA.

    PubMed

    Simbahan, Jessica; Drijber, Rhae; Blum, Paul

    2004-09-01

    A thermo-acidophilic Gram-positive bacterium, strain CsHg2T, which grows aerobically at 35-65 degrees C (optimum 55 degrees C) and at pH 2.0-6.0 (optimum 4.0), was isolated from a geothermal pool located in Coso Hot Springs in the Mojave Desert, California, USA. Phylogenetic analysis of 16S rRNA gene sequences showed that this bacterium was most closely related to the type strains of Alicyclobacillus acidocaldarius (97.8 % identity) and Alicyclobacillus sendaiensis (96.9 %), three Japanese strains denoted as UZ-1, KHA-31 and MIH 332 (96.1-96.5 %) and Alicyclobacillus genomic species FR-6 (96.3 %). Phenotypic characteristics including temperature and pH optima, G+C composition, acid production from a variety of carbon sources and sensitivity to different metal salts distinguished CsHg2T from A. acidocaldarius, A. sendaiensis and FR-6. The cell lipid membrane was composed mainly of omega-cyclohexyl fatty acid, consistent with membranes from other Alicyclobacillus species. Very low DNA-DNA hybridization values between CsHg2T and the type strains of Alicyclobacillus indicate that CsHg2T represents a distinct species. On the basis of these results, the name Alicyclobacillus vulcanalis sp. nov. is proposed for this organism. The type strain is CsHg2T (ATCC BAA-915T = DSM 16176T).

  20. Extreme Ionizing-Radiation-Resistant Bacterium

    NASA Technical Reports Server (NTRS)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.; Schwendner, Petra

    2012-01-01

    potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

  1. Extreme Ionizing-Radiation-Resistant Bacterium

    NASA Technical Reports Server (NTRS)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.; Schwendner, Petra

    2013-01-01

    potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

  2. Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana

    PubMed Central

    Pradhan, Nirakar; Dipasquale, Laura; d’Ippolito, Giuliana; Panico, Antonio; Lens, Piet N. L.; Esposito, Giovanni; Fontana, Angelo

    2015-01-01

    As the only fuel that is not chemically bound to carbon, hydrogen has gained interest as an energy carrier to face the current environmental issues of greenhouse gas emissions and to substitute the depleting non-renewable reserves. In the last years, there has been a significant increase in the number of publications about the bacterium Thermotoga neapolitana that is responsible for production yields of H2 that are among the highest achievements reported in the literature. Here we present an extensive overview of the most recent studies on this hyperthermophilic bacterium together with a critical discussion of the potential of fermentative production by this bacterium. The review article is organized into sections focused on biochemical, microbiological and technical issues, including the effect of substrate, reactor type, gas sparging, temperature, pH, hydraulic retention time and organic loading parameters on rate and yield of gas production. PMID:26053393

  3. Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana.

    PubMed

    Pradhan, Nirakar; Dipasquale, Laura; d'Ippolito, Giuliana; Panico, Antonio; Lens, Piet N L; Esposito, Giovanni; Fontana, Angelo

    2015-06-04

    As the only fuel that is not chemically bound to carbon, hydrogen has gained interest as an energy carrier to face the current environmental issues of greenhouse gas emissions and to substitute the depleting non-renewable reserves. In the last years, there has been a significant increase in the number of publications about the bacterium Thermotoga neapolitana that is responsible for production yields of H2 that are among the highest achievements reported in the literature. Here we present an extensive overview of the most recent studies on this hyperthermophilic bacterium together with a critical discussion of the potential of fermentative production by this bacterium. The review article is organized into sections focused on biochemical, microbiological and technical issues, including the effect of substrate, reactor type, gas sparging, temperature, pH, hydraulic retention time and organic loading parameters on rate and yield of gas production.

  4. Microbiological study of lactic acid fermentation of Caper berries by molecular and culture-dependent methods.

    PubMed

    Pérez Pulido, Rubén; Ben Omar, Nabil; Abriouel, Hikmate; Lucas López, Rosario; Martínez Cañamero, Magdalena; Gálvez, Antonio

    2005-12-01

    Fermentation of capers (the fruits of Capparis sp.) was studied by molecular and culture-independent methods. A lactic acid fermentation occurred following immersion of caper berries in water, resulting in fast acidification and development of the organoleptic properties typical of this fermented food. A collection of 133 isolates obtained at different times of fermentation was reduced to 75 after randomly amplified polymorphic DNA (RAPD)-PCR analysis. Isolates were identified by PCR or 16S rRNA gene sequencing as Lactobacillus plantarum (37 isolates), Lactobacillus paraplantarum (1 isolate), Lactobacillus pentosus (5 isolates), Lactobacillus brevis (9 isolates), Lactobacillus fermentum (6 isolates), Pediococcus pentosaceus (14 isolates), Pediococcus acidilactici (1 isolate), and Enterococcus faecium (2 isolates). Cluster analysis of RAPD-PCR patterns revealed a high degree of diversity among lactobacilli (with four major groups and five subgroups), while pediococci clustered in two closely related groups. A culture-independent analysis of fermentation samples by temporal temperature gradient electrophoresis (TTGE) also indicated that L. plantarum is the predominant species in this fermentation, in agreement with culture-dependent results. The distribution of L. brevis and L. fermentum in samples was also determined by TTGE, but identification of Pediococcus at the species level was not possible. TTGE also allowed a more precise estimation of the distribution of E. faecium, and the detection of Enterococcus casseliflavus (which was not revealed by the culture-dependent analysis). Results from this study indicate that complementary data from molecular and culture-dependent analysis provide a more accurate determination of the microbial community dynamics during caper fermentation.

  5. Crassaminicella profunda gen. nov., sp. nov., an anaerobic marine bacterium isolated from deep-sea sediments.

    PubMed

    Lakhal, Raja; Pradel, Nathalie; Postec, Anne; Ollivier, Bernard; Cayol, Jean-Luc; Godfroy, Anne; Fardeau, Marie-Laure; Galés, Grégoire

    2015-09-01

    A novel, anaerobic, chemo-organotrophic bacterium, designated strain Ra1766H(T), was isolated from sediments of the Guaymas basin (Gulf of California, Mexico) taken from a depth of 2002  m. Cells were thin, motile, Gram-stain-positive, flexible rods forming terminal endospores. Strain Ra1766H(T) grew at temperatures of 25-45 °C (optimum 30 °C), pH 6.7-8.1 (optimum 7.5) and in a salinity of 5-60 g l(-1) NaCl (optimum 30 g l(-1)). It was an obligate heterotrophic bacterium fermenting carbohydrates (glucose and mannose) and organic acids (pyruvate and succinate). Casamino acids and amino acids (glutamate, aspartate and glycine) were also fermented. The main end products from glucose fermentation were acetate, butyrate, ethanol, H2 and CO2. Sulfate, sulfite, thiosulfate, elemental sulfur, fumarate, nitrate, nitrite and Fe(III) were not used as terminal electron acceptors. The predominant cellular fatty acids were C14  : 0, C16 : 1ω7, C16 : 1ω7 DMA and C16 : 0. The main polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phospholipids. The G+C content of the genomic DNA was 33.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Ra1766H(T) was affiliated to cluster XI of the order Clostridiales, phylum Firmicutes. The closest phylogenetic relative of Ra1766H(T) was Geosporobacter subterraneus (94.2% 16S rRNA gene sequence similarity). On the basis of phylogenetic inference and phenotypic properties, strain Ra1766H(T) ( = DSM 27501(T) = JCM 19377(T)) is proposed to be the type strain of a novel species of a novel genus, named Crassaminicella profunda.

  6. Pontibacter diazotrophicus sp. nov., a Novel Nitrogen-Fixing Bacterium of the Family Cytophagaceae

    PubMed Central

    Xu, Linghua; Zeng, Xian-Chun; Nie, Yao; Luo, Xuesong; Zhou, Enmin; Zhou, Lingli; Pan, Yunfan; Li, Wenjun

    2014-01-01

    Few diazotrophs have been found to belong to the family Cytophagaceae so far. In the present study, a Gram-negative, rod-shaped bacterium that forms red colonies, was isolated from sands of the Takalamakan desert. It was designated H4XT. Phylogenetic and biochemical analysis indicated that the isolate is a new species of the genus Pontibacter. The 16S rRNA gene of H4XT displays 94.2–96.8% sequence similarities to those of other strains in Pontibacter. The major respiratory quinone is menaquinone-7 (MK-7). The DNA G+C content is 46.6 mol%. The major cellular fatty acids are iso-C15∶0, C16∶1ω5c, summed feature 3 (containing C16∶1ω6c and/or C16∶1ω7c) and summed feature 4 (comprising anteiso-C17∶1B and/or iso-C17∶1I). The major polar lipids are phosphatidylethanolamine (PE), one aminophospholipid (APL) and some unknown phospholipids (PLs). It is interesting to see that this bacterium can grow very well in a nitrogen-free medium. PCR amplification suggested that the bacterium possesses at least one type of nitrogenase gene. Acetylene reduction assay showed that H4XT actually possesses nitrogen-fixing activity. Therefore, it can be concluded that H4XT is a new diazotroph. We thus referred it to as Pontibacter diazotrophicus sp. nov. The type strain is H4XT ( = CCTCC AB 2013049T = NRRL B-59974T). PMID:24647674

  7. Adhesive properties of a symbolic bacterium from a wood-boreing marine shipworm

    SciTech Connect

    Imam, S.H.; Greene, R.V.; Griffin, H.L. )

    1990-05-01

    Adhesive properties of cellulolytic, nitrogen-fixing bacterium isolated from a marine shipworm are described. {sup 35}S-labeled cells of the shipworm bacterium bound preferentially Whatman no.1 cellulose filter paper, compared with its binding to other cellulose substrata or substrata lacking cellulose. The ability of the bacteria to bind to Whatman no. 1 filter paper was significantly reduced by glutaraldehyde or heat treatment of cells. Pretreatment of cells with azide, valinomycin, gramicidin-D, bis-hexafluoroacetylacetone (1799), or carbonyl cyanide-p-trifluoromethoxyphenylhydrazone inhibited adhesion activity. Cells pretreated with pronase or trypsin also exhibited reduced binding activity, but chymotrypsin and peptidase had no effect on adhesion activity. Cellodextrins and methyl cellulose 15 inhibited the adhesion of the shipworm bacteria to filter paper, whereas glucose, cellobiose, and soluble carboxymethyl cellulose had no significant effect. The divalent cation chelators EDTA and EGTA (ethylene hlycol-bis({beta}-aminoethyl ether)-N,N,N{prime}N{prime}-tetraacetic acid) had little or no effect on adhesive properties of shipworm bacteria. Also, preabsorbing the substratum with extracellular endoglucanase isolated from the ship worm bacterium or 1% bovine serum albumin had no apparent effect on bacterial binding. Low concentration (0.01%) of sodium dodecyl sulfate solubilized a fraction from whole cells, which appeared to be involved in cellular binding activity. After removal of sodium dodecyl, sulfate, several proteins in this fraction associated with intact cells. These cells exhibited up to 50% enhanced binding to filter paper in comparison to cells which had not been exposed to the sodium dodecyl sulfate-solubilized fraction.

  8. Chitin Utilization by the Insect-Transmitted Bacterium Xylella fastidiosa▿ †

    PubMed Central

    Killiny, Nabil; Prado, Simone S.; Almeida, Rodrigo P. P.

    2010-01-01

    Xylella fastidiosa is an insect-borne bacterium that colonizes xylem vessels of a large number of host plants, including several crops of economic importance. Chitin is a polysaccharide present in the cuticle of leafhopper vectors of X. fastidiosa and may serve as a carbon source for this bacterium. Biological assays showed that X. fastidiosa reached larger populations in the presence of chitin. Additionally, chitin induced phenotypic changes in this bacterium, notably increasing adhesiveness. Quantitative PCR assays indicated transcriptional changes in the presence of chitin, and an enzymatic assay demonstrated chitinolytic activity by X. fastidiosa. An ortholog of the chitinase A gene (chiA) was identified in the X. fastidiosa genome. The in silico analysis revealed that the open reading frame of chiA encodes a protein of 351 amino acids with an estimated molecular mass of 40 kDa. chiA is in a locus that consists of genes implicated in polysaccharide degradation. Moreover, this locus was also found in the genomes of closely related bacteria in the genus Xanthomonas, which are plant but not insect associated. X. fastidiosa degraded chitin when grown on a solid chitin-yeast extract-agar medium and grew in liquid medium with chitin as the sole carbon source; ChiA was also determined to be secreted. The gene encoding ChiA was cloned into Escherichia coli, and endochitinase activity was detected in the transformant, showing that the gene is functional and involved in chitin degradation. The results suggest that X. fastidiosa may use its vectors' foregut surface as a carbon source. In addition, chitin may trigger X. fastidiosa's gene regulation and biofilm formation within vectors. Further work is necessary to characterize the role of chitin and its utilization in X. fastidiosa. PMID:20656858

  9. Lactic acid bacteria in Hamei and Marcha of North East India.

    PubMed

    Tamang, J P; Dewan, S; Tamang, B; Rai, A; Schillinger, U; Holzapfel, W H

    2007-06-01

    Hamei and Marcha are mixed dough inocula used as starters for preparation of various indigenous alcoholic beverages in Manipur and Sikkim in India, respectively. These starters are traditionally prepared from rice with wild herbs and spices. Samples of Hamei and Marcha, collected from Manipur and Sikkim, respectively, were analysed for lactic acid bacterial composition. The population of lactic acid bacteria (LAB) was 6.9 and 7.1 Log cfu/g in Hamei and Marcha, respectively. On the basis of phenotypic and genotypic characters, LAB strains isolated from Hamei and Marcha were identified as Pediococcus pentosaceus, Lactobacillus plantarum and Lactobacillus brevis. Technological properties of LAB such as antimicrobial properties, effect on acidification, ability to produce biogenic amines and ethanol, degree of hydrophobicity and enzymatic activities were also performed. Pediococcus pentosaceus HS: B1, isolated from Hamei, was found to produce bacteriocin. None of the strains produced biogenic amines. LAB strains showed a strong acidifying ability and they also produced a wide spectrum of enzymes.

  10. Nesterenkonia sp. strain F, a halophilic bacterium producing acetone, butanol, and ethanol under aerobic conditions

    PubMed Central

    Amiri, Hamid; Azarbaijani, Reza; Parsa Yeganeh, Laleh; Shahzadeh Fazeli, Abolhassan; Tabatabaei, Meisam; Hosseini Salekdeh, Ghasem; Karimi, Keikhosro

    2016-01-01

    The moderately halophilic bacterium Nesterenkonia sp. strain F, which was isolated from Aran-Bidgol Lake (Iran), has the ability to produce acetone, butanol, and ethanol (ABE) as well as acetic and butyric acids under aerobic and anaerobic conditions. This result is the first report of ABE production with a wild microorganism from a family other than Clostridia and also the first halophilic species shown to produce butanol under aerobic cultivation. The cultivation of Nesterenkonia sp. strain F under anaerobic conditions with 50 g/l of glucose for 72 h resulted in the production of 105 mg/l of butanol, 122 mg/l of acetone, 0.2 g/l of acetic acid, and 2.5 g/l of butyric acid. Furthermore, the strain was cultivated on media with different glucose concentrations (20, 50, and 80 g/l) under aerobic and anaerobic conditions. Through fermentation with a 50 g/l initial glucose concentration under aerobic conditions, 66 mg/l of butanol, 125 mg/l of acetone, 291 mg/l of ethanol, 5.9 g/l of acetic acid, and 1.2 g/l of butyric acid were produced. The enzymes pertaining to the fermentation pathway in the strain were compared with the enzymes of Clostridium spp., and the metabolic pathway of fermentation used by Nesterenkonia sp. strain F was investigated. PMID:26725518

  11. Cellobiohydrolase B, a second exo-cellobiohydrolase from the cellulolytic bacterium Cellulomonas fimi.

    PubMed Central

    Shen, H; Gilkes, N R; Kilburn, D G; Miller, R C; Warren, R A

    1995-01-01

    The gene cbhB from the cellulolytic bacterium Cellulomonas fimi encodes a polypeptide of 1090 amino acids. Cellobiohydrolase B (CbhB) is 1037 amino acids long, with a calculated molecular mass of 109765 Da. The enzyme comprises five domains: an N-terminal catalytic domain of 643 amino acids, three fibronectin type III repeats of 97 amino acids each, and a C-terminal cellulose-binding domain of 104 amino acids. The catalytic domain belongs to family 48 of glycosyl hydrolases. CbhB has a very low activity on CM-cellulose. Viscometric analysis of CM-cellulose hydrolysis indicates that the enzyme is an exoglucanase. Cellobiose is the major product of hydrolysis of cellulose. In common with two other exoglycanases from C. fimi, CbhB has low but detectable endoglucanase activity. CbhB is the second exo-cellobiohydrolase found in C. fimi. Therefore, the cellulase system of C. fimi resembles those of fungi in comprising multiple endoglucanases and cellobiohydrolases. Images Figure 5 PMID:7575482

  12. Nesterenkonia sp. strain F, a halophilic bacterium producing acetone, butanol, and ethanol under aerobic conditions.

    PubMed

    Amiri, Hamid; Azarbaijani, Reza; Parsa Yeganeh, Laleh; Shahzadeh Fazeli, Abolhassan; Tabatabaei, Meisam; Salekdeh, Ghasem Hosseini; Karimi, Keikhosro

    2016-01-04

    The moderately halophilic bacterium Nesterenkonia sp. strain F, which was isolated from Aran-Bidgol Lake (Iran), has the ability to produce acetone, butanol, and ethanol (ABE) as well as acetic and butyric acids under aerobic and anaerobic conditions. This result is the first report of ABE production with a wild microorganism from a family other than Clostridia and also the first halophilic species shown to produce butanol under aerobic cultivation. The cultivation of Nesterenkonia sp. strain F under anaerobic conditions with 50 g/l of glucose for 72 h resulted in the production of 105 mg/l of butanol, 122 mg/l of acetone, 0.2 g/l of acetic acid, and 2.5 g/l of butyric acid. Furthermore, the strain was cultivated on media with different glucose concentrations (20, 50, and 80 g/l) under aerobic and anaerobic conditions. Through fermentation with a 50 g/l initial glucose concentration under aerobic conditions, 66 mg/l of butanol, 125 mg/l of acetone, 291 mg/l of ethanol, 5.9 g/l of acetic acid, and 1.2 g/l of butyric acid were produced. The enzymes pertaining to the fermentation pathway in the strain were compared with the enzymes of Clostridium spp., and the metabolic pathway of fermentation used by Nesterenkonia sp. strain F was investigated.

  13. Complete Genome of the Cellulolytic Ruminal Bacterium Ruminococcus albus 7

    SciTech Connect

    Suen, Garret; Stevenson, David M; Bruce, David; Chertkov, Olga; Copeland, A; Cheng, Jan-Fang; Detter, J. Chris; Goodwin, Lynne A.; Han, Cliff; Hauser, Loren John; Ivanova, N; Kyrpides, Nikos C; Land, Miriam L; Lapidus, Alla L.; Lucas, Susan; Ovchinnikova, Galina; Pitluck, Sam; Tapia, Roxanne; Woyke, Tanja; Boyum, Julie; Mead, David; Weimer, Paul J

    2011-01-01

    Ruminococcus albus 7 is a highly cellulolytic ruminal bacterium that is a member of the phylum Firmicutes. Here, we describe the complete genome of this microbe. This genome will be useful for rumen microbiology and cellulosome biology and in biofuel production, as one of its major fermentation products is ethanol.

  14. Complete genome of the cellulolytic ruminal bacterium Ruminococcus albus 7

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ruminococcus albus 7 is a highly cellulolytic rumen bacterium that is a member of the phylum Firmicutes. Here, we describe the complete genome for this microbe. This genome will be useful for rumen microbiology, cellulosome biology, and in biofuel production, as one of its major fermentation product...

  15. Gut bacterium of Dendrobaena veneta (Annelida: Oligochaeta) possesses antimycobacterial activity.

    PubMed

    Fiołka, Marta J; Zagaja, Mirosław P; Piersiak, Tomasz D; Wróbel, Marek; Pawelec, Jarosław

    2010-09-01

    The new bacterial strain with antimycobacterial activity has been isolated from the midgut of Dendrobaena veneta (Annelida). Biochemical and molecular characterization of isolates from 18 individuals identified all as Raoultella ornithinolytica genus with 99% similarity. The bacterium is a possible symbiont of the earthworm D. veneta. The isolated microorganism has shown the activity against four strains of fast-growing mycobacteria: Mycobacterium butiricum, Mycobacterium jucho, Mycobacterium smegmatis and Mycobacterium phlei. The multiplication of the gut bacterium on plates with Sauton medium containing mycobacteria has caused a lytic effect. After the incubation of the cell free extract prepared from the gut bacterium with four strains of mycobacteria in liquid Sauton medium, the cells of all tested strains were deformed and divided to small oval forms and sometimes created long filaments. The effect was observed by the use of light, transmission and scanning microscopy. Viability of all examined species of mycobacteria was significantly decreased. The antimycobacterial effect was probably the result of the antibiotic action produced by the gut bacterium of the earthworm. The application of ultrafiltration procedure allowed to demonstrate that antimicrobial substance with strong antimycobacterial activity from bacterial culture supernatant, is a protein with the molecular mass above 100 kDa.

  16. (Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage

    PubMed Central

    Mehboob, Farrakh; van Gelder, Antonie H.; Rijpstra, W. Irene C.; Damsté, Jaap S. Sinninghe; Stams, Alfons J. M.

    2010-01-01

    A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5–0.8 μm in diameter, and 2–8 μm in length, growing as single cells or in pairs. The cells grew optimally at 37°C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H2/CO2 to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO2. The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts. PMID:20680263

  17. Asticcacaulis benevestitus sp. nov., a psychrotolerant, dimorphic, prosthecate bacterium from tundra wetland soil.

    PubMed

    Vasilyeva, Lina V; Omelchenko, Marina V; Berestovskaya, Yulia Y; Lysenko, Anatolii M; Abraham, Wolf-Rainer; Dedysh, Svetlana N; Zavarzin, George A

    2006-09-01

    A Gram-negative, aerobic, heterotrophic, non-pigmented, dimorphic prosthecate bacterium was isolated from tundra wetland soil and designated strain Z-0023(T). Cells of this strain had a dimorphic life cycle and developed a non-adhesive stalk at a site not coincident with the centre of the cell pole, a characteristic typical of representatives of the genus Asticcacaulis. A highly distinctive feature of cells of strain Z-0023(T) was the presence of a conical, bell-shaped sheath when grown at low temperature. This prosthecate bacterium was a psychrotolerant, moderately acidophilic organism capable of growth between 4 and 28 degrees Celsius (optimum 15-20 degrees Celsius) and between pH 4.5 and 8.0 (optimum 5.6-6.0). The major phospholipid fatty acid was 18 : 1omega7c and the major phospholipids were phosphatidylglycerols. The G+C content of the DNA was 60.4 mol%. On the basis of 16S rRNA gene sequence similarity, strain Z-0023(T) was most closely related to Asticcacaulis biprosthecium (98 % similarity), Asticcacaulis taihuensis (98 %) and Asticcacaulis excentricus (95 %). However, low levels of DNA-DNA relatedness to these organisms and a number of distinctive features of the tundra wetland isolate indicated that it represented a novel species of the genus Asticcacaulis, for which the name Asticcacaulis benevestitus sp. nov. is proposed. The type strain is Z-0023(T) (=DSM 16100(T)=ATCC BAA-896(T)).

  18. (Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage.

    PubMed

    Balk, Melike; Mehboob, Farrakh; van Gelder, Antonie H; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; Stams, Alfons J M

    2010-09-01

    A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5-0.8 microm in diameter, and 2-8 microm in length, growing as single cells or in pairs. The cells grew optimally at 37 degrees C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H(2)/CO(2) to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO(2). The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts.

  19. Non-specific immune response of bullfrog Rana catesbeiana to intraperitoneal injection of bacterium Aeromonas hydrophila

    NASA Astrophysics Data System (ADS)

    Zhang, Junjie; Zou, Wenzheng; Yan, Qingpi

    2008-08-01

    Non-specific immune response of bullfrog Rana catesbeiana to pathogenic Aeromonas hydrophila was studied to 60 individuals in two groups. Each bullfrog in bacterium-injected group was injected intraperitoneally (i.p.) with 0.2 ml bacterial suspension at a density of 5.2 × 106 CFU/ml, while each one in control group injected i.p. with 0.2 ml sterile saline solution (0.85%, w/v). Three bullfrogs in both groups were sampled at 0, 1, 3, 7, 11, 15 and 20 days post-injection (dpi) for the evaluation of non-specific immune parameters. It was observed that intraperitoneal injection of A. hydrophila significantly increased the number of leucocytes and that of NBT-positive cells in peripheral blood. Significant increases in serum bactericidal activity and serum acid phosphatase activity were also observed in the bacterium-injected frogs when compared with those in the control group. However, a significant reduction was detected in vitro in phagocytosis activity of peripheral blood phagocytes. No significant difference in changes in the number of peripheral erythrocytes, serum superoxide dismutase (SOD) activity, and lysozyme activity was detected between the two groups. It is suggested that bullfrogs may produce a series of non-specific immune reactions in response to the A. hydrophila infection.

  20. Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium

    USGS Publications Warehouse

    Caccavo, F.; Coates, J.D.; Rossello-Mora, R. A.; Ludwig, W.; Schleifer, K.H.; Lovley, D.R.; McInerney, M.J.

    1996-01-01

    A new, phylogenetically distinct, dissimilatory, Fe(III)-reducing bacterium was isolated from surface sediment of a hydrocarbon-contaminated ditch. The isolate, designated strain PAL-1, was an obligately anaerobic, non-fermentative, motile, gram-negative vibrio. PAL-1 grew in a defined medium with acetate as electron donor and ferric pyrophosphate, ferric oxyhydroxide, ferric citrate, Co(III)-EDTA, or elemental sulfur as sole electron acceptor. PAL-1 also used proline, hydrogen, lactate, propionate, succinate, fumarate, pyruvate, or yeast extract as electron donors for Fe(III) reduction. It is the first bacterium known to couple the oxidation of an amino acid to Fe(III) reduction. PAI-1 did not reduce oxygen, Mn(IV), U(VI), Cr(VI), nitrate, sulfate, sulfite, or thiosulfate with acetate as the electron donor. Cell suspensions of PAL-1 exhibited dithionite-reduced minus air-oxidized difference spectra that were characteristic of c-type cytochromes. Analysis of the 16S rRNA gene sequence of PAL-1 showed that the strain is not related to any of the described metal-reducing bacteria in the Proteobacteria and, together with Flexistipes sinusarabici, forms a separate line of descent within the Bacteria. Phenotypically and phylogenetically, strain PAI-1 differs from all other described bacteria, and represents the type strain of a new genus and species. Geovibrio ferrireducens.

  1. Involvement of a novel fermentative bacterium in acidification in a thermophilic anaerobic digester.

    PubMed

    Hori, Tomoyuki; Akuzawa, Masateru; Haruta, Shin; Ueno, Yoshiyuki; Ogata, Atsushi; Ishii, Masaharu; Igarashi, Yasuo

    2014-12-01

    Acidification results from the excessive accumulation of volatile fatty acids and the breakthrough of buffering capacity in anaerobic digesters. However, little is known about the identity of the acidogenic bacteria involved. Here, we identified an active fermentative bacterium during acidification in a thermophilic anaerobic digester by sequencing and phylogenetic analysis of isotopically labeled rRNA. The digestion sludge retrieved from the beginning of pH drop in the laboratory-scale anaerobic digester was incubated anaerobically at 55 °C for 4 h during which (13)C-labeled glucose was supplemented repeatedly. (13)CH4 and (13)CO2 were produced after substrate addition. RNA extracts from the incubated sludge was density-separated by ultracentrifugation, and then bacterial communities in the density fractions were screened by terminal restriction fragment length polymorphism and clone library analyses based on 16S rRNA transcripts. Remarkably, a novel lineage within the genus Thermoanaerobacterium became abundant with increasing the buoyant density and predominated in the heaviest fraction of RNA. The results in this study indicate that a thermoacidophilic bacterium exclusively fermented the simple carbohydrate glucose, thereby playing key roles in acidification in the thermophilic anaerobic digester.

  2. The bacterial transformation of abietic acid

    PubMed Central

    Cross, B. E.; Myers, P. L.

    1968-01-01

    An Alcaligenes species, which was isolated from soil, can utilize abietic acid as its sole carbon source. During growth, the bacterium transforms abietic acid into 5α-hydroxyabietic acid (I, R=OH), a product considered to be 7β-hydroxy-13-isopropyl-8ξ-podocarp-13-en-15-oic acid (II, R=H) and a compound, C20H28O3, which is believed to be an epoxy-γ-lactone. PMID:5665894

  3. Addition of microbially-treated sugar beet residue and a native bacterium increases structural stability in heavy metal-contaminated Mediterranean soils.

    PubMed

    Carrasco, L; Caravaca, F; Azcón, R; Kohler, J; Roldán, A

    2009-10-15

    A mesocosm experiment was conducted to investigate the effect of the addition of Aspergillus niger-treated sugar beet waste, in the presence of rock phosphate, and inoculation with a native, metal-tolerant bacterium, Bacillus thuringiensis, on the stabilisation of soil aggregates of two mine tailings, with differing pH values, from a semiarid Mediterranean area and on the stimulation of growth of Piptatherum miliaceum. Bacterium combined with organic amendment enhanced structural stability (38% in acidic soil and 106% in neutral soil compared with their corresponding controls). Only the organic amendment increased pH, electrical conductivity, water-soluble C, water-soluble carbohydrates and plant growth, in both soils. While in neutral soil both organic amendment and bacterium increased dehydrogenase activity, only organic amendment had a significant effect in acidic soil. This study demonstrates that the use of P. miliaceum in combination with organic amendment and bacterium is a suitable tool for the stabilisation of the soil structure of degraded mine tailings, although its effectiveness is dependent on soil pH.

  4. Isolation, characterization and evaluation of probiotic lactic acid bacteria for potential use in animal production.

    PubMed

    García-Hernández, Yaneisy; Pérez-Sánchez, Tania; Boucourt, Ramón; Balcázar, José L; Nicoli, Jacques R; Moreira-Silva, João; Rodríguez, Zoraya; Fuertes, Héctor; Nuñez, Odalys; Albelo, Nereyda; Halaihel, Nabil

    2016-10-01

    In livestock production, lactic acid bacteria (LAB) are the most common microorganisms used as probiotics. For such use, these bacteria must be correctly identified and characterized to ensure their safety and efficiency. In the present study, LAB were isolated from broiler excreta, where a fermentation process was used. Nine among sixteen isolates were identified by biochemical and molecular (sequencing of the 16S rRNA gene) methods as Lactobacillus crispatus (n=1), Lactobacillus pentosus (n=1), Weissella cibaria (n=1), Pediococcus pentosaceus (n=2) and Enterococcus hirae (n=4). Subsequently, these bacteria were characterized for their growth capabilities, lactic acid production, acidic pH and bile salts tolerance, cell surface hydrophobicity, antimicrobial susceptibility and antagonistic activity. Lactobacillus pentosus strain LB-31, which showed the best characteristics, was selected for further analysis. This strain was administered to broilers and showed the ability of modulating the immune response and producing beneficial effects on morpho-physiological, productive and health indicators of the animals.

  5. Stomatobaculum longum gen. nov., sp. nov., an obligately anaerobic bacterium from the human oral cavity

    PubMed Central

    Muller, Paul; Panikov, Nicolai; Mandalakis, Manolis; Hohmann, Tine; Hazen, Amanda; Fowle, William; Prozorov, Tanya; Bazylinski, Dennis A.

    2013-01-01

    A strictly anaerobic Gram-stain-variable but positive by structure, non-spore-forming bacterium designated Lachnospiraceae bacterium ACC2 strain DSM 24645T was isolated from human subgingival dental plaque. Bacterial cells were 4–40 µm long non-motile rods, often swollen and forming curved filaments up to 200 µm. Cells contained intracellular, poorly crystalline, nanometre-sized iron- and sulfur-rich particles. The micro-organism was able to grow on yeast extract, trypticase peptone, milk, some sugars and organic acids. The major metabolic end-products of glucose fermentation were butyrate, lactate, isovalerate and acetate. The growth temperature and pH ranges were 30–42 °C and 4.9–7.5, respectively. Major fatty acids were C14 : 0, C14 : 0 DMA (dimethyl aldehyde), C16 : 0, C16 : 1ω7c DMA. The whole-cell hydrolysate contained meso-diaminopimelic acid, indicating peptidoglycan type A1γ. The DNA G+C content was calculated to be 55.05 mol% from the whole-genome sequence and 55.3 mol% as determined by HPLC. There were no predicted genes responsible for biosynthesis of respiratory lipoquinones, mycolic acids and lipopolysaccharides. Genes associated with synthesis of teichoic and lipoteichoic acids, diaminopimelic acid, polar lipids and polyamines were present. According to the 16S rRNA gene sequence phylogeny, strain DSM 24645T formed, together with several uncultured oral clones, a separate branch within the family Lachnospiraceae, with the highest sequence similarity to the type strain of Moryella indoligenes at 94.2 %. Based on distinct phenotypic and genotypic characteristics, we suggest that strain DSM 24645T represents a novel species in a new genus, for which the name Stomatobaculum longum gen. nov., sp. nov. is proposed. The type strain of Stomatobaculum longum is DSM 24645T ( = HM-480T; deposited in BEI Resources, an NIH collection managed by the ATCC). PMID:22843721

  6. Stomatobaculum longum gen. nov., sp. nov., an obligately anaerobic bacterium from the human oral cavity.

    PubMed

    Sizova, Maria V; Muller, Paul; Panikov, Nicolai; Mandalakis, Manolis; Hohmann, Tine; Hazen, Amanda; Fowle, William; Prozorov, Tanya; Bazylinski, Dennis A; Epstein, Slava S

    2013-04-01

    A strictly anaerobic Gram-stain-variable but positive by structure, non-spore-forming bacterium designated Lachnospiraceae bacterium ACC2 strain DSM 24645(T) was isolated from human subgingival dental plaque. Bacterial cells were 4-40 µm long non-motile rods, often swollen and forming curved filaments up to 200 µm. Cells contained intracellular, poorly crystalline, nanometre-sized iron- and sulfur-rich particles. The micro-organism was able to grow on yeast extract, trypticase peptone, milk, some sugars and organic acids. The major metabolic end-products of glucose fermentation were butyrate, lactate, isovalerate and acetate. The growth temperature and pH ranges were 30-42 °C and 4.9-7.5, respectively. Major fatty acids were C14 : 0, C14 : 0 DMA (dimethyl aldehyde), C16 : 0, C16 : 1ω7c DMA. The whole-cell hydrolysate contained meso-diaminopimelic acid, indicating peptidoglycan type A1γ. The DNA G+C content was calculated to be 55.05 mol% from the whole-genome sequence and 55.3 mol% as determined by HPLC. There were no predicted genes responsible for biosynthesis of respiratory lipoquinones, mycolic acids and lipopolysaccharides. Genes associated with synthesis of teichoic and lipoteichoic acids, diaminopimelic acid, polar lipids and polyamines were present. According to the 16S rRNA gene sequence phylogeny, strain DSM 24645(T) formed, together with several uncultured oral clones, a separate branch within the family Lachnospiraceae, with the highest sequence similarity to the type strain of Moryella indoligenes at 94.2 %. Based on distinct phenotypic and genotypic characteristics, we suggest that strain DSM 24645(T) represents a novel species in a new genus, for which the name Stomatobaculum longum gen. nov., sp. nov. is proposed. The type strain of Stomatobaculum longum is DSM 24645(T) ( = HM-480(T); deposited in BEI Resources, an NIH collection managed by the ATCC).

  7. The genome of Erwinia tasmaniensis strain Et1/99, a non-pathogenic bacterium in the genus Erwinia.

    PubMed

    Kube, Michael; Migdoll, Alexander Michael; Müller, Ines; Kuhl, Heiner; Beck, Alfred; Reinhardt, Richard; Geider, Klaus

    2008-09-01

    The complete genome of the bacterium Erwinia tasmaniensis strain Et1/99 consisting of a 3.9 Mb circular chromosome and five plasmids was sequenced. Strain Et1/99 represents an epiphytic plant bacterium related to Erwinia amylovora and E. pyrifoliae, which are responsible for the important plant diseases fire blight and Asian pear shoot blight, respectively. Strain Et1/99 is a non-pathogenic bacterium and is thought to compete with these and other bacteria when occupying the same habitat during initial colonization. Genome analysis revealed tools for colonization, cellular communication and defence modulation, as well as genes coding for the synthesis of levan and a not detected capsular exopolysaccharide. Strain Et1/99 may secrete indole-3-acetic acid to increase availability of nutrients provided on plant surfaces. These nutrients are subsequently accessed and metabolized. Secretion systems include the hypersensitive response type III pathway present in many pathogens. Differences or missing parts within the virulence-related factors distinguish strain Et1/99 from pathogens such as Pectobacterium atrosepticum and the related Erwinia spp. Strain Et1/99 completely lacks the sorbitol operon, which may also affect its inability to invade fire blight host plants. Erwinia amylovora in contrast depends for virulence on utilization of sorbitol, the dominant carbohydrate in rosaceous plants. The presence of other virulence-associated factors in strain Et1/99 indicates the ancestral genomic background of many plant-associated bacteria.

  8. A Mutant Strain of a Surfactant-Producing Bacterium with Increased Emulsification Activity

    NASA Astrophysics Data System (ADS)

    Liu, Qingmei; Yao, Jianming; Pan, Renrui; Yu, Zengliang

    2005-06-01

    As reported in this paper, a strain of oil-degrading bacterium Sp-5-3 was determined to belong to Enterobacteriaceae, which would be useful for microbial enhanced oil recovery (MEOR). The aim of our study was to generate a mutant using low energy N+ beam implantation. With 10 keV of energy and 5.2 × 1014 N+/cm2 of dose - the optimum condition, a mutant, S-34, was obtained, which had nearly a 5-fold higher surface and a 13-fold higher of emulsification activity than the wild type. The surface activity was measured by two methods, namely, a surface tension measuring instrument and a recording of the repulsive circle of the oil film; the emulsification activity was scaled through measuring the separating time of the oil-fermentation mixture. The metabolic acid was determined as methane by means of gas chromatography.

  9. Biodegradation of nitrobenzene in a lysogeny broth medium by a novel halophilic bacterium Bacillus licheniformis.

    PubMed

    Li, Tian; Deng, Xinping; Wang, Jinjun; Chen, Yucheng; He, Lin; Sun, Yuchuan; Song, Caixia; Zhou, Zhifeng

    2014-12-15

    The Bacillus licheniformis strain YX2, a novel nitrobenzene-degrading halophilic bacterium, was isolated from active sludge obtained from a pesticide factory. Strain YX2 can withstand highly acidic and alkaline conditions and high temperatures. Degradation of nitrobenzene (200mgL(-1)) by YX2 exceeded 70% after 72h in lysogeny broth medium (pH 4-9). Under optimal degradation conditions (33°C, pH 7 in LB medium) YX2 degraded 50, 100, 200, and 600mgL(-1) nitrobenzene within 36, 36, 72, and 156h, respectively. Even in the presence of benzene, phenol or aniline, strain YX2 efficiently degraded nitrobenzene. Furthermore, strain YX2 completely degraded 600mgL(-1) nitrobenzene in 7% NaCl (w/w). Thus, our data show that strain YX2 may have promise for removing nitrobenzene from complex wastewaters with high salinity and variable pH.

  10. Continuous synthesis and excretion of the compatible solute ectoine by a transgenic, nonhalophilic bacterium.

    PubMed

    Schubert, Torsten; Maskow, Thomas; Benndorf, Dirk; Harms, Hauke; Breuer, Uta

    2007-05-01

    The compatible solute 1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid (ectoine) acts in microorganisms as an osmotic counterweight against halostress and has attracted commercial attention as a protecting agent. Its production and application are restricted by the drawbacks of the discontinuous harvesting procedure involving salt shocks, which reduces volumetric yield, increases reactor corrosion, and complicates downstream processing. In order to synthesize ectoine continuously in less-aggressive media, we introduced the ectoine genes ectABC of the halophilic bacterium Chromohalobacter salexigens into an Escherichia coli strain using the expression vector pASK-IBA7. Under the control of a tet promoter, the transgenic E. coli synthesized 6 g liter-1 ectoine with a space-time yield of 40 mg liter-1 h-1, with the vast majority of the ectoine being excreted.

  11. Biosynthesis and characterization of polyhydroxyalkanoates in the polysaccharide-degrading marine bacterium Saccharophagus degradans ATCC 43961.

    PubMed

    González-García, Yolanda; Nungaray, Jesús; Córdova, Jesús; González-Reynoso, Orfil; Koller, Martin; Atlic, Aid; Braunegg, Gerhart

    2008-06-01

    The marine bacterium Saccharophagus degradans was investigated for the synthesis of polyhydroxyalkanoates (PHAs), using glucose as the sole source of carbon in a two-step batch culture. In the first step the microorganism grew under nutrient balanced conditions; in the second step the cells were cultivated under limitation of nitrogen source. The biopolymer accumulated in S. degradans cells was detected by Nile red staining and FT-IR analysis. From GC-MS analysis, it was found that this strain produced a homopolymer of 3-hydroxybutyric acid. The cellular polymer concentration, its molecular mass, glass transition temperature, melting point and heat of fusion were 17.2+/-2.7% of dry cell weight, 54.2+/-0.6 kDa, 37.4+/-6.0 degrees C, 165.6+/-5.5 degrees C and 59.6+/-2.2 J g(-1), respectively. This work is the first report determining the capacity of S. degradans to synthesize PHAs.

  12. Expression of multiple complex polysaccharide-degrading enzyme systems by marine bacterium strain 2-40.

    PubMed

    Ensor; Stosz; Weiner

    1999-08-01

    Saprophytic marine bacterium strain 2-40 (2-40) can degrade numerous complex polysaccharides (CP) including agar, alginic acid, carrageenan, carboxymethylcellulose, chitin, beta-glucan, laminarin, pectin, pullulan, starch, and xylan. The growth of 2-40 was assessed in minimal media containing one of 16 CP or simple carbohydrates, with the result that all supported growth. Each of the carbohydrase systems was elicited at highest levels by the homologous substrate. Each, excluding amylase, was repressed when 2-40 was cultured in glucose minimal synthetic media. Cyclic adenosine monophosphate alleviated the repression. Agarose as sole carbon source supported the synthesis of the most heterologous complex carbohydrase systems, although, generally, at a lower level of activity than the homologous CP.

  13. Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil.

    PubMed

    Rice, Marlen C; Norton, Jeanette M; Valois, Frederica; Bollmann, Annette; Bottomley, Peter J; Klotz, Martin G; Laanbroek, Hendrikus J; Suwa, Yuichi; Stein, Lisa Y; Sayavedra-Soto, Luis; Woyke, Tanja; Shapiro, Nicole; Goodwin, Lynne A; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Kyrpides, Nikos; Varghese, Neha; Mikhailova, Natalia; Markowitz, Victor; Palaniappan, Krishna; Ivanova, Natalia; Stamatis, Dimitrios; Reddy, T B K; Ngan, Chew Yee; Daum, Chris

    2016-01-01

    Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments.

  14. Bioethanol production from mannitol by a newly isolated bacterium, Enterobacter sp. JMP3.

    PubMed

    Wang, Jing; Kim, Young Mi; Rhee, Hong Soon; Lee, Min Woo; Park, Jong Moon

    2013-05-01

    In this study a new bacterium capable of growing on brown seaweed Laminaria japonica, Enterobacter sp. JMP3 was isolated from the gut of turban shell, Batillus cornutus. In anaerobic condition, it produced high yields of ethanol (1.15 mol-EtOH mol-mannitol(-1)) as well as organic acids from mannitol, the major carbohydrate component of L. japonica. Based on carbon distribution and metabolic flux analysis, it was revealed that mannitol was more favorable than glucose for ethanol production due to their different redox states. This indicates that L. japonica is one of the promising feedstock for bioethanol production. Additionally, the mannitol dehydrogenation pathway in Enterobacter sp. JMP3 was examined and verified. Finally, an attempt was made to explore the possibility of controlling ethanol production by altering the redox potential via addition of external NADH in mannitol fermentation.

  15. Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus.

    PubMed

    Bolotin, Alexander; Quinquis, Benoît; Renault, Pierre; Sorokin, Alexei; Ehrlich, S Dusko; Kulakauskas, Saulius; Lapidus, Alla; Goltsman, Eugene; Mazur, Michael; Pusch, Gordon D; Fonstein, Michael; Overbeek, Ross; Kyprides, Nikos; Purnelle, Bénédicte; Prozzi, Deborah; Ngui, Katrina; Masuy, David; Hancy, Frédéric; Burteau, Sophie; Boutry, Marc; Delcour, Jean; Goffeau, André; Hols, Pascal

    2004-12-01

    The lactic acid bacterium Streptococcus thermophilus is widely used for the manufacture of yogurt and cheese. This dairy species of major economic importance is phylogenetically close to pathogenic streptococci, raising the possibility that it has a potential for virulence. Here we report the genome sequences of two yogurt strains of S. thermophilus. We found a striking level of gene decay (10% pseudogenes) in both microorganisms. Many genes involved in carbon utilization are nonfunctional, in line with the paucity of carbon sources in milk. Notably, most streptococcal virulence-related genes that are not involved in basic cellular processes are either inactivated or absent in the dairy streptococcus. Adaptation to the constant milk environment appears to have resulted in the stabilization of the genome structure. We conclude that S. thermophilus has evolved mainly through loss-of-function events that remarkably mirror the environment of the dairy niche resulting in a severely diminished pathogenic potential.

  16. Legionnaires' disease: isolation of a bacterium and demonstration of its role in other respiratory disease.

    PubMed

    McDade, J E; Shepard, C C; Fraser, D W; Tsai, T R; Redus, M A; Dowdle, W R

    1977-12-01

    To identify the etiologic agent of Legionnaire's disease, we examined patients' serum and tissue specimens in a search for toxins, bacteria, fungi, chlamydiae, rickettsiae and viruses. From the lungs of four of six patients we isolated a gram-negative, non-acid-fast bacillus in guinea pigs. The bacillus could be transferred to yolk sacs of embryonated eggs. Classification of this organism is incomplete. We used yolk-sac cultures of the bacillus as antigen to survey suspected serum specimens, employing antihuman-globulin fluorescent antibody. When compared to controls, specimens from 101 to 111 patients meeting clinical criteria of Legionnaires' disease showed diagnostic increases in antibody titers. Diagnostic increases were also found in 54 recent sporadic cases of severe pneumonia and, retrospectively, in stored serum from most patients in two other previously unsolved outbreaks of respiratory disease. We conclude that Legionnaires' disease is caused by a gram-negative bacterium that may be responsible for widespread infection.

  17. Gordonibacter urolithinfaciens sp. nov., a urolithin-producing bacterium isolated from the human gut.

    PubMed

    Selma, María V; Tomás-Barberán, Francisco A; Beltrán, David; García-Villalba, Rocio; Espín, Juan C

    2014-07-01

    Urolithins are dibenzopyranone metabolites that exert anti-inflammatory activity in vivo and are produced by the gut microbiota from the dietary polyphenols ellagic acid (EA) and ellagitannins. However, the bacteria involved in this process remain unknown. We report here a novel bacterium, strain CEBAS 1/15P(T), capable of metabolizing EA to urolithins, that was isolated from healthy human faeces and characterized by determining phenotypic, biochemical and molecular methods. The strain was related to Gordonibacter pamelaeae 7-10-1-b(T), the type and only reported strain of the only species of the genus Gordonibacter, with about 97% 16S rRNA gene sequence similarity; they were both obligately anaerobic, non-spore-forming, Gram-stain-positive, short-rods/coccobacilli and metabolized only small numbers of carbon sources. L-Fucose, D-fructose, turanose, D-galacturonic acid and α-ketobutyric acid were metabolized by strain CEBAS 1/15P(T), while G. pamelaeae was negative for metabolism of these compounds. The whole-cell fatty acids consisted predominantly of saturated fatty acids (70%); strain CEBAS 1/15P(T) differed significantly from G. pamelaeae in the major fatty acid, which was C18 : 1ω9c, while anteiso-C15 : 0 was the major component for G. pamelaeae. The presence of a number of different fatty acid peaks, especially C19 : 0 cyclo and C18 : 1ω6c, was also indicative of distinct species. Six glycolipids (GL1-6) were recognized, while, in G. pamelaeae, only four glycolipids were described. On the basis of these data, the novel species Gordonibacter urolithinfaciens sp. nov. is described, with strain CEBAS 1/15P(T) ( = DSM 27213(T) = CCUG 64261(T)) as the type strain.

  18. Desulfovibrio alaskensis sp. nov., a sulphate-reducing bacterium from a soured oil reservoir.

    PubMed

    Feio, Maria J; Zinkevich, Vitaly; Beech, Iwona B; Llobet-Brossa, Enric; Eaton, Peter; Schmitt, Jürgen; Guezennec, Jean

    2004-09-01

    A novel sulphate-reducing bacterium (Al1T) was recovered from a soured oil well in Purdu Bay, Alaska. Light and atomic force microscopy observations revealed that cells were Gram-negative, vibrio-shaped and motile by means of a single polar flagellum. The carbon and energy sources used by the isolate and the salinity, temperature and pH ranges facilitating its growth proved to be typical of a partial lactate-oxidizing, moderately halophilic, mesophilic, sulphate-reducing bacterium. Analysis of the fatty acid profile revealed that C(18 : 0), isoC(15 : 0) and isoC(17 : 1)omega7c were the predominant species. Fatty acid profile and complete 16S rRNA gene sequencing demonstrated the similarity between strain Al1T and members of the genus Desulfovibrio. The position of strain Al1T within the phylogenetic tree indicated that it clustered closely with Desulfovibrio vietnamensis DSM 10520T (98.9 % sequence similarity), a strain recovered from a similar habitat. However, whole-cell protein profiles, Fourier-transform infrared studies and DNA-DNA hybridization demonstrated that, in spite of the high level of 16S rRNA gene sequence similarity, there is sufficient dissimilarity at the DNA sequence level between D. vietnamensis DSM 10520T and strain Al1T (10.2 % similarity) to propose that strain Al1T belongs to a separate species within the genus Desulfovibrio. Based on the results obtained, the name Desulfovibrio alaskensis sp. nov. is therefore proposed, with Al1T (= NCIMB 13491T = DSM 16109T) as the type strain.

  19. Luteimonas padinae sp. nov., an epiphytic bacterium isolated from an intertidal macroalga.

    PubMed

    Verma, Ashish; Ojha, Anup Kumar; Kumari, Parveen; Sundharam, Shiva S; Mayilraj, Shanmugam; Krishnamurthi, Srinivasan

    2016-12-01

    A Gram-stain-negative, rod-shaped bacterium, forming yellow colonies and designated CDR SL 15T, was isolated from the surface of Padina sp., a brown macroalga, which grows in the Western coastal regions of the state of Goa, India. The 16S rRNA gene sequence phylogeny placed the strain in the genus Luteimonas and it showed closest sequence similarity to Luteimonas terricola BZ92rT (97.6 %) and <97.0 % to other species of the genus Luteimonas. Chemotaxonomic features, such as having iso-C15 : 0 and summed feature 9 (C16 : 0 10-methyl/iso-C17 : 1ω9c) as the major fatty acids and Q-8 as the only ubiquinone further supported its placement within this genus. There were some critical differences in phenotypic properties between Luteimonas padinae sp. nov. CDR SL 15T and L. terricola DSM 22344T i.e. temperature range for growth and salinity range and optimum for growth (L. terricola is a psychrotolerant bacterium with a lower optimum temperature for growth), acid production and assimilation of substrates, enzyme activities and resistance to certain antibiotics. The DNA-DNA relatedness value of the novel strain with its closest phylogenetic relative was only 40 %, below the 70 % threshold value recommended for species delineation. All these characteristics are consistent with strain CDR SL 15T representing a novel species of the genus Luteimonas, for which the name Luteimonas padinae sp. nov. is proposed. The type strain is CDR SL 15T (=DSM 101536T=KCTC 52403T).

  20. Molecular Characterization and In Vitro Analyses of a Sporogenous Bacterium with Potential Probiotic Properties.

    PubMed

    Sen, Ramkrishna; Pal, Dibyarupa; Kodali, Vidya Prabhakar; Das, Subhasish; Ghosh, Sudip Kumar

    2010-10-01

    The Gram-positive thin rods of a Bacillus species were identified and designated as Bacillus coagulans RK - 02 through the standard microbiological and biochemical characterization procedures, followed by data analysis and comparison with the characteristics given in Bergey's manual of systematic bacteriology. The culture was further characterized and confirmed as Bacillus coagulans by 16S rDNA sequence analysis wherein about 755 nucleotides of 16S rDNA was amplified and cloned in pGEM-T vector and subsequently sequenced. Sequence was blasted against the nr database of NCBI. Multiple alignments were done with some selected and related sequences using Clustal W. Phylogenetic trees were drawn with the same software after the distances were determined by neighbor-joining algorithm. The in vitro studies on the probiotic properties demonstrated that our isolate could prove to be a potential probiotic with spore-forming and lactic acid-producing abilities coupled with acid and bile tolerance properties and antimicrobial action. In addition to these characteristics, the bacterium also produced enzymes such as amylase, cellulase, lipase, protease, lactase and catalase, which can help in improving digestion and overall health, alleviate lactose intolerance and remove oxidative stresses, required for the well-being of the consumers. In our previously reported studies, an exopolysaccharide (EPS), a probioactive molecule produced by the same bacterium, showed very significant antioxidant, antihyperglycemic and emulsification activities. Thus, Bacillus coagulans RK - 02 is a well-characterized promising probiotic for its potential commercial applications to pharmaceutical, nutraceutical and functional food formulations with care-free storage.

  1. Isolation of a bacterium capable of degrading peanut hull lignin

    SciTech Connect

    Kerr, T.A.; Kerr, R.D.; Benner, R.

    1983-11-01

    Thirty-seven bacterial strains capable of degrading peanut hull lignin were isolated by using four types of lignin preparations and hot-water-extracted peanut hulls. One of the isolates, tentatively identified as Arthrobacter species, was capable of utilizing all four lignin preparations as well as extracted peanut hulls as a sole source of carbon. The bacterium was also capable of degrading specifically labeled (/sup 14/C) lignin-labeled lignocellulose and (/sup 14/C)cellulose-labeled lignocellulose from the cordgrass Spartina alterniflora and could also degrade (/sup 14/C) Kraft lignin from slash pine. After 10 days of incubation with (/sup 14/C) cellulose-labeled lignocellulose or (/sup 14/C) lignin-labeled lignocellulose from S. alterniflora, the bacterium mineralized 6.5% of the polysaccharide component and 2.9% of the lignin component. (Refs. 24).

  2. A Streamlined Strategy for Biohydrogen Production with an Alkaliphilic Bacterium

    SciTech Connect

    Elias, Dwayne A; Wall, Judy D.; Mormile, Dr. Melanie R.; Begemann, Matthew B

    2012-01-01

    Biofuels are anticipated to enable a shift from fossil fuels for renewable transportation and manufacturing fuels, with biohydrogen considered attractive since it could offer the largest reduction of global carbon budgets. Currently, biohydrogen production remains inefficient and heavily fossil fuel-dependent. However, bacteria using alkali-treated biomass could streamline biofuel production while reducing costs and fossil fuel needs. An alkaliphilic bacterium, Halanaerobium strain sapolanicus, is described that is capable of biohydrogen production at levels rivaling neutrophilic strains, but at pH 11 and hypersaline conditions. H. sapolanicus ferments a variety of 5- and 6- carbon sugars derived from hemicellulose and cellulose including cellobiose, and forms the end products hydrogen and acetate. Further, it can also produce biohydrogen from switchgrass and straw pretreated at temperatures far lower than any previously reported and in solutions compatible with growth. Hence, this bacterium can potentially increase the efficiency and efficacy of biohydrogen production from renewable biomass resources.

  3. Cloning, sequence analysis and expression of the F1F0-ATPase beta-subunit from wine lactic acid bacteria.

    PubMed

    Sievers, Martin; Uermösi, Christina; Fehlmann, Marc; Krieger, Sibylle

    2003-09-01

    The nucleotide sequences of the genes encoding the F1F0-ATPase beta-subunit from Oenococcus oeni, Leuconostoc mesenteroides subsp. mesenteroides, Pediococcus damnosus, Pediococcus parvulus, Lactobacillus brevis and Lactobacillus hilgardii were determined. Their deduced amino acid sequences showed homology values of 79-98%. Data from the alignment and ATPase tree indicated that O. oeni and L. mesenteroides subsp. mesenteroides formed a group well-separated from P. damnosus and P. parvulus and from the group comprises L. brevis and L. hilgardii. The N-terminus of the F1F0-ATPase beta-subunit of O. oeni contains a stretch of additional 38 amino acid residues. The catalytic site of the ATPase beta-subunit of the investigated strains is characterized by the two conserved motifs GGAGVGKT and GERTRE. The amplified atpD coding sequences were inserted into the pCRT7/CT-TOPO vector using TA-cloning strategy and transformed in Escherichia coli. SDS-PAGE and Western blot analyses confirmed that O. oeni has an ATPase beta-subunit protein which is larger in size than the corresponding molecules from the investigated strains.

  4. Thermostable purified endoglucanase from thermophilic bacterium acidothermus cellulolyticus

    DOEpatents

    Tucker, Melvin P.; Grohmann, Karel; Himmel, Michael E.; Mohagheghi, Ali

    1992-01-01

    A substantially purified high molecular weight cellulase enzyme having a molecular weight of between about 156,000 to about 203,400 daltons isolated from the bacterium Acidothermus cellulolyticus (ATCC 43068) and a method of producing it are disclosed. The enzyme is water soluble, possesses both C.sub.1 and C.sub.x types of enzymatic activity, has a high degree of stability toward heat and exhibits both a high optimum temperature activity and high inactivation characteristics.

  5. Isolation and Characterization of a Chlorinated-Pyridinol-Degrading Bacterium

    PubMed Central

    Feng, Y.; Racke, K. D.; Bollag, J.

    1997-01-01

    The isolation of a pure culture of bacteria able to use 3,5,6-trichloro-2-pyridinol (TCP) as a sole source of carbon and energy under aerobic conditions was achieved for the first time. The bacterium was identified as a Pseudomonas sp. and designated ATCC 700113. [2,6-(sup14)C]TCP degradation yielded (sup14)CO(inf2), chloride, and unidentified polar metabolites. PMID:16535719

  6. Initiation of Chromosomal Replication in Predatory Bacterium Bdellovibrio bacteriovorus

    PubMed Central

    Makowski, Łukasz; Donczew, Rafał; Weigel, Christoph; Zawilak-Pawlik, Anna; Zakrzewska-Czerwińska, Jolanta

    2016-01-01

    Bdellovibrio bacteriovorus is a small Gram-negative predatory bacterium that attacks other Gram-negative bacteria, including many animal, human, and plant pathogens. This bacterium exhibits a peculiar biphasic life cycle during which two different types of cells are produced: non-replicating highly motile cells (the free-living phase) and replicating cells (the intracellular-growth phase). The process of chromosomal replication in B. bacteriovorus must therefore be temporally and spatially regulated to ensure that it is coordinated with cell differentiation and cell cycle progression. Recently, B. bacteriovorus has received considerable research interest due to its intriguing life cycle and great potential as a prospective antimicrobial agent. Although, we know that chromosomal replication in bacteria is mainly regulated at the initiation step, no data exists about this process in B. bacteriovorus. We report the first characterization of key elements of initiation of chromosomal replication – DnaA protein and oriC region from the predatory bacterium, B. bacteriovorus. In vitro studies using different approaches demonstrate that the B. bacteriovorus oriC (BdoriC) is specifically bound and unwound by the DnaA protein. Sequence comparison of the DnaA-binding sites enabled us to propose a consensus sequence for the B. bacteriovorus DnaA box [5′-NN(A/T)TCCACA-3′]. Surprisingly, in vitro analysis revealed that BdoriC is also bound and unwound by the host DnaA proteins (relatively distantly related from B. bacteriovorus). We compared the architecture of the DnaA–oriC complexes (orisomes) in homologous (oriC and DnaA from B. bacteriovorus) and heterologous (BdoriC and DnaA from prey, Escherichia coli or Pseudomonas aeruginosa) systems. This work provides important new entry points toward improving our understanding of the initiation of chromosomal replication in this predatory bacterium. PMID:27965633

  7. [Fractionation of sulfur isotopes by phototrophic sulfur bacterium Ectothiorhodospira shaposhnikovii].

    PubMed

    Ivanov, M V; Gogotova, G I; Matrosov, A G; Ziakun, A M

    1976-01-01

    Two processes of sulphur isotope fractionation have been found in experiments with the sulphur purple bacterium Ectothiorhodospira shaposhnikovii. As a result, a light isotope, 32S, is concentrated in residual hydrogen sulphide, and a heavy isotope, 34S, in elementary suphur which is deposited outside the cell. The sulphate produced is lighter than elementary sulphur. Fractionation of sulphur isotopes is observed in natural conditions and is confined to places of mass growth of photosynthetic sulphur bacteria.

  8. Bacillus coreaensis sp. nov.: a xylan-hydrolyzing bacterium isolated from the soil of Jeju Island, Republic of Korea.

    PubMed

    Chi, Won-Jae; Youn, Young Sang; Park, Jae-Seon; Hong, Soon-Kwang

    2015-07-01

    A xylan-degrading bacterium, designated as MS5(T) strain, was isolated from soil collected from the Jeju Island, Republic of Korea. Strain MS5(T) was Gram-stain-positive, aerobic, and motile by polar flagellum. The major fatty acids identified in this bacterium were iso-C15:0 (32.3%), C16:0 (27.3%), and anteiso-C15:0 (10.2%). A similarity search based on the 16S rRNA gene sequence revealed that the strain belongs to the class Bacilli and shared the highest similarity with the type strains Bacillus beringensis BR035(T) (98.7%) and Bacillus korlensis ZLC-26(T) (98.6%) which form a coherent cluster in a neighbor-joining phylogenetic tree. The DNA G+C content of strain MS5(T) was 43.0 mol%. The major menaquinone was MK-7 and the diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The DNADNA relatedness values between strain MS5(T) and two closely related species, B. beringensis BR035(T) and B. korlensis ZLC-26(T), were less than 70%. DNA-DNA relatedness analysis and 16S rRNA sequence similarity, as well as phenotypic and chemotaxonomic characteristics suggest that the strain MS5(T) constitutes a novel Bacillus species, for which the name Bacillus coreaensis sp. nov. is proposed. The type strain is MS5(T) (=DSM25506(T) =KCTC13895(T)).

  9. Degradation of high loads of crystalline cellulose and of unpretreated plant biomass by the thermophilic bacterium Caldicellulosiruptor bescii.

    PubMed

    Basen, Mirko; Rhaesa, Amanda M; Kataeva, Irina; Prybol, Cameron J; Scott, Israel M; Poole, Farris L; Adams, Michael W W

    2014-01-01

    The thermophilic bacterium Caldicellulosiruptor bescii grows at 78 °C on high concentrations (200 g L(-1)) of both crystalline cellulose and unpretreated switchgrass, while low concentrations (<20 g L(-1)) of acid-pretreated switchgrass inhibit growth. Degradation of crystalline cellulose, but not that of unpretreated switchgrass, was limited by nitrogen and vitamin (folate) availability. Under optimal conditions, C. bescii solubilized approximately 60% of the crystalline cellulose and 30% of the unpretreated switchgrass using initial substrate concentrations of 50 g L(-1). Further fermentation of crystalline cellulose and of switchgrass was inhibited by organic acid end-products and by a specific inhibitor of C. bescii growth that did not affect other thermophilic bacteria, respectively. Soluble mono- and oligosaccharides, organic acids, carbon dioxide, and microbial biomass, quantitatively accounted for the crystalline cellulose and plant biomass carbon utilized. C. bescii therefore degrades industrially-relevant concentrations of lignocellulosic biomass that have not undergone pretreatment thereby demonstrating its potential utility in biomass conversion.

  10. Characterization and Determination of Origin of Lactic Acid Bacteria from a Sorghum-Based Fermented Weaning Food by Analysis of Soluble Proteins and Amplified Fragment Length Polymorphism Fingerprinting

    PubMed Central

    Kunene, Nokuthula F.; Geornaras, Ifigenia; von Holy, Alexander; Hastings, John W.

    2000-01-01

    The group that includes the lactic acid bacteria is one of the most diverse groups of bacteria known, and these organisms have been characterized extensively by using different techniques. In this study, 180 lactic acid bacterial strains isolated from sorghum powder (44 strains) and from corresponding fermented (93 strains) and cooked fermented (43 strains) porridge samples that were prepared in 15 households were characterized by using biochemical and physiological methods, as well as by analyzing the electrophoretic profiles of total soluble proteins. A total of 58 of the 180 strains were Lactobacillus plantarum strains, 47 were Leuconostoc mesenteroides strains, 25 were Lactobacillus sake-Lactobacillus curvatus strains, 17 were Pediococcus pentosaceus strains, 13 were Pediococcus acidilactici strains, and 7 were Lactococcus lactis strains. L. plantarum and L. mesenteroides strains were the dominant strains during the fermentation process and were recovered from 87 and 73% of the households, respectively. The potential origins of these groups of lactic acid bacteria were assessed by amplified fragment length polymorphism fingerprint analysis. PMID:10698775

  11. Screening, selection and characterization of phytic acid degrading lactic acid bacteria from chicken intestine.

    PubMed

    Raghavendra, Ponnala; Halami, Prakash M

    2009-07-31

    This study was undertaken to screen and select potent phytate degrading lactic acid bacteria and to evaluate their additional characteristic features. Forty lactic acid bacterial strains were isolated from different sources and screened for their ability to degrade myo-inositol hexaphosphate or IP(6) by cobalt chloride staining (plate assay) method, using calcium or sodium salt of phytic acid as substrate. All the forty isolates were able to degrade calcium phytate. However, only two Pediococcus pentosaceus strains (CFR R38 and CFR R35) were found to degrade sodium phytate. These strains showed phytase activity of 213 and 89 U at 50 degrees C, respectively and poor acid phosphatase activity. These strains were further evaluated for additional characteristic features. At pH 2, P. pentosaceus strains CFR R38 and CFR R35 showed 50.7 and 48.5 percentage survivability after 2 h of incubation respectively and they could also withstand 0.3% ox-bile. These cultures exhibited 54.6 and 44.8% of hydrophobicity to xylene, antibacterial activity against food borne pathogens and possessed beta-galactosidase activity. The resistance pattern to several antibiotics was also analyzed. The present study indicates that these strains, having phytate degrading ability and other characteristic features can be exploited as starter cultures in fermented foods to improve the mineral bioavailability.

  12. Coexistence of and interaction relationships between an aflatoxin-producing fungus and a bacterium.

    PubMed

    Yan, Quan-Hong; Zhou, Jian-Xiang; Li, Hong-Zhou; Zhi, Qing-Qing; Zhou, Xiao-Ping; He, Zhu-Mei

    2015-07-01

    The interactions between aflatoxin-producing fungi and bacteria have opened up a new avenue for identifying biological agents suitable for controlling aflatoxin contamination. In this study, we analysed the interactions between A. flavus and the bacterium Burkholderia gladioli M3 that coexist in rice that is naturally contaminated with A. flavus. Our results showed that a cell-free culture filtrate (CCF) and the metabolite bongkrekic acid of the M3 strain potently suppressed the mycelial growth and spore production, and then affected the production of aflatoxin of A. flavus. Bongkrekic acid secreted by the M3 strain exhibited higher antifungal activity than did analogues. The CCF of the M3 strain and its metabolite bongkrekic acid can inhibit the growth of A. flavus, but the metabolites of A. flavus, aflatoxins, exerted no inhibitory effect on the growth of the M3 strain. Furthermore, we determined that the M3 cells could use the dead mycelia of A. flavus as energy sources for reproduction, while A. flavus could not grow in a solution containing dead M3 cells. In summary, these results indicated that B. gladioli has a competitive advantage in survival when it coexists with its fungal partner A. flavus.

  13. Paenibacillus pinihumi sp. nov., a cellulolytic bacterium isolated from the rhizosphere of Pinus densiflora.

    PubMed

    Kim, Byung-Chun; Lee, Kang Hyun; Kim, Mi Na; Kim, Eun-Mi; Rhee, Moon-Soo; Kwon, O-Yu; Shin, Kee-Sun

    2009-10-01

    A novel cellulolytic bacterium, strain S23(T), was isolated from the rhizosphere of the pine trees in Daejeon, Republic of Korea. This isolate was Gram-positive, strictly aerobic, rod-shaped, catalase-negative, oxidase-positive, motile by means of peritrichous flagella, and tested positive for alkaline phosphatase, esterase lipase, leucine arylamidase, alpha-galactosidase, and beta-galactosidase activities. The DNA G+C content was 49.5 mol%. The main cellular fatty acids were anteiso-C(15:0) (51.9%), iso-C(16:0) (14.7%), and iso-C(15:0) (13.2%). The major isoprenoid quinone was menaquinone 7 (MK-7). Diagnostic diamino acid in the cell-wall pepti-doglycan was meso-diaminopimelic acid. Comparative 16S rRNA gene sequence analysis showed that this strain clustered with Paenibacillus species. The 16S rRNA gene sequence similarity values between S23(T) and other Paenibacillus species were between 89.9% and 95.9%, and S23(T) was most closely related to Paenibacillus tarimensis SA-7-6(T). On the basis of phylogenetic and phenotypic properties of strain S23(T), the isolate is considered as a novel species belonging to the genus Paenibacillus. Therefore, the name, Paenibacillus pinihumi sp. nov., is proposed for the rhizosphere isolate; the type strain is S23(T) (=KCTC 13695(T) =KACC 14199(T) =JCM 16419(T)).

  14. Paenibacillus puernese sp. nov., a β-glucosidase-producing bacterium isolated from Pu'er tea.

    PubMed

    Wang, Dan-Dan; Kim, Yeon-Ju; Hoang, Van-An; Nguyen, Ngoc-Lan; Singh, Priyanka; Wang, Chao; Chun-Yang, Deok

    2016-04-01

    A Gram-staining-positive, endospore-forming, aerobic, rod-shaped bacterium, designated as DCY97(T), was isolated from ripened Pu'er tea and was identified by using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain DCY97(T) was closely related to Paenibacillus dongdonensis KUDC0114(T) (98.0 %), Paenibacillus oceanisediminis L10(T) (97.7 %), and Paenibacillus barcinonensis BP-23(T) (97.2 %). The phenotypic and chemotaxonomic characteristics of strain DCY97(T) matched with the characteristics of members belonging to the genus Paenibacillus. The major identified polar lipids included phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant quinone was MK-7. The major fatty acids were anteiso-C15:0 (35.1 %), anteiso-C16:0 (19.0 %), and iso-C16:0 (13.9 %). The peptidoglycan cell wall was composed of meso-diaminopimelic acids, alanine, and D-glutamic acid. The genomic DNA G + C content was determined to be 46.7 mol%. The DNA-DNA relatedness between strain DCY97(T) and Paenibacillus dongdonensis KCTC 33221(T), Paenibacillus oceanisediminis KACC 16023(T), Paenibacillus barcinonensis KCTC 13019(T) were 27, 19, and 10 %, respectively. Based on the genotypic, phenotypic, and chemotaxonomic characteristics, strain DCY97(T) is considered as a novel species of the genus Paenibacillus, for which the name Paenibacillus puernese sp. nov. is proposed. The type strain is DCY97(T) (=KCTC 33596(T) = JCM 140369(T)).

  15. In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella

    PubMed Central

    Sheik, Abdul R; Muller, Emilie EL; Audinot, Jean-Nicolas; Lebrun, Laura A; Grysan, Patrick; Guignard, Cedric; Wilmes, Paul

    2016-01-01

    Microorganisms in biological wastewater treatment plants require adaptive strategies to deal with rapidly fluctuating environmental conditions. At the population level, the filamentous bacterium Candidatus Microthrix parvicella (Ca. M. parvicella) has been found to fine-tune its gene expression for optimized substrate assimilation. Here we investigated in situ substrate assimilation by single cells of Ca. M. parvicella using nano-scale secondary-ion mass spectrometry (nanoSIMS). NanoSIMS imaging highlighted phenotypic heterogeneity among Ca. M. parvicella cells of the same filament, whereby 13C-oleic acid and 13C-glycerol-3-phosphate assimilation occurred in ≈21–55% of cells, despite non-assimilating cells being intact and alive. In response to alternating aerobic–anoxic regimes, 13C-oleic acid assimilation occurred among subpopulations of Ca. M. parvicella cells (≈3–28% of cells). Furthermore, Ca. M. parvicella cells exhibited two temperature optima for 13C-oleic acid assimilation and associated growth rates. These results suggest that phenotypic heterogeneity among Ca. M. parvicella cells allows the population to adapt rapidly to fluctuating environmental conditions facilitating its widespread occurrence in biological wastewater treatment plants. PMID:26505828

  16. Connecting phenome to genome in Pseudomonas stutzeri 5190: an artwork biocleaning bacterium.

    PubMed

    Bosch-Roig, Pilar; Decorosi, Francesca; Giovannetti, Luciana; Ranalli, Giancarlo; Viti, Carlo

    Research on biotechnology applications for cultural heritage restoration has shown how microorganisms can be efficient at cleaning particularly complex or ingrained substances through the process called "biocleaning". Bacteria are able to synthesize groups of specific enzymes for the degradation of complex materials present on artwork. Biocleaning has been shown to be less hazardous than some traditional mechanical or chemical techniques for the artwork, to be environmentally-friendly and safe for restorers to use. In order to improve our knowledge of the metabolic mechanisms involved in biocleaning, we analyzed the relationship between the genome and phenome of Pseudomonas stutzeri 5190 in order to identify and confirm the benefits and drawbacks of this bacterium used on on-site artwork as a biocleaning agent. Main phenotype microarray (PM) assays showed that P. stutzeri 5190 was able to use: i) 51 of the 190 carbon sources tested, where 32 were used efficiently, among which there were six amino acids (l-proline, l-alanine, d-alanine, l-glutamic acid, l-asparagine and l-glutamine); ii) 74 of the 95 nitrogen sources tested, where 50 compounds were used efficiently, among which were 28 amino acids and the inorganic nitrate and nitrite compounds, supporting the hypothesis of the strain's ability to remove nitrate salt efflorescence from frescoes. Furthermore, high tolerance to osmotic stress, to basic pH and to toxic compounds was revealed by PM. Putative genes compatible with these phenotypes are described.

  17. Biodegradation of bisphenol A and other bisphenols by a gram-negative aerobic bacterium

    SciTech Connect

    Lobos, J.H.; Leib, T.K. ); Tahmun Su )

    1992-06-01

    A novel bacterium designated strain MV1 was isolated from a sludge enrichmet takes from the wastewater treatment plant at a plastics manufacturing facility and shown to degrade 2,2-bis(4-hydroxyphenyl)propane (4,4[prime]-isopropylidenediphenol or bisphenol A). Strain MV1 is a gram-negative, aerobic bacillus that grows on bisphenol A as a sole source of carbon and energy. Total carbon analysis for bisphenol A degradation demonstrated that 60% of the carbon was mineralized to CO[sub 2], 20% was associated with the bacterial cells, and 20% was converted to soluble organic compounds. Metabolic intermediates detected in the culture medium during growth on bisphenol A were identified as 4-hydroxybenzoic acid, 4-hydroxyacetophenone, 2,2-bis(4-hydroxyphenyl)-1-propanol, and 2,3-bis(4-hydroxyphenyl)-1,2-propanediol. Most of the bisphenol A degraded by strain MV1 is cleaved in some way to form 4-hydroxybenzoic acid and 4-hydroxyacetophenone, which are subsequently mineralized or assimilated into cell carbon. In addition, about 20% of the bisphenol A is hydroxylated to form 2,2-bis(4-hydroxyphenyl)-1-propanol, which is slowly biotransformed to 2,3-bis(4-hydroxyphenyl)-1,2-propanediol. Cells that were grown on bisphenol A degraded a variety of bisphenol alkanes, hydroxylated benzoic acids, and hydroxylated acetophenones during resting-cell assays. Transmission electron microscopy of cells grown on bisphenol A revealed lipid storage granules and intracytoplasmic membranes.

  18. Cloning, expression, and characterization of a new phytase from the phytopathogenic bacterium Pectobacterium wasabiae DSMZ 18074.

    PubMed

    Shao, Na; Huang, Huoqing; Meng, Kun; Luo, Huiying; Wang, Yaru; Yang, Peilong; Yao, Bin

    2008-07-01

    The soft rot bacterium Pectobacterium wasabiae is an economically important pathogen of many crops. A new phytase gene, appA, was cloned from P. wasabiae by degenerate PCR and TAIL-PCR. The open reading frame of appA consisted of 1,302 bp encoding 433 amino acid residues, including 27 residues of a putative signal peptide. The mature protein had a molecular mass of 45 kDa and a theoretical pI of 5.5. The amino acid sequence contained the conserved active site residues RHGXRXP and HDTN of typical histidine acid phosphatases, and showed the highest identity of 48.5% to PhyM from Pseudomonas syringae. The gene fragment encoding the mature phytase was expressed in Escherichia coli BL21 (DE3), and the purified recombinant phytase had a specific activity of 1,072+/-47 U/mg for phytate substrate. The optimum pH and temperature for the purified phytase were pH 5.0 and 50 degrees C, respectively. The Km value was 0.17 mM, with a Vmax of 1,714 micromol/min/mg. This is the first report of the identification and isolation of phytase from Pectobacterium.

  19. Use of autochthonous lactic acid bacteria starters to ferment mango juice for promoting its probiotic roles.

    PubMed

    Liao, Xue-Yi; Guo, Li-Qiong; Ye, Zhi-Wei; Qiu, Ling-Yan; Gu, Feng-Wei; Lin, Jun-Fang

    2016-05-18

    Strains of Leuconostoc mesenteroides, Pediococcus pentosaceus, and Lactobacillus brevis were identified from mango fruits by partial 16S rDNA gene sequence. Based on the ability of producing mannitol and diacetyl, Leuconostoc mesenteroides MPL18 and MPL39 were selected within the lactic acid bacteria isolates, and used as mixed starters to ferment mango juice (MJ). Both the autochthonous strains grew well in fermented mango juice (FMJ) and remained viable at 9.81 log cfu mL(-1) during 30 days of storage at 4°C. The content of total sugar of FMJ was lower than that of MJ, while the concentration of mannitol was higher than that of MJ, and the concentration of diacetyl was 3.29 ± 0.12 mg L(-1). Among detected organic acids including citric acid, gallic acid, lactic acid, and acetic acid, only citric acid and gallic acid were found in MJ, while all detected organic acids were found in FMJ. The concentration of lactic acid of FMJ was the highest (78.62 ± 13.66 mM) among all detected organic acids. The DPPH radical scavenging capacity of FMJ was higher than that of MJ. Total phenolic compounds were better preserved in FMJ. The acidity and sweetness had a noticeable impact on the overall acceptance of the treated sample.

  20. Exploitation of sweet cherry (Prunus avium L.) puree added of stem infusion through fermentation by selected autochthonous lactic acid bacteria.

    PubMed

    Di Cagno, Raffaella; Surico, Rosalinda Fortunata; Minervini, Giovanna; Rizzello, Carlo Giuseppe; Lovino, Raffaella; Servili, Maurizio; Taticchi, Agnese; Urbani, Sefania; Gobbetti, Marco

    2011-08-01

    Strains of Lactobacillus plantarum, Pediococcus acidilactici, Pediococcus pentosaceus and Leuconostoc mesenteroides subsp. mesenteroides were identified from 8 cultivars of sweet cherry by partial 16S rRNA gene sequence and subjected to typing by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) analysis. Representative isolates from each species and each cultivar were screened based on the kinetics of growth on cherry puree added of (10%, v/v) stem infusion (CP-SI). A protocol for processing and storage of CP-SI, which included fermentation by selected autochthonous P. pentosaceus SWE5 and L. plantarum FP3 (started CP-SI) or spontaneous fermentation (unstarted CP-SI), was set up. Starters grew and remained viable at elevated cell numbers (ca. 9.0 log cfu g(-1)) during 60 days of storage at 4 °C. The number of presumptive lactic acid bacteria of the unstarted CP-SI did not exceed the value of ca. 3.0 log cfu g(-1). Consumption of carbohydrates (e.g., glucose and fructose) by starter lactic acid bacteria was limited as well as it was the lactic acid fermentation. Consumption of organic acids (e.g., malic acid) and free amino acids was evident, especially, throughout storage. Compared to CP-SI before processing, the concentrations of total phenolic compounds and anthocyanins did not vary in the started CP-SI. The concentration of anthocyanins slightly decreased in the unstarted CP-SI. The antioxidant activity, expressed as the scavenging activity toward DPPH radical, was found at highest level in the started CP-SI which approached that found in CP-SI before processing. During storage, viscosity and, especially, color indexes of started CP-SI were higher than those found in the unstarted CP-SI. Fermentation by autochthonous lactic acid bacteria seemed to also positively interfere with the sensory attributes of CP-SI.

  1. Change in mineral weathering behaviors of a bacterium Chitinophaga jiangningensis JN53 under different nutrition conditions.

    PubMed

    Cheng, Cheng; Wang, Qi; He, Linyan; Sheng, Xiafang

    2017-04-01

    Bacteria play important roles in mineral weathering and soil formation. However, little is known about the nutrition-related changes in mineral weathering potential and pattern of bacteria. In this study, mineral weathering behaviors of a novel mineral-weathering bacterium Chitinophaga jiangningensis JN53 were characterized in the presence of three contrasting biotite or potassium feldspar-added media. C. jiangningensis JN53 increased more Fe release from the minerals in the M-BHm (nutrition-poor medium) than in the SSKM (nutrition-rich medium) and BHm (nutrition-moderate medium), while C. jiangningensis JN53 released more Al from the minerals and Si from biotite in the SSKM. Similar Si release from potassium feldspar by C. jiangningensis JN53 was observed in the SSKM, BHm, and M-BHm. K releasing ability of C. jiangningensis JN53 was significantly higher in the biotite-added M-BHm. Highest and lowest growth of C. jiangningensis JN53 was observed in the SSKM and M-BHm, respectively. In the presence of the minerals, C. jiangningensis JN53 mainly produced gluconic acid in the SSKM and acetic acid in the BHm and M-BHm. C. jiangningensis JN53 also produced large amount of succinic acid in the biotite-added SSKM and oxalic acid in the potassium feldspar-added M-BHm. The results showed the growth, production of organic acids, and mineral weathering ability of C. jiangningensis JN53 in the three contrasting nutrition conditions. The results also suggested the change in the mineral weathering behaviors of C. jiangningensis JN53 under different levels of nutrition conditions.

  2. Anaeromicrobium sediminis gen. nov., sp. nov., a fermentative bacterium isolated from deep-sea sediment.

    PubMed

    Zhang, Xiaobo; Zeng, Xiang; Li, Xi; Alain, Karine; Jebbar, Mohamed; Shao, Zongze

    2016-12-14

    A novel anaerobic, mesophilic,heterotrophic bacterium, designated strain DY2726DT, was isolated from West Pacific Ocean sediments. Cells were long rods (0.5-0.8 μm wide,4-15 μm long),Gram-positive and motile by means of flagella. The temperature and pH ranges for growth were 25-40 °C and pH 6.5-9.0,while optimal growth occurred at 37 °C and pH 7.5, with a generation time 76 minutes. The strain required sea salts for growth from 10 to 30 g L-1 (optimum at 20 g L-1). Substrates used as carbon sources were yeast extract, tryptone, glucose, cellobiose, starch, gelatin, dextrin, fructose, fucose, galactose, galacturonic acid, gentiobiose, glucosaminic acid, mannose, melibiose, palatinose and rhamnose. Products of fermentation were carbon dioxide, acetic acid and butyric acid. Strain DY2726DT was able to reduce amorphous iron hydroxide, goethite, amorphous iron oxides, AQDS and crotonate, but did not reduce sulfur, sulfate, thiosulfate, sulfite and nitrate. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain DY2726DT was affiliated to the family Clostridiaceae and is most closely related to Alkaliphilus transvaalensis (90.0% similarity), Alkaliphilus oremlandii (89.6%). The genomic DNA G + C content, was 33.4 mol%. The major cellular fatty acids of strain DY2726DT were C16:1, C14:0 and C16:0. On the basis of its phenotypic and genotypic properties, strain DY2726DT is suggested to represent a novel species of a new genus in the family Clostridiaceae, for which the name Anaeromicrobium sediminis gen. nov., sp. nov. is proposed. The type strain of Anaeromicrobium sediminis is DY2726DT (=JCM 30224T =MCCC 1A00776T).

  3. Metabolic strategies of beer spoilage lactic acid bacteria in beer.

    PubMed

    Geissler, Andreas J; Behr, Jürgen; von Kamp, Kristina; Vogel, Rudi F

    2016-01-04

    Beer contains only limited amounts of readily fermentable carbohydrates and amino acids. Beer spoilage lactic acid bacteria (LAB) have to come up with metabolic strategies in order to deal with selective nutrient content, high energy demand of hop tolerance mechanisms and a low pH. The metabolism of 26 LAB strains of 6 species and varying spoilage potentialwas investigated in order to define and compare their metabolic capabilities using multivariate statistics and outline possible metabolic strategies. Metabolic capabilities of beer spoilage LAB regarding carbohydrate and amino acids did not correlate with spoilage potential, but with fermentation type (heterofermentative/homofermentative) and species. A shift to mixed acid fermentation by homofermentative (hof) Pediococcus claussenii and Lactobacillus backii was observed as a specific feature of their growth in beer. For heterofermentative (hef) LAB a mostly versatile carbohydrate metabolism could be demonstrated, supplementing the known relevance of organic acids for their growth in beer. For hef LAB a distinct amino acid metabolism, resulting in biogenic amine production, was observed, presumably contributing to energy supply and pH homeostasis.

  4. Survival Strategies of the Plant-Associated Bacterium Enterobacter sp. Strain EG16 under Cadmium Stress.

    PubMed

    Chen, Yanmei; Chao, Yuanqing; Li, Yaying; Lin, Qingqi; Bai, Jun; Tang, Lu; Wang, Shizhong; Ying, Rongrong; Qiu, Rongliang

    2016-01-04

    Plant-associated bacteria are of great interest because of their potential use in phytoremediation. However, their ability to survive and promote plant growth in metal-polluted soils remains unclear. In this study, a soilborne Cd-resistant bacterium was isolated and identified as Enterobacter sp. strain EG16. It tolerates high external Cd concentrations (Cd(2+) MIC, >250 mg liter(-1)) and is able to produce siderophores and the plant hormone indole-3-acetic acid (IAA), both of which contribute to plant growth promotion. Surface biosorption in this strain accounted for 31% of the total Cd accumulated. The potential presence of cadmium sulfide, shown by energy-dispersive X-ray (EDX) analysis, suggested intracellular Cd binding as a Cd response mechanism of the isolate. Cd exposure resulted in global regulation at the transcriptomic level, with the bacterium switching to an energy-conserving mode by inhibiting energy-consuming processes while increasing the production of stress-related proteins. The stress response system included increased import of sulfur and iron, which become deficient under Cd stress, and the redirection of sulfur metabolism to the maintenance of intracellular glutathione levels in response to Cd toxicity. Increased production of siderophores, responding to Cd-induced Fe deficiency, not only is involved in the Cd stress response systems of EG16 but may also play an important role in promoting plant growth as well as alleviating the Cd-induced inhibition of IAA production. The newly isolated strain EG16 may be a suitable candidate for microbially assisted phytoremediation due to its high resistance to Cd and its Cd-induced siderophore production, which is likely to contribute to plant growth promotion.

  5. Geobacter luticola sp. nov., an Fe(III)-reducing bacterium isolated from lotus field mud.

    PubMed

    Viulu, Samson; Nakamura, Kohei; Okada, Yurina; Saitou, Sakiko; Takamizawa, Kazuhiro

    2013-02-01

    A novel species of Fe(III)-reducing bacterium, designated strain OSK6(T), belonging to the genus Geobacter, was isolated from lotus field mud in Japan. Strain OSK6(T) was isolated using a solid medium containing acetate, Fe(III)-nitrilotriacetate (NTA) and gellan gum. The isolate is a strictly anaerobic, gram-negative, motile, straight rod-shaped bacterium, 0.6-1.9 µm long and 0.2-0.4 µm wide. The growth of the isolate occurred at 20-40 °C with optima of 30-37 °C and pH 6.5-7.5 in the presence of up to 0.5 g NaCl l(-1). The G+C content of the genomic DNA was determined by HPLC to be 59.7 mol%. The major respiratory quinone was MK-8. The major fatty acids were 16 : 1ω7c and 16 : 0. Strain OSK6(T) was able to grow with Fe(III)-NTA, ferric citrate, amorphous iron (III) hydroxide and nitrate, but not with fumarate, malate or sulfate as electron acceptors. Among examined substrates grown with Fe(III)-NTA, the isolate grew on acetate, lactate, pyruvate and succinate. Analysis of the near full-length 16S rRNA gene sequence revealed that strain OSK6(T) is closely related to Geobacter daltonii and Geobacter toluenoxydans with 95.6 % similarity to the type strains of these species. On the basis of phylogenetic analysis and physiological tests, strain OSK6(T) is described as a representative of a novel species, Geobacter luticola sp. nov.; the type strain is OSK6(T) ( = DSM 24905(T) = JCM 17780(T)).

  6. Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice.

    PubMed

    Vance, Tyler D R; Olijve, Luuk L C; Campbell, Robert L; Voets, Ilja K; Davies, Peter L; Guo, Shuaiqi

    2014-07-04

    The large size of a 1.5-MDa ice-binding adhesin [MpAFP (Marinomonas primoryensis antifreeze protein)] from an Antarctic Gram-negative bacterium, M. primoryensis, is mainly due to its highly repetitive RII (Region II). MpAFP_RII contains roughly 120 tandem copies of an identical 104-residue repeat. We have previously determined that a single RII repeat folds as a Ca2+-dependent immunoglobulin-like domain. Here, we solved the crystal structure of RII tetra-tandemer (four tandem RII repeats) to a resolution of 1.8 Å. The RII tetra-tandemer reveals an extended (~190-Å × ~25-Å), rod-like structure with four RII-repeats aligned in series with each other. The inter-repeat regions of the RII tetra-tandemer are strengthened by Ca2+ bound to acidic residues. SAXS (small-angle X-ray scattering) profiles indicate the RII tetra-tandemer is significantly rigidified upon Ca2+ binding, and that the protein's solution structure is in excellent agreement with its crystal structure. We hypothesize that >600 Ca2+ help rigidify the chain of ~120 104-residue repeats to form a ~0.6 μm rod-like structure in order to project the ice-binding domain of MpAFP away from the bacterial cell surface. The proposed extender role of RII can help the strictly aerobic, motile bacterium bind ice in the upper reaches of the Antarctic lake where oxygen and nutrients are most abundant. Ca2+-induced rigidity of tandem Ig-like repeats in large adhesins might be a general mechanism used by bacteria to bind to their substrates and help colonize specific niches.

  7. Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice

    PubMed Central

    Vance, Tyler D. R.; Olijve, Luuk L. C.; Campbell, Robert L.; Voets, Ilja K.; Davies, Peter L.; Guo, Shuaiqi

    2014-01-01

    The large size of a 1.5-MDa ice-binding adhesin [MpAFP (Marinomonas primoryensis antifreeze protein)] from an Antarctic Gram-negative bacterium, M. primoryensis, is mainly due to its highly repetitive RII (Region II). MpAFP_RII contains roughly 120 tandem copies of an identical 104-residue repeat. We have previously determined that a single RII repeat folds as a Ca2+-dependent immunoglobulin-like domain. Here, we solved the crystal structure of RII tetra-tandemer (four tandem RII repeats) to a resolution of 1.8 Å. The RII tetra-tandemer reveals an extended (~190-Å × ~25-Å), rod-like structure with four RII-repeats aligned in series with each other. The inter-repeat regions of the RII tetra-tandemer are strengthened by Ca2+ bound to acidic residues. SAXS (small-angle X-ray scattering) profiles indicate the RII tetra-tandemer is significantly rigidified upon Ca2+ binding, and that the protein's solution structure is in excellent agreement with its crystal structure. We hypothesize that >600 Ca2+ help rigidify the chain of ~120 104-residue repeats to form a ~0.6 μm rod-like structure in order to project the ice-binding domain of MpAFP away from the bacterial cell surface. The proposed extender role of RII can help the strictly aerobic, motile bacterium bind ice in the upper reaches of the Antarctic lake where oxygen and nutrients are most abundant. Ca2+-induced rigidity of tandem Ig-like repeats in large adhesins might be a general mechanism used by bacteria to bind to their substrates and help colonize specific niches. PMID:24892750

  8. Psychrobacter fjordensis sp. nov., a psychrotolerant bacterium isolated from an Arctic fjord in Svalbard.

    PubMed

    Zeng, Yin-Xin; Yu, Yong; Li, Hui-Rong; Luo, Wei

    2015-12-01

    A Gram-negative, non-motile, non-spore-forming, psychrotolerant and halotolerant bacterium designated BSw21516B(T), was obtained from seawater in Kongsfjorden, a glacial fjord in the Arctic Svalbard and subjected to taxonomic analysis using a polyphasic approach. This bacterium was observed to optimally grow at 25-29 °C; between at 4 and 34 °C, but not at >35 °C; and in the presence of 0-8 % (w/v) NaCl at an optimum concentration of 2-5 % (w/v) NaCl. Strain BSw21516B(T) was found to contain Ubiquinone-8 (Q-8) as a predominant respiratory lipoquinone and C18:1 ω9c and summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) as predominant cellular fatty acids. Phylogenetic analysis of 16S rRNA and gyrB gene sequences showed that this isolate belongs to the genus Psychrobacter and is closely related to Psychrobacter fozii LMG 21280(T), which was isolated from a sediment sample in Antarctica. DNA hybridization experiments revealed a low level of DNA-DNA relatedness (less than 58.6 %) between strain BSw21516B(T) and its closest relatives. Based on these results a new species Psychrobacter fjordensis sp. nov. is proposed (type strain BSw21516B(T) = KCTC 42279(T) = CCTCC AB 2014020(T)).

  9. Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

    PubMed Central

    Taghavi, Safiyh; van der Lelie, Daniel; Hoffman, Adam; Zhang, Yian-Biao; Walla, Michael D.; Vangronsveld, Jaco; Newman, Lee; Monchy, Sébastien

    2010-01-01

    Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa×deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT–PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to

  10. Production of polyhydroxybutyrate by the marine photosynthetic bacterium Rhodovulum sulfidophilum P5

    NASA Astrophysics Data System (ADS)

    Cai, Jinling; Wei, Ying; Zhao, Yupeng; Pan, Guanghua; Wang, Guangce

    2012-07-01

    The effects of different NaCl concentrations, nitrogen sources, carbon sources, and carbon to nitrogen molar ratios on biomass accumulation and polyhydroxybutyrate (PHB) production were studied in batch cultures of the marine photosynthetic bacterium Rhodovulum sulfidophilum P5 under aerobic-dark conditions. The results show that the accumulation of PHB in strain P5 is a growth-associated process. Strain P5 had maximum biomass and PHB accumulation at 2%-3% NaCl, suggesting that the bacterium can maintain growth and potentially produce PHB at natural seawater salinity. In the nitrogen source test, the maximum biomass accumulation (8.10±0.09 g/L) and PHB production (1.11±0.13 g/L and 14.62%±2.2 of the cell dry weight) were observed when peptone and ammonium chloride were used as the sole nitrogen source. NH{4/+}-N was better for PHB production than other nitrogen sources. In the carbon source test, the maximum biomass concentration (7.65±0.05 g/L) was obtained with malic acid as the sole carbon source, whereas the maximum yield of PHB (5.03±0.18 g/L and 66.93%±1.69% of the cell dry weight) was obtained with sodium pyruvate as the sole carbon source. In the carbon to nitrogen ratios test, sodium pyruvate and ammonium chloride were selected as the carbon and nitrogen sources, respectively. The best carbon to nitrogen molar ratio for biomass accumulation (8.77±0.58 g/L) and PHB production (6.07±0.25 g/L and 69.25%±2.05% of the cell dry weight) was 25. The results provide valuable data on the production of PHB by R. sulfidophilum P5 and further studies are on-going for best cell growth and PHB yield.

  11. Flavobacterium arsenitoxidans sp. nov., an arsenite-oxidizing bacterium from Thai soil.

    PubMed

    Khianngam, Saowapar; Akaracharanya, Ancharida; Lee, Jung-Sook; Lee, Keun Chul; Kim, Kyoung-Woong; Tanasupawat, Somboon

    2014-12-01

    An arsenite-oxidizing bacterium, strain S2-3H(T), was isolated from arsenic-contaminated soil sample collected from Dantchaeng district, Suphanburi province, Thailand and was characterized based on polyphasic taxonomic study. The strain was observed to be a Gram-stain negative, aerobic, yellow pigmented, non-spore forming and rod-shaped bacterium. Major menaquinone was MK-6. Iso-C15:0, iso-C15:0 3OH, C16:1 ω7c/C16:1 ω6c, C16:0, iso-C17:0 3OH, and C16:0 3OH were the predominant cellular fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, unidentified phospholipids and unidentified aminophospholipids. The DNA G+C content was 37.0 mol%. Phylogenetic analysis using 16S rRNA sequence showed that strain S2-3H(T) is affiliated to the genus Flavobacterium, and is closely related to F. defluvii KCTC 12612(T) (97.0 %) and F. johnsoniae NBRC 14942(T) (97.0 %). The strain S2-3H(T) could be clearly distinguished from the related Flavobacterium species by its physiological and biochemical characteristics as well as its phylogenetic position and DNA-DNA relatedness. Therefore, the strain represents a novel species of the genus Flavobacterium, for which the name Flavobacterium arsenitoxidans sp. nov. (type strain S2-3H(T) = KCTC 22507(T) = NBRC 109607(T) = PCU 331(T) = TISTR 2238(T)) is proposed.

  12. Survival Strategies of the Plant-Associated Bacterium Enterobacter sp. Strain EG16 under Cadmium Stress

    PubMed Central

    Chen, Yanmei; Li, Yaying; Lin, Qingqi; Bai, Jun; Tang, Lu; Wang, Shizhong; Ying, Rongrong

    2016-01-01

    Plant-associated bacteria are of great interest because of their potential use in phytoremediation. However, their ability to survive and promote plant growth in metal-polluted soils remains unclear. In this study, a soilborne Cd-resistant bacterium was isolated and identified as Enterobacter sp. strain EG16. It tolerates high external Cd concentrations (Cd2+ MIC, >250 mg liter−1) and is able to produce siderophores and the plant hormone indole-3-acetic acid (IAA), both of which contribute to plant growth promotion. Surface biosorption in this strain accounted for 31% of the total Cd accumulated. The potential presence of cadmium sulfide, shown by energy-dispersive X-ray (EDX) analysis, suggested intracellular Cd binding as a Cd response mechanism of the isolate. Cd exposure resulted in global regulation at the transcriptomic level, with the bacterium switching to an energy-conserving mode by inhibiting energy-consuming processes while increasing the production of stress-related proteins. The stress response system included increased import of sulfur and iron, which become deficient under Cd stress, and the redirection of sulfur metabolism to the maintenance of intracellular glutathione levels in response to Cd toxicity. Increased production of siderophores, responding to Cd-induced Fe deficiency, not only is involved in the Cd stress response systems of EG16 but may also play an important role in promoting plant growth as well as alleviating the Cd-induced inhibition of IAA production. The newly isolated strain EG16 may be a suitable candidate for microbially assisted phytoremediation due to its high resistance to Cd and its Cd-induced siderophore production, which is likely to contribute to plant growth promotion. PMID:26729719

  13. Interactions of nisin and pediocin PA-1 with closely related lactic acid bacteria that manifest over 100-fold differences in bacteriocin sensitivity.

    PubMed Central

    Bennik, M H; Verheul, A; Abee, T; Naaktgeboren-Stoffels, G; Gorris, L G; Smid, E J

    1997-01-01

    The natural variation in the susceptibilities of gram-positive bacteria towards the bacteriocins nisin and pediocin PA-1 is considerable. This study addresses the factors associated with this variability for closely related lactic acid bacteria. We compared two sets of nonbacteriocinogenic strains for which the MICs of nisin and pediocin PA-1 differed 100- to 1,000-fold: Lactobacillus sake DSM20017 and L. sake DSM20497 and Pediococcus dextrinicus and Pediococcus pentosaccus. Strikingly, the bacteriocin-sensitive and -insensitive strains showed a similar concentration-dependent dissipation of their membrane potential (delta psi) after exposure to these bacteriocins. The bacteriocin-induced dissipation of delta psi below the MICs for the insensitive strains did not coincide with a reduction of intracellular ATP pools and glycolytic rates. This was not observed with the sensitive strains. Analysis of membrane lipid properties revealed minor differences in the phospho- and glycolipid compositions of both sets of strains. The interactions of the bacteriocins with strain-specific lipids were not significantly different in a lipid monolayer assay. Further lipid analysis revealed higher in situ membrane fluidity of the bacteriocin-sensitive Pediococcus strain compared with that for the insensitive strain, but the opposite was found for the L. sake strains. Our results provide evidence that the association of bacteriocins with the cell membrane and their subsequent insertion take place in a similar way for cells that have a high or a low natural tolerance towards bacteriocins. For insensitive strains, overall membrane constitution rather than mere membrane fluidity may preclude the formation of pores with sufficient diameters and lifetimes to ultimately cause cell death. PMID:9293015

  14. Gene identification and molecular characterization of solvent stable protease from a moderately haloalkaliphilic bacterium, Geomicrobium sp. EMB2.

    PubMed

    Karan, Ram; Singh, Raj Kumar Mohan; Kapoor, Sanjay; Khare, S K

    2011-02-01

    Cloning and characterization of the gene encoding a solvent-tolerant protease from the haloalkaliphilic bacterium Geomicrobium sp. EMB2 are described. Primers designed based on the N-terminal amino acid sequence of the purified EMB2 protease helped in the amplification of a 1,505-bp open reading frame that had a coding potential of a 42.7-kDa polypeptide. The deduced EMB2 protein contained a 35.4-kDa mature protein of 311 residues, with a high proportion of acidic amino acid residues. Phylogenetic analysis placed the EMB2 gene close to a known serine protease from Bacillus clausii KSM-K16. Primary sequence analysis indicated a hydrophobic inclination of the protein; and the 3D structure modeling elucidated a relatively higher percentage of small (glycine, alanine, and valine) and borderline (serine and threonine) hydrophobic residues on its surface. The structure analysis also highlighted enrichment of acidic residues at the cost of basic residues. The study indicated that solvent and salt stabilities in Geomicrobium sp. protease may be accorded to different structural features; that is, the presence of a number of small hydrophobic amino acid residues on the surface and a higher content of acidic amino acid residues, respectively.

  15. 9,10-Phenanthrenedione biodegradation by a soil bacterium and identification of transformation products by LC/ESI-MS/MS.

    PubMed

    Kanaly, Robert A; Hamamura, Natsuko

    2013-09-01

    Transformation of 9,10-phenanthrenedione, a cytotoxic derivative of phenanthrene, was shown to occur by a soil bacterium belonging to the genus Sphingobium. Phenanthrene-grown cells of this strain were exposed to 50mgL(-1) 9,10-phenanthrenedione in liquid cultures, extracted, and extracts were analyzed by liquid chromatography electrospray ionization mass spectrometry in negative ionization mode. Full scan analyses of exposed cells over the range from m/z 50 to m/z 500 were compared to abiotic and biotic controls. Product and precursor ion scan mode analyses indicated that at least three aromatic ring-cleavage transformation products of 9,10-phenanthrenedione were present and structures for these products, corresponding to [M-H](-)=271, [M-H](-)=241, and [M-H](-)=339 were proposed to be 4-(1-hydroxy-3,4-dioxo-2-naphthyl)-2-oxo-but-3-enoic acid, 2,2'-diphenic acid and 2-[(6-carboxy-2,3-dihydroxy-phenyl)-hydroxy-methyl]-5-oxo-hex-3-enedioic acid. The identity of 2,2'-diphenic acid was confirmed by comparison to an authentic standard and when the strain was exposed to 50mgL(-1) 2,2'-diphenic acid in separate assays, a transformation product with a similar mass spectrum as 9,10-phenanthrenedione-derived [M-H](-)=339 was revealed. Based upon these results, pathways for the transformation of 9,10-phenanthrenedione by strain KK22 were proposed. Strain KK22 appeared unable to use 9,10-phenanthrenedione as a growth substrate under these conditions. This is the first report of potential biotransformation pathways of 9,10-phenanthrenedione by a bacterium.

  16. Transcriptome Sequence and Plasmid Copy Number Analysis of the Brewery Isolate Pediococcus claussenii ATCC BAA-344T during Growth in Beer

    PubMed Central

    Pittet, Vanessa; Phister, Trevor G.; Ziola, Barry

    2013-01-01

    Growth of specific lactic acid bacteria in beer leads to spoiled product and economic loss for the brewing industry. Microbial growth is typically inhibited by the combined stresses found in beer (e.g., ethanol, hops, low pH, minimal nutrients); however, certain bacteria have adapted to grow in this harsh environment. Considering little is known about the mechanisms used by bacteria to grow in and spoil beer, transcriptome sequencing was performed on a variant of the beer-spoilage organism Pediococcusclaussenii ATCC BAA-344T (Pc344-358). Illumina sequencing was used to compare the transcript levels in Pc344-358 growing mid-exponentially in beer to those in nutrient-rich MRS broth. Various operons demonstrated high gene expression in beer, several of which are involved in nutrient acquisition and overcoming the inhibitory effects of hop compounds. As well, genes functioning in cell membrane modification and biosynthesis demonstrated significantly higher transcript levels in Pc344-358 growing in beer. Three plasmids had the majority of their genes showing increased transcript levels in beer, whereas the two cryptic plasmids showed slightly decreased gene expression. Follow-up analysis of plasmid copy number in both growth environments revealed similar trends, where more copies of the three non-cryptic plasmids were found in Pc344-358 growing in beer. Transcriptome sequencing also enabled the addition of several genes to the P. claussenii ATCC BAA-344T genome annotation, some of which are putatively transcribed as non-coding RNAs. The sequencing results not only provide the first transcriptome description of a beer-spoilage organism while growing in beer, but they also highlight several targets for future exploration, including genes that may have a role in the general stress response of lactic acid bacteria. PMID:24040005

  17. Isolation of an algal morphogenesis inducer from a marine bacterium.

    PubMed

    Matsuo, Yoshihide; Imagawa, Hiroshi; Nishizawa, Mugio; Shizuri, Yoshikazu

    2005-03-11

    Ulva and Enteromorpha are cosmopolitan and familiar marine algal genera. It is well known that these green macroalgae lose their natural morphology during short-term cultivation under aseptic conditions and during long-term cultivation in nutrient-added seawater and adopt an unusual form instead. These phenomena led to the belief that undefined morphogenetic factors that were indispensable to the foliaceous morphology of macroalgae exist throughout the oceans. We characterize a causative factor, named thallusin, isolated from an epiphytic marine bacterium. Thallusin induces normal germination and morphogenesis of green macroalgae.

  18. Inorganic nitrogen assimilation by the photosynthetic bacterium Rhodopseudomonas capsulata.

    PubMed Central

    Johansson, B C; Gest, H

    1976-01-01

    The photosynthetic bacterium Rhodopseudomonas capsulata lacks glutamate dehydrogenase and normally uses the glutamine synthetase/glutamate synthase sequence of reactions for assimilation of N2 and ammonia. The glutamine synthetase in cell-free extracts of the organism is completely sedimented by centrifugation at 140,000 X g for 2 h, is inhibited by L-alanine but not by adenosine 5'-monophosphate, and exhibits two apparent Km values for ammonia (ca. 13 muM and 1 mM). PMID:10281

  19. Triazine herbicide resistance in the photosynthetic bacterium Rhodopseudomonas sphaeroides

    PubMed Central

    Brown, Alfred E.; Gilbert, Carl W.; Guy, Rachel; Arntzen, Charles J.

    1984-01-01

    The photoaffinity herbicide azidoatrazine (2-azido-4-ethylamino-6-isopropylamino-s-triazine) selectively labels the L subunit of the reaction center of the photosynthetic bacterium Rhodopseudomonas sphaeroides. Herbicide-resistant mutants retain the L subunit and have altered binding properties for methylthio- and chloro-substituted triazines as well as altered equilibrium constants for electron transfer between primary and secondary electron acceptors. We suggest that a subtle alteration in the L subunit is responsible for herbicide resistance and that the L subunit is the functional analog of the 32-kDa QB protein of chloroplast membranes. Images PMID:16593520

  20. Factors Affecting Zebra Mussel Kill by the Bacterium Pseudomonas fluorescens

    SciTech Connect

    Daniel P. Molloy

    2004-02-24

    The specific purpose of this research project was to identify factors that affect zebra mussel kill by the bacterium Pseudomonas fluorescens. Test results obtained during this three-year project identified the following key variables as affecting mussel kill: treatment concentration, treatment duration, mussel siphoning activity, dissolved oxygen concentration, water temperature, and naturally suspended particle load. Using this latter information, the project culminated in a series of pipe tests which achieved high mussel kill inside power plants under once-through conditions using service water in artificial pipes.

  1. The metagenome of the marine anammox bacterium ‘Candidatus Scalindua profunda’ illustrates the versatility of this globally important nitrogen cycle bacterium

    PubMed Central

    van de Vossenberg, Jack; Woebken, Dagmar; Maalcke, Wouter J; Wessels, Hans J C T; Dutilh, Bas E; Kartal, Boran; Janssen-Megens, Eva M; Roeselers, Guus; Yan, Jia; Speth, Daan; Gloerich, Jolein; Geerts, Wim; van der Biezen, Erwin; Pluk, Wendy; Francoijs, Kees-Jan; Russ, Lina; Lam, Phyllis; Malfatti, Stefanie A; Tringe, Susannah Green; Haaijer, Suzanne C M; Op den Camp, Huub J M; Stunnenberg, Henk G; Amann, Rudi; Kuypers, Marcel M M; Jetten, Mike S M

    2013-01-01

    Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the ‘Candidatus Scalindua’ species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by ‘Candidatus Scalindua profunda’ to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater ‘Candidatus Kuenenia stuttgartiensis’. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K. stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm. PMID:22568606

  2. Proteome analysis of the plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae.

    PubMed

    Xu, Shu; Luo, Jianying; Pan, Xiayan; Liang, Xiaoyu; Wu, Jian; Zheng, Wenjun; Chen, Changjun; Hou, Yiping; Ma, Hongyu; Zhou, Mingguo

    2013-08-01

    The plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of bacterial blight, which is one of the most serious diseases of rice. Xoo has been studied for over one century, and much has been learned about it, but proteomic investigation has been neglected. In this study, proteome reference maps of Xoo were constructed by two-dimensional gel electrophoresis, and 628 spots in the gels representing 469 different protein species were identified with MALDI-TOF/TOF MS. The identified spots were assigned to 15 functional categories according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the annotations from the National Center for Biotechnology Information (NCBI) database. The data set has been deposited in the World-2DPAGE database (Database ID: 0044). In addition, comparative proteomic analysis revealed that proteins related to the TonB-dependent transportation system and energy metabolism are involved in the phenazine-1-carboxylic acid resistance in Xoo. In conclusion, we have established a proteome database for Xoo and have used this database in a comparative proteomic analysis that identified proteins potentially contributing to phenazine-1-carboxylic acid resistance in Xoo.

  3. Propionate-degrading bacterium, Syntrophobacter wolinii sp. nov. gen. nov. , from methanogenic ecosystems

    SciTech Connect

    Boone, D.R.; Bryant, M.P.

    1980-09-01

    A new genus and species of a nonmotile gram-negative rod, Syntrophobacter wolinii, is the first bacterium described which degrades propionate only in coculture with an H/sub 2/-using organism and in the absence of light or exogenous electron acceptors such as O/sub 2/, sulfate, or nitrate. It was isolated from methanogenic enrichments from an anaerobic municipal sewage digestor, using anaerobic roll tubes containing a medium with propionate as the energy source in association with an H/sub 2/-using, sulfate-reducing Desulfovibrio sp. which cannot utilize fatty acids other than formate. S. wolinii produced acetate and, presumably, CO/sub 2/ and H/sub 2/ (or formate) from propionate. In media without sulfate and with Methanospirillum hungatei, a methanogen that uses only H/sub 2/-CO/sub 2/ or formate as an energy source, acetate, methane, and, presumably, CO/sub 2/ were produced from propionate and only small amounts of Desulfovibrio sp. were present. Isolation in coculture with the methanogen was not successful. S. wolinii does not use other saturated fatty acids as energy sources. 2 figures, 3 tables.

  4. A new κ-carrageenase CgkS from marine bacterium Shewanella sp. Kz7

    NASA Astrophysics Data System (ADS)

    Wang, Linna; Li, Shangyong; Zhang, Shilong; Li, Jiejing; Yu, Wengong; Gong, Qianhong

    2015-08-01

    A new κ-carrageenase gene cgkS was cloned from marine bacterium Shewanella sp. Kz7 by using degenerate and site-finding PCR. The gene was comprised of an open reading frame of 1224 bp, encoding 407 amino acid residues, with a signal peptide of 24 residues. Based on the deduced amino acid sequence, the κ-carrageenase CgkS was classified into the Glycoside Hydrolase family 16. The cgkS gene was expressed in Escherichia coli, and the recombinant enzyme was purified to homogeneity with a specific activity of 716.8 U mg-1 and a yield of 69%. Recombinant CgkS was most active at 45°C and pH 8.0. It was stable at pH 6.0-9.0 and below 30°C. The enzyme did not require NaCl for activity, although its activity was enhanced by NaCl. CgkS degraded κ-carrageenan in an endo-fashion releasing tetrasaccharides and disaccharides as main hydrolysis products.

  5. Identification of salt-inducible peptide with putative kinase activity in halophilic bacterium Virgibacillus halodenitrificans.

    PubMed

    Rafiee, Mahmoud-Reza; Sokhansanj, Ashrafaddin; Yoosefi, Mitra; Naghizadeh, Mohammad-Ali

    2007-09-01

    Strain XII, a moderately halophilic bacterium, expressed a peptide in response to saline media. This peptide was designated as salt-inducible factor (Sif-A). The purpose of this study is to describe Sif-A, which might be involved in the osmoresistance mechanism of strain XII. The complete sequence of sif-A was determined using PCR. sif-A codes for a polypeptide of 20.518 kDa. The polypeptide has a putative signal peptide of 27 amino acids (2.667 kDa) preceding the mature protein (17.869 kDa). Motif analysis of the deduced amino acid sequence indicated that there is a p-loop NTPase domain on the C-terminal of the peptide, which might correlate with its function. The sequence of the 16S rRNA gene was analyzed phylogenetically to classify strain XII. This organism was found to have the closest association with Virgibacillus halodenitrificans, which was proven by its phenotypic characteristics.

  6. Protein inclusions produced by the entomopathogenic bacterium Xenorhabdus nematophilus subsp. nematophilus.

    PubMed Central

    Couche, G A; Gregson, R P

    1987-01-01

    The entomopathogenic bacterium Xenorhabdus nematophilus subsp. nematophilus produces two types of intracellular inclusion bodies during in vitro culture. Large cigar-shaped inclusions (designated type 1) and smaller ovoid inclusions (designated type 2) were purified from cell lysates, using differential centrifugation in discontinuous glycerol gradients and isopycnic density gradient centrifugation in sodium diatrizoate. The inclusions, composed almost exclusively of protein, are readily soluble at high and low pH values and in the presence of cation chelators such as EDTA, anionic detergents (sodium dodecyl sulfate), or protein denaturants (urea, NaBr). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of purified inclusions revealed a single 26-kilodalton protein (IP-1) in type 1 inclusions and a 22-kilodalton protein (IP-2) in type 2 inclusions. Analysis of these proteins by isoelectric focusing in the presence of 8 M urea showed that IP-1 is acidic and IP-2 is neutral. Furthermore, each protein occurred in multiple forms differing slightly in isoelectric point. Other variations in peptides released by trypsin digestion, immunological properties, and amino acid composition revealed significant structural differences between IP-1 and IP-2. Kinetic studies using light microscopy, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and immunoblotting procedures showed that inclusion protein synthesis occurs only during the second half of exponential culture growth. Synthesis of inclusion proteins and their aggregation to form inclusions occurred concurrently. Possible functions for these abundant proteins are discussed. Images PMID:3667532

  7. Application of Lactobacillus fermentum HL57 and Pediococcus acidilactici SP979 as potential probiotics in the manufacture of traditional Iberian dry-fermented sausages.

    PubMed

    Ruiz-Moyano, Santiago; Martín, Alberto; Benito, María José; Hernández, Alejandro; Casquete, Rocio; de Guia Córdoba, María

    2011-08-01

    The purpose of this study was to investigate the potential of implanting the probiotics Lactobacillus fermentum HL57 and P. acidilactici SP979 during manufacture of Iberian dry-fermented sausages, and their effect on the sensory properties of these meat products. Microbial counts were studied in sausages inoculated with these strains and compared with a control batch. To detect the presence of probiotic strains at high counts (>7 log CFU/g) in the inoculated sausages, specific PCR and (RAPD)-PCR techniques were carried out. Changes due to probiotic inoculations on parameters and compounds related to fermentation, and nitrogen and lipid fractions were determined, and the impact on sensory quality evaluated by descriptive and hedonic tests. Iberian dry-fermented sausages inoculated with L. fermentum HL57 and P. acidilactici SP979 may be considered as functional products according to the counts of these strains found at the end of processing. However, inoculation with L. fermentum HL57 increased the amount of acetic acid and lipid degradation products such as malonaldehyde in Iberian dry-fermented sausages, resulting in a negative impact on relevant sensory parameters related to colour and taste. On the contrary, P. acidilactici SP979 did not notably modify the physicochemical parameters or the sensory quality of Iberian dry-fermented sausages when compared to the autochthonous microbial population present in the control batch.

  8. Intestinimonas butyriciproducens gen. nov., sp. nov., a butyrate-producing bacterium from the mouse intestine.

    PubMed

    Kläring, Karoline; Hanske, Laura; Bui, Nam; Charrier, Cédric; Blaut, Michael; Haller, Dirk; Plugge, Caroline M; Clavel, Thomas

    2013-12-01

    A Gram-positive, spore-forming, non-motile, strictly anaerobic rod-shaped bacterium was isolated from the caecal content of a TNF(deltaARE) mouse. The isolate, referred to as strain SRB-521-5-I(T), was originally cultured on a reduced agar medium containing yeast extract, rumen fluid and lactic acid as main energy and carbon sources. Phylogenetic analysis of partial 16S rRNA genes revealed that the species most closely related to strain SRB-521-5-I(T) were Flavonifractor plautii and Pseudoflavonifractor capillosus (<95 % sequence similarity; 1436 bp). In contrast to F. plautii and P. capillosus, strain SRB-521-5-I(T) contained a substantial amount of C18 : 0 dimethylacetal. Additional major fatty acids were C14 : 0 methyl ester, C16 : 0 dimethylacetal and C18 : 0 aldehyde. Strain SRB-521-5-I(T) differed in its enzyme profile from F. plautii and P. capillosus by being positive for dextrin, maltotriose, turanose, dl-lactic acid and d-lactic acid methyl ester but negative for d-fructose. In reduced Wilkins-Chalgren-Anaerobe broth, strain SRB-521-5-I(T) produced approximately 8 mM butyrate and 4 mM acetate. In contrast to F. plautii, the strain did not metabolize flavonoids. It showed intermediate resistance towards the antibiotics ciprofloxacin, colistin and tetracycline. Based on genotypic and phenotypic characteristics, we propose the name Intestinimonas butyriciproducens gen. nov., sp. nov. to accommodate strain SRB-521-5-I(T) ( = DSM 26588(T) = CCUG 63529(T)) as the type strain.

  9. Genome Sequence and Analysis of the Oral Bacterium Fusobacterium nucleatum Strain ATCC 25586

    PubMed Central

    Kapatral, Vinayak; Anderson, Iain; Ivanova, Natalia; Reznik, Gary; Los, Tamara; Lykidis, Athanasios; Bhattacharyya, Anamitra; Bartman, Allen; Gardner, Warren; Grechkin, Galina; Zhu, Lihua; Vasieva, Olga; Chu, Lien; Kogan, Yakov; Chaga, Oleg; Goltsman, Eugene; Bernal, Axel; Larsen, Niels; D'Souza, Mark; Walunas, Theresa; Pusch, Gordon; Haselkorn, Robert; Fonstein, Michael; Kyrpides, Nikos; Overbeek, Ross

    2002-01-01

    We present a complete DNA sequence and metabolic analysis of the dominant oral bacterium Fusobacterium nucleatum. Although not considered a major dental pathogen on its own, this anaerobe facilitates the aggregation and establishment of several other species including the dental pathogens Porphyromonas gingivalis and Bacteroides forsythus. The F. nucleatum strain ATCC 25586 genome was assembled from shotgun sequences and analyzed using the ERGO bioinformatics suite (http://www.integratedgenomics.com). The genome contains 2.17 Mb encoding 2,067 open reading frames, organized on a single circular chromosome with 27% GC content. Despite its taxonomic position among the gram-negative bacteria, several features of its core metabolism are similar to that of gram-positive Clostridium spp., Enterococcus spp., and Lactococcus spp. The genome analysis has revealed several key aspects of the pathways of organic acid, amino acid, carbohydrate, and lipid metabolism. Nine very-high-molecular-weight outer membrane proteins are predicted from the sequence, none of which has been reported in the literature. More than 137 transporters for the uptake of a variety of substrates such as peptides, sugars, metal ions, and cofactors have been identified. Biosynthetic pathways exist for only three amino acids: glutamate, aspartate, and asparagine. The remaining amino acids are imported as such or as di- or oligopeptides that are subsequently degraded in the cytoplasm. A principal source of energy appears to be the fermentation of glutamate to butyrate. Additionally, desulfuration of cysteine and methionine yields ammonia, H2S, methyl mercaptan, and butyrate, which are capable of arresting fibroblast growth, thus preventing wound healing and aiding penetration of the gingival epithelium. The metabolic capabilities of F. nucleatum revealed by its genome are therefore consistent with its specialized niche in the mouth. PMID:11889109

  10. Gracilibacillus boraciitolerans sp. nov., a highly boron-tolerant and moderately halotolerant bacterium isolated from soil.

    PubMed

    Ahmed, Iftikhar; Yokota, Akira; Fujiwara, Toru

    2007-04-01

    A motile, Gram-positive, boron-tolerant and moderately halotolerant rod-shaped bacterium was isolated from a soil naturally high in boron minerals found in the Hisarcik area of Turkey. The novel isolate, designated T-16X(T), produced spherical or ellipsoidal endospores in a non-bulging or slightly swollen sporangium in a terminal position and survived in a medium containing up to 450 mM boron. Whereas it tolerated 11 % (w/v) NaCl, it also grew without NaCl or boron. The temperature range for growth was 16-37 degrees C (optimum 25-28 degrees C) and the pH range for growth was 6.0-10.0 (optimum pH 7.5-8.5). The DNA G+C content was 35.8 mol% and the major cellular fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0) at 18.2 and 45.7 % of the total fatty acids, respectively. MK-7 (90 %) was the predominant respiratory quinone system and meso-diaminopimelic acid was the predominant diamino acid of the cell-wall peptidoglycan. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the novel strain is closely related to the type strains of Gracilibacillus orientalis (96.7 % similarity), G. halotolerans (95.5 %) and G. dipsosauri (95.4 %). However, the maximum DNA hybridization value for this strain with these closely related strains was less than 26.2 %. On the basis of 16S rRNA gene sequence data and chemotaxonomic and physiological features, the organism T-16X(T) (=DSM 17256(T)=IAM 15263(T)=ATCC BAA-1190(T)) is proposed to be a member of the genus Gracilibacillus as the type strain of the novel species Gracilibacillus boraciitolerans sp. nov.

  11. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus

    DOE PAGES

    Gardner, Jeffrey G.

    2016-06-04

    Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. Furthermore, this review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkablemore » ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.« less

  12. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus.

    PubMed

    Gardner, Jeffrey G

    2016-07-01

    Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. This review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkable ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.

  13. Molybdate Reduction to Molybdenum Blue by an Antarctic Bacterium

    PubMed Central

    Ahmad, S. A.; Shukor, M. Y.; Shamaan, N. A.; Mac Cormack, W. P.; Syed, M. A.

    2013-01-01

    A molybdenum-reducing bacterium from Antarctica has been isolated. The bacterium converts sodium molybdate or Mo6+ to molybdenum blue (Mo-blue). Electron donors such as glucose, sucrose, fructose, and lactose supported molybdate reduction. Ammonium sulphate was the best nitrogen source for molybdate reduction. Optimal conditions for molybdate reduction were between 30 and 50 mM molybdate, between 15 and 20°C, and initial pH between 6.5 and 7.5. The Mo-blue produced had a unique absorption spectrum with a peak maximum at 865 nm and a shoulder at 710 nm. Respiratory inhibitors such as antimycin A, sodium azide, potassium cyanide, and rotenone failed to inhibit the reducing activity. The Mo-reducing enzyme was partially purified using ion exchange and gel filtration chromatography. The partially purified enzyme showed optimal pH and temperature for activity at 6.0 and 20°C, respectively. Metal ions such as cadmium, chromium, copper, silver, lead, and mercury caused more than 95% inhibition of the molybdenum-reducing activity at 0.1 mM. The isolate was tentatively identified as Pseudomonas sp. strain DRY1 based on partial 16s rDNA molecular phylogenetic assessment and the Biolog microbial identification system. The characteristics of this strain would make it very useful in bioremediation works in the polar and temperate countries. PMID:24381945

  14. Rare bacterium of new genus isolated with prolonged enrichment culture.

    PubMed

    Hashizume, Akiko; Fudou, Ryosuke; Jojima, Yasuko; Nakai, Ryohsuke; Hiraishi, Akira; Tabuchi, Akira; Sen, Kikuo; Shibai, Hiroshiro

    2004-01-01

    Dynamic change in microbial flora was monitored with an oxygen electrode. The 1st phase microorganisms, which first grew well in LB medium, were followed by the 2nd phase microorganisms, which supposedly assimilated microbial cells of the 1st phase and their metabolites. In a similar way, a change in microbial flora was observed from the 1st phase to the 4th phase in 84 hr. Based on this observation, prolonged enrichment culture was done for as long as two months to increase the ratio of existence of rare microorganisms. From these culture liquids, four slow-growing bacteria (provisionally named Shinshu-ah1, -ah2, -ah3, and -ah4), which formed scarcely visible small colonies, were isolated. Sequence analysis of their 16S rDNA showed that Shinshu-ah1 had 97% homology with Bradyrhizobium japonicum and uncultured alpha proteobacterium clone blaii 16, Shinshu-ah2 91% with Rasbo bacterium, Alpha proteobacterium 34619, Bradyrhizobium genosp. P, Afipia felis and an unidentified bacterium, Shinshu-ah3 99% with Methylobacterium mesophilicum, and Shinshu-ah4 95% with Agromyces ramosus DSM 43045. Phylogenetic study indicated that Shinshu-ah2 had a possibility to form a new family, Shinshu-ah1 a new genus, and Shinshu-ah4 a new species.

  15. Further characterization of o-nitrobenzaldehyde degrading bacterium Pseudomonas sp. ONBA-17 and deduction on its metabolic pathway.

    PubMed

    Yu, Fang-Bo; Li, Xiao-Dan; Ali, Shinawar Waseem; Shan, Sheng-Dao; Luo, Lin-Ping; Guan, Li-Bo

    2014-01-01

    A previously reported o-nitrobenzaldehyde (ONBA) degrading bacterium Pseudomonas sp. ONBA-17 was further identified and characterized. Based on results of DNA base composition and DNA-DNA hybridization, the strain was identified as P. putida. Its degradation effect enhanced with increase of inoculum amount and no lag phase was observed. Higher removal rate was achieved under shaking conditions. All tested ONBA with different initial concentrations could be completely degraded within 5 d. In addition, degradative enzyme(s) involved was confirmed as intra-cellular distributed and constitutively expressed. Effects of different compounds on relative activity of degradative enzyme(s) within cell-free extract were also evaluated. Finally, 2-nitrobenzoic acid and 2, 3-dihydroxybenzoic acid were detected as metabolites of ONBA degradation by P. putida ONBA-17, and relevant metabolic pathway was preliminary proposed. This study might help with future research in better understanding of nitroaromatics biodegradation.

  16. Biosynthesis of vitamins and cofactors in bacterium-harbouring trypanosomatids depends on the symbiotic association as revealed by genomic analyses.

    PubMed

    Klein, Cecilia C; Alves, João M P; Serrano, Myrna G; Buck, Gregory A; Vasconcelos, Ana Tereza R; Sagot, Marie-France; Teixeira, Marta M G; Camargo, Erney P; Motta, Maria Cristina M

    2013-01-01

    Some non-pathogenic trypanosomatids maintain a mutualistic relationship with a betaproteobacterium of the Alcaligenaceae family. Intensive nutritional exchanges have been reported between the two partners, indicating that these protozoa are excellent biological models to study metabolic co-evolution. We previously sequenced and herein investigate the entire genomes of five trypanosomatids which harbor a symbiotic bacterium (SHTs for Symbiont-Haboring Trypanosomatids) and the respective bacteria (TPEs for Trypanosomatid Proteobacterial Endosymbiont), as well as two trypanosomatids without symbionts (RTs for Regular Trypanosomatids), for the presence of genes of the classical pathways for vitamin biosynthesis. Our data show that genes for the biosynthetic pathways of thiamine, biotin, and nicotinic acid are absent from all trypanosomatid genomes. This is in agreement with the absolute growth requirement for these vitamins in all protozoa of the family. Also absent from the genomes of RTs are the genes for the synthesis of pantothenic acid, folic acid, riboflavin, and vitamin B6. This is also in agreement with the available data showing that RTs are auxotrophic for these essential vitamins. On the other hand, SHTs are autotrophic for such vitamins. Indeed, all the genes of the corresponding biosynthetic pathways were identified, most of them in the symbiont genomes, while a few genes, mostly of eukaryotic origin, were found in the host genomes. The only exceptions to the latter are: the gene coding for the enzyme ketopantoate reductase (EC:1.1.1.169) which is related instead to the Firmicutes bacteria; and two other genes, one involved in the salvage pathway of pantothenic acid and the other in the synthesis of ubiquinone, that are related to Gammaproteobacteria. Their presence in trypanosomatids may result from lateral gene transfer. Taken together, our results reinforce the idea that the low nutritional requirement of SHTs is associated with the presence of the

  17. Production of amino acids using auxotrophic mutants of methylotrophic bacillus

    DOEpatents

    Hanson, Richard S.; Flickinger, Michael C.; Schendel, Frederick J.; Guettler, Michael V.

    2001-07-17

    A method of producing amino acids by culturing an amino acid auxotroph of a biologically pure strain of a type I methylotrophic bacterium of the genus Bacillus which exhibits sustained growth at 50.degree. C. using methanol as a carbon and energy source and requiring vitamin B.sub.12 and biotin is provided.

  18. Selection of lactic acid bacteria isolated from Tunisian cereals and exploitation of the use as starters for sourdough fermentation.

    PubMed

    Mamhoud, Asma; Nionelli, Luana; Bouzaine, Taroub; Hamdi, Moktar; Gobbetti, Marco; Rizzello, Carlo Giuseppe

    2016-05-16

    Wheat bread is the most popular staple food consumed in Tunisia and, despite the niche production of some typical breads (e.g. Tabouna, Mlawi, Mtabga), the major part is currently produced with baker's yeast at industrial or, mainly, at artisanal level, while the use of sourdough fermentation is rarely reported. Considering the growing national demand for cereal baked goods, it can be hypothesized that sourdough fermentation through the use of selected lactic acid bacteria as starters could improve the overall quality and the diversification of local products. Different cereal grains were collected from the regions of Ariana, Bizerta, Beja Nabeul, and Seliana, and the autochthonous lactic acid bacteria were isolated, identified, characterized and selected on the basis of the kinetics of acidification, the proteolytic activity, and the quotient of fermentation. Lactobacillus curvatus MA2, Pediococcus pentosaceus OA2, and Pediococcus acidilactici O1A1 were used together as mixed starter to obtain a selected sourdough. According to the backslopping procedure, a type I sourdough was made from a Tunisian flour (spontaneous sourdough). Compared to the use of the spontaneous sourdough, the one obtained with selected and mixed starters by a unique fermentation step, favored the increase of the concentrations of organic acids, phenols, and total free amino acids, the most suitable quotient of fermentation, and the most intense phytase and antioxidant activities, that increased ca. 20% compared to the control. Moreover, the selected starters improved the in vitro protein digestibility (ca. 82% when selected sourdough was used), textural and sensory features of the breads, as determined by textural profile analysis and panel test, respectively. This study aimed at exploiting the potential of selected autochthonous lactic acid bacteria and extending the use of a sourdough (type II), thanks to the set-up of a two-step fermentation protocol designed for application at the

  19. Structure and morphology of magnetite anaerobically-produced by a marine magnetotactic bacterium and a dissimilatory iron-reducing bacterium

    USGS Publications Warehouse

    Sparks, N.H.C.; Mann, S.; Bazylinski, D.A.; Lovley, D.R.; Jannasch, H.W.; Frankel, R.B.

    1990-01-01

    Intracellular crystals of magnetite synthesized by cells of the magnetotactic vibroid organism, MV-1, and extracellular crystals of magnetite produced by the non-magnetotactic dissimilatory iron-reducing bacterium strain GS-15, were examined using high-resolution transmission electron microscopy, electron diffraction and 57Fe Mo??ssbauer spectroscopy. The magnetotactic bacterium contained a single chain of approximately 10 crystals aligned along the long axis of the cell. The crystals were essentially pure stoichiometric magnetite. When viewed along the crystal long axis the particles had a hexagonal cross-section whereas side-on they appeared as rectangules or truncated rectangles of average dimension, 53 ?? 35 nm. These findings are explained in terms of a three-dimensional morphology comprising a hexagonal prism of {110} faces which are capped and truncated by {111} end faces. Electron diffraction and lattice imaging studies indicated that the particles were structurally well-defined single crystals. In contrast, magnetite particles produced by the strain, GS-15 were irregular in shape and had smaller mean dimensions (14 nm). Single crystals were imaged but these were not of high structural perfection. These results highlight the influence of intracellular control on the crystallochemical specificity of bacterial magnetites. The characterization of these crystals is important in aiding the identification of biogenic magnetic materials in paleomagnetism and in studies of sediment magnetization. ?? 1990.

  20. Silica-Induced Protein (Sip) in Thermophilic Bacterium Thermus thermophilus Responds to Low Iron Availability

    PubMed Central

    Fujino, Yasuhiro; Nagayoshi, Yuko; Iwase, Makoto; Yokoyama, Takushi; Ohshima, Toshihisa

    2016-01-01

    ABSTRACT Thermus thermophilus HB8 expresses silica-induced protein (Sip) when cultured in medium containing supersaturated silicic acids. Using genomic information, Sip was identified as a Fe3+-binding ABC transporter. Detection of a 1-kb hybridized band in Northern analysis revealed that sip transcription is monocistronic and that sip has its own terminator and promoter. The sequence of the sip promoter showed homology with that of the σA-dependent promoter, which is known as a housekeeping promoter in HB8. Considering that sip is transcribed when supersaturated silicic acids are added, the existence of a repressor is presumed. DNA microarray analysis suggested that supersaturated silicic acids and iron deficiency affect Thermus cells similarly, and enhanced sip transcription was detected under both conditions. This suggested that sip transcription was initiated by iron deficiency and that the ferric uptake regulator (Fur) controlled the transcription. Three Fur gene homologues (TTHA0255, TTHA0344, and TTHA1292) have been annotated in the HB8 genome, and electrophoretic mobility shift assays revealed that the TTHA0344 product interacts with the sip promoter region. In medium containing supersaturated silicic acids, free Fe3+ levels were decreased due to Fe3+ immobilization on colloidal silica. This suggests that, because Fe3+ ions are captured by colloidal silica in geothermal water, Thermus cells are continuously exposed to the risk of iron deficiency. Considering that Sip is involved in iron acquisition, Sip production may be a strategy to survive under conditions of low iron availability in geothermal water. IMPORTANCE The thermophilic bacterium Thermus thermophilus HB8 produces silica-induced protein (Sip) in the presence of supersaturated silicic acids. Sip has homology with iron-binding ABC transporter; however, the mechanism by which Sip expression is induced by silicic acids remains unexplained. We demonstrate that Sip captures iron and its transcription

  1. A Halotolerant Bacterium Bacillus licheniformis HSW-16 Augments Induced Systemic Tolerance to Salt Stress in Wheat Plant (Triticum aestivum)

    PubMed Central

    Singh, Rajnish P.; Jha, Prabhat N.

    2016-01-01

    Certain plant growth promoting bacteria can protect associated plants from harmful effects of salinity. We report the isolation and characterization of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase bacterium Bacillus licheniformis HSW-16 capable of ameliorating salt (NaCl) stress in wheat plants. The bacterium was isolated from the water of Sambhar salt lake, Rajasthan, India. The presence of ACC deaminase activity was confirmed by enzyme assay and analysis of AcdS gene, a structural gene for ACC deaminase. Inoculation of B. licheniformis HSW-16 protected wheat plants from growth inhibition caused by NaCl and increased plant growth (6-38%) in terms of root length, shoot length, fresh weight, and dry weight. Ionic analysis of plant samples showed that the bacterial inoculation decreased the accumulation of Na+ content (51%), and increased K+ (68%), and Ca2+ content (32%) in plants at different concentration of NaCl. It suggested that bacterial inoculation protected plants from the effect of NaCl by decreasing the level of Na+ in plants. Production of exopolysaccharide by the B. licheniformis HSW-16 can also protect from Na+ by binding this ion. Moreover, application of test isolate resulted in an increase in certain osmolytes such as total soluble sugar, total protein content, and a decrease in malondialdehyde content, illustrating their role in the protection of plants. The ability of B. licheniformis HSW-16 to colonize plant root surface was examined by staining the bacterium with acridine orange followed by fluorescence microscopy and polymerase chain reaction-based DNA finger printing analysis. These results suggested that B. licheniformis HSW-16 could be used as a bioinoculant to improve the productivity of plants growing under salt stress. PMID:28018415

  2. Draft Genome Sequence of Ensifer adhaerens M78, a Mineral-Weathering Bacterium Isolated from Soil

    PubMed Central

    Wang, Yuanli; Chen, Wei; He, Linyan; Wang, Qi

    2016-01-01

    Ensifer adhaerens M78, a bacterium isolated from soil, can weather potash feldspar and release Fe, Si, and Al from rock under nutrient-poor conditions. Here, we report the draft genome sequence of strain M78, which may facilitate a better understanding of the molecular mechanism involved in mineral weathering by the bacterium. PMID:27609930

  3. Draft Genome Sequence of Ensifer adhaerens M78, a Mineral-Weathering Bacterium Isolated from Soil.

    PubMed

    Wang, Yuanli; Chen, Wei; He, Linyan; Wang, Qi; Sheng, Xia-Fang

    2016-09-08

    Ensifer adhaerens M78, a bacterium isolated from soil, can weather potash feldspar and release Fe, Si, and Al from rock under nutrient-poor conditions. Here, we report the draft genome sequence of strain M78, which may facilitate a better understanding of the molecular mechanism involved in mineral weathering by the bacterium.

  4. Genome Sequence of the Antarctic Psychrophile Bacterium Planococcus antarcticus DSM 14505

    PubMed Central

    Margolles, Abelardo; Gueimonde, Miguel

    2012-01-01

    Planococcus antarcticus DSM 14505 is a psychrophile bacterium that was isolated from cyanobacterial mat samples, originally collected from ponds in McMurdo, Antarctica. This orange-pigmented bacterium grows at 4°C and may possess interesting enzymatic activities at low temperatures. Here we report the first genomic sequence of P. antarcticus DSM 14505. PMID:22843594

  5. Near-complete genome sequence of the cellulolytic Bacterium Bacteroides (Pseudobacteroides) cellulosolvens ATCC 35603

    DOE PAGES

    Dassa, Bareket; Utturkar, Sagar M.; Hurt, Richard A.; ...

    2015-09-24

    We report the single-contig genome sequence of the anaerobic, mesophilic, cellulolytic bacterium, Bacteroides cellulosolvens. The bacterium produces a particularly elaborate cellulosome system, whereas the types of cohesin-dockerin interactions are opposite of other known cellulosome systems: cell-surface attachment is thus mediated via type-I interactions whereas enzymes are integrated via type-II interactions.

  6. Kinetic study of trichloroethylene and toluene degradation by a bioluminescent reporter bacterium

    SciTech Connect

    Kelly, C.J.; Sanseverino, J.; Bienkowski, P.R.; Sayler, G.S.

    1995-12-31

    A constructed bioluminescent reporter bacterium, Pseudomonas putida B2, is very briefly described in this paper. The bacterium degrades toluene and trichloroethylene (TCE), and produces light in the presence of toluene. The light response is an indication of cellular viability and expression of the genes encoding toluene and TCE degrading enzymes.

  7. Draft Genome Sequence of Pseudomonas aeruginosa Strain RB, a Bacterium Capable of Synthesizing Cadmium Selenide Nanoparticles.

    PubMed

    Ayano, Hiroyuki; Kuroda, Masashi; Soda, Satoshi; Ike, Michihiko

    2014-05-15

    Pseudomonas aeruginosa strain RB is a bacterium capable of synthesizing cadmium selenide (CdSe) nanoparticles and was isolated from a soil sample. Here, we present the draft genome sequence of P. aeruginosa strain RB. To the best of our knowledge, this is the first report of a draft genome of a CdSe-synthesizing bacterium.

  8. Bacillus shacheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil.

    PubMed

    Lei, Zuchao; Qiu, Peng; Ye, Renyuan; Tian, Jiewei; Liu, Yang; Wang, Lei; Tang, Shu-Kun; Li, Wen-Jun; Tian, Yongqiang

    2014-01-01

    A moderately halophilic bacterium, strain HNA-14(T), was isolated from a saline-alkali soil sample collected in Shache County, Xinjiang Province. On the basis of the polyphasic taxonomic data, the isolate was considered to be a member of the genus Bacillus. The organism grew optimally at 30 °C and pH 8.0. It was moderately halophilic and its optimum growth occurred at 5-10% NaCl. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid and the predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15:0 and iso-C15:0 and the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and two unknown phospholipids. The G+C content of the genomic DNA was 48.6 mol%. Strain HNA-14(T) exhibited a low 16S rRNA gene sequence similarity of 96% with its nearest neighbors [Bacillus clausii KSM-K16 (96.5%), Bacillus xiaoxiensis DSM 21943(T)(96.2%), Bacillus clausii DSM 8716(T) (96.1%), Bacillus patagoniensis PAT05(T) (96.1%), Bacillus lehensis MLB-2(T) (96.0%), Bacillus oshimensis K11(T) (95.9%) and Bacillus hunanensis DSM 23008(T) (95.8%)] and the phenotypic characteristics indicate that strain HNA-14(T) can be distinguished from them. Therefore, a novel species of the genus Bacillus, Bacillus shacheensis sp. nov. (type strain, HNA-14(T) = KCTC 33145 = DSM 26902) is proposed.

  9. Bacillus salitolerans sp. nov., a novel bacterium isolated from a salt mine in Xinjiang province, China.

    PubMed

    Zhang, Wei-Yan; Hu, Jing; Zhang, Xin-Qi; Zhu, Xu-Fen; Wu, Min

    2015-08-01

    A novel aerobic bacterium, KC1(T), was isolated from a salt mine in Kuche county, Xinjiang province, China. Cells were observed to be Gram-positive, rod-shaped, endospore-forming and motile with flagella. Strain KC1(T) was found to grow at 25-45 °C (optimum 37 °C), pH 6.5-9.0 (optimum 8.0) and NaCl 0-10 % (v/v) (optimum 4 %). The major fatty acids were identified as anteiso-C15:0 and anteiso-C17:0. Menaquinone-7 (MK-7) was found to be the predominant isoprenoid quinone. The cell-wall diamino acid was found to be meso-diaminopimelic acid. Polar lipid analysis revealed the presence of phosphatidylglycerol and a glycolipid. The 16S rRNA gene sequence of strain KC1(T) showed low similarity (<96 %) to other validly named species. The phylogenetic trees showed that strain KC1(T) is closely related to Bacillus azotoformans DSM 1046(T) and Bacillus methanolicus DSM 16454(T). Both these type strains showed 95.4 % 16S rRNA gene sequence similarity to strain KC1(T). The DNA G+C content of strain KC1(T) was determined to be 39.0 mol%. On the basis of its phenotypic, chemotaxonomic and genotypic characteristics, strain KC1(T) is considered to represent a novel species of the genus Bacillus, for which the name Bacillus salitolerans sp. nov. is proposed. The type strain is KC1(T) (=JCM 19760(T) = CGMCC 1.12810(T)).

  10. Thermoactinomyces khenchelensis sp. nov., a filamentous bacterium isolated from soil sediment of a terrestrial hot spring.

    PubMed

    Mokrane, Salim; Bouras, Noureddine; Meklat, Atika; Lahoum, Abdelhadi; Zitouni, Abdelghani; Verheecke, Carol; Mathieu, Florence; Schumann, Peter; Spröer, Cathrin; Sabaou, Nasserdine; Klenk, Hans-Peter

    2016-02-01

    A novel thermophilic filamentous bacterium, designated strain T36(T), was isolated from soil sediment sample from a hot spring source collected in Khenchela province, Algeria. Strain T36(T) was identified as a member of the genus Thermoactinomyces by a polyphasic approach. Strain T36(T) was observed to form white aerial mycelium and non-coloured to pale yellow substrate mycelium, both producing endospores, sessile or borne by short sporophores. The optimum growth temperature and pH were found to be 37-55 °C and 7.0-9.0, respectively and the optimum NaCl concentration for growth was found to be 0-7 % (w/v). The diagnostic diamino acid in the cell wall peptidoglycan was identified as meso-diaminopimelic acid. The predominant menaquinone of strain T36(T) was identified as MK-7 (H0). The major fatty acids were found to be iso-C15:0 and iso-C17:0. The phospholipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphoglycolipid. The chemotaxonomic properties of strain T36(T) are consistent with those shared by members of the genus Thermoactinomyces. 16S rRNA gene sequence analysis indicated that the sequence similarities between strain T36(T) and Thermoactinomyces species with validly published names were less than 98 %. Based on the combined genotypic and phenotypic evidence, it is proposed that strain T36(T) should be classified as representative of a novel species, for which the name Thermoactinomyces khenchelensis sp. nov. is proposed. The type strain is T36(T) (=DSM 45951(T) = CECT 8579(T)).

  11. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene

    SciTech Connect

    Maymo-Gatell, X.; Chien, Yueh-tyng; Zinder, S.H.

    1997-06-06

    Tetrachloroethene is a prominent groundwater pollutant that can be reductively dechlorinated by mixed anaerobic microbial populations to the nontoxic product ethene. Strain 195, a coccoid bacterium that dechlorinates tetrachlorethene to ethene, was isolated and characterized. Growth of strain 195 with H{sub 2} and tetrachloroethene as the electron donor and acceptor pair required extracts from mixed microbial cultures. Growth of strain 195 was resistant to ampicillin and vancomycin; its cell wall did not react with a peptidoglycan-specific lectin and its ultrastructure resembled S-layers of Archaea. Analysis of the 16S ribosomal DNA sequence of strain 195 indicated that it is a eubacterium without close affiliation to any known groups. 24 refs., 4 figs., 1 tab.

  12. Genome analysis of the Anerobic Thermohalophilic bacterium Halothermothrix orenii

    SciTech Connect

    Mavromatis, Konstantinos; Ivanova, Natalia; Anderson, Iain; Lykidis, Athanasios; Hooper, Sean D.; Sun, Hui; Kunin, Victor; Lapidus, Alla; Hugenholtz, Philip; Patel, Bharat; Kyrpides, Nikos C.

    2008-11-03

    Halothermothirx orenii is a strictly anaerobic thermohalophilic bacterium isolated from sediment of a Tunisian salt lake. It belongs to the order Halanaerobiales in the phylum Firmicutes. The complete sequence revealed that the genome consists of one circular chromosome of 2578146 bps encoding 2451 predicted genes. This is the first genome sequence of an organism belonging to the Haloanaerobiales. Features of both Gram positive and Gram negative bacteria were identified with the presence of both a sporulating mechanism typical of Firmicutes and a characteristic Gram negative lipopolysaccharide being the most prominent. Protein sequence analyses and metabolic reconstruction reveal a unique combination of strategies for thermophilic and halophilic adaptation. H. orenii can serve as a model organism for the study of the evolution of the Gram negative phenotype as well as the adaptation under thermohalophilic conditions and the development of biotechnological applications under conditions that require high temperatures and high salt concentrations.

  13. Characterization of the quinones in purple sulfur bacterium Thermochromatium tepidum.

    PubMed

    Kimura, Yuuka; Kawakami, Tomoaki; Yu, Long-Jiang; Yoshimura, Miku; Kobayashi, Masayuki; Wang-Otomo, Zheng-Yu

    2015-07-08

    Quinone distributions in the thermophilic purple sulfur bacterium Thermochromatium tepidum have been investigated at different levels of the photosynthetic apparatus. Here we show that, on average, the intracytoplasmic membrane contains 18 ubiquinones (UQ) and 4 menaquinones (MQ) per reaction center (RC). About one-third of the quinones are retained in the light-harvesting-reaction center core complex (LH1-RC) with a similar ratio of UQ to MQ. The numbers of quinones essentially remains unchanged during crystallization of the LH1-RC. There are 1-2 UQ and 1 MQ associated with the RC-only complex in the purified solution sample. Our results suggest that a large proportion of the quinones are confined to the core complex and at least five UQs remain invisible in the current LH1-RC crystal structure.

  14. Real-time RNA profiling within a single bacterium.

    PubMed

    Le, Thuc T; Harlepp, Sébastien; Guet, Calin C; Dittmar, Kimberly; Emonet, Thierry; Pan, Tao; Cluzel, Philippe

    2005-06-28

    Characterizing the dynamics of specific RNA levels requires real-time RNA profiling in a single cell. We show that the combination of a synthetic modular genetic system with fluorescence correlation spectroscopy allows us to directly measure in real time the activity of any specific promoter in prokaryotes. Using a simple inducible gene expression system, we found that induced RNA levels within a single bacterium of Escherichia coli exhibited a pulsating profile in response to a steady input of inducer. The genetic deletion of an efflux pump system, a key determinant of antibiotic resistance, altered the pulsating transcriptional dynamics and caused overexpression of induced RNA. In contrast with population measurements, real-time RNA profiling permits identifying relationships between genotypes and transcriptional dynamics that are accessible only at the level of the single cell.

  15. Endocytosis-like protein uptake in the bacterium Gemmata obscuriglobus

    PubMed Central

    Lonhienne, Thierry G. A.; Sagulenko, Evgeny; Webb, Richard I.; Lee, Kuo-Chang; Franke, Josef; Devos, Damien P.; Nouwens, Amanda; Carroll, Bernard J.; Fuerst, John A.

    2010-01-01

    Endocytosis is a process by which extracellular material such as macromolecules can be incorporated into cells via a membrane-trafficking system. Although universal among eukaryotes, endocytosis has not been identified in Bacteria or Archaea. However, intracellular membranes are known to compartmentalize cells of bacteria in the phylum Planctomycetes, suggesting the potential for endocytosis and membrane trafficking in members of this phylum. Here we show that cells of the planctomycete Gemmata obscuriglobus have the ability to uptake proteins present in the external milieu in an energy-dependent process analogous to eukaryotic endocytosis, and that internalized proteins are associated with vesicle membranes. Occurrence of such ability in a bacterium is consistent with autogenous evolution of endocytosis and the endomembrane system in an ancestral noneukaryote cell. PMID:20566852

  16. Mechanism of anaerobic degradation of triethanolamine by a homoacetogenic bacterium.

    PubMed

    Speranza, Giovanna; Morelli, Carlo F; Cairoli, Paola; Müller, Britta; Schink, Bernhard

    2006-10-20

    Triethanolamine (TEA) is converted into acetate and ammonia by a strictly anaerobic, gram-positive Acetobacterium strain LuTria3. Fermentation experiments with resting cell suspensions and specifically deuterated substrates indicate that in the acetate molecule the carboxylate and the methyl groups correspond to the alcoholic function and to its adjacent methylene group, respectively, of the 2-hydroxyethyl unit of TEA. A 1,2 shift of a hydrogen (deuterium) atom from -CH2-O- to =N-CH2- without exchange with the medium was observed. This fact gives evidence that a radical mechanism occurs involving the enzyme and/or coenzyme molecule as a hydrogen carrier. Such a biodegradation appears analogous to the conversion of 2-phenoxyethanol into acetate mediated by another strain of the anaerobic homoacetogenic bacterium Acetobacterium.

  17. Mechanism of anaerobic degradation of triethanolamine by a homoacetogenic bacterium

    SciTech Connect

    Speranza, Giovanna . E-mail: giovanna.speranza@unimi.it; Morelli, Carlo F.; Cairoli, Paola; Mueller, Britta; Schink, Bernhard

    2006-10-20

    Triethanolamine (TEA) is converted into acetate and ammonia by a strictly anaerobic, gram-positive Acetobacterium strain LuTria3. Fermentation experiments with resting cell suspensions and specifically deuterated substrates indicate that in the acetate molecule the carboxylate and the methyl groups correspond to the alcoholic function and to its adjacent methylene group, respectively, of the 2-hydroxyethyl unit of TEA. A 1,2 shift of a hydrogen (deuterium) atom from -CH{sub 2} -O- to =N-CH{sub 2} - without exchange with the medium was observed. This fact gives evidence that a radical mechanism occurs involving the enzyme and/or coenzyme molecule as a hydrogen carrier. Such a biodegradation appears analogous to the conversion of 2-phenoxyethanol into acetate mediated by another strain of the anaerobic homoacetogenic bacterium Acetobacterium.

  18. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.

    PubMed

    White, O; Eisen, J A; Heidelberg, J F; Hickey, E K; Peterson, J D; Dodson, R J; Haft, D H; Gwinn, M L; Nelson, W C; Richardson, D L; Moffat, K S; Qin, H; Jiang, L; Pamphile, W; Crosby, M; Shen, M; Vamathevan, J J; Lam, P; McDonald, L; Utterback, T; Zalewski, C; Makarova, K S; Aravind, L; Daly, M J; Minton, K W; Fleischmann, R D; Ketchum, K A; Nelson, K E; Salzberg, S; Smith, H O; Venter, J C; Fraser, C M

    1999-11-19

    The complete genome sequence of the radiation-resistant bacterium Deinococcus radiodurans R1 is composed of two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base pairs), and a small plasmid (45,704 base pairs), yielding a total genome of 3,284, 156 base pairs. Multiple components distributed on the chromosomes and megaplasmid that contribute to the ability of D. radiodurans to survive under conditions of starvation, oxidative stress, and high amounts of DNA damage were identified. Deinococcus radiodurans represents an organism in which all systems for DNA repair, DNA damage export, desiccation and starvation recovery, and genetic redundancy are present in one cell.

  19. Characterization of the Genes Encoding d-Amino Acid Transaminase and Glutamate Racemase, Two d-Glutamate Biosynthetic Enzymes of Bacillus sphaericus ATCC 10208

    PubMed Central

    Fotheringham, Ian G.; Bledig, Stefan A.; Taylor, Paul P.

    1998-01-01

    In Bacillus sphaericus and other Bacillus spp., d-amino acid transaminase has been considered solely responsible for biosynthesis of d-glutamate, an essential component of cell wall peptidoglycan, in contrast to the glutamate racemase employed by many other bacteria. We report here the cloning of the dat gene encoding d-amino acid transaminase and the glr gene encoding a glutamate racemase from B. sphaericus ATCC 10208. The glr gene encodes a 28.8-kDa protein with 40 to 50% sequence identity to the glutamate racemases of Lactobacillus, Pediococcus, and Staphylococcus species. The dat gene encodes a 31.4-kDa peptide with 67% primary sequence homology to the d-amino acid transaminase of the thermophilic Bacillus sp. strain YM1. PMID:9696787

  20. Isolation and Characterization of a Purple Non-Sulfur Photosynthetic Bacterium Rhodopseudomonas faecalis Strain A from Swine Sewage Wastewater.

    PubMed

    Wei, Hongyi; Okunishi, Suguru; Yoshikawa, Takeshi; Kamei, Yuto; Maeda, Hiroto

    2016-01-01

    A purple non-sulfur photosynthetic bacterium (PNSB), PSB Strain A was isolated from swine sewage wastewater. Phylogenetic analysis revealed that PSB Strain A was most closely related to Rhodopseudomonas faecalis. Growth of the isolate under anaerobic-light conditions with a variety of carbon sources was investigated. Both PSB Strain A and the standard strain showed good growth with acetic acid, propionic acid, and n-butyric acid at a concentration of 20 mM. At the high concentration of 200 mM, PSB Strain A showed better growth in pyruvate, acetate, propionate, succinate and malate. By applying PSB Strain A to treat swine sewage wastewater, the concentration of VFAs, which were acetic acid and propionic acid, decreased from 158.0 mM to 120.2±2.9 mM, and 14.9 mM to 9.3±0.9 mM, respectively, after 216-h incubation. After 330-h incubation, the concentrations of TOC and ammonia nitrogen dropped from 4508.0 mg/L to 3104.0±451.5 mg/L, and 629.7 mg/L to 424.1±7.4 mg/L, respectively. The isolated PSB Strain A showed almost the same efficiency compared with the standard strain on the removal of VFAs and TOC. The results suggest the possibility of using the isolated strain to treat swine sewage wastewater.

  1. Detection of arc genes related with the ethyl carbamate precursors in wine lactic acid bacteria.

    PubMed

    Araque, Isabel; Gil, Joana; Carreté, Ramon; Bordons, Albert; Reguant, Cristina

    2009-03-11

    Trace amounts of the carcinogen ethyl carbamate can appear in wine by the reaction of ethanol with compounds such as citrulline and carbamyl phosphate, which are produced from arginine degradation by some wine lactic acid bacteria (LAB). In this work, the presence of arc genes for the arginine-deiminase pathway was studied in several strains of different species of LAB. Their ability to degrade arginine was also studied. To detect the presence of arc genes, degenerate primers were designed from the alignment of protein sequences in already sequenced LAB. The usefulness of these degenerate primers has been proven by sequencing some of the amplified PCR fragments and searching for homologies with published sequences of the same species and related ones. Correlation was found between the presence of genes and the ability to degrade arginine. Degrading strains included all heterofermentative lactobacilli, Oenococcus oeni , Pediococcus pentosaceus , and some strains of Leuconostoc mesenteroides and Lactobacillus plantarum .

  2. Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24

    PubMed Central

    Yun, Sung Ho; Choi, Chi-Won; Yi, Yoon-Sun; Kim, Jonghyun; Chung, Young-Ho; Park, Edmond Changkyun; Kim, Seung Il

    2016-01-01

    Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, is a soil bacterium capable of utilizing aniline as its sole carbon and nitrogen source. Genomic sequence analysis revealed that this bacterium possesses putative gene clusters for biodegradation of various monocyclic aromatic hydrocarbons (MAHs), including benzene, toluene, and xylene (BTX), as well as aniline. We verified the proposed MAH biodegradation pathways by dioxygenase activity assays, RT-PCR, and LC/MS-based quantitative proteomic analyses. This proteogenomic approach revealed four independent degradation pathways, all converging into the citric acid cycle. Aniline and p-hydroxybenzoate degradation pathways converged into the β-ketoadipate pathway. Benzoate and toluene were degraded through the benzoyl-CoA degradation pathway. The xylene isomers, i.e., o-, m-, and p-xylene, were degraded via the extradiol cleavage pathways. Salicylate was degraded through the gentisate degradation pathway. Our results show that Burkholderia sp. K24 possesses versatile biodegradation pathways, which may be employed for efficient bioremediation of aniline and BTX. PMID:27124467

  3. Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24.

    PubMed

    Lee, Sang-Yeop; Kim, Gun-Hwa; Yun, Sung Ho; Choi, Chi-Won; Yi, Yoon-Sun; Kim, Jonghyun; Chung, Young-Ho; Park, Edmond Changkyun; Kim, Seung Il

    2016-01-01

    Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, is a soil bacterium capable of utilizing aniline as its sole carbon and nitrogen source. Genomic sequence analysis revealed that this bacterium possesses putative gene clusters for biodegradation of various monocyclic aromatic hydrocarbons (MAHs), including benzene, toluene, and xylene (BTX), as well as aniline. We verified the proposed MAH biodegradation pathways by dioxygenase activity assays, RT-PCR, and LC/MS-based quantitative proteomic analyses. This proteogenomic approach revealed four independent degradation pathways, all converging into the citric acid cycle. Aniline and p-hydroxybenzoate degradation pathways converged into the β-ketoadipate pathway. Benzoate and toluene were degraded through the benzoyl-CoA degradation pathway. The xylene isomers, i.e., o-, m-, and p-xylene, were degraded via the extradiol cleavage pathways. Salicylate was degraded through the gentisate degradation pathway. Our results show that Burkholderia sp. K24 possesses versatile biodegradation pathways, which may be employed for efficient bioremediation of aniline and BTX.

  4. Anaerobranca californiensis sp. nov., an anaerobic, alkalithermophilic, fermentative bacterium isolated from a hot spring on Mono Lake.

    PubMed

    Gorlenko, Vladimir; Tsapin, Alexandre; Namsaraev, Zorigto; Teal, Tracy; Tourova, Tatyana; Engler, Diane; Mielke, Randy; Nealson, Kenneth

    2004-05-01

    A novel, obligately anaerobic, alkalithermophilic, chemo-organotrophic bacterium was isolated from the sediment of an alkaline hot spring located on Paoha Island in Mono Lake, California, USA. This rod-shaped bacterium was motile via peritrichous flagella. Isolated strains grew optimally in 5-25 g NaCl l(-1), at pH 9.0-9.5 and at a temperature of 58 degrees C and were fermentative and mainly proteolytic, utilizing peptone, Casamino acids and yeast extract. Optimal growth was seen in the presence of elemental sulfur, polysulfide or thiosulfate with concomitant reduction to hydrogen sulfide. Sulfite was also formed in an equal ratio to sulfide during reduction of thiosulfate. The novel isolate could also reduce Fe(III) and Se(IV) in the presence of organic matter. On the basis of physiological properties, 16S rRNA gene sequence and DNA-DNA hybridization data, strain PAOHA-1(T) (=DSM 14826(T)=UNIQEM 227(T)) belongs to the genus Anaerobranca and represents a novel species, Anaerobranca californiensis sp. nov.

  5. Clostridium tunisiense sp. nov., a new proteolytic, sulfur-reducing bacterium isolated from an olive mill wastewater contaminated by phosphogypse.

    PubMed

    Thabet, Olfa Ben Dhia; Fardeau, Marie-Laure; Joulian, Catherine; Thomas, Pierre; Hamdi, Moktar; Garcia, Jean-Louis; Ollivier, Bernard

    2004-06-01

    A new sporulated fermentative bacterium designated strain E1(T) (T=type strain), was isolated from an anaerobic mud of an olive mill wastewater basin contaminated by phosphogypse produced by a Tunisian factory. Strain E1(T) was a motile Gram-positive slightly curved rod with spherical terminal spore swelling the cell. It grew between 18 degrees C and 43 degrees C with an optimum at 37 degrees C and pH 7.8 (range 5.5-8.7), without NaCl (range 0-3%). Strain E1(T) was a chemoorganotrophic anaerobic bacterium fermenting only proteins and amino acids. Yeast extract was required for growth. Elemental sulfur was used as terminal electron acceptor. The G+C content of the DNA was 32.6 mol%. The closest phylogenetical relatives of strain E1(T) were Clostridium thiosulfatireducens and C. subterminale (97.3% similarity for partial rRNA gene sequences). DNA-DNA hybridization values between strain E1(T) and both species were 17% and 20.8%, respectively. On the basis of differences in genotypic and phenotypic characteristics, strain E1(T) (DSM 15206(T), CIP 107666(T)) is proposed as the type strain of a new species, C. tunisiense sp. nov. GenBank accession number for the 16S rRNA gene sequence of strain E1(T) is AY187622.

  6. Candidatus Desulfofervidus auxilii, a hydrogenotrophic sulfate-reducing bacterium involved in the thermophilic anaerobic oxidation of methane.

    PubMed

    Krukenberg, Viola; Harding, Katie; Richter, Michael; Glöckner, Frank Oliver; Gruber-Vodicka, Harald R; Adam, Birgit; Berg, Jasmine S; Knittel, Katrin; Tegetmeyer, Halina E; Boetius, Antje; Wegener, Gunter

    2016-09-01

    The anaerobic oxidation of methane (AOM) is mediated by consortia of anaerobic methane-oxidizing archaea (ANME) and their specific partner bacteria. In thermophilic AOM consortia enriched from Guaymas Basin, members of the ANME-1 clade are associated with bacteria of the HotSeep-1 cluster, which likely perform direct electron exchange via nanowires. The partner bacterium was enriched with hydrogen as sole electron donor and sulfate as electron acceptor. Based on phylogenetic, genomic and metabolic characteristics we propose to name this chemolithoautotrophic sulfate reducer Candidatus Desulfofervidus auxilii. Ca. D. auxilii grows on hydrogen at temperatures between 50°C and 70°C with an activity optimum at 60°C and doubling time of 4-6 days. Its genome draft encodes for canonical sulfate reduction, periplasmic and soluble hydrogenases and autotrophic carbon fixation via the reductive tricarboxylic acid cycle. The presence of genes for pili formation and cytochromes, and their similarity to genes of Geobacter spp., indicate a potential for syntrophic growth via direct interspecies electron transfer when the organism grows in consortia with ANME. This first ANME-free enrichment of an AOM partner bacterium and its characterization opens the perspective for a deeper understanding of syntrophy in anaerobic methane oxidation.

  7. Identification of volatile compounds produced by the bacterium Burkholderia tropica that inhibit the growth of fungal pathogens

    PubMed Central

    Tenorio-Salgado, Silvia; Tinoco, Raunel; Vazquez-Duhalt, Rafael; Caballero-Mellado, Jesus; Perez-Rueda, Ernesto

    2013-01-01

    It has been documented that bacteria from the Burkholderia genera produce different kinds of compounds that inhibit plant pathogens, however in Burkholderia tropica, an endophytic diazotrophic and phosphate-solubilizing bacterium isolated from a wide diversity of plants, the capacity to produce antifungal compounds has not been evaluated. In order to expand our knowledge about Burkholderia tropica as a potential biological control agent, we analyzed 15 different strains of this bacterium to evaluate their capacities to inhibit the growth of four phytopathogenic fungi, Colletotrichum gloeosporioides, Fusarium culmorum, Fusarium oxysporum and Sclerotium rolffsi. Diverse analytical techniques, including plant root protection and dish plate growth assays and gas chromatography-mass spectroscopy showed that the fungal growth inhibition was intimately associated with the volatile compounds produced by B. tropica and, in particular, two bacterial strains (MTo293 and TTe203) exhibited the highest radial mycelial growth inhibition. Morphological changes associated with these compounds, such as disruption of fungal hyphae, were identified by using photomicrographic analysis. By using gas chromatography-mass spectroscopy technique, 18 volatile compounds involved in the growth inhibition mechanism were identified, including α-pinene and limonene. In addition, we found a high proportion of bacterial strains that produced siderophores during growth with different carbon sources, such as alanine and glutamic acid; however, their roles in the antagonism mechanism remain unclear. PMID:23680857

  8. Alcaligenes faecalis subsp. phenolicus subsp. nov. a phenol-degrading, denitrifying bacterium isolated from a graywater bioprocessor.

    PubMed

    Rehfuss, Marc; Urban, James

    2005-07-01

    A Gram (-) coccobacillary bacterium, J(T), was isolated from a graywater bioprocessor. 16S rRNA and biochemical analysis has revealed strain J(T) closely resembles Alcaligenes faecalis ATCC 8750T and A. faecalis subsp. parafaecalis DSM 13975T, but is a distinct, previously uncharacterized isolate. Strain J(T), along with the type strain of A. faecalis and its previously described subspecies share the ability to aerobically degrade phenol. The degradation rates of phenol for strain J(T) and reference phenol degrading bacteria were determined by photometrically measuring the change in optical density when grown on 0.1% phenol as the sole carbon source, followed by addition of Gibb's reagent to measure depletion of substrate. The phenol degradation rates of strain J(T) was found to exceed that of the phenol hydroxylase group III bacterium Pseudomonas pseudoalcaligenes, with isolate J(T) exhibiting a doubling time of 4.5 h. The presence of the large subunit of the multicomponent phenol hydroxylase gene in strain J(T) was confirmed by PCR. The presence of the nirK nitrite reductase gene as demonstrated by PCR as well as results obtained from nitrite media indicated denitrification at least to N2O. Based on phenotypic, phylogenetic, fatty acid analysis and results from DNA DNA hybridization, we propose assigning a novel subspecies of Alcaligenes faecalis, to be named Alcaligenes faecalis subsp. phenolicus with the type strain J(T) (= DSM 16503) (= NRRL B-41076).

  9. The effects of Lactobacillus buchneri with or without a homolactic bacterium on the fermentation and aerobic stability of corn silages made at different locations.

    PubMed

    Schmidt, R J; Kung, L

    2010-04-01

    Whole-plant corn (31 to 39% dry matter) from several locations was chopped, treated with nothing (U), Lactobacillus buchneri 40788 (4 x 10(5) cfu/g; LB), or L. buchneri (4 x 10(5) cfu/g) and Pediococcus pentosaceus (1 x 10(5) cfu/g; LBPP), and packed into quadruplicate 20-L silos to determine their effects on silage fermentation and aerobic stability after 120 d of storage. The experiment was a randomized complete block design with main effects of treatment (T), block (location; L), and T x L interaction. Dry matter recovery was different among locations but unaffected by T. The population of lactic acid bacteria was greater in LB and LBPP than in U, and the opposite was true regarding the population of yeasts. Numbers of L. buchneri (colony-forming unit equivalents), determined by a real-time quantitative polymerase chain reaction, were higher in 4 of 5 locations for LB and LBPP compared with U (T x L interaction) with an average 6.70 log cfu/g for LB and LBPP versus 4.87 log cfu/g for U. Silages inoculated with LB and LBPP had higher silage pH and higher concentrations of acetic acid and 1,2 propanediol but lower concentrations of ethanol and water-soluble carbohydrates; there was a T x L interaction for all these variables. Aerobic stability was improved by LB and LBPP (mean of 136 h) compared with U (44 h), but there was an interaction between T x L. In general, locations with the highest population of L. buchneri had the largest increases in acetic acid and, consequently, the greatest improvements in aerobic stability. The addition of L. buchneri 40788 alone or with P. pentosaceus resulted in similar effects on silage fermentation and aerobic stability, but the effects were variable among locations, suggesting that unidentified factors; for example, in the field or on the forage crop, may alter the effectiveness of microbial inoculation.

  10. Aurantibacter crassamenti gen. nov., sp. nov., a bacterium isolated from marine sediment.

    PubMed

    Yoon, Jaewoo; Kasai, Hiroaki

    2017-01-01

    A Gram-stain-negative, strictly aerobic, orange-colored, rod-shaped, chemoheterotrophic bacterium, designated HG732(T), was isolated from marine sediment in Japan. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the novel marine strain was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it shared the highest (94.1 %) sequence similarity with Kriegella aquimaris KMM 3665(T). The strain could be differentiated phenotypically from related members of the family Flavobacteriaceae. Major fatty acids of strain HG732(T) were iso-C15:1 G, iso-C15:0 and iso-C17:0 3-OH. The polar lipid profile consisted of phosphatidylglycerol, three unidentidied aminolipids and two unidentified lipids. The DNA G+C content of the strain was determined to be 35.2 mol%, and the major respiratory quinone was identified as menaquinone 6 (MK-6). From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus in the family Flavobacteriaceae, for which the name Aurantibacter crassamenti gen. nov., sp. nov. is proposed. The type strain of A. crassamenti gen. nov., sp. nov. is HG732(T) (= KCTC 52207(T) = NBRC 112211(T)).

  11. Thorsellia anophelis is the dominant bacterium in a Kenyan population of adult Anopheles gambiae mosquitoes.

    PubMed

    Briones, Aurelio M; Shililu, Josephat; Githure, John; Novak, Robert; Raskin, Lutgarde

    2008-01-01

    Anopheles gambiae mosquitoes are not known to harbor endosymbiotic bacteria. Here we show, using nucleic acid-based methods, that 16S rRNA gene sequences specific to a recently described mosquito midgut bacterium, Thorsellia anophelis, is predominant in the midgut of adult An. gambiae s.l. mosquitoes captured in residences in central Kenya, and also occurs in the aquatic rice paddy environment nearby. PCR consistently detected T. anophelis in the surface microlayer of rice paddies, which is also consistent with the surface-feeding behavior of A. gambiae s.l. larvae. Phylogenetic analysis of cloned environmental 16S rRNA genes identified four major Thorsellia lineages, which are closely affiliated to an insect endosymbiont of the genus Arsenophonus. Physiological characterizations support the hypothesis that T. anophelis is well adapted to the female anopheline midgut by utilizing blood and tolerating the alkaline conditions in this environment. The results suggest that aquatically derived bacteria such as T. anophelis can persist through mosquito metamorphosis and become well-established in the adult mosquito midgut.

  12. Marinomonas arctica sp. nov., a psychrotolerant bacterium isolated from the Arctic.

    PubMed

    Zhang, De-Chao; Li, Hui-Rong; Xin, Yu-Hua; Liu, Hong-Can; Chen, Bo; Chi, Zhen-Ming; Zhou, Pei-Jin; Yu, Yong

    2008-07-01

    A novel psychrotolerant, Gram-negative, motile bacterium, designated strain 328(T), was isolated from sea-ice samples collected off the Canadian Basin of the Arctic Ocean (7 degrees 23' 14'' N 14 degrees 06' 55'' W). Strain 328(T) was able to grow at 0-37 degrees C, with optimum growth at 25-27 degrees C. It possessed phosphatidylethanolamine and phosphatidylglycerol as major phospholipids and C(10 : 0) 3-OH (31.78 %), C(18 : 1)omega7c (27.50 %) and iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c (19.22 %) as predominant cellular fatty acids. The DNA G+C content of strain 328(T) was 45.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 328(T) was a member of the genus Marinomonas (92.7-96.0 % 16S rRNA gene sequence similarity). On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain 328(T) was considered to represent a novel species of the genus Marinomonas. The name Marinomonas arctica sp. nov. is proposed, with strain 328(T) (=CGMCC 1.6498(T)=JCM 14976(T)) as the type strain.

  13. Sporosarcina antarctica sp. nov., a psychrophilic bacterium isolated from the Antarctic.

    PubMed

    Yu, Yong; Xin, Yu-Hua; Liu, Hong-Can; Chen, Bo; Sheng, Jun; Chi, Zhen-Ming; Zhou, Pei-Jin; Zhang, De-Chao

    2008-09-01

    A Gram-positive, psychrophilic, rod-shaped bacterium, designated strain N-05(T), was isolated from soil samples collected off King George Island, west Antarctica (6 degrees 13' 31'' S 5 degrees 57' 08'' W). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain N-05(T) was related to members of the genus Sporosarcina and had highest 16S rRNA gene sequence similarity with the type strain of Sporosarcina macmurdoensis (98.0%). The temperature range for growth of strain N-05(T) was 0-23 degrees C, with optimum growth occurring at 17-18 degrees C and approximately pH 6.0-8.0. Strain N-05(T) had MK-7 as the major menaquinone and anteiso-C(15:0) and C(16:1)omega7c alcohol as major fatty acids. The genomic DNA G+C content was 39.2 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain N-05(T) is considered to represent a novel species of the genus Sporosarcina, for which the name Sporosarcina antarctica is proposed. The type strain is N-05(T) (=CGMCC 1.6503(T)=JCM 14646(T)).

  14. Sphingomonas psychrolutea sp. nov., a psychrotolerant bacterium isolated from glacier ice.

    PubMed

    Liu, Qing; Liu, Hong-Can; Zhang, Jian-Li; Zhou, Yu-Guang; Xin, Yu-Hua

    2015-09-01

    A Gram-stain-negative, rod-shaped, orange bacterium (strain MDB1-A(T)) was isolated from ice samples collected from Midui glacier in Tibet, south-west China. Cells were aerobic and psychrotolerant (growth occurred at 0-25 °C). Phylogenetic analysis based on 16S rRNA gene sequences showed that it was a member of the genus Sphingomonas, with its closest relative being Sphingomonas glacialis C16y(T) (98.9% similarity). Q-10 was the predominant ubiquinone. C17 : 1ω6c and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) were the major cellular fatty acids. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid. The polyamines detected were sym-homospermidine, spermidine and spermine. The G+C content of the genomic DNA was 63.6%. Based on data from this polyphasic analysis, strain MDB1-A(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas psychrolutea sp. nov. is proposed. The type strain is MDB1-A(T) ( = CGMCC 1.10106(T) = NBRC 109639(T)).

  15. A serine hydroxymethyltransferase from marine bacterium Shewanella algae: Isolation, purification, characterization and l-serine production.

    PubMed

    Jiang, Wei; Xia, Bingzhao; Liu, Ziduo

    2013-10-01

    Currently, l-serine is mainly produced by enzymatic conversion, in which serine hydroxymethyltransferase (SHMT) is the key enzyme, suggesting the importance of searching for a SHMT with high activity. Shewanella algae, a methanol-utilizing marine bacterium showing high SHMT activity, was selected based on screening bacterial strains and comparison of the activities of SHMTs. A glyA was isolated from the S. algae through thermal asymmetric interlaced PCR (TAIL-PCR) and it encoded a 417 amino acid polypeptide. The SaSHMT, encoded by the glyA, showed the optimal activity at 50°C and pH 7.0, and retained over 45% of its maximal activity after incubation at 40°C for 3h. The enzyme showed better stability under alkaline environment (pH 6.5-9.0) than Hyphomicrobium methylovorum GM2's SHMT (pH 6.0-7.5). The SaSHMT can produce 77.76mM of l-serine by enzymatic conversion, with the molecular conversion rate in catalyzing glycine to l-serine being 1.41-fold higher than that of Escherichia coli. Therefore, the SaSHMT has the potential for industrial applications due to its tolerance of alkaline environment and a relatively high enzymatic conversion rate.

  16. Bacillus seohaeanensis sp. nov., a halotolerant bacterium that contains L-lysine in its cell wall.

    PubMed

    Lee, Jae-Chan; Lim, Jee-Min; Park, Dong-Jin; Jeon, Che Ok; Li, Wen-Jun; Kim, Chang-Jin

    2006-08-01

    A halotolerant, round-endospore-forming, aerobic, Gram-positive bacterium, designated BH724(T), was isolated from a solar saltern at Taean in Korea. Cells of this strain were rod-shaped and found to be non-motile. Strain BH724(T) grew at salinities of 0-10 % (w/v) NaCl with an optimum of 3 % (w/v) NaCl and at temperatures of 15-50 degrees C with an optimum of 40 degrees C. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BH724(T) belonged to the genus Bacillus and that Bacillus aquimaris TF-12(T), Bacillus marisflavi TF-11(T) and Bacillus vietnamensis JCM 11124(T) were its closest neighbours, sharing 97.3, 97.2 and 97.0 % 16S rRNA gene sequence similarity, respectively. The genomic DNA G+C content was 39 mol% and the predominant menaquinone was MK-7. Its major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0), iso-C(16 : 0) and iso-C(14 : 0). The peptidoglycan type was A1alpha, linked directly through l-lysine. On the basis of morphological, chemotaxonomic, physiological and phylogenetic properties, strain BH724(T) represents a novel species of the genus Bacillus, for which the name Bacillus seohaeanensis sp. nov. is proposed. The type strain is BH724(T) (=KCTC 3913(T)=DSM 16464(T)).

  17. Capture of Arginine at Low Concentrations by a Marine Psychrophilic Bacterium

    PubMed Central

    Geesey, Gill G.; Morita, Richard Y.

    1979-01-01

    The cells of the marine bacterium Ant-300 were found to take up arginine when this substrate was at low concentrations. The cells possessed an uptake system(s) that specifically transported l-arginine. The kinetic parameters for uptake appeared to differ when the cells were exposed to nanomolar and micromolar concentrations of the amino acid. Uptake over this concentration range functioned in the absence of an exogenous energy source, even after the cells had been preincubated in unsupplemented artificial seawater. Respiratory activity appeared to be a more important driving force for arginine uptake than adenosine 5′-triphosphate hydrolysis. The cells also exhibited chemotaxis toward l-arginine. The minimum arginine concentration needed to elicit a chemotactic response was between 10−5 and 10−6 M. It is proposed that the capture of arginine by cells of Ant-300 in nutrient-depleted waters, which are typical of the open ocean, proceeds via high-affinity active transport, whereas in substrate-enriched seawater, capture involves chemotaxis and an active transport mechanism with reduced affinity for the substrate. PMID:16345475

  18. Improved manganese-oxidizing activity of DypB, a peroxidase from a lignolytic bacterium

    PubMed Central

    Singh, Rahul; Grigg, Jason C.; Qin, Wei; Kadla, John F.; Murphy, Michael E.P.; Eltis, Lindsay D.

    2013-01-01

    DypB, a dye-decolorizing peroxidase from the lignolytic soil bacterium Rhodococcus jostii RHA1, catalyzes the peroxide-dependent oxidation of divalent manganese (Mn2+), albeit less efficiently than fungal manganese peroxidases. Substitution of Asn246, a distal heme residue, with alanine, increased the enzyme’s apparent kcat and kcat/Km values for Mn2+ by 80- and 15-fold, respectively. A 2.2 Å resolution X-ray crystal structure of the N246A variant revealed the Mn2+ to be bound within a pocket of acidic residues at the heme edge, reminiscent of the binding site in fungal manganese peroxidase and very different to that of another bacterial Mn2+-oxidizing peroxidase. The first coordination sphere was entirely comprised of solvent, consistent with the variant’s high Km for Mn2+ (17 ± 2 mM). N246A catalyzed the manganese-dependent transformation of hard wood kraft lignin and its solvent-extracted fractions. Two of the major degradation products were identified as 2,6-dimethoxybenzoquinone and 4-hydroxy-3,5-dimethoxybenzaldehyde, respectively. These results highlight the potential of bacterial enzymes as biocatalysts to transform lignin. PMID:23305326

  19. Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal

    NASA Astrophysics Data System (ADS)

    Vreeland, Russell H.; Rosenzweig, William D.; Powers, Dennis W.

    2000-10-01

    Bacteria have been found associated with a variety of ancient samples, however few studies are generally accepted due to questions about sample quality and contamination. When Cano and Borucki isolated a strain of Bacillus sphaericus from an extinct bee trapped in 25-30 million-year-old amber, careful sample selection and stringent sterilization techniques were the keys to acceptance. Here we report the isolation and growth of a previously unrecognized spore-forming bacterium (Bacillus species, designated 2-9-3) from a brine inclusion within a 250million-year-old salt crystal from the Permian Salado Formation. Complete gene sequences of the 16S ribosomal DNA show that the organism is part of the lineage of Bacillus marismortui and Virgibacillus pantothenticus. Delicate crystal structures and sedimentary features indicate the salt has not recrystallized since formation. Samples were rejected if brine inclusions showed physical signs of possible contamination. Surfaces of salt crystal samples were sterilized with strong alkali and acid before extracting brines from inclusions. Sterilization procedures reduce the probability of contamination to less than 1 in 10 9.

  20. Improved manganese-oxidizing activity of DypB, a peroxidase from a lignolytic bacterium.

    PubMed

    Singh, Rahul; Grigg, Jason C; Qin, Wei; Kadla, John F; Murphy, Michael E P; Eltis, Lindsay D

    2013-04-19

    DypB, a dye-decolorizing peroxidase from the lignolytic soil bacterium Rhodococcus jostii RHA1, catalyzes the peroxide-dependent oxidation of divalent manganese (Mn(2+)), albeit less efficiently than fungal manganese peroxidases. Substitution of Asn246, a distal heme residue, with alanine increased the enzyme's apparent k(cat) and k(cat)/K(m) values for Mn(2+) by 80- and 15-fold, respectively. A 2.2 Å resolution X-ray crystal structure of the N246A variant revealed the Mn(2+) to be bound within a pocket of acidic residues at the heme edge, reminiscent of the binding site in fungal manganese peroxidase and very different from that of another bacterial Mn(2+)-oxidizing peroxidase. The first coordination sphere was entirely composed of solvent, consistent with the variant's high K(m) for Mn(2+) (17 ± 2 mM). N246A catalyzed the manganese-dependent transformation of hard wood kraft lignin and its solvent-extracted fractions. Two of the major degradation products were identified as 2,6-dimethoxybenzoquinone and 4-hydroxy-3,5-dimethoxybenzaldehyde, respectively. These results highlight the potential of bacterial enzymes as biocatalysts to transform lignin.

  1. Photobacterium galatheae sp. nov., a bioactive bacterium isolated from a mussel in the Solomon Sea.

    PubMed

    Machado, Henrique; Giubergia, Sonia; Mateiu, Ramona Valentina; Gram, Lone

    2015-12-01

    A novel, Gram-negative marine bacterium, S2753T, was isolated from a mussel of the Solomon Sea, Solomon Islands. Analysis of the 16S rRNA gene sequence and whole genome sequence data placed strain S2753T in the genus Photobacterium with the closest relative being Photobacterium halotolerans DSM 18316T (97.7 % 16S rRNA gene similarity). Strain S2753T was able to grow from 15 to 40 °C and in NaCl concentrations of 0.5 to 9 % (w/v). The predominant fatty acids were 16 : 1ω7c/16 : 1ω6c (27.9 %), 16 : 0 (22.1 %) and 18 : 1ω7c/8 : 1ω6c (21.4 %). The genomic DNA G+C mol content was 49.5 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic differences, strain S2753T is considered to represent a novel species of the genus Photobacterium. Furthermore, whole genome sequence analysis comparing S2753T and type-strains of closely related species of the genus Photobacterium also demonstrated that the strain is genomically distinct enough to be considered a novel species. The name Photobacterium galatheae is proposed and the type-strain is S2753T( = LMG 28894T = DSM 100496T).

  2. Haloanaerobium kushneri sp. nov., an obligately halophilic, anaerobic bacterium from an oil brine

    NASA Technical Reports Server (NTRS)

    Bhupathiraju, V. K.; McInerney, M. J.; Woese, C. R.; Tanner, R. S.

    1999-01-01

    Three strains, designated VS-751T, VS-511 and VS-732, of a strictly anaerobic, moderately halophilic, Gram-negative, rod-shaped bacterium were isolated from a highly saline (15-20%) brine from an oil reservoir in central Oklahoma, USA. The optimal concentration of NaCl for growth of these three strains was 2 M (12%), and the strains also grew in the presence of an additional 1 M MgCl2. The strains were mesophilic and grew at a pH range of 6-8. Carbohydrates used by all three strains included glucose, fructose, arabinose, galactose, maltose, mannose, cellobiose, sucrose and inulin. Glucose fermentation products included ethanol, acetate, H2 and CO2, with formate produced by two of the three strains. Differences were noted among strains in the optimal temperature and pH for growth, the maximum and minimum NaCl concentration that supported growth, substrate utilization and cellular fatty acid composition. Despite the phenotypic differences among the three strains, analysis of the 16S rRNA gene sequences and DNA-DNA hybridizations showed that these three strains were members of the same genospecies which belonged to the genus Haloanaerobium. The phenotypic and genotypic characteristics of strains VS-751T, VS-511 and VS-732 are different from those of previously described species of Haloanaerobium. It is proposed that strain VS-751T (ATCC 700103T) be established as the type strain of a new species, Haloanaerobium kushneri.

  3. Collagenolytic subtilisin-like protease from the deep-sea bacterium Alkalimonas collagenimarina AC40T.

    PubMed

    Kurata, Atsushi; Uchimura, Kohsuke; Kobayashi, Tohru; Horikoshi, Koki

    2010-03-01

    A new alkaline protease (AcpII) was purified from a culture of the deep-sea bacterium Alkalimonas collagenimarina AC40(T). AcpII degraded collagen three times faster than it degraded casein. The optimal pH was 8.5-9, and the optimal temperature was 45 degrees C for the degradation of collagen. AcpII was completely inhibited by phenylmethylsulfonyl fluoride and partially by EDTA. Cloning and sequencing the gene for AcpII revealed a 2,283-bp open reading frame encoding a protein of 760 amino acids. AcpII comprises a prepropeptide, a catalytic domain that includes a protease-associated domain (PA domain), and tandem repeat prepeptidase C-terminal domains. To elucidate the role of the PA domain of AcpII, we constructed genes for two enzyme derivatives that possessed the catalytic domains with or without the PA domain and expressed them in Escherichia coli. The derivative without the PA domain showed increased specific activities toward all proteinaceous substrates tested, including gelatin, casein, and collagen, compared with those of the derivative with the PA domain.

  4. Enterobacter siamensis sp. nov., a transglutaminase-producing bacterium isolated from seafood processing wastewater in Thailand.

    PubMed

    Khunthongpan, Suwannee; Bourneow, Chaiwut; H-Kittikun, Aran; Tanasupawat, Somboon; Benjakul, Soottawat; Sumpavapol, Punnanee

    2013-01-01

    A novel strain of Enterobacter, C2361(T), a Gram-negative, non-spore-forming, rod-shaped and facultative anaerobic bacterium with the capability to produce transglutaminase, was isolated from seafood processing wastewater collected from a treatment pond of a seafood factory in Songkhla Province, Thailand. Phylogenetic analyses and phenotypic characteristics, including chemotaxonomic characteristics, showed that the strain was a member of the genus Enterobacter. The 16S rRNA gene sequence similarities between strain C2361(T) and Enterobacter cloacae subsp. cloacae ATCC 13047(T) and Enterobacter cloacae subsp. dissolvens LMG 2683(T) were 97.5 and 97.5%, respectively. Strain C2361(T) showed a low DNA-DNA relatedness with the above-mentioned species. The major fatty acids were C16:0, C17:0cyclo and C14:0. The DNA G+C content was 53.0 mol%. On the basis of the polyphasic evidence gathered in this study, it should be classified as a novel species of the genus Enterobacter for which the name Enterobacter siamensis sp. nov. is proposed. The type strain is C2361(T) (= KCTC 23282(T) = NBRC 107138(T)).

  5. Isolation and characterization of comprehensive polychlorinated biphenyl degrading bacterium, Enterobacter sp. LY402.

    PubMed

    Jia, Ling-Yun; Zheng, Ai-Ping; Xu, Li; Huang, Xiao-Dong; Zhang, Qing; Yang, Feng-Lin

    2008-05-01

    A Gram-negative bacterium, named LY402, was isolated from contaminated soil. 16S rDNA sequencing and measurement of the physiological and biochemical characteristics identified it as belonging to the genus Enterobacter. Degradation experiments showed that LY402 had the ability to aerobically transform 79 of the 91 major congeners of Aroclor 1242, 1254, and 1260. However, more interestingly, the strain readily degraded certain highly chlorinated and recalcitrant polychlorinated biphenyls (PCBs). Almost all the tri- and tetra-chlorobiphenyls (CBs), except for 3,4,3',4'-CB, were degraded in 3 days, whereas 73% of 3,4,3',4'-, 92% of the penta-, 76% of the hexa-, and 37% of the hepta-CBs were transformed after 6 days. In addition, among 12 octa-CBs, 2,2',3,3',5,5',6,6- CB was obviously degraded, and 2,2',3,3',4,5,6,6'- and 2,2',3,3',4,5,5',6'-CB were slightly transformed. In a metabolite analysis, mono- and di-chlorobenzoic acids (CBAs) were identified, and parts of them were also transformed by strain LY402. Analysis of PCB degradation indicated that strain LY402 could effectively degrade PCB congeners with chlorine substitutions in both ortho- and para-positions. Consequently, this is the first report of an Enterobacteria that can efficiently degrade both low and highly chlorinated PCBs under aerobic conditions.

  6. Hydrogen peroxide-dependent uptake of iodine by marine Flavobacteriaceae bacterium strain C-21.

    PubMed

    Amachi, Seigo; Kimura, Koh; Muramatsu, Yasuyuki; Shinoyama, Hirofumi; Fujii, Takaaki

    2007-12-01

    The cells of the marine bacterium strain C-21, which is phylogenetically closely related to Arenibacter troitsensis, accumulate iodine in the presence of glucose and iodide (I-). In this study, the detailed mechanism of iodine uptake by C-21 was determined using a radioactive iodide tracer, 125I-. In addition to glucose, oxygen and calcium ions were also required for the uptake of iodine. The uptake was not inhibited or was only partially inhibited by various metabolic inhibitors, whereas reducing agents and catalase strongly inhibited the uptake. When exogenous glucose oxidase was added to the cell suspension, enhanced uptake of iodine was observed. The uptake occurred even in the absence of glucose and oxygen if hydrogen peroxide was added to the cell suspension. Significant activity of glucose oxidase was found in the crude extracts of C-21, and it was located mainly in the membrane fraction. These findings indicate that hydrogen peroxide produced by glucose oxidase plays a key role in the uptake of iodine. Furthermore, enzymatic oxidation of iodide strongly stimulated iodine uptake in the absence of glucose. Based on these results, the mechanism was considered to consist of oxidation of iodide to hypoiodous acid by hydrogen peroxide, followed by passive translocation of this uncharged iodine species across the cell membrane. Interestingly, such a mechanism of iodine uptake is similar to that observed in iodine-accumulating marine algae.

  7. Developmentally regulated cleavage of tRNAs in the bacterium Streptomyces coelicolor

    PubMed Central

    Haiser, Henry J.; Karginov, Fedor V.; Hannon, Gregory J.; Elliot, Marie A.

    2008-01-01

    The ability to sense and respond to environmental and physiological signals is critical for the survival of the soil-dwelling Gram-positive bacterium Streptomyces coelicolor. Nutrient deprivation triggers the onset of a complex morphological differentiation process that involves the raising of aerial hyphae and formation of spore chains, and coincides with the production of a diverse array of clinically relevant antibiotics and other secondary metabolites. These processes are tightly regulated; however, the genes and signals involved have not been fully elucidated. Here, we report a novel tRNA cleavage event that follows the same temporal regulation as morphological and physiological differentiation, and is growth medium dependent. All tRNAs appear to be susceptible to cleavage; however, there appears to be a bias towards increased cleavage of those tRNAs that specify highly utilized codons. In contrast to what has been observed in eukaryotes, accumulation of tRNA halves in S. coelicolor is not significantly affected by amino acid starvation, and is also not affected by induction of the stringent response or inhibition of ribosome function. Mutants defective in aerial development and antibiotic production exhibit altered tRNA cleavage profiles relative to wild-type strains. PMID:18084030

  8. Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus Udaeobacter copiosus'.

    PubMed

    Brewer, Tess E; Handley, Kim M; Carini, Paul; Gilbert, Jack A; Fierer, Noah

    2016-10-31

    Although bacteria within the Verrucomicrobia phylum are pervasive in soils around the world, they are under-represented in both isolate collections and genomic databases. Here, we describe a single verrucomicrobial group within the class Spartobacteria that is not closely related to any previously described taxa. We examined more than 1,000 soils and found this spartobacterial phylotype to be ubiquitous and consistently one of the most abundant soil bacterial phylotypes, particularly in grasslands, where it was typically the most abundant. We reconstructed a nearly complete genome of this phylotype from a soil metagenome for which we propose the provisional name 'Candidatus Udaeobacter copiosus'. The Ca. U. copiosus genome is unusually small for a cosmopolitan soil bacterium, estimated by one measure to be only 2.81 Mbp, compared to the predicted effective mean genome size of 4.74 Mbp for soil bacteria. Metabolic reconstruction suggests that Ca. U. copiosus is an aerobic heterotroph with numerous putative amino acid and vitamin auxotrophies. The large population size, relatively small genome and multiple putative auxotrophies characteristic of Ca. U. copiosus suggest that it may be undergoing streamlining selection to minimize cellular architecture, a phenomenon previously thought to be restricted to aquatic bacteria. Although many soil bacteria need relatively large, complex genomes to be successful in soil, Ca. U. copiosus appears to use an alternative strategy, sacrificing metabolic versatility for efficiency to become dominant in the soil environment.

  9. The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. UW4

    PubMed Central

    Duan, Jin; Jiang, Wei; Cheng, Zhenyu; Heikkila, John J.; Glick, Bernard R.

    2013-01-01

    The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated “housekeeping” genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup. PMID:23516524

  10. Isolation and Characterization of Intracellular Protein Inclusions Produced by the Entomopathogenic Bacterium Photorhabdus luminescens

    PubMed Central

    Bowen, David J.; Ensign, Jerald C.

    2001-01-01

    Cells of the entomopathogenic bacterium Photorhabdus luminescens contain two types of morphologically distinct crystalline inclusion proteins. The larger rectangular inclusion (type 1) and a smaller bipyramid-shaped inclusion (type 2) were purified from cell lysates by differential centrifugation and isopycnic density gradient centrifugation. Both structures are composed of protein and are readily soluble at pH 11 and 4 in 1% sodium dodecyl sulfate (SDS) and in 8 M urea. Electrophoretic analysis reveals that each inclusion is composed of a single protein subunit with a molecular mass of 11,000 Da. The proteins differ in amino acid composition, protease digestion pattern, and immunological cross-reactivity. The protein inclusions are first visible in the cells at the time of late exponential growth. Western blot analyses showed that the proteins appeared in cells during mid- to late exponential growth. When at maximum size in stationary-phase cells, the proteins constitute 40% of the total cellular protein. The protein inclusions are not used during long-term starvation of the cells and were not toxic when injected into or fed to Galleria mellonella larvae. PMID:11571191

  11. Streptococcus danieliae sp. nov., a novel bacterium isolated from the caecum of a mouse.

    PubMed

    Clavel, Thomas; Charrier, Cédric; Haller, Dirk

    2013-01-01

    We report the characterization of one novel bacterium, strain ERD01G(T), isolated from the cecum of a TNF(deltaARE) mouse. The strain was found to belong to the genus Streptococcus based on phylogenetic analysis of partial 16S rRNA gene sequences. The bacterial species with standing name in nomenclature that was most closely related to our isolate was Streptococcus alactolyticus (97 %). The two bacteria were characterized by a DNA-DNA hybridization similarity value of 35 %, demonstrating that they belong to different species. The new isolate was negative for acetoin production, esculin hydrolysis, urease, α-galactosidase and β-glucosidase, was able to produce acid from starch and trehalose, grew as beta-hemolytic coccobacilli on blood agar, did not grow at >40 °C, did not survive heat treatment at 60 °C for 20 min and showed negative agglutination in Lancefield tests. On the basis of these characteristics, strain ERD01G(T) differed from the most closely related species S. alactolyticus, Streptococcus gordonii, Streptococcus intermedius and Streptococcus sanguinis. Thus, based on genotypic and phenotypic evidence, we propose that the isolate belongs to a novel bacterial taxon within the genus Streptococcus, for which the name Streptococcus danieliae is proposed. The type strain is ERD01G(T) (= DSM 22233(T) = CCUG 57647(T)).

  12. Pseudomonas glareae sp. nov., a marine sediment-derived bacterium with antagonistic activity.

    PubMed

    Romanenko, Lyudmila A; Tanaka, Naoto; Svetashev, Vassilii I; Mikhailov, Valery V

    2015-06-01

    An aerobic, Gram-negative, motile, rod-shaped bacterium designated KMM 9500(T) was isolated from a sediment sample collected from the Sea of Japan seashore. Comparative 16S rRNA gene sequence analysis affiliated strain KMM 9500(T) to the genus Pseudomonas as a distinct subline clustered with Pseudomonas marincola KMM 3042(T) and Pseudomonas segetis KCTC 12331(T) sharing the highest similarities of 98 and 97.9 %, respectively. Strain KMM 9500(T) was characterized by mainly possessing ubiquinone Q-9, and by the predominance of C18:1 ω7c, C16:1 ω7c, and C16:0 followed by C12:0 in its fatty acid profile. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid, and unknown phospholipids. Strain KMM 9500(T) was found to inhibit growth of Gram-negative and Gram-positive indicatory microorganisms. Based on the phylogenetic analysis and distinctive phenotypic characteristics, strain 9500(T) is concluded to represent a novel species of the genus Pseudomonas, for which the name Pseudomonas glareae sp. nov. is proposed. The type strain of the species is strain KMM 9500(T) (=NRIC 0939(T)).

  13. Roseimarinus sediminis gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from coastal sediment.

    PubMed

    Wu, Wen-Jie; Liu, Qian-Qian; Chen, Guan-Jun; Du, Zong-Jun

    2015-07-01

    A Gram-stain-negative, facultatively anaerobic, non-motile and pink-pigmented bacterium, designated strain HF08(T), was isolated from marine sediment of the coast of Weihai, China. Cells were rod-shaped, and oxidase- and catalase-positive. The isolate grew optimally at 33 °C, at pH 7.5-8.0 and with 2-3% (w/v) NaCl. The dominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C14 : 0. Menaquinone 7 (MK-7) was the major respiratory quinone and the DNA G+C content was 44.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the class Bacteroidia, and shared 88-90% sequence similarity with the closest genera Sunxiuqinia, Prolixibacter, Draconibacterium, Mariniphaga and Meniscus. Based on the phylogenetic and phenotypic evidence presented, a novel species in a new genus of the family Prolixibacteraceae is proposed, with the name Roseimarinus sediminis gen. nov., sp. nov. The type strain of Roseimarinus sediminis is HF08(T) ( = KCTC 42261(T) = CICC 10901(T)).

  14. Brassicibacter thermophilus sp. nov., a thermophilic bacterium isolated from coastal sediment.

    PubMed

    Wang, Bing; Ji, Shi-Qi; Tian, Xin-Xin; Qu, Ling-Yun; Li, Fu-Li

    2015-09-01

    A novel thermophilic, obligately anaerobic bacterium, strain Cel2f(T), was isolated from a cellulolytic community enriched from coastal marine sediment. Cells were Gram-stain-negative, non-motile, non-spore-forming and rod-shaped. Optimal growth temperature and pH of strain Cel2f(T) were 55 °C and pH 7.0, respectively. NaCl was essential for the growth of strain Cel2f(T) and the strain showed enhanced growth in the presence of sea salt; the optimum sea salt concentration for growth was 7% (w/v). Thiosulfate, sulfate and sulfite were potential electron acceptors. The major fatty acids of strain Cel2f(T) were iso-C15 : 0, C16 : 0, and C18 : 0. Polar lipid analysis indicated the presence of phosphatidylethanolamine and phosphatidylglycerol. Strain Cel2f(T) contained menaquinone MK-7 as the isoprenoid quinone, and the DNA G+C content was 31.3 mol%. Phylogenetic analysis revealed that the nearest relative of strain Cel2f(T) was Brassicibacter mesophilus BM(T) with 93.8% 16S rRNA gene sequence similarity. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, strain Cel2f(T) represents a novel species of genus Brassicibacter, for which the name Brassicibacter thermophilus sp. nov. is proposed. The type strain is Cel2f(T) ( = JCM 30480(T) = CGMCC 1.5200(T)).

  15. Melghiribacillus thermohalophilus gen. nov., sp. nov., a novel filamentous, endospore-forming, thermophilic and halophilic bacterium.

    PubMed

    Addou, Nariman Ammara; Schumann, Peter; Spröer, Cathrin; Ben Hania, Wajdi; Hacene, Hocine; Fauque, Guy; Cayol, Jean-Luc; Fardeau, Marie-Laure

    2015-04-01

    A novel filamentous, endospore-forming, thermophilic and moderately halophilic bacterium designated strain Nari2A(T) was isolated from soil collected from an Algerian salt lake, Chott Melghir. The novel isolate was Gram-staining-positive, aerobic, catalase-negative and oxidase-positive. Optimum growth occurred at 50-55 °C, 7-10% (w/v) NaCl and pH 7-8. The strain exhibited 95.4, 95.4 and 95.2% 16S rRNA gene sequence similarity to Thalassobacillus devorans G19.1(T), Sediminibacillus halophilus EN8d(T) and Virgibacillus kekensis YIM-kkny16(T), respectively. The major menaquinone was MK-7. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, three unknown phosphoglycolipids and two unknown phospholipids. The predominant cellular fatty acids were iso-C(15 : 0) and iso-C(17 : 0). The DNA G+C content was 41.9 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain Nari2A(T) is considered to represent a novel species of a new genus in the family Bacillaceae , order Bacillales , for which the name Melghiribacillus thermohalophilus gen. nov., sp. nov. is proposed. The type strain of Melghiribacillus thermohalophilus is Nari2A(T) ( = DSM 25894(T) = CCUG 62543(T)).

  16. Arthrobacter nitrophenolicus sp. nov. a new 2-chloro-4-nitrophenol degrading bacterium isolated from contaminated soil.

    PubMed

    Arora, Pankaj Kumar; Jain, Rakesh Kumar

    2013-02-01

    Strain SJCon(T), a 2-chloro-4-nitrophenol (2C4NP) degrading bacterium, was isolated from soil collected from a pesticide-contaminated site in Punjab, India. The strain, which stained Gram positive, displayed a rod-coccus life cycle, and possessed a type A3α peptidoglycan (L-Lys-L-Ala3), MK-9(H2) as the major menaquinone, anteiso-C15 and iso-C15:0 as the major cellular fatty acids, and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and a glycolipid as the major polar lipids, showed morphological and chemotaxonomic properties consistent with those reported for members of the genus Arthrobacter. Phylogenetic analysis of the 16S rRNA gene sequence of strain SJCon(T) confirmed that it was a member of this genus with Arthrobacter globiformis DSM 20124(T) being the closest relative (sequence similarity of 97 %). The DNA G + C content of strain SJCon(T) was 69 ± 1 mol% and DNA homology with A. globiformis DSM 20124(T) was 45 %, suggesting that strain SJCon(T) represented a novel species of the genus Arthrobacter, which we have named Arthrobacter nitrophenolicus sp. nov The type strain is SJCon(T) (=MTCC 10104(T) =DSM 23165(T)).

  17. Iron and carbon metabolism by a mineral-oxidizing Alicyclobacillus-like bacterium.

    PubMed

    Yahya, Adibah; Hallberg, Kevin B; Johnson, D Barrie

    2008-04-01

    A novel iron-oxidizing, moderately thermophilic, acidophilic bacterium (strain "GSM") was isolated from mineral spoil taken from a gold mine in Montana. Biomolecular analysis showed that it was most closely related to Alicyclobacillus tolerans, although the two bacteria differed in some key respects, including the absence (in strain GSM) of varpi-alicyclic fatty acids and in their chromosomal base compositions. Isolate GSM was able to grow in oxygen-free media using ferric iron as terminal electron acceptor confirming that it was a facultative anaerobe, a trait not previously described in Alicyclobacillus spp.. The acidophile used both organic and inorganic sources of energy and carbon, although growth and iron oxidation by isolate GSM was uncoupled in media that contained both fructose and ferrous iron. Fructose utilization suppressed iron oxidation, and oxidation of ferrous iron occurred only when fructose was depleted. In contrast, fructose catabolism was suppressed when bacteria were harvested while actively oxidizing iron, suggesting that both ferrous iron- and fructose-oxidation are inducible in this acidophile. Isolate GSM accelerated the oxidative dissolution of pyrite in liquid media either free of, or amended with, organic carbon, although redox potentials were significantly different in these media. The potential of this isolate for commercial mineral processing is discussed.

  18. Desulfuromonas thiophila sp. nov., a new obligately sulfur-reducing bacterium from anoxic freshwater sediment

    USGS Publications Warehouse

    Finster, K.; Coates, J.D.; Liesack, W.; Pfennig, N.

    1997-01-01

    A mesophilic, acetate-oxidizing, sulfur-reducing bacterium, strain NZ27(T), was isolated from anoxic mud from a freshwater sulfur spring. The cells were ovoid, motile, and gram negative. In addition to acetate, the strain oxidized pyruvate, succinate, and fumarate. Sulfur flower could be replaced by polysulfide as an electron acceptor. Ferric nitrilotriacetic acid was reduced in the presence of pyruvate; however, this reduction did not sustain growth. These phenotypic characteristics suggested that strain NZ27(T) is affiliated with the genus Desulfuromonas. A phylogenetic analysis based on the results of comparative 16S ribosomal DNA sequencing confirmed that strain NZ27(T) belongs to the Desulfuromonas cluster in the recently proposed family 'Geobacteraceae' in the delta subgroup of the Proteobacteria. In addition, the results of DNA-DNA hybridization studies confirmed that strain NZ27(T) represents a novel species. Desulfuromonas thiophila, a name tentatively used in previous publications, is the name proposed for strain NZ27(T) in this paper.

  19. Relationship between ion requirements for respiration and membrane transport in a marine bacterium.

    PubMed

    Khanna, G; DeVoe, L; Brown, L; Niven, D F; MacLeod, R A

    1984-01-01

    Intact cells of the marine bacterium Alteromonas haloplanktis 214 oxidized NADH, added to the suspending medium, by a process which was stimulated by Na+ or Li+ but not K+. Toluene-treated cells oxidized NADH at three times the rate of untreated cells by a mechanism activated by Na+ but not by Li+ or K+. In the latter reaction, K+ spared the requirement for Na+. Intact cells of A. haloplanktis oxidized ethanol by a mechanism stimulated by either Na+ or Li+. The uptake of alpha-aminoisobutyric acid by intact cells of A. haloplanktis in the presence of either NADH or ethanol as an oxidizable substrate required Na+, and neither Li+ nor K+ could replace it. The results indicate that exogenous and endogenous NADH and ethanol are oxidized by A. haloplanktis by processes distinguishable from one another by their requirements for alkali metal ions and from the ion requirements for membrane transport. Intact cells of Vibrio natriegens and Photobacterium phosphoreum oxidized NADH, added externally, by an Na+-activated process, and intact cells of Vibrio fischeri oxidized NADH, added externally, by a K+-activated process. Toluene treatment caused the cells of all three organisms to oxidize NADH at much faster rates than untreated cells by mechanisms which were activated by Na+ and spared by K+.

  20. Brevibacillus ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field.

    PubMed

    Baek, Sang-Hoon; Im, Wan-Taek; Oh, Hyun Woo; Lee, Jung-Sook; Oh, Hee-Mock; Lee, Sung-Taik

    2006-11-01

    A Gram-positive, rod-shaped, spore-forming bacterium, Gsoil 3088T, was isolated from soil from a ginseng field in Pocheon Province in South Korea and characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 3088T was shown to belong to the family Paenibacillaceae, being related to Brevibacillus centrosporus (96.6%), Brevibacillus borstelensis (96.3%), Brevibacillus parabrevis (96.1%), Brevibacillus formosus (96.1%), Brevibacillus brevis (96.1%) and Brevibacillus laterosporus (96.0%). The phylogenetic distances from other validly described species within the genus Brevibacillus were greater than 4.0% (i.e. there was less than 96.0% similarity). The G+C content of the genomic DNA was 52.1 mol%. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; fatty acid profile, iso-C15:0, iso-C14:0 and anteiso-C15:0) supported the affiliation of strain Gsoil 3088T to the genus Brevibacillus. The results of physiological and biochemical tests allowed strain Gsoil 3088T to be distinguished genotypically and phenotypically from Brevibacillus species with validly published names. Strain Gsoil 3088T, therefore, represents a novel species of the genus Brevibacillus, for which the name Brevibacillus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3088T (=KCTC 13938T=LMG 23403T).

  1. Evidence for quorum sensing and differential metabolite production by a marine bacterium in response to DMSP

    PubMed Central

    Johnson, Winifred M; Kido Soule, Melissa C; Kujawinski, Elizabeth B

    2016-01-01

    Microbes, the foundation of the marine foodweb, do not function in isolation, but rather rely on molecular level interactions among species to thrive. Although certain types of interactions between autotrophic and heterotrophic microorganisms have been well documented, the role of specific organic molecules in regulating inter-species relationships and supporting growth are only beginning to be understood. Here, we examine one such interaction by characterizing the metabolic response of a heterotrophic marine bacterium, Ruegeria pomeroyi DSS-3, to growth on dimethylsulfoniopropionate (DMSP), an abundant organosulfur metabolite produced by phytoplankton. When cultivated on DMSP, R. pomeroyi synthesized a quorum-sensing molecule, N-(3-oxotetradecanoyl)-l-homoserine lactone, at significantly higher levels than during growth on propionate. Concomitant with the production of a quorum-sensing molecule, we observed differential production of intra- and extracellular metabolites including glutamine, vitamin B2 and biosynthetic intermediates of cyclic amino acids. Our metabolomics data indicate that R. pomeroyi changes regulation of its biochemical pathways in a manner that is adaptive for a cooperative lifestyle in the presence of DMSP, in anticipation of phytoplankton-derived nutrients and higher microbial density. This behavior is likely to occur on sinking marine particles, indicating that this response may impact the fate of organic matter. PMID:26882264

  2. Flavobacterium arsenatis sp. nov., a novel arsenic-resistant bacterium from high-arsenic sediment.

    PubMed

    Ao, Lian; Zeng, Xian-Chun; Nie, Yao; Mu, Yao; Zhou, Lingli; Luo, Xuesong

    2014-10-01

    A novel bacterial strain Z(T) was isolated from the high-arsenic sediment in Jianghan Plain, China. The strain was Gram-staining-negative, rod-shaped and formed yellow colonies. This bacterium is capable of tolerating arsenate and arsenite, with MICs of 40 mM and 20 mM, respectively. The strain also possesses catalase and does not produce oxidase. The nucleotide sequence of the 16S rRNA gene of the isolate showed the highest similarity (96.9%) to that of the type strain of Flavobacterium soli. On the basis of the 16S rRNA gene sequence analysis and the phenotypic properties of strain Z(T), it was assigned to the genus Flavobacterium. The major respiratory menaquinone was MK-6 and the predominant fatty acids were iso-C15:0, summed feature 3 (containing C16:1ω6c and/or C16:1ω7c) and iso-C15:1G. The major polar lipids were phosphatidylethanolamine, three uncharacterized aminophospholipids and four unidentified phospholipids. The DNA G+C content was 32.1 mol%. Based on the phenotypic and genotypic data presented in this article, it can be concluded that this isolate represents a novel species of the genus Flavobacterium, for which the name Flavobacterium arsenatis sp. nov. is proposed. The type strain is Z(T) ( = CCTCC AB 2013048(T) = KCTC 32397(T)).

  3. Flavobacterium noncentrifugens sp. nov., a psychrotolerant bacterium isolated from glacier meltwater.

    PubMed

    Zhu, Lang; Liu, Qing; Liu, Hongcan; Zhang, Jianli; Dong, Xiuzhu; Zhou, Yuguang; Xin, Yuhua

    2013-06-01

    A non-motile, Gram-stain-negative bacterium, designated R-HLS-17(T), was isolated from the meltwater of Hailuogou Glacier located in Sichuan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Flavobacterium, with the closest relatives being Flavobacterium antarcticum JCM 12383(T) (95.5% 16S rRNA gene sequence similarity), F. omnivorum JCM 11313(T) (95.0%) and F. fryxellicola LMG 22022(T) (95.2%). Growth occurred at 0-29 °C (optimum, 10-20 °C) and pH 6.0-8.5 (optimum, 7.0-8.0). The DNA G+C content was 46.5 mol%. The major cellular fatty acids were iso-C15:0, iso-C15:1 G, summed feature 9 (comprising iso-C17:1ω9c and/or 10-methyl C16:0), iso-C17:0 3-OH and iso-C15:0 3-OH. The predominant menaquinone was MK-6. Based on the genotypic and phenotypic characteristics, we propose that strain R-HLS-17(T) represents a novel species of the genus Flavobacterium, Flavobacterium noncentrifugens sp. nov. The type strain is R-HLS-17(T) (=CGMCC 1.10076(T)=NBRC 108844(T)).

  4. A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus

    PubMed Central

    Wielgoss, Sébastien; Didelot, Xavier; Chaudhuri, Roy R; Liu, Xuan; Weedall, Gareth D; Velicer, Gregory J; Vos, Michiel

    2016-01-01

    The bacterium Myxococcus xanthus glides through soil in search of prey microbes, but when food sources run out, cells cooperatively construct and sporulate within multicellular fruiting bodies. M. xanthus strains isolated from a 16 × 16-cm-scale patch of soil were previously shown to have diversified into many distinct compatibility types that are distinguished by the failure of swarming colonies to merge upon encounter. We sequenced the genomes of 22 isolates from this population belonging to the two most frequently occurring multilocus sequence type (MLST) clades to trace patterns of incipient genomic divergence, specifically related to social divergence. Although homologous recombination occurs frequently within the two MLST clades, we find an almost complete absence of recombination events between them. As the two clades are very closely related and live in sympatry, either ecological or genetic barriers must reduce genetic exchange between them. We find that the rate of change in the accessory genome is greater than the rate of amino-acid substitution in the core genome. We identify a large genomic tract that consistently differs between isolates that do not freely merge and therefore is a candidate region for harbouring gene(s) responsible for self/non-self discrimination. PMID:27046334

  5. Variovorax ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field.

    PubMed

    Im, Wan-Taek; Liu, Qing-Mei; Lee, Kang-Jin; Kim, Se-Young; Lee, Sung-Taik; Yi, Tae-Hoo

    2010-07-01

    A Gram-negative, aerobic or facultatively anaerobic, non-spore-forming, motile, rod-shaped bacterium (strain Gsoil 3165(T)) was isolated from soil of a ginseng field in Pocheon, South Korea. Its taxonomic position was determined by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain Gsoil 3165(T) was shown to belong to the family Comamonadaceae, class Betaproteobacteria, and was related most closely to the type strains of Variovorax boronicumulans (98.9 % similarity), Variovorax paradoxus (98.3 %), Variovorax soli (98.2 %) and Variovorax dokdonensis (96.6 %). Levels of 16S rRNA gene sequence similarity between strain Gsoil 3165(T) and the type strains of other species in the family Comamonadaceae were less than 97.0 %. The G+C content of the genomic DNA of strain Gsoil 3165(T) was 66 mol%. Phenotypic and chemotaxonomic data (Q-8 as the major ubiquinone; C(16 : 0) and C(17 : 0) cyclo as major fatty acids) supported the affiliation of strain Gsoil 3165(T) to the genus Variovorax. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain Gsoil 3165(T) from recognized Variovorax species. Gsoil 3165(T) is therefore considered to represent a novel species of the genus Variovorax, for which the name Variovorax ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3165(T) (=KCTC 12583(T) =LMG 23392(T)).

  6. Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soil.

    PubMed

    Miwa, Hiroki; Ahmed, Iftikhar; Yoon, Jaewoo; Yokota, Akira; Fujiwara, Toru

    2008-01-01

    A non-spore-forming, Gram-negative, motile, rod-shaped, boron-accumulating bacterium isolated from soil was characterized by polyphasic taxonomy. The strain, designated BAM-48(T), was positive for catalase and oxidase activities and grew at 4-37 degrees C, 0-1% NaCl and pH 5-9. Comparative analysis of the 16S rRNA gene sequence demonstrated that the novel isolate BAM-48(T) was closely related to Variovorax paradoxus IAM 12373(T) (99.3% sequence similarity), Variovorax soli GH9-3(T) (98.3%) and Variovorax dokdonensis DS-43(T) (97.0%). DNA-DNA hybridization values between strain BAM-48(T) and V. paradoxus NBRC 15149(T), V. soli KACC 11579(T) and V. dokdonensis KCTC 12544(T) were only 49.1, 25.4 and 24.6%, respectively. The major respiratory quinone was ubiquinone 8 (Q-8). The DNA G+C content was 71.2 mol%. Strain BAM-48(T) contained C(16:0) (36.1%), C(16:1)omega7c (21.4%) and C(17:0) cyclo (19.0%) as the major fatty acids. Based on phenotypic, chemotaxonomic and phylogenetic data, strain BAM-48(T) should be classified as a member of a novel species in the genus Variovorax, for which the name Variovorax boronicumulans sp. nov. is proposed. The type strain is BAM-48(T) (=NBRC 103145(T) =KCTC 22010(T)).

  7. Microbial desulfonation of substituted naphthalenesulfonic acids and benzenesulfonic acids.

    PubMed Central

    Zürrer, D; Cook, A M; Leisinger, T

    1987-01-01

    Sulfur-limited batch enrichment cultures containing one of nine multisubstituted naphthalenesulfonates and an inoculum from sewage yielded several taxa of bacteria which could quantitatively utilize 19 sulfonated aromatic compounds as the sole sulfur source for growth. Growth yields were about 4 kg of protein per mol of sulfur. Specific degradation rates were about 4 to 14 mu kat/kg of protein. A Pseudomonas sp., an Arthrobacter sp., and an unidentified bacterium were examined. Each desulfonated at least 16 aromatic compounds, none of which served as a carbon source. Pseudomonas sp. strain S-313 converted 1-naphthalenesulfonic acid, 2-naphthalenesulfonic acid, 5-amino-1-naphthalenesulfonic acid, benzenesulfonic acid, and 3-aminobenzenesulfonic acid to 1-naphthol, 2-naphthol, 5-amino-1-naphthol, phenol, and 3-aminophenol, respectively. Experiments with 18O2 showed that the hydroxyl group was derived from molecular oxygen. PMID:3662502

  8. A Novel Treatment Protects Chlorella at Commercial Scale from the Predatory Bacterium Vampirovibrio chlorellavorus

    PubMed Central

    Ganuza, Eneko; Sellers, Charles E.; Bennett, Braden W.; Lyons, Eric M.; Carney, Laura T.

    2016-01-01

    The predatory bacterium, Vampirovibrio chlorellavorus, can destroy a Chlorella culture in just a few days, rendering an otherwise robust algal crop into a discolored suspension of empty cell walls. Chlorella is used as a benchmark for open pond cultivation due to its fast growth. In nature, V. chlorellavorus plays an ecological role by controlling this widespread terrestrial and freshwater microalga, but it can have a devastating effect when it attacks large commercial ponds. We discovered that V. chlorellavorus was associated with the collapse of four pilot commercial-scale (130,000 L volume) open-pond reactors. Routine microscopy revealed the distinctive pattern of V. chlorellavorus attachment to the algal cells, followed by algal cell clumping, culture discoloration and ultimately, growth decline. The “crash” of the algal culture coincided with increasing proportions of 16s rRNA sequencing reads assigned to V. chlorellavorus. We designed a qPCR assay to predict an impending culture crash and developed a novel treatment to control the bacterium. We found that (1) Chlorella growth was not affected by a 15 min exposure to pH 3.5 in the presence of 0.5 g/L acetate, when titrated with hydrochloric acid and (2) this treatment had a bactericidal effect on the culture (2-log decrease in aerobic counts). Therefore, when qPCR results indicated a rise in V. chlorellavorus amplicons, we found that the pH-shock treatment prevented the culture crash and doubled the productive longevity of the culture. Furthermore, the treatment could be repeatedly applied to the same culture, at the beginning of at least two sequential batch cycles. In this case, the treatment was applied preventively, further increasing the longevity of the open pond culture. In summary, the treatment reversed the infection of V. chlorellavorus as confirmed by observations of bacterial attachment to Chlorella cells and by detection of V. chlorellavorus by 16s rRNA sequencing and qPCR assay. The p

  9. Genotypic characterization and safety assessment of lactic acid bacteria from indigenous African fermented food products

    PubMed Central

    2012-01-01

    Background Indigenous fermented food products play an essential role in the diet of millions of Africans. Lactic acid bacteria (LAB) are among the predominant microbial species in African indigenous fermented food products and are used for different applications in the food and biotechnology industries. Numerous studies have described antimicrobial susceptibility profiles of LAB from different parts of the world. However, there is limited information on antimicrobial resistance profiles of LAB from Africa. The aim of this study was to characterize 33 LAB previously isolated from three different African indigenous fermented food products using (GTG)5-based rep-PCR, sequencing of the 16S rRNA gene and species-specific PCR techniques for differentiation of closely related species and further evaluate their antibiotic resistance profiles by the broth microdilution method and their haemolytic activity on sheep blood agar plates as indicators of safety traits among these bacteria. Results Using molecular biology based methods and selected phenotypic tests such as catalase reaction, CO2 production from glucose, colonies and cells morphology, the isolates were identified as Lactobacillus delbrueckii, Lactobacillus fermentum, Lactobacillus ghanensis, Lactobacillus plantarum, Lactobacillus salivarius, Leuconostoc pseudomesenteroides, Pediococcus acidilactici, Pediococcus pentosaceus and Weissella confusa. The bacteria were susceptible to ampicillin, chloramphenicol, clindamycin and erythromycin but resistant to vancomycin, kanamycin and streptomycin. Variable sensitivity profiles to tetracycline and gentamicin was observed among the isolates with Lb. plantarum, Lb. salivarius, W. confusa (except strain SK9-5) and Lb. fermentum strains being susceptible to tetracycline whereas Pediococcus strains and Lb. ghanensis strains were resistant. For gentamicin, Leuc. pseudomesenteroides, Lb. ghanensis and Ped. acidilactici strains were resistant to 64 mg/L whereas some W. confusa

  10. Caenibacillus caldisaponilyticus gen. nov., sp. nov., a thermophilic, spore-forming and phospholipid-degrading bacterium isolated from acidulocompost.

    PubMed

    Tsujimoto, Yoshiyuki; Saito, Ryo; Furuya, Hiroto; Ishihara, Daisuke; Sahara, Takehiko; Kimura, Nobutada; Nishino, Tokuzo; Tsuruoka, Naoki; Shigeri, Yasushi; Watanabe, Kunihiko

    2016-07-01

    A thermophilic and phospholipid-degrading bacterium, designated strain B157T, was isolated from acidulocompost, a garbage compost processed under acidic conditions at moderately high temperature. The organism was Gram-stain-positive, aerobic, spore-forming and rod-shaped. Growth was observed to occur at 40-65 °C and pH 4.8-8.1 (optimum growth: 50-60 °C, pH 6.2). The strain was catalase- and oxidase-positive. The cell wall contained meso-diaminopimelic acid, alanine, glutamic acid and galactose. The predominant respiratory quinone was menaquinone-7 (MK-7) and the major fatty acids were anteiso-C17 : 0 and iso-C17 : 0. Comparative 16S rRNA gene sequence analysis showed that strain B157T was related most closely to Tuberibacillus calidus 607T (94.8 % identity), and the phylogenetic analysis revealed that it belonged to the family Sporolactobacillaceae. The DNA G+C content was determined as 51.8 mol%. In spite of many similarities with the type strains of members of the family Sporolactobacillaceae, genotypic analyses suggest that strain B157T represents a novel species of a new genus, Caenibacilluscaldisaponilyticus gen. nov., sp. nov. The type strain of Caenibacilluscaldisaponilyticus is B157T (=NBRC 111400T=DSM 101100T).

  11. ppc, the gene for phosphoenolpyruvate carboxylase from an extremely thermophilic bacterium, Rhodothermus obamensis: cloning, sequencing and overexpression in Escherichia coli.

    PubMed

    Takai, K; Sako, Y; Uchida, A

    1998-05-01

    The ppc gene, which encodes phosphoenolpyruvate carboxylase (PEPC) of an extremely thermophilic bacterium, Rhodothermus obamensis, was directly sequenced by the thermal asymmetric interlaced (TAIL) PCR method. An ORF for a 937 amino acid polypeptide was found in the gene. The ppc gene had a high G+C content (66.2 mol%) and the third position of the codon exhibited strong preference for G or C usage (85.0 mol%). The calculated molecular mass was 107,848 Da, which was consistent with the molecular mass of the enzyme as determined by SDS-PAGE (100 kDa). The amino acid sequence of R. obamensis PEPC was closely related to that of PEPC from another thermophile, a Thermus sp., and from a mesophile, Corynebacterium glutamicum, exhibiting 45.3% or 37.7% identity and 61.5% or 56.5% similarity, respectively. By Southern analysis, the ppc gene was found to be present in a single copy in the genomic DNA of this organism. The cloned gene was expressed in Escherichia coli using a pET expression vector system and a thermostable recombinant PEPC was obtained. Comparison of the deduced amino acid sequences of the thermophilic and mesophilic PEPCs revealed distinct or common preferences for specific amino acid composition and substitutions in the two thermophilic enzymes.

  12. A Novel Eliminase from a Marine Bacterium That Degrades Hyaluronan and Chondroitin Sulfate*

    PubMed Central

    Han, Wenjun; Wang, Wenshuang; Zhao, Mei; Sugahara, Kazuyuki; Li, Fuchuan

    2014-01-01

    Lyases cleave glycosaminoglycans (GAGs) in an eliminative mechanism and are important tools for the structural analysis and oligosaccharide preparation of GAGs. Various GAG lyases have been identified from terrestrial but not marine organisms even though marine animals are rich in GAGs with unique structures and functions. Herein we isolated a novel GAG lyase for the first time from the marine bacterium Vibrio sp. FC509 and then recombinantly expressed and characterized it. It showed strong lyase activity toward hyaluronan (HA) and chondroitin sulfate (CS) and was designated as HA and CS lyase (HCLase). It exhibited the highest activities to both substrates at pH 8.0 and 0.5 m NaCl at 30 °C. Its activity toward HA was less sensitive to pH than its CS lyase activity. As with most other marine enzymes, HCLase is a halophilic enzyme and very stable at temperatures from 0 to 40 °C for up to 24 h, but its activity is independent of divalent metal ions. The specific activity of HCLase against HA and CS reached a markedly high level of hundreds of thousands units/mg of protein under optimum conditions. The HCLase-resistant tetrasaccharide Δ4,5HexUAα1-3GalNAc(6-O-sulfate)β1-4GlcUA(2-O-sulfate)β1-3GalNAc(6-O-sulfate) was isolated from CS-D, the structure of which indicated that HCLase could not cleave the galactosaminidic linkage bound to 2-O-sulfated d-glucuronic acid (GlcUA) in CS chains. Site-directed mutagenesis indicated that HCLase may work via a catalytic mechanism in which Tyr-His acts as the Brønsted base and acid. Thus, the identification of HCLase provides a useful tool for HA- and CS-related research and applications. PMID:25122756

  13. Transverse and lateral distribution of phospholipids and glycolipids in the membrane of the bacterium Micrococcus luteus

    SciTech Connect

    de Bony, J.; Lopez, A.; Gilleron, M.; Welby, M.; Laneelle, G.; Rousseau, B.; Beaucourt, J.P.; Tocanne, J.F. )

    1989-05-02

    The photodimerization of anthracene was used to investigate the transverse and lateral distribution of lipids in the membrane of the Gram-positive bacterium Micrococcus luteus. 9-(2-Anthryl)nonanoic acid (9-AN) is incorporated at a high rate into various membrane lipids of M. luteus. On irradiation of intact bacteria at 360 nm, anthracene-labeled lipids form stable photodimers which can be extracted and separated by thin-layer chromatography. We present here the results of a study on the distribution of two major lipids, phosphatidylglycerol (PG) and dimannosyldiacylglycerol (DMDG), within each leaflet of the membrane lipid bilayer. After metabolic incorporation of a tritiated derivative of 9-AN in M. luteus, the radioactivity associated with the photodimers issued from PG and DMDG was counted. In the bacterial membrane, the ratio of PG-DMDG heterodimer with respect to PG-PG and DMDG-DMDG homodimers is around half of what should be obtained for a homogeneous mixture of the two lipids. In order to find out whether this was due to an asymmetric distribution of the two lipids between the two membrane leaflets or a heterogeneous distribution of the two lipids within the same membrane leaflet, the transverse distribution of PG and DMDG was also investigated. This was carried out by following the kinetics of oxidation of the two lipids by periodic acid in the membrane of M. luteus protoplasts. PG predominated slightly in the outer layer (60%), while DMDG was found to be symmetrically distributed between the two leaflets. By itself, this lipid asymmetry cannot account for the lipid distribution determined from the photodimerization experiments. This indicates that PG and DMDG are not homogeneously distributed in the plane of the bacterial membrane.

  14. Nocardioides caricicola sp. nov., an endophytic bacterium isolated from a halophyte, Carex scabrifolia Steud.

    PubMed

    Song, Geun Cheol; Yasir, Muhammad; Bibi, Fehmida; Chung, Eu Jin; Jeon, Che Ok; Chung, Young Ryun

    2011-01-01

    A Gram-staining-positive, coccoid to rod-shaped bacterium, designated strain YC6903(T), was isolated from a halophytic plant (Carex scabrifolia Steud.) collected from sand dunes at Namhae Island, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain YC6903(T) grew optimally at 30 °C and at pH 8.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YC6903(T) belongs to the genus Nocardioides in the family Nocardioidaceae. Strain YC6903(T) was related most closely to Nocardioides pyridinolyticus OS4(T) (97.0 % 16S rRNA gene sequence similarity), Nocardioides dokdonensis FR1436(T) (96.6 %), Nocardioides aquiterrae GW-9(T) (96.6 %) and Nocardioides hankookensis DS-30(T) (96.6 %). The cell-wall peptidoglycan contained LL-diaminopimelic acid and MK-8(H(4)) was the major respiratory quinone. The mean (±SD) level of DNA-DNA relatedness between strain YC6903(T) and N. pyridinolyticus OS4(T) was 53.5±5.5 %. The predominant cellular fatty acid of strain YC6903(T) was iso-C(16 : 0) (28.9 %). The DNA G+C content was 71.7 mol%. Phenotypic, phylogenetic and chemotaxonomic data indicated that strain YC6903(T) represents a novel species of the genus Nocardioides, for which the name Nocardioides caricicola sp. nov. is proposed. The type strain is YC6903(T) (=KACC 13778(T) =DSM 22177(T)).

  15. Discovery of a novel iota carrageenan sulfatase isolated from the marine bacterium Pseudoalteromonas carrageenovora

    PubMed Central

    Genicot, Sabine M.; Groisillier, Agnès; Rogniaux, Hélène; Meslet-Cladière, Laurence; Barbeyron, Tristan; Helbert, William

    2014-01-01

    Carrageenans are sulfated polysaccharides extracted from the cell wall of some marine red algae. These polysaccharides are widely used as gelling, stabilizing, and viscosifying agents in the food and pharmaceutical industries. Since the rheological properties of these polysaccharides depend on their sulfate content, we screened several isolated marine bacteria for carrageenan specific sulfatase activity, in the aim of developing enzymatic bioconversion of carrageenans. As a result of the screening, an iota-carrageenan sulfatase was detected in the cell-free lysate of the marine bacterium Pseudoalteromonas carrageenovora strain PscT. It was purified through Phenyl Sepharose and Diethylaminoethyl Sepharose chromatography. The pure enzyme, Psc ι-CgsA, was characterized. It had a molecular weight of 115.9 kDaltons and exhibited an optimal activity/stability at pH ~8.3 and at 40 ± 5°C. It was inactivated by phenylmethylsulfonyl fluoride but not by ethylene diamine tetraacetic acid. Psc ι-CgsA specifically catalyzes the hydrolysis of the 4-S sulfate of iota-carrageenan. The purified enzyme could transform iota-carrageenan into hybrid iota-/alpha- or pure alpha-carrageenan under controlled conditions. The gene encoding Psc ι-CgsA, a protein of 1038 amino acids, was cloned into Escherichia coli, and the sequence analysis revealed that Psc ι-CgsA has more than 90% sequence identity with a putative uncharacterized protein Q3IKL4 from the marine strain Pseudoalteromonas haloplanktis TAC 125, but besides this did not share any homology to characterized sulfatases. Phylogenetic studies show that P. carrageenovora sulfatase thus represents the first characterized member of a new sulfatase family, with a C-terminal domain having strong similarity with the superfamily of amidohydrolases, highlighting the still unexplored diversity of marine polysaccharide modifying enzymes. PMID:25207269

  16. Discovery of a novel iota carrageenan sulfatase isolated from the marine bacterium Pseudoalteromonas carrageenovora

    NASA Astrophysics Data System (ADS)

    Genicot, Sabine; Groisillier, Agnès; Rogniaux, Hélène; Meslet-Cladière, Laurence; Barbeyron, Tristan; Helbert, William

    2014-08-01

    Carrageenans are sulfated polysaccharides extracted from the cell wall of some marine red algae. These polysaccharides are widely used as gelling, stabilizing, and viscosifying agents in the food and pharmaceutical industries. Since the rheological properties of these polysaccharides depend on their sulfate content, we screened several isolated marine bacteria for carrageenan specific sulfatase activity, in the aim of developing enzymatic bioconversion of carrageenans. As a result of the screening, an iota-carrageenan sulfatase was detected in the cell-free lysate of the marine bacterium Pseudoalteromonas carrageenovora strain PscT. It was purified through Phenyl Sepharose and Diethylaminoethyl Sepharose chromatography. The pure enzyme, Psc ?-CgsA, was characterized. It had a molecular weight of 115.9 kDaltons and exhibited an optimal activity/stability at pH ~8.3 and at 40°C ± 5°C. It was inactivated by phenylmethylsulfonyl fluoride but not by ethylene diamine tetraacetic acid. Psc ?-CgsA specifically catalyzes the hydrolysis of the 4-S sulfate of iota-carrageenan. The purified enzyme could transform iota-carrageenan into hybrid iota-/alpha- or pure alpha-carrageenan under controlled conditions. The gene encoding Psc ?-CgsA, a protein of 1038 amino acids, was cloned into Escherichia coli, and the sequence analysis revealed that Psc ?-CgsA has more than 90% sequence identity with a putative uncharacterized protein Q3IKL4 from the marine strain Pseudoalteromonas haloplanktis TAC 125, but besides this did not share any homology to characterized sulfatases. Phylogenetic studies show that P. carrageenovora sulfatase thus represents the first characterized member of a new sulfatase family, with a C-terminal domain having strong similarity with the superfamily of amidohydrolases, highlighting the still unexplored diversity of marine polysaccharide modifying enzymes.

  17. Chloroflexus islandicus sp. nov., a thermophilic filamentous anoxygenic phototrophic bacterium from geyser Strokkur (Iceland).

    PubMed

    Gaisin, Vasil A; Kalashnikov, Alexander M; Grouzdev, Denis S; Sukhacheva, Marina V; Kuznetsov, Boris B; Gorlenko, Vladimir M

    2017-01-23

    A novel, thermophilic filamentous anoxygenic phototrophic bacterium, strain isl-2T, was isolated from the Strokkur Geyser, Iceland. Strain isl-2T formed unbranched multicellular filaments with gliding motility. The cells formed no spores and stained Gram-negative. The existence of pili was described in Chloroflexus spp. for the first time. Optimal growth occurred in a pH range of 7.5-7.7 and at a temperature of 55°C. Strain isl-2T grew photoheterotrophically under anaerobic conditions in the light and chemoheterotrophically under aerobic conditions in the dark. The major cellular fatty acids were C18:1ω9, C16:0, C18:0, and C18:0-OH. The major quinone was menaquinone-10. The photosynthetic pigments were bacteriochlorophylls c and a as well as β- and γ-carotenes. Phylogenetic analysis of the 16S rRNA gene sequences placed strain isl-2T into the genus Chloroflexus of the phylum Chloroflexi with Chloroflexus aggregans DSM 9485T as the closest relative (97.0% identity). The whole-genome sequence of strain isl-2T was determined. Average nucleotide identity values obtained for strain isl-2T in comparison to available genomic sequences of other strains of Chloroflexus spp. were ≤81.4% and digital DNA-DNA hybridisation values ≤ 22.8%. Additional phylogenetic analysis of the PufLM and BchG amino acid sequences supported the separate position of the isl-2T phylotype from other Chloroflexus phylotypes. Based on physiological and phylogenetic data as well as on genomic data, it was suggested that strain isl-2T represents a novel species within the genus Chloroflexus, with the proposed name Chloroflexus islandicus sp. nov. The type strain of the species is isl-2T (=VKM B-2978T, =DSM 29225T, =JCM 30533T).

  18. Global Transcriptome Analysis of Gracilaria changii (Rhodophyta) in Response to Agarolytic Enzyme and Bacterium.

    PubMed

    Lim, Ee-Leen; Siow, Rouh-San; Abdul Rahim, Raha; Ho, Chai-Ling

    2016-04-01

    Many bacterial epiphytes of agar-producing seaweeds secrete agarase that degrade algal cell wall matrix into oligoagars which elicit defense-related responses in the hosts. The molecular defense responses of red seaweeds are largely unknown. In this study, we surveyed the defense-related transcripts of an agarophyte, Gracilaria changii, treated with β-agarase through next generation sequencing (NGS). We also compared the defense responses of seaweed elicited by agarase with those elicited by an agarolytic bacterium isolated from seaweed, by profiling the expression of defense-related genes using quantitative reverse transcription real-time PCR (qRT-PCR). NGS detected a total of 391 differentially expressed genes (DEGs) with a higher abundance (>2-fold change with a p value <0.001) in the agarase-treated transcriptome compared to that of the non-treated G. changii. Among these DEGs were genes related to signaling, bromoperoxidation, heme peroxidation, production of aromatic amino acids, chorismate, and jasmonic acid. On the other hand, the genes encoding a superoxide-generating NADPH oxidase and related to photosynthesis were downregulated. The expression of these DEGs was further corroborated by qRT-PCR results which showed more than 90 % accuracy. A comprehensive analysis of their gene expression profiles between 1 and 24 h post treatments (hpt) revealed that most of the genes analyzed were consistently upregulated or downregulated by both agarase and agarolytic bacterial treatments, indicating that the defense responses induced by both treatments are highly similar except for genes encoding vanadium bromoperoxidase and animal heme peroxidase. Our study has provided the first glimpse of the molecular defense responses of G. changii to agarase and agarolytic bacterial treatments.

  19. Bacillus mesophilum sp. nov., strain IITR-54T, a novel 4-chlorobiphenyl dechlorinating bacterium.

    PubMed

    Manickam, Natesan; Singh, Nitin Kumar; Bajaj, Abhay; Kumar, Rajendran Mathan; Kaur, Gurwinder; Kaur, Navjot; Bala, Monu; Kumar, Anand; Mayilraj, Shanmugam

    2014-07-01

    The taxonomic position of a Gram-positive, endospore-forming bacterium isolated from soil sample collected from an industrial site was analyzed by a polyphasic approach. The strain designated as IITR-54T matched most of the phenotypic and chemical characteristics of the genus Bacillus and represents a novel species. It was found to biodegrade 4-chlorobiphenyl through dechlorination and was isolated through enrichment procedure from an aged polychlorinated biphenyl-contaminated soil. Both resting cell assay and growth under aerobic liquid conditions using 4-chlorobiphenyl as sole source of carbon along with 0.01% yeast extract, formation of chloride ions was measured. 16S rRNA (1,489 bases) nucleotide sequence of isolated strain was compared with those of closely related Bacillus type strains and confirmed that the strain belongs to the genus Bacillus. Strain IITR-54T differs from all other species of Bacillus by at least 2.1% at the 16S rRNA level, and the moderately related species are Bacillus oceanisediminis (97.9%) followed by Bacillus infantis (97.7%), Bacillus firmus (97.4%), Bacillus drentensis (97.3%), Bacillus circulans (97.2%), Bacillus soli (97.1%), Bacillus horneckiae (97.1%), Bacillus pocheonensis (97.1%) and Bacillus bataviensis (97.1%), respectively. The cell wall peptidoglycan contained meso-diaminopimelic acid and the major isoprenoid quinone was MK-7. Major fatty acids are iso-C15:0 (32.4%) and anteiso-C15:0 (27.4%). Predominant polar lipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The results of physiological and biochemical tests allowed the genotypic and phenotypic distinctiveness of strain IITR-54T with its phylogenetic relatives and suggest that the strain IITR-54T should be recognized as a novel species, for which the name Bacillus mesophilum sp. nov. is proposed. The type strain is IITR-54T (=MTCC 11060T=JCM 19208T).

  20. Saccharofermentans acetigenes gen. nov., sp. nov., an anaerobic bacterium isolated from sludge treating brewery wastewater.

    PubMed

    Chen, Shuangya; Niu, Lili; Zhang, Yongxiang

    2010-12-01

    A spore-forming anaerobic bacterium, designated strain P6(T), was isolated from the sludge of an up-flow anaerobic sludge blanket reactor treating brewery wastewater. Cells were Gram-positive, oval and 0.6-0.9 μm by 1.2-1.8 μm in size. Growth was observed at 20-42 °C and at pH 5.0-7.5. It fermented several hexoses, polysaccharides and alcohols. Sucrose and aesculin could also be fermented. The main end products of fermentation from glucose were acetate, lactate and fumarate; trace CO(2) and H(2) were also produced. The DNA G+C content of strain P6(T) was 55.6 mol%. The major cellular fatty acids were iso-C(15 : 0), anteiso-C(15 : 0) and iso-C(14 : 0) 3-OH. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain P6(T) represented a novel phyletic sublineage in clostridial cluster III, and showed <91 % similarity to the type strains of recognized species in this cluster. Phenotypically, the new isolate was distinguished from its phylogenetic relatives (e.g. Clostridium straminisolvens, Clostridium thermocellum, Acetivibrio cellulolyticus and Clostridium aldrichii) by producing acid from glucose and its inability to degrade cellulose. On the basis of evidence from this polyphasic study, strain P6(T) is considered to represent a novel species of a new genus, for which the name Saccharofermentans acetigenes gen. nov., sp. nov. is proposed. The type strain of Saccharofermentans acetigenes is P6(T) (=JCM 14006(T) =AS 1.5064(T)).

  1. Brassicibacter mesophilus gen. nov., sp. nov., a strictly anaerobic bacterium isolated from food industry wastewater.

    PubMed

    Fang, Ming-Xu; Zhang, Wen-Wu; Zhang, Yan-Zhou; Tan, Hai-Qin; Zhang, Xin-Qi; Wu, Min; Zhu, Xu-Fen

    2012-12-01

    A novel mesophilic, strictly anaerobic bacterium, strain BM(T), was isolated from food industry wastewater. The cells were motile, non-spore-forming rods and stained Gram-negative. Growth of strain BM(T) was observed at 16-44 °C (optimum 37 °C) and pH 6.0-9.0 (optimum pH 7.5). The NaCl concentration range for growth was 0-8% (optimum 1.5%, w/v). Strain BM(T) was chemo-organotrophic, using a few sugars and amino acids as sole carbon and energy sources. The fermentation products from peptone-yeast extract broth were propionate, formate, acetate, ethanol and isovalerate. Indole, NH(3) and H(2)S were produced from peptone. No respiratory quinones could be detected. The major fatty acids were iso-C(15:0) (39.3%), iso-C(15:0) dimethyl acetal (10.1%), anteiso-C(15:0) (7.6%), C(14:0) (6.1%) and C(16:0) (5.6%). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and a number of unidentified aminoglycolipids, glycolipids and phospholipids. The DNA G+C content was 28.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain BM(T) was related to various genera of the family Clostridiaceae, and its closest relatives were Sporosalibacterium faouarense SOL3f37(T) (94.3% 16S rRNA gene sequence similarity), Proteiniborus ethanoligenes GW(T) (92.1%) and Clostridiisalibacter paucivorans 37HS60(T) (92.0%). In recognition of its distinct phenotypic and genotypic characteristics, isolate BM(T) is proposed to represent a novel species of a new genus, Brassicibacter mesophilus gen. nov., sp. nov. The type strain of Brassicibacter mesophilus is BM(T) ( = JCM 16868(T)  = DSM 24659(T)).

  2. Self-trapping of a single bacterium in its own chemoattractant

    NASA Astrophysics Data System (ADS)

    Tsori, Y.; de Gennes, P.-G.

    2004-05-01

    Bacteria (e.g., E. coli) are very sensitive to certain chemoattractants (e.g., asparate) which they themselves produce. This leads to chemical instabilities in a uniform population. We discuss here the different case of a single bacterium, following the general scheme of Brenner, Levitov and Budrene. We show that in one and two dimensions (in a capillary or in a thin film) the bacterium can become self-trapped in its cloud of attractant. This should occur if a certain coupling constant g is larger than unity. We then estimate the reduced diffusion Deff of the bacterium in the strong-coupling limit, and find Deff ~ g-1.

  3. Ecology and metabolism of the beneficial intestinal commensal bacterium Faecalibacterium prausnitzii.

    PubMed

    Miquel, Sylvie; Martín, Rebeca; Bridonneau, Chantal; Robert, Véronique; Sokol, Harry; Bermúdez-Humarán, Luis G; Thomas, Muriel; Langella, Philippe

    2014-01-01

    Faecalibacterium prausnitzii is a major commensal bacterium, and its prevalence is often decreased in conditions of intestinal dysbiosis. The phylogenic identity of this bacterium was described only recently. It is still poorly characterized, and its specific growth requirements in the human gastrointestinal tract are not known. In this review, we consider F. prausnitzii metabolism, its ecophysiology in both humans and animals, and the effects of drugs and nutrition on its population. We list important questions about this beneficial and ubiquitous commensal bacterium that it would be valuable to answer.

  4. Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

    SciTech Connect

    Taghavi, S.; van der Lelie, D.; Hoffman, A.; Zhang, Y.-B.; Walla, M. D.; Vangronsveld, J.; Newman, L.; Monchy, S.

    2010-05-13

    Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa x deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT-PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to

  5. Investigation of the mechanism of iron acquisition by the marine bacterium Alteromonas luteoviolaceus: Characterization of siderophore production

    SciTech Connect

    Reid, R.T.; Butler, A. )

    1991-12-01

    Iron availability in the ocean ranges from one to four orders of magnitude below typical growth requirements of bacteria. The discrepancy between Fe availability and requirements raises questions about the mechanisms that marine bacteria use to sequester Fe{sup 3+}. Surprisingly little is known about the siderophores produced by marine bacteria. Growth conditions of an open-ocean bacterial isolate, Alteromonas luteoviolaceus, were investigated to determine the conditions which enhance siderophore production. Methods to isolate and purify the siderophores were determined. The siderophores produced by A. luteoviolaceus were partially characterized by mass spectral analysis, amino acid analysis, qualitative analytical tests, chemical degradation, and nuclear magnetic resonance. A new set of outer membrane proteins was also produced when the bacterium was grown under Fe-limited conditions.

  6. Regulation of Pyrroloquinoline Quinone-Dependent Glucose Dehydrogenase Activity in the Model Rhizosphere-Dwelling Bacterium Pseudomonas putida KT2440

    PubMed Central

    An, Ran

    2016-01-01

    ABSTRACT Soil-dwelling microbes solubilize mineral phosphates by secreting gluconic acid, which is produced from glucose by a periplasmic glucose dehydrogenase (GDH) that requires pyrroloquinoline quinone (PQQ) as a redox coenzyme. While GDH-dependent phosphate solubilization has been observed in numerous bacteria, little is known concerning the mechanism by which this process is regulated. Here we use the model rhizosphere-dwelling bacterium Pseudomonas putida KT2440 to explore GDH activity and PQQ synthesis, as well as gene expression of the GDH-encoding gene (gcd) and PQQ biosynthesis genes (pqq operon) while under different growth conditions. We also use reverse transcription-PCR to identify transcripts from the pqq operon to more accurately map the operon structure. GDH specific activity and PQQ levels vary according to growth condition, with the highest levels of both occurring when glucose is used as the sole carbon source and under conditions of low soluble phosphate. Under these conditions, however, PQQ levels limit in vitro phosphate solubilization. GDH specific activity data correlate well with gcd gene expression data, and the levels of expression of the pqqF and pqqB genes mirror the levels of PQQ synthesized, suggesting that one or both of these genes may serve to modulate PQQ levels according to the growth conditions. The pqq gene cluster (pqqFABCDEG) encodes at least two independent transcripts, and expression of the pqqF gene appears to be under the control of an independent promoter and terminator. IMPORTANCE Plant growth promotion can be enhanced by soil- and rhizosphere-dwelling bacteria by a number of different methods. One method is by promoting nutrient acquisition from soil. Phosphorus is an essential nutrient that plants obtain through soil, but in many cases it is locked up in forms that are not available for plant uptake. Bacteria such as the model bacterium Pseudomonas putida KT2440 can solubilize insoluble soil phosphates by secreting

  7. Structural Study of MPN387, an Essential Protein for Gliding Motility of a Human-Pathogenic Bacterium, Mycoplasma pneumoniae

    PubMed Central

    Kawakita, Yoshito; Kinoshita, Miki; Furukawa, Yukio; Tulum, Isil; Tahara, Yuhei O.; Katayama, Eisaku

    2016-01-01

    ABSTRACT Mycoplasma pneumoniae is a human pathogen that glides on host cell surfaces with repeated catch and release of sialylated oligosaccharides. At a pole, this organism forms a protrusion called the attachment organelle, which is composed of surface structures, including P1 adhesin and the internal core structure. The core structure can be divided into three parts, the terminal button, paired plates, and bowl complex, aligned in that order from the front end of the protrusion. To elucidate the gliding mechanism, we focused on MPN387, a component protein of the bowl complex which is essential for gliding but dispensable for cytadherence. The predicted amino acid sequence showed that the protein features a coiled-coil region spanning residue 72 to residue 290 of the total of 358 amino acids in the protein. Recombinant MPN387 proteins were isolated with and without an enhanced yellow fluorescent protein (EYFP) fusion tag and analyzed by gel filtration chromatography, circular dichroism spectroscopy, analytical ultracentrifugation, partial proteolysis, and rotary-shadowing electron microscopy. The results showed that MPN387 is a dumbbell-shaped homodimer that is about 42.7 nm in length and 9.1 nm in diameter and includes a 24.5-nm-long central parallel coiled-coil part. The molecular image was superimposed onto the electron micrograph based on the localizing position mapped by fluorescent protein tagging. A proposed role of this protein in the gliding mechanism is discussed. IMPORTANCE Human mycoplasma pneumonia is caused by a pathogenic bacterium, Mycoplasma pneumoniae. This tiny, 2-μm-long bacterium is suggested to infect humans by gliding on the surface of the trachea through binding to sialylated oligosaccharides. The mechanism underlying mycoplasma “gliding motility” is not related to any other well-studied motility systems, such as bacterial flagella and eukaryotic motor proteins. Here, we isolated and analyzed the structure of a key protein which is

  8. Does S-Metolachlor Affect the Performance of Pseudomonas sp. Strain ADP as Bioaugmentation Bacterium for Atrazine-Contaminated Soils?

    PubMed Central

    Viegas, Cristina A.; Costa, Catarina; André, Sandra; Viana, Paula; Ribeiro, Rui; Moreira-Santos, Matilde

    2012-01-01

    Atrazine (ATZ) and S-metolachlor (S-MET) are two herbicides widely used, often as mixtures. The present work examined whether the presence of S-MET affects the ATZ-biodegradation activity of the bioaugmentation bacterium Pseudomonas sp. strain ADP in a crop soil. S-MET concentrations were selected for their relevance in worst-case scenarios of soil contamination by a commercial formulation containing both herbicides. At concentrations representative of application of high doses of the formulation (up to 50 µg g−1 of soil, corresponding to a dose approximately 50× higher than the recommended field dose (RD)), the presence of pure S-MET significantly affected neither bacteria survival (∼107 initial viable cells g−1 of soil) nor its ATZ-mineralization activity. Consistently, biodegradation experiments, in larger soil microcosms spiked with 20× or 50×RD of the double formulation and inoculated with the bacterium, revealed ATZ to be rapidly (in up to 5 days) and extensively (>96%) removed from the soil. During the 5 days, concentration of S-MET decreased moderately to about 60% of the initial, both in inoculated and non-inoculated microcosms. Concomitantly, an accumulation of the two metabolites S-MET ethanesulfonic acid and S-MET oxanilic acid was found. Despite the dissipation of almost all the ATZ from the treated soils, the respective eluates were still highly toxic to an aquatic microalgae species, being as toxic as those from the untreated soil. We suggest that this high toxicity may be due to the S-MET and/or its metabolites remaining in the soil. PMID:22615921

  9. High cell density cultivation of the chemolithoautotrophic bacterium Nitrosomonas europaea.

    PubMed

    Papp, Benedek; Török, Tibor; Sándor, Erzsébet; Fekete, Erzsébet; Flipphi, Michel; Karaffa, Levente

    2016-05-01

    Nitrosomonas europaea is a chemolithoautotrophic nitrifier, a gram-negative bacterium that can obtain all energy required for growth from the oxidation of ammonia to nitrite, and this may be beneficial for various biotechnological and environmental applications. However, compared to other bacteria, growth of ammonia oxidizing bacteria is very slow. A prerequisite to produce high cell density N. europaea cultures is to minimize the concentrations of inhibitory metabolic by-products. During growth on ammonia nitrite accumulates, as a consequence, N. europaea cannot grow to high cell concentrations under conventional batch conditions. Here, we show that single-vessel dialysis membrane bioreactors can be used to obtain substantially increased N. europaea biomasses and substantially reduced nitrite levels in media initially containing high amounts of the substrate. Dialysis membrane bioreactor fermentations were run in batch as well as in continuous mode. Growth was monitored with cell concentration determinations, by assessing dry cell mass and by monitoring ammonium consumption as well as nitrite formation. In addition, metabolic activity was probed with in vivo acridine orange staining. Under continuous substrate feed, the maximal cell concentration (2.79 × 10(12)/L) and maximal dry cell mass (0.895 g/L) achieved more than doubled the highest values reported for N. europaea cultivations to date.

  10. Presence of an unusual methanogenic bacterium in coal gasification waste.

    PubMed

    Tomei, F A; Rouse, D; Maki, J S; Mitchell, R

    1988-12-01

    Methanogenic bacteria growing on a pilot-scale, anaerobic filter processing coal gasification waste were enriched in a mineral salts medium containing hydrogen and acetate as potential energy sources. Transfer of the enrichments to methanol medium resulted in the initial growth of a strain of Methanosarcina barkeri, but eventually small cocci became dominant. The cocci growing on methanol produced methane and exhibited the typical fluorescence of methanogenic bacteria. They grew in the presence of the cell wall synthesis-inhibiting antibiotics d-cycloserine, fosfomycin, penicillin G, and vancomycin as well as in the presence of kanamycin, an inhibitor of protein synthesis in eubacteria. The optimal growth temperature was 37 degrees C, and the doubling time was 7.5 h. The strain lysed after reaching stationary phase. The bacterium grew poorly with hydrogen as the energy source and failed to grow on acetate. Morphologically, the coccus shared similarities with Methanosarcina sp. Cells were 1 mum wide, exhibited the typical thick cell wall and cross-wall formation, and formed tetrads. Packets and cysts were not formed.

  11. Hydrodynamics and collective behavior of the tethered bacterium Thiovulum majus

    PubMed Central

    Petroff, Alexander; Libchaber, Albert

    2014-01-01

    The ecology and dynamics of many microbial systems, particularly in mats and soils, are shaped by how bacteria respond to evolving nutrient gradients and microenvironments. Here we show how the response of the sulfur-oxidizing bacterium Thiovulum majus to changing oxygen gradients causes cells to organize into large-scale fronts. To study this phenomenon, we develop a technique to isolate and enrich these bacteria from the environment. Using this enrichment culture, we observe the formation and dynamics of T. majus fronts in oxygen gradients. We show that these dynamics can be understood as occurring in two steps. First, chemotactic cells moving up the oxygen gradient form a front that propagates with constant velocity. We then show, through observation and mathematical analysis, that this front becomes unstable to changes in cell density. Random perturbations in cell density create oxygen gradients. The response of cells magnifies these gradients and leads to the formation of millimeter-scale fluid flows that actively pull oxygenated water through the front. We argue that this flow results from a nonlinear instability excited by stochastic fluctuations in the density of cells. Finally, we show that the dynamics by which these modes interact can be understood from the chemotactic response of cells. These results provide a mathematically tractable example of how collective phenomena in ecological systems can arise from the individual response of cells to a shared resource. PMID:24459183

  12. Bioconversion of methane to lactate by an obligate methanotrophic bacterium

    SciTech Connect

    Henard, Calvin A.; Smith, Holly; Dowe, Nancy; Kalyuzhnaya, Marina G.; Pienkos, Philip T.; Guarnieri, Michael T.

    2016-02-23

    Methane is the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. Microbial conversion of methane to fuels and value-added chemicals offers a means to reduce GHG emissions, while also valorizing this otherwise squandered high-volume, high-energy gas. However, to date, advances in methane biocatalysis have been constrained by the low-productivity and limited genetic tractability of natural methane-consuming microbes. Here, leveraging recent identification of a novel, tractable methanotrophic bacterium, Methylomicrobium buryatense, we demonstrate microbial biocatalysis of methane to lactate, an industrial platform chemical. Heterologous overexpression of a Lactobacillus helveticus L-lactate dehydrogenase in M. buryatense resulted in an initial titer of 0.06 g lactate/L from methane. Cultivation in a 5 L continuously stirred tank bioreactor enabled production of 0.8 g lactate/L, representing a 13-fold improvement compared to the initial titer. The yields (0.05 g lactate/g methane) and productivity (0.008 g lactate/L/h) indicate the need and opportunity for future strain improvement. Additionally, real-time analysis of methane utilization implicated gas-to-liquid transfer and/or microbial methane consumption as process limitations. This work opens the door to develop an array of methanotrophic bacterial strain-engineering strategies currently employed for biocatalytic sugar upgrading to “green” chemicals and fuels.

  13. Bioconversion of methane to lactate by an obligate methanotrophic bacterium

    DOE PAGES

    Henard, Calvin A.; Smith, Holly; Dowe, Nancy; ...

    2016-02-23

    Methane is the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. Microbial conversion of methane to fuels and value-added chemicals offers a means to reduce GHG emissions, while also valorizing this otherwise squandered high-volume, high-energy gas. However, to date, advances in methane biocatalysis have been constrained by the low-productivity and limited genetic tractability of natural methane-consuming microbes. Here, leveraging recent identification of a novel, tractable methanotrophic bacterium, Methylomicrobium buryatense, we demonstrate microbial biocatalysis of methane to lactate, an industrial platform chemical. Heterologous overexpression of a Lactobacillus helveticus L-lactate dehydrogenase in M. buryatense resultedmore » in an initial titer of 0.06 g lactate/L from methane. Cultivation in a 5 L continuously stirred tank bioreactor enabled production of 0.8 g lactate/L, representing a 13-fold improvement compared to the initial titer. The yields (0.05 g lactate/g methane) and productivity (0.008 g lactate/L/h) indicate the need and opportunity for future strain improvement. Additionally, real-time analysis of methane utilization implicated gas-to-liquid transfer and/or microbial methane consumption as process limitations. This work opens the door to develop an array of methanotrophic bacterial strain-engineering strategies currently employed for biocatalytic sugar upgrading to “green” chemicals and fuels.« less

  14. Novel Rickettsiella bacterium in the leafhopper Orosius albicinctus (Hemiptera: Cicadellidae).

    PubMed

    Iasur-Kruh, Lilach; Weintraub, Phyllis G; Mozes-Daube, Netta; Robinson, Wyatt E; Perlman, Steve J; Zchori-Fein, Einat

    2013-07-01

    Bacteria in the genus Rickettsiella (Coxiellaceae), which are mainly known as arthropod pathogens, are emerging as excellent models to study transitions between mutualism and pathogenicity. The current report characterizes a novel Rickettsiella found in the leafhopper Orosius albicinctus (Hemiptera: Cicadellidae), a major vector of phytoplasma diseases in Europe and Asia. Denaturing gradient gel electrophoresis (DGGE) and pyrosequencing were used to survey the main symbionts of O. albicinctus, revealing the obligate symbionts Sulcia and Nasuia, and the facultative symbionts Arsenophonus and Wolbachia, in addition to Rickettsiella. The leafhopper Rickettsiella is allied with bacteria found in ticks. Screening O. albicinctus from the field showed that Rickettsiella is highly prevalent, with over 60% of individuals infected. A stable Rickettsiella infection was maintained in a leafhopper laboratory colony for at least 10 generations, and fluorescence microscopy localized bacteria to accessory glands of the female reproductive tract, suggesting that the bacterium is vertically transmitted. Future studies will be needed to examine how Rickettsiella affects host fitess and its ability to vector phytopathogens.

  15. Hydrodynamics and collective behavior of the tethered bacterium Thiovulum majus.

    PubMed

    Petroff, Alexander; Libchaber, Albert

    2014-02-04

    The ecology and dynamics of many microbial systems, particularly in mats and soils, are shaped by how bacteria respond to evolving nutrient gradients and microenvironments. Here we show how the response of the sulfur-oxidizing bacterium Thiovulum majus to changing oxygen gradients causes cells to organize into large-scale fronts. To study this phenomenon, we develop a technique to isolate and enrich these bacteria from the environment. Using this enrichment culture, we observe the formation and dynamics of T. majus fronts in oxygen gradients. We show that these dynamics can be understood as occurring in two steps. First, chemotactic cells moving up the oxygen gradient form a front that propagates with constant velocity. We then show, through observation and mathematical analysis, that this front becomes unstable to changes in cell density. Random perturbations in cell density create oxygen gradients. The response of cells magnifies these gradients and leads to the formation of millimeter-scale fluid flows that actively pull oxygenated water through the front. We argue that this flow results from a nonlinear instability excited by stochastic fluctuations in the density of cells. Finally, we show that the dynamics by which these modes interact can be understood from the chemotactic response of cells. These results provide a mathematically tractable example of how collective phenomena in ecological systems can arise from the individual response of cells to a shared resource.

  16. Bioconversion of methane to lactate by an obligate methanotrophic bacterium.

    PubMed

    Henard, Calvin A; Smith, Holly; Dowe, Nancy; Kalyuzhnaya, Marina G; Pienkos, Philip T; Guarnieri, Michael T

    2016-02-23

    Methane is the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. Microbial conversion of methane to fuels and value-added chemicals offers a means to reduce GHG emissions, while also valorizing this otherwise squandered high-volume, high-energy gas. However, to date, advances in methane biocatalysis have been constrained by the low-productivity and limited genetic tractability of natural methane-consuming microbes. Here, leveraging recent identification of a novel, tractable methanotrophic bacterium, Methylomicrobium buryatense, we demonstrate microbial biocatalysis of methane to lactate, an industrial platform chemical. Heterologous overexpression of a Lactobacillus helveticus L-lactate dehydrogenase in M. buryatense resulted in an initial titer of 0.06 g lactate/L from methane. Cultivation in a 5 L continuously stirred tank bioreactor enabled production of 0.8 g lactate/L, representing a 13-fold improvement compared to the initial titer. The yields (0.05 g lactate/g methane) and productivity (0.008 g lactate/L/h) indicate the need and opportunity for future strain improvement. Additionally, real-time analysis of methane utilization implicated gas-to-liquid transfer and/or microbial methane consumption as process limitations. This work opens the door to develop an array of methanotrophic bacterial strain-engineering strategies currently employed for biocatalytic sugar upgrading to "green" chemicals and fuels.

  17. Novel Trypanosomatid-Bacterium Association: Evolution of Endosymbiosis in Action

    PubMed Central

    Kostygov, Alexei Y.; Dobáková, Eva; Grybchuk-Ieremenko, Anastasiia; Váhala, Dalibor; Maslov, Dmitri A.; Votýpka, Jan

    2016-01-01

    ABSTRACT We describe a novel symbiotic association between a kinetoplastid protist, Novymonas esmeraldas gen. nov., sp. nov., and an intracytoplasmic bacterium, “Candidatus Pandoraea novymonadis” sp. nov., discovered as a result of a broad-scale survey of insect trypanosomatid biodiversity in Ecuador. We characterize this association by describing the morphology of both organisms, as well as their interactions, and by establishing their phylogenetic affinities. Importantly, neither partner is closely related to other known organisms previously implicated in eukaryote-bacterial symbiosis. This symbiotic association seems to be relatively recent, as the host does not exert a stringent control over the number of bacteria harbored in its cytoplasm. We argue that this unique relationship may represent a suitable model for studying the initial stages of establishment of endosymbiosis between a single-cellular eukaryote and a prokaryote. Based on phylogenetic analyses, Novymonas could be considered a proxy for the insect-only ancestor of the dixenous genus Leishmania and shed light on the origin of the two-host life cycle within the subfamily Leishmaniinae. PMID:26980834

  18. Bioconversion of methane to lactate by an obligate methanotrophic bacterium

    PubMed Central

    Henard, Calvin A.; Smith, Holly; Dowe, Nancy; Kalyuzhnaya, Marina G.; Pienkos, Philip T.; Guarnieri, Michael T.

    2016-01-01

    Methane is the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. Microbial conversion of methane to fuels and value-added chemicals offers a means to reduce GHG emissions, while also valorizing this otherwise squandered high-volume, high-energy gas. However, to date, advances in methane biocatalysis have been constrained by the low-productivity and limited genetic tractability of natural methane-consuming microbes. Here, leveraging recent identification of a novel, tractable methanotrophic bacterium, Methylomicrobium buryatense, we demonstrate microbial biocatalysis of methane to lactate, an industrial platform chemical. Heterologous overexpression of a Lactobacillus helveticus L-lactate dehydrogenase in M. buryatense resulted in an initial titer of 0.06 g lactate/L from methane. Cultivation in a 5 L continuously stirred tank bioreactor enabled production of 0.8 g lactate/L, representing a 13-fold improvement compared to the initial titer. The yields (0.05 g lactate/g methane) and productivity (0.008 g lactate/L/h) indicate the need and opportunity for future strain improvement. Additionally, real-time analysis of methane utilization implicated gas-to-liquid transfer and/or microbial methane consumption as process limitations. This work opens the door to develop an array of methanotrophic bacterial strain-engineering strategies currently employed for biocatalytic sugar upgrading to “green” chemicals and fuels. PMID:26902345

  19. Kinetics of a chlorate-accumulating, perchlorate-reducing bacterium.

    PubMed

    Dudley, Margaret; Salamone, Anna; Nerenberg, Robert

    2008-05-01

    Kinetics parameters for perchlorate and chlorate reduction were determined for Dechlorosoma sp. HCAP-C, also known as Dechlorosoma sp. PCC, a novel perchlorate-reducing bacterium (PCRB) that accumulates significant amounts of chlorate during perchlorate reduction. This is the first report of such behavior, and we hypothesized the perchlorate reduction kinetics would be markedly different from other PCRB. In batch tests with initial perchlorate concentrations ranging from 200 to around 1400 mg/L, maximum chlorate accumulation ranged from 41 to 279 mg/L, and were consistently around 20% of the initial perchlorate concentration. For perchlorate, parameters were determined using a competitive inhibition model. The maximum specific substrate degradation rate qmaxP was 11.5mgClO4-/mgdry weight (DW)-d, and the half-maximum rate constant KP was 193 mgClO4-/L. For chlorate, the qmaxC was 8.3 mgClO3-/mgDW-d and the KC was 58.3 mgClO3-/L. The high KP values relative to conventional PCRB, values suggests that HCAP-C does not play a significant role at low perchlorate concentrations. However, the relatively high qmaxP, and the potential for syntrophic relationships with chlorate-reducing bacteria that relieve the effects of chlorate inhibition, suggest that HCAP-C could play a significant role at high perchlorate concentrations.

  20. Heavy Metal Induced Antibiotic Resistance in Bacterium LSJC7.

    PubMed

    Chen, Songcan; Li, Xiaomin; Sun, Guoxin; Zhang, Yingjiao; Su, Jianqiang; Ye, Jun

    2015-09-29

    Co-contamination of antibiotics and heavy metals prevails in the environment, and may play an important role in disseminating bacterial antibiotic resistance, but the selective effects of heavy metals on bacterial antibiotic resistance is largely unclear. To investigate this, the effects of heavy metals on antibiotic resistance were studied in a genome-sequenced bacterium, LSJC7. The results showed that the presence of arsenate, copper, and zinc were implicated in fortifying the resistance of LSJC7 towards tetracycline. The concentrations of heavy metals required to induce antibiotic resistance, i.e., the minimum heavy metal concentrations (MHCs), were far below (up to 64-fold) the minimum inhibition concentrations (MIC) of LSJC7. This finding indicates that the relatively low heavy metal levels in polluted environments and in treated humans and animals might be sufficient to induce bacterial antibiotic resistance. In addition, heavy metal induced antibiotic resistance was also observed for a combination of arsenate and chloramphenicol in LSJC7, and copper/zinc and tetracycline in antibiotic susceptible strain Escherichia coli DH5α. Overall, this study implies that heavy metal induced antibiotic resistance might be ubiquitous among various microbial species and suggests that it might play a role in the emergence and spread of antibiotic resistance in metal and antibiotic co-contaminated environments.

  1. Mechanisms of gold biomineralization in the bacterium Cupriavidus metallidurans

    PubMed Central

    Reith, Frank; Etschmann, Barbara; Grosse, Cornelia; Moors, Hugo; Benotmane, Mohammed A.; Monsieurs, Pieter; Grass, Gregor; Doonan, Christian; Vogt, Stefan; Lai, Barry; Martinez-Criado, Gema; George, Graham N.; Nies, Dietrich H.; Mergeay, Max; Pring, Allan; Southam, Gordon; Brugger, Joël

    2009-01-01

    While the role of microorganisms as main drivers of metal mobility and mineral formation under Earth surface conditions is now widely accepted, the formation of secondary gold (Au) is commonly attributed to abiotic processes. Here we report that the biomineralization of Au nanoparticles in the metallophillic bacterium Cupriavidus metallidurans CH34 is the result of Au-regulated gene expression leading to the energy-dependent reductive precipitation of toxic Au(III)-complexes. C. metallidurans, which forms biofilms on Au grains, rapidly accumulates Au(III)-complexes from solution. Bulk and microbeam synchrotron X-ray analyses revealed that cellular Au accumulation is coupled to the formation of Au(I)-S complexes. This process promotes Au toxicity and C. metallidurans reacts by inducing oxidative stress and metal resistances gene clusters (including a Au-specific operon) to promote cellular defense. As a result, Au detoxification is mediated by a combination of efflux, reduction, and possibly methylation of Au-complexes, leading to the formation of Au(I)-C-compounds and nanoparticulate Au0. Similar particles were observed in bacterial biofilms on Au grains, suggesting that bacteria actively contribute to the formation of Au grains in surface environments. The recognition of specific genetic responses to Au opens the way for the development of bioexploration and bioprocessing tools. PMID:19815503

  2. Heavy Metal Induced Antibiotic Resistance in Bacterium LSJC7

    PubMed Central

    Chen, Songcan; Li, Xiaomin; Sun, Guoxin; Zhang, Yingjiao; Su, Jianqiang; Ye, Jun

    2015-01-01

    Co-contamination of antibiotics and heavy metals prevails in the environment, and may play an important role in disseminating bacterial antibiotic resistance, but the selective effects of heavy metals on bacterial antibiotic resistance is largely unclear. To investigate this, the effects of heavy metals on antibiotic resistance were studied in a genome-sequenced bacterium, LSJC7. The results showed that the presence of arsenate, copper, and zinc were implicated in fortifying the resistance of LSJC7 towards tetracycline. The concentrations of heavy metals required to induce antibiotic resistance, i.e., the minimum heavy metal concentrations (MHCs), were far below (up to 64-fold) the minimum inhibition concentrations (MIC) of LSJC7. This finding indicates that the relatively low heavy metal levels in polluted environments and in treated humans and animals might be sufficient to induce bacterial antibiotic resistance. In addition, heavy metal induced antibiotic resistance was also observed for a combination of arsenate and chloramphenicol in LSJC7, and copper/zinc and tetracycline in antibiotic susceptible strain Escherichia coli DH5α. Overall, this study implies that heavy metal induced antibiotic resistance might be ubiquitous among various microbial species and suggests that it might play a role in the emergence and spread of antibiotic resistance in metal and antibiotic co-contaminated environments. PMID:26426011

  3. Anoxybacillus calidus sp. nov., a thermophilic bacterium isolated from soil near a thermal power plant.

    PubMed

    Cihan, Arzu Coleri; Cokmus, Cumhur; Koc, Melih; Ozcan, Birgul

    2014-01-01

    A novel thermophilic, Gram-stain-positive, facultatively anaerobic, endospore-forming, motile, rod-shaped bacterium, strain C161ab(T), was isolated from a soil sample collected near Kizildere, Saraykoy-Buharkent power plant in Denizli. The isolate could grow at temperatures between 35 and 70 °C (optimum 55 °C), at pH 6.5-9.0 (optimum pH 8.0-8.5) and with 0-2.5 % NaCl (optimum 0.5 %, w/v). The strain formed cream-coloured, circular colonies and tolerated up to 70 mM boron. Its DNA G+C content was 37.8 mol%. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. Strain C161ab(T) contained menaquinones MK-7 (96 %) and MK-6 (4 %). The major cellular fatty acids were iso-branched fatty acids: iso-C15 : 0 (52.2 %) and iso-C17 : 0 (28.0 %,) with small amounts of C16 : 0 (7.4 %). Phylogenetic analysis based on the 16S rRNA gene revealed 94.6-96.8 % sequence similarity with all recognized species of the genus Anoxybacillus. Strain C161ab(T) showed the greatest sequence similarity to Anoxybacillus rupiensis DSM 17127(T) and Anoxybacillus voinovskiensis DSM 17075(T), both had 96.8 % similarity to strain C161ab(T), as well as to Anoxybacillus caldiproteolyticus DSM 15730(T) (96.6 %). DNA-DNA hybridization revealed low levels of relatedness with the closest relatives of strain C161ab(T), A. rupiensis (21.2 %) and A. voinovskiensis (16.5 %). On the basis of the results obtained from phenotypic, chemotaxonomic, genomic fingerprinting, phylogenetic and hybridization analyses, the isolate is proposed to represent a novel species, Anoxybacillus calidus sp. nov. (type strain C161ab(T) = DSM 25520(T) = NCIMB 14851(T)).

  4. Fervidicella metallireducens gen. nov., sp. nov., a thermophilic, anaerobic bacterium from geothermal waters.

    PubMed

    Ogg, Christopher D; Patel, Bharat K C

    2010-06-01

    A strictly anaerobic, thermophilic bacterium, designated strain AeB(T), was isolated from microbial mats colonizing a run-off channel formed by free-flowing thermal water from a bore well (registered number 17263) of the Great Artesian Basin, Australia. Cells of strain AeB(T) were slightly curved rods (2.5-6.0x1.0 mum) that stained Gram-negative and formed spherical terminal to subterminal spores. The strain grew optimally in tryptone-yeast extract-Casamino acids medium at 50 degrees C (range 37-55 degrees C) and pH 7 (range pH 5-9). Strain AeB(T) grew poorly on yeast extract (0.2 %) and tryptone (0.2 %) as sole carbon sources, which were obligately required for growth on other energy sources. Growth of strain AeB(T) increased in the presence of various carbohydrates and amino acids, but not organic acids. End products detected from glucose fermentation were ethanol, acetate, CO2 and H2. In the presence of 0.2 % yeast extract, iron(III), manganese(IV), vanadium(V) and cobalt(III) were reduced, but not sulfate, thiosulfate, sulfite, elemental sulfur, nitrate or nitrite. Iron(III) was also reduced in the presence of tryptone, peptone, Casamino acids and amyl media (Research Achievement), but not starch, xylan, chitin, glycerol, ethanol, pyruvate, benzoate, lactate, acetate, propionate, succinate, glycine, serine, lysine, threonine, arginine, glutamate, valine, leucine, histidine, alanine, aspartate, isoleucine or methionine. Growth was inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin and NaCl concentrations >2 %. The DNA G+C content was 35.4+/-1 mol%, as determined by the thermal denaturation method. 16S rRNA gene sequence analysis indicated that strain AeB(T) is a member of the family Clostridiaceae, class Clostridia, phylum 'Firmicutes', and is positioned approximately equidistantly between the genera Sarcina, Anaerobacter, Caloramator and Clostridium (16S rRNA gene similarity values of 87.8-90.9 %). On the basis of 16S rRNA gene

  5. Anaerobaculum mobile sp. nov., a novel anaerobic, moderately thermophilic, peptide-fermenting bacterium that uses crotonate as an electron acceptor, and emended description of the genus Anaerobaculum.

    PubMed

    Menes, Rodolfo Javier; Muxí, Lucía

    2002-01-01

    A novel anaerobic, moderately thermophilic, peptide-fermenting bacterium, strain NGA(T), was isolated from an anaerobic wool-scouring wastewater treatment lagoon. The cells were gram-negative, straight rods of 0.5-1.0 x 2.0-4.0 microm, motile by means of a single flagellum. The DNA G+C content was 51.5 mol%. The optimum pH and temperature range for growth were 6.6-7.3 and 55-60 degrees C, respectively. The optimum NaCl concentration was 0.08 g l(-1). The bacterium fermented organic acids (malate, tartrate, pyruvate, glycerol and fumarate), a few carbohydrates (starch, glucose, fructose and gluconate), Casamino acids, tryptone and yeast extract. Carbohydrates and organic acids were converted to acetate, hydrogen and CO2. The bacterium oxidized leucine to isovalerate with crotonate as an electron acceptor, but not in co-culture with Methanothermobacter thermoautotrophicus DSM 3720T. Thiosulfate, sulfur and cystine were reduced to sulfide and crotonate was reduced to butyrate with glucose and tryptone-yeast extract as electron donors. Phylogenetic analysis of the 16S rRNA gene indicated that strain NGA(T) was related to Anaerobaculum thermoterrenum (98% similarity), the only described species of the genus. The DNA-DNA hybridization value for strain NGA(T) and A. thermoterrenum ACM 5076T was 40.8%. On the basis of these results, strain NGA(T) is proposed as a novel species of the genus Anaerobaculum, namely Anaerobaculum mobile sp. nov. The type strain is NGA(T) (= DSM 13181T =ATCC BAA-54T).

  6. Cold adaptation of the mononuclear molybdoenzyme periplasmic nitrate reductase from the Antarctic bacterium Shewanella gelidimarina

    SciTech Connect

    Simpson, Philippa J.L.; Codd, Rachel

    2011-11-04

    Highlights: Black-Right-Pointing-Pointer Cold-adapted phenotype of NapA from the Antarctic bacterium Shewanella gelidimarina. Black-Right-Pointing-Pointer Protein homology model of NapA from S. gelidimarina and mesophilic homologue. Black-Right-Pointing-Pointer Six amino acid residues identified as lead candidates governing NapA cold adaptation. Black-Right-Pointing-Pointer Molecular-level understanding of designing cool-temperature in situ oxyanion sensors. -- Abstract: The reduction of nitrate to nitrite is catalysed in bacteria by periplasmic nitrate reductase (Nap) which describes a system of variable protein subunits encoded by the nap operon. Nitrate reduction occurs in the NapA subunit, which contains a bis-molybdopterin guanine dinucleotide (Mo-MGD) cofactor and one [4Fe-4S] iron-sulfur cluster. The activity of periplasmic nitrate reductase (Nap) isolated as native protein from the cold-adapted (psychrophilic) Antarctic bacterium Shewanella gelidimarina (Nap{sub Sgel}) and middle-temperature adapted (mesophilic) Shewanella putrefaciens (Nap{sub Sput}) was examined at varied temperature. Irreversible deactivation of Nap{sub Sgel} and Nap{sub Sput} occurred at 54.5 and 65 Degree-Sign C, respectively. When Nap{sub Sgel} was preincubated at 21-70 Degree-Sign C for 30 min, the room-temperature nitrate reductase activity was maximal and invariant between 21 and 54 Degree-Sign C, which suggested that Nap{sub Sgel} was poised for optimal catalysis at modest temperatures and, unlike Nap{sub Sput}, did not benefit from thermally-induced refolding. At 20 Degree-Sign C, Nap{sub Sgel} reduced selenate at 16% of the rate of nitrate reduction. Nap{sub Sput} did not reduce selenate. Sequence alignment showed 46 amino acid residue substitutions in Nap{sub Sgel} that were conserved in NapA from mesophilic Shewanella, Rhodobacter and Escherichia species and could be associated with the Nap{sub Sgel} cold-adapted phenotype. Protein homology modeling of Nap{sub Sgel} using a

  7. Characterization of a Neochlamydia-like Bacterium Associated with Epitheliocystis in Cultured Artic Char Salvelinus alpinus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Infections of branchial epithelium by intracellular gram-negative bacteria, termed epitheliocystis, have limited culture of Arctic char (Salvelinus alpinus). To characterize a bacterium associated with epitheliocystis in cultured char, gills were sampled for histopathologic examination, conventional...

  8. Draft Genome Sequence of the Versatile Alkane-Degrading Bacterium Aquabacterium sp. Strain NJ1.

    PubMed

    Masuda, Hisako; Shiwa, Yuh; Yoshikawa, Hirofumi; Zylstra, Gerben J

    2014-12-04

    The draft genome sequence of a soil bacterium, Aquabacterium sp. strain NJ1, capable of utilizing both liquid and solid alkanes, was deciphered. This is the first report of an Aquabacterium genome sequence.

  9. Enhancement of xylose utilization from corn stover by a recombinant bacterium for ethanol production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recombinant ethanologenic Escherichia coli ferments glucose, xylose and arabinose to ethanol. However, the bacterium preferentially utilizes glucose first, then arabinose and finally xylose (sequential utilization of sugars) during fermentation of lignocellulosic hydrolyzates to ethanol making the p...

  10. Draft Genome Sequence of the Fast-Growing Bacterium Vibrio natriegens Strain DSMZ 759.

    PubMed

    Maida, Isabel; Bosi, Emanuele; Perrin, Elena; Papaleo, Maria Cristiana; Orlandini, Valerio; Fondi, Marco; Fani, Renato; Wiegel, Juergen; Bianconi, Giovanna; Canganella, Francesco

    2013-08-22

    Vibrio natriegens is a Gram-negative bacterium known for its extremely short doubling time. Here we present the annotated draft genome sequence of Vibrio natriegens strain DSMZ 759, with the aim of providing insights about its high growth rate.

  11. IN SITU RT-PCR WITH A SULFATE-REDUCING BACTERIUM ISOLATED FROM SEAGRASS ROOTS

    EPA Science Inventory

    Bacteria considered to be obligate anaerobes internally colonize roots of the submerged macrophyte Halodule wrightii. A sulfate reducing bacterium, Summer lac 1, was isolated on lactate from H. wrightii roots. The isolate has physiological characteristics typical of Desulfovibri...

  12. Identification and Analysis of a Novel Group of Bacteriophages Infecting the Lactic Acid Bacterium Streptococcus thermophilus

    PubMed Central

    McDonnell, Brian; Mahony, Jennifer; Neve, Horst; Hanemaaijer, Laurens; Noben, Jean-Paul; Kouwen, Thijs

    2016-01-01

    ABSTRACT We present the complete genome sequences of four members of a novel group of phages infecting Streptococcus thermophilus, designated here as the 987 group. Members of this phage group appear to have resulted from genetic exchange events, as evidenced by their “hybrid” genomic architecture, exhibiting DNA sequence relatedness to the morphogenesis modules of certain P335 group Lactococcus lactis phages and to the replication modules of S. thermophilus phages. All four identified members of the 987 phage group were shown to elicit adsorption affinity to both their cognate S. thermophilus hosts and a particular L. lactis starter strain. The receptor binding protein of one of these phages (as a representative of this novel group) was defined using an adsorption inhibition assay. The emergence of a novel phage group infecting S. thermophilus highlights the continuous need for phage monitoring and development of new phage control measures. IMPORTANCE Phage predation of S. thermophilus is an important issue for the dairy industry, where viral contamination can lead to fermentation inefficiency or complete fermentation failure. Genome information and phage-host interaction studies of S. thermophilus phages, particularly those emerging in the marketplace, are an important part of limiting the detrimental impact of these viruses in the dairy environment. PMID:27316953

  13. Biodiversity of yeasts, lactic acid bacteria and acetic acid bacteria in the fermentation of "Shanxi aged vinegar", a traditional Chinese vinegar.

    PubMed

    Wu, Jia Jia; Ma, Ying Kun; Zhang, Fen Fen; Chen, Fu Sheng

    2012-05-01

    Shanxi aged vinegar is a famous traditional Chinese vinegar made from several kinds of cereal by spontaneous solid-state fermentation techniques. In order to get a comprehensive understanding of culturable microorganism's diversity present in its fermentation, the indigenous microorganisms including 47 yeast isolates, 28 lactic acid bacteria isolates and 58 acetic acid bacteria isolates were recovered in different fermenting time and characterized based on a combination of phenotypic and genotypic approaches including inter-delta/PCR, PCR-RFLP, ERIC/PCR analysis, as well as 16S rRNA and 26S rRNA partial gene sequencing. In the alcoholic fermentation, the dominant yeast species Saccharomyces (S.) cerevisiae (96%) exhibited low phenotypic and genotypic diversity among the isolates, while Lactobacillus (Lb.) fermentum together with Lb. plantarum, Lb. buchneri, Lb. casei, Pediococcus (P.) acidilactici, P. pentosaceus and Weissella confusa were predominated in the bacterial population at the same stage. Acetobacter (A.) pasteurianus showing great variety both in genotypic and phenotypic tests was the dominant species (76%) in the acetic acid fermentation stage, while the other acetic acid bacteria species including A. senegalensis, A. indonesiensis, A. malorum and A. orientalis, as well as Gluconobacter (G.) oxydans were detected at initial point of alcoholic and acetic acid fermentation stage respectively.

  14. Genome sequence of Pseudomonas parafulva CRS01-1, an antagonistic bacterium isolated from rice field.

    PubMed

    Liu, Qunen; Zhang, Yingxin; Yu, Ning; Bi, Zhenzhen; Zhu, Aike; Zhan, Xiaodeng; Wu, Weixun; Yu, Ping; Chen, Daibo; Cheng, Shihua; Cao, Liyong

    2015-07-20

    Pseudomonas parafulva (formerly known as Pseudomonas fulva) is an antagonistic bacterium against several rice bacterial and fungal diseases. The total genome size of P. parafulva CRS01-1 is 5,087,619 bp with 4389 coding sequences (CDSs), 77 tRNAs, and 7 rRNAs. The annotated full genome sequence of the P. parafulva CRS01-1 strain might shed light on its role as an antagonistic bacterium.

  15. Vibrio damsela, a Marine Bacterium, Causes Skin Ulcers on the Damselfish Chromis punctipinnis.

    PubMed

    Love, M; Teebken-Fisher, D; Hose, J E; Farmer, J J; Hickman, F W; Fanning, G R

    1981-12-04

    A previously undescribed marine bacterium, Vibrio damsela, was isolated from naturally occurring skin ulcers on a species of temperate-water damselfish, the blacksmith (Chromis punctipinnis). Laboratory infection of the blacksmith with Vibrio damsela produced similar ulcers. Vibrio damsela was pathogenic for four other species of damselfish but not for members of other families of fish. The bacterium has also been isolated from water and from two human wounds and may be a cause of human disease.

  16. Naphthalecin, a novel antibiotic produced by the anaerobic bacterium, Sporotalea colonica sp. nov.

    PubMed

    Ezaki, Masami; Muramatsu, Hideyuki; Takase, Shigehiro; Hashimoto, Michizane; Nagai, Koji

    2008-04-01

    A novel antibiotic naphthalecin was purified and isolated from the cells of an anaerobic bacterium isolated from a soil sample. This antibiotic contained a naphthalene moiety, so named as naphthalecin, and showed antibacterial activity against gram positive species. The producing strain, an obligate anaerobe, was identified as a new species of the genus Sporotalea. Identification of the bacterium, cultivation, purification, structure determination, and antibacterial activity are shown.

  17. Cultivable microbiota of Lithobates catesbeianus and advances in the selection of lactic acid bacteria as biological control agents in raniculture.

    PubMed

    Mendoza, Gabriela Montel; Pasteris, Sergio E; Ale, Cesar E; Otero, María C; Bühler, Marta I; Nader-Macías, María E Fátima

    2012-12-01

    The cultivable microbiota of skin and cloaca of captive Lithobates catesbeianus includes microorganisms generally accepted as beneficial and potentially pathogenic bacteria. In order to select a group of potentially probiotic bacteria, 136 isolates were evaluated for their surface properties and production of antagonistic metabolites. Then, 11 lactic acid bacteria (LAB) strains were selected and identified as Lactobacillus plantarum, Lb. brevis, Pediococcus pentosaceus, Lactococcus lactis, L. garvieae and Enterococcus gallinarum. Studies of compatibility indicate that all the strains could be included in a multi-strain probiotic, with the exception of Ent. gallinarum CRL 1826 which inhibited LAB species through a bacteriocin-like metabolite. These results contribute to the design of a probiotic product to improve the sanitary status of bullfrogs in intensive culture systems, to avoid the use of antibiotics and thus to reduce production costs. It could also be an alternative to prevent infectious diseases during the ex situ breeding of amphibian species under threat of extinction.

  18. Phytase activity of lactic acid bacteria and their impact on the solubility of minerals from wholemeal wheat bread.

    PubMed

    Cizeikiene, Dalia; Juodeikiene, Grazina; Bartkiene, Elena; Damasius, Jonas; Paskevicius, Algimantas

    2015-01-01

    The objective of this study was to determinate phytase activity of bacteriocins producing lactic acid bacteria previously isolated from spontaneous rye sourdough. The results show that the highest extracellular phytase activity produces Pediococcus pentosaceus KTU05-8 and KTU05-9 strains with a volumetric phytase activity of 32 and 54 U/ml, respectively, under conditions similar to leavening of bread dough (pH 5.5 and 30 °C). In vitro studies in simulated gastrointestinal tract media pH provide that bioproducts prepared with P. pentosaceus strains used in wholemeal wheat bread preparation increase solubility of iron, zinc, manganese, calcium and phosphorus average 30%. Therefore, P. pentosaceus KTU05-9 and KTU05-8 strains could be recommended to use as a starter for sourdough preparation for increasing of mineral bioavailability from wholemeal wheat bread.

  19. Metabolomics evaluation of the impact of smokeless tobacco exposure on the oral bacterium Capnocytophaga sputigena.

    PubMed

    Sun, Jinchun; Jin, Jinshan; Beger, Richard D; Cerniglia, Carl E; Yang, Maocheng; Chen, Huizhong

    2016-10-01

    The association between exposure to smokeless tobacco products (STP) and oral diseases is partially due to the physiological and pathological changes in the composition of the oral microbiome and its metabolic profile. However, it is not clear how STPs affect the physiology and ecology of oral microbiota. A UPLC/QTof-MS-based metabolomics study was employed to analyze metabolic alterations in oral bacterium, Capnocytophaga sputigena as a result of smokeless tobacco exposure and to assess the capability of the bacterium to metabolize nicotine. Pathway analysis of the metabolome profiles indicated that smokeless tobacco extracts caused oxidative stress in the bacterium. The metabolomics data also showed that the arginine-nitric oxide pathway was perturbed by the smokeless tobacco treatment. Results also showed that LC/MS was useful in identifying STP constituents and additives, including caffeine and many flavoring compounds. No significant changes in levels of nicotine and its major metabolites were found when C. sputigena was cultured in a nutrient rich medium, although hydroxylnicotine and cotinine N-oxide were detected in the bacterial metabolites suggesting that nicotine metabolism might be present as a minor degradation pathway in the bacterium. Study results provide new insights regarding the physiological and toxicological effects of smokeless tobacco on oral bacterium C. sputigena and associated oral health as well as measuring the ability of the oral bacterium to metabolize nicotine.

  20. Antifungal Activity of Lactic Acid Bacteria Strains Isolated from Natural Honey against Pathogenic Candida Species

    PubMed Central

    Bulgasem, Bulgasem Y.; Lani, Mohd Nizam; Wan Yusoff, Wan Mohtar; Fnaish, Sumaya G.

    2016-01-01

    The role of lactic acid bacteria (LAB) in honey as antifungal activity has received little attention and their mechanism of inhibitory of fungi is not fully understood. In this study, LAB were isolated from honey samples from Malaysia, Libya, Saudi Arabia, and Yemen. Twenty-five isolates were confirmed LAB by catalase test and Gram staining, and were screened for antifungal activity. Four LAB showed inhibitory activity against Candida spp. using the dual agar overlay method. And they were identified as Lactobacillus plantarum HS isolated from Al-Seder honey, Lactobacillus curvatus HH isolated from Al-Hanon honey, Pediococcus acidilactici HC isolated from Tualang honey and Pediococcus pentosaceus HM isolated from Al-Maray honey by the 16S rDNA sequence. The growth of Candida glabrata ATCC 2001 was strongly inhibited (>15.0 mm) and (10~15 mm) by the isolates of L. curvatus HH and P. pentosaceus HM, respectively. The antifungal activity of the crude supernatant (cell free supernatant, CFS) was evaluated using well diffusion method. The CFS showed high antifungal activity against Candida spp. especially The CFS of L. curvatus HH was significantly (p < 0.05) inhibited growth of C. glabrata ATCC 2001, C. parapsilosis ATCC 2201, and C. tropicalis ATCC 750 with inhibitory zone 22.0, 15.6, and 14.7 mm, respectively. While CFS of P. pentosaceus HM was significantly (p < 0.05) effective against C. krusei, C. glabrata, and C. albicans with inhibition zone 17.2, 16.0, and 13.3 mm, respectively. The results indicated that LAB isolated from honey produced compounds which can be used to inhibit the growth of the pathogenic Candida species. PMID:28154488

  1. Antifungal Activity of Lactic Acid Bacteria Strains Isolated from Natural Honey against Pathogenic Candida Species.

    PubMed

    Bulgasem, Bulgasem Y; Lani, Mohd Nizam; Hassan, Zaiton; Wan Yusoff, Wan Mohtar; Fnaish, Sumaya G

    2016-12-01

    The role of lactic acid bacteria (LAB) in honey as antifungal activity has received little attention and their mechanism of inhibitory of fungi is not fully understood. In this study, LAB were isolated from honey samples from Malaysia, Libya, Saudi Arabia, and Yemen. Twenty-five isolates were confirmed LAB by catalase test and Gram staining, and were screened for antifungal activity. Four LAB showed inhibitory activity against Candida spp. using the dual agar overlay method. And they were identified as Lactobacillus plantarum HS isolated from Al-Seder honey, Lactobacillus curvatus HH isolated from Al-Hanon honey, Pediococcus acidilactici HC isolated from Tualang honey and Pediococcus pentosaceus HM isolated from Al-Maray honey by the 16S rDNA sequence. The growth of Candida glabrata ATCC 2001 was strongly inhibited (>15.0 mm) and (10~15 mm) by the isolates of L. curvatus HH and P. pentosaceus HM, respectively. The antifungal activity of the crude supernatant (cell free supernatant, CFS) was evaluated using well diffusion method. The CFS showed high antifungal activity against Candida spp. especially The CFS of L. curvatus HH was significantly (p < 0.05) inhibited growth of C. glabrata ATCC 2001, C. parapsilosis ATCC 2201, and C. tropicalis ATCC 750 with inhibitory zone 22.0, 15.6, and 14.7 mm, respectively. While CFS of P. pentosaceus HM was significantly (p < 0.05) effective against C. krusei, C. glabrata, and C. albicans with inhibition zone 17.2, 16.0, and 13.3 mm, respectively. The results indicated that LAB isolated from honey produced compounds which can be used to inhibit the growth of the pathogenic Candida species.

  2. Biodiversity of lactic acid bacteria and yeasts in spontaneously-fermented buckwheat and teff sourdoughs.

    PubMed

    Moroni, Alice V; Arendt, Elke K; Dal Bello, Fabio

    2011-05-01

    In this study, four different laboratory scale gluten-free (GF) sourdoughs were developed from buckwheat or teff flours. The fermentations were initiated by the spontaneous biota of the flours and developed under two technological conditions (A and B). Sourdoughs were propagated by continuous back-slopping until the stability was reached. The composition of the stable biota occurring in each sourdough was assessed using both culture-dependent and -independent techniques. Overall, a broad spectrum of lactic acid bacteria (LAB) and yeasts species, belonging mainly to the genera Lactobacillus, Pediococcus, Leuconostoc, Kazachstania and Candida, were identified in the stable sourdoughs. Buckwheat and teff sourdoughs were dominated mainly by obligate or facultative heterofermentative LAB, which are commonly associated with traditional wheat or rye sourdoughs. However, the spontaneous fermentation of the GF flours resulted also in the selection of species which are not consider endemic to traditional sourdoughs, i.e. Pediococcus pentosaceus, Leuconostoc holzapfelii, Lactobacillus gallinarum, Lactobacillus vaginalis, Lactobacillus sakei, Lactobacillus graminis and Weissella cibaria. In general, the composition of the stable biota was strongly affected by the fermentation conditions, whilst Lactobacillus plantarum dominated in all buckwheat sourdoughs. Lactobacillus pontis is described for the first time as dominant species in teff sourdough. Among yeasts, Saccharomyces cerevisiae and Candida glabrata dominated teff sourdoughs, whereas the solely Kazachstania barnetti was isolated in buckwheat sourdough developed under condition A. This study allowed the identification and isolation of LAB and yeasts species which are highly competitive during fermentation of buckwheat or teff flours. Representatives of these species can be selected as starters for the production of sourdough destined to GF bread production.

  3. Cloning of a Novel 6-Chloronicotinic Acid Chlorohydrolase from the Newly Isolated 6-Chloronicotinic Acid Mineralizing Bradyrhizobiaceae Strain SG-6C

    PubMed Central

    Pandey, Rinku; Khan, Fazlurrahman; Dorrian, Susan J.; Balotra, Sahil; Russell, Robyn J.; Oakeshott, John G.; Pandey, Gunjan

    2012-01-01

    A 6-chloronicotinic acid mineralizing bacterium was isolated from enrichment cultures originating from imidacloprid-contaminated soil samples. This Bradyrhizobiaceae, designated strain SG-6C, hydrolytically dechlorinated 6-chloronicotinic acid to 6-hydroxynicotinic acid, which was then further metabolised via the nicotinic acid pathway. This metabolic pathway was confirmed by growth and resting cell assays using HPLC and LC-MS studies. A candidate for the gene encoding the initial dechlorination step, named cch2 (for 6-chloronicotinic acid chlorohydrolase), was identified using genome sequencing and its function was confirmed using resting cell assays on E. coli heterologously expressing this gene. The 464 amino acid enzyme was found to be a member of the metal dependent hydrolase superfamily with similarities to the TRZ/ATZ family of chlorohydrolases. We also provide evidence that cch2 was mobilized into this bacterium by an Integrative and Conjugative Element (ICE) that feeds 6-hydroxynicotinic acid into the existing nicotinic acid mineralization pathway. PMID:23226482

  4. Role of specific components from commercial inactive dry yeast winemaking preparations on the growth of wine lactic acid bacteria.

    PubMed

    Andújar-Ortiz, Inmaculada; Pozo-Bayón, Maria Angeles; García-Ruiz, Almudena; Moreno-Arribas, M Victoria

    2010-07-28

    The role of specific components from inactive dry yeast preparations widely used in winemaking on the growth of three representative wine lactic acid bacteria (Oenococcus oeni, Lactobacillus hilgardii and Pediococcus pentosaceus) has been studied. A pressure liquid extraction technique using solvents of different polarity was employed to obtain extracts with different chemical composition from the inactive dry yeast preparations. Each of the extracts was assayed agai