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Sample records for gordonia jacobaea mv-26

  1. Influence of culture conditions of Gordonia jacobaea MV-26 on canthaxanthin production.

    PubMed

    Veiga-Crespo, Patricia; Blasco, Lucia; Rosa-Dos-Santos, Fernando; Poza, Margarita; Villa, Tomas G

    2005-03-01

    Commercial interest in the use of natural pigments isolated from microorganisms has increased in recent years; hence, molecules belonging to the polyisoprenoid group (i.e. beta-carotene, astaxanthin, and canthaxanthin) have been the focus of much attention. The bacterium Gordonia jacobaea readily synthesizes and accumulates large amounts of canthaxanthin (beta-beta'-carotene-4,4'-dione), which is widely used in the food and cosmetics industries. In the present work, the effects of different low-cost raw materials on fermentation and canthaxanthin accumulation by a hyperpigmented strain of G. jacobaea were studied. Canthaxanthin production and peak levels of accumulation varied according to the different media used. PMID:15906262

  2. Analysis of canthaxanthin production by Gordonia jacobaea.

    PubMed

    Veiga-Crespo, Patricia; Vinuesa, Teresa; Viñas, Miquel; Villa, Tomás G

    2012-01-01

    Commercial interest in the use of natural pigments isolated from microorganisms has increased in recent years; hence, molecules belonging to the polyisoprenoid group (i.e., β-carotene, astaxanthin, and canthaxanthin) have been the focus of much attention. The bacterium Gordonia jacobaea readily synthesizes and accumulates large amounts of canthaxanthin (β-β'-carotene-4,4'-dione), which is widely used in the food and cosmetics industries. In the present work, the integral process of canthaxanthin production by G. jacobaea is analyzed together with its application as natural sources for the industry. A great influence of culture media is observed on canthaxanthin levels. Also, the ability is found of extract the pigments with ethanol from bacteria. The concentration of the samples is a crucial point of the process, being mandatory to discard any process of heating the samples, because this provoked the pigment degradation. Despite this, the described method allows to consider G. jacobaea as a potential canthaxanthin producer for the industry. PMID:22623301

  3. Draft Genome Sequence of the Bacterium Gordonia jacobaea, a New Member of the Gordonia Genus.

    PubMed

    Jiménez-Galisteo, G; Villa, T G; Vinuesa, T; Viñas, M; Domínguez, A; Muñoz, E

    2015-01-01

    Gordonia jacobaea was isolated and characterized in the Department of Microbiology, University of Santiago de Compostela, in 2000. Here we present the draft genome sequence of this species, which will improve our understanding of the diversity and the relation of the cell wall proteins of G. jacobaea with other mycolata. PMID:26337890

  4. Draft Genome Sequence of the Bacterium Gordonia jacobaea, a New Member of the Gordonia Genus

    PubMed Central

    Jiménez-Galisteo, G.; Villa, T. G.; Vinuesa, T.; Viñas, M.; Domínguez, A.

    2015-01-01

    Gordonia jacobaea was isolated and characterized in the Department of Microbiology, University of Santiago de Compostela, in 2000. Here we present the draft genome sequence of this species, which will improve our understanding of the diversity and the relation of the cell wall proteins of G. jacobaea with other mycolata. PMID:26337890

  5. Analysis of canthaxanthin and related pigments from Gordonia jacobaea mutants.

    PubMed

    de Miguel, T; Sieiro, C; Poza, M; Villa, T G

    2001-03-01

    A collection of 43 mutant strains of the bacterium Gordonia jacobaea was obtained by means of ethyl methanesulfonate treatment, and the strains were selected for their different pigmentation with respect to the wild-type strain. None of the mutants showed auxotrophy. They all showed good genetic stability and a growth rate similar to that of the parental strain. Canthaxanthin and other carotenoids from these mutants were extracted with acetone and ethanol and separated by high-performance liquid chromatography (HPLC). These HPLC analyses, together with spectrophotometric detection at 480 nm, revealed variations in the pigment contents of the different mutant strains. PMID:11312835

  6. Isolation and taxonomic study of a new canthaxanthin-containing bacterium, Gordonia jacobaea MV-1 sp. nov.

    PubMed

    de Miguel, T; Sieiro, C; Poza, M; Villa, T G

    2000-06-01

    This article describes the isolation and taxonomic study of a coryneform isolate of a new Gordonia species (G. jacobaea), strain MV-1, which accumulates several carotenoids, including the ketocarotenoid trans-canthaxanthin. Identification of this new isolate by morphobiochemical methods did not allow unambiguous taxon assignment, but sequencing of the 16S rRNA gene clearly pointed to the genus Gordonia, Gordonia sputi being the closest fit. Differences in certain transversions/transitions in otherwise very well-conserved sequences of the described Gordonia species supported the proposal of this new taxon. The fact that both the best growth and best pigmentation were obtained with glucose, an inexpensive carbon source and at an industrially suitable temperature, suggests that this new bacterial strain may have good potential for the industrial production of canthaxanthin. PMID:11001540

  7. Gordonia otitidis sp. nov., isolated from a patient with external otitis.

    PubMed

    Iida, Soji; Taniguchi, Hiroko; Kageyama, Akiko; Yazawa, Katsukiyo; Chibana, Hiroji; Murata, Shota; Nomura, Fumio; Kroppenstedt, Reiner M; Mikami, Yuzuru

    2005-09-01

    The taxonomic positions of two clinically isolated actinomycetes were established using a polyphasic approach. The two strains, IFM 10032(T), isolated from ear discharge of a 28-year-old Japanese female patient with external otitis, and IFM 10148, isolated from pleural fluid of a 60-year-old Japanese male patient with bronchitis, possessed meso-diaminopimelic acid as the diagnostic amino acid, MK-9(H(2)) as the predominant menaquinone and mycolic acids ranging from 58 to 64 carbons. The 16S rRNA gene sequences of the two strains were most closely related to those of Gordonia aichiensis, Gordonia sputi and 'Gordonia jacobaea'. Differences in several phenotypic characteristics together with genotypic distinctiveness distinguish strains IFM 10032(T) and IFM 10148 from these three species. DNA-DNA hybridization results and the combination of genotypic and phenotypic data showed that the two strains belong to a single species, and merit recognition of a novel species within the genus Gordonia. The name proposed for this taxon is Gordonia otitidis sp. nov.; the type strain is IFM 10032(T) (=DSM 44809(T)=JCM 12355(T)=NBRC 100426(T)). PMID:16166681

  8. Genome Sequence of Gordonia Phage Yvonnetastic.

    PubMed

    Pope, Welkin H; Bandyopadhyay, Anshika; Carlton, Meghan L; Kane, Meghan T; Panchal, Niyati J; Pham, Yvonne C; Reynolds, Zachary J; Sapienza, Michael S; German, Brian A; McDonnell, Jill E; Schafer, Claire E; Yu, Victor J; Furbee, Emily C; Grubb, Sarah R; Warner, Marcie H; Montgomery, Matthew T; Garlena, Rebecca A; Russell, Daniel A; Jacobs-Sera, Deborah; Hatfull, Graham F

    2016-01-01

    Gordonia bacteriophage Yvonnetastic was isolated from soil in Pittsburgh, PA, using Gordonia terrae 3612 as a host. Yvonnetastic has siphoviral morphology and a genome of 98,136 bp, with 198 predicted protein-coding genes and five tRNA genes. Yvonnetastic does not share substantial sequence similarity with other sequenced bacteriophage genomes. PMID:27389265

  9. Genome Sequence of Gordonia Phage Yvonnetastic

    PubMed Central

    Bandyopadhyay, Anshika; Carlton, Meghan L.; Kane, Meghan T.; Panchal, Niyati J.; Pham, Yvonne C.; Reynolds, Zachary J.; Sapienza, Michael S.; German, Brian A.; McDonnell, Jill E.; Schafer, Claire E.; Yu, Victor J.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Montgomery, Matthew T.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2016-01-01

    Gordonia bacteriophage Yvonnetastic was isolated from soil in Pittsburgh, PA, using Gordonia terrae 3612 as a host. Yvonnetastic has siphoviral morphology and a genome of 98,136 bp, with 198 predicted protein-coding genes and five tRNA genes. Yvonnetastic does not share substantial sequence similarity with other sequenced bacteriophage genomes. PMID:27389265

  10. Genome Sequence of Gordonia Bacteriophage Lucky10

    PubMed Central

    Brown, Aleks K.; Fisher, Daniel J.; Okwiya, Nicholas H.; Savage, Kaitlyn A.; German, Brian A.; McDonnell, Jill E.; Schafer, Claire E.; Yu, Victor J.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Montgomery, Matthew T.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2016-01-01

    Lucky10 is a newly isolated phage of Gordonia terrae 3612 that was recovered from a soil sample in Pittsburgh, PA. Lucky10 has siphoviral morphology and a double-stranded DNA (dsDNA) genome of 42,979 bp, with 70 predicted protein-coding genes. Lucky10 shows little similarity to previously reported Gordonia phages. PMID:27365346

  11. Genome Sequence of Gordonia Phage Emalyn

    PubMed Central

    Guido, Madeline J.; Iyengar, Pragnya; Nigra, Jonathan T.; Serbin, Matthew B.; Kasturiarachi, Naomi S.; Pressimone, Catherine A.; Schiebel, Johnathon G.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Montgomery, Matthew T.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2016-01-01

    Emalyn is a newly isolated bacteriophage of Gordonia terrae 3612 and has a double-stranded DNA genome 43,982 bp long with 67 predicted protein-encoding genes, 32 of which we can assign putative functions. Emalyn has a prolate capsid and has extensive nucleotide similarity with several previously sequenced phages. PMID:27516499

  12. Genome Sequence of Gordonia Phage Emalyn.

    PubMed

    Pope, Welkin H; Guido, Madeline J; Iyengar, Pragnya; Nigra, Jonathan T; Serbin, Matthew B; Kasturiarachi, Naomi S; Pressimone, Catherine A; Schiebel, Johnathon G; Furbee, Emily C; Grubb, Sarah R; Warner, Marcie H; Montgomery, Matthew T; Garlena, Rebecca A; Russell, Daniel A; Jacobs-Sera, Deborah; Hatfull, Graham F

    2016-01-01

    Emalyn is a newly isolated bacteriophage of Gordonia terrae 3612 and has a double-stranded DNA genome 43,982 bp long with 67 predicted protein-encoding genes, 32 of which we can assign putative functions. Emalyn has a prolate capsid and has extensive nucleotide similarity with several previously sequenced phages. PMID:27516499

  13. Chemical ecology of the cinnabar moth ( Tyria jacobaeae ) on a newly recorded host Senecio adonidifolius

    NASA Astrophysics Data System (ADS)

    Vrieling, Klaas

    2006-09-01

    The cinnabar moth ( Tyria jacobaeae, Arctiidae) normally feeds on Senecio jacobaea in the field. For the first time, naturally occurring populations of T. jacobaeae have been found thriving on Senecio adonidifolius, even though the moth's preferred host, S. jacobaea, is available within 50-400 m. In the laboratory, the cinnabar moth has been shown to feed on and develop on S. adonidifolius despite its different leaf morphology, pyrrolizidine alkaloid (PA) profile and a large taxonomic distance to S. jacobaea. Here I examined whether T. jacobaeae has adapted to this new host in the field using adult oviposition behavior and plant acquired defense chemistry in pupae as criteria. Choice tests indicated local adaptation to this newly recorded host. T. jacobaeae reared on S. adonidifolius hosts laid more egg batches and total eggs on it than T. jacobaeae from S. jacobaea. The egg batches were smaller on S. adonidifolius possibly due to highly pinnate thread-like structure of its leaves. The bouquet of plant acquired PAs and the insect metabolized callimorphine in pupae differed widely between pupae collected from the two hosts. T. jacobaeae pupae taken from S. adonidifolius hosts contained more of the insect metabolized callimorphine than pupae taken from S. jacobaea hosts, but they did not differ in total PA concentration. Pupae taken from S. jacobaea hosts contained more unmetabolized plant PA's than pupae from S. adonidifolius hosts. Additionally, 10% of T. jacobaeae larvae taken from S. adonidifolius in Biausse were infested with Carcelia dubia, a parasitic and rare tachinid fly that typically attacks arctiid moths.

  14. Genome Sequences of Gordonia Phages Bowser and Schwabeltier

    PubMed Central

    Montgomery, Matthew T.; Arnold, Zachary M.; Basina, Aleksandra; Iyer, Ankitha M.; Stoner, Ty H.; Kasturiarachi, Naomi S.; Pressimone, Catherine A.; Schiebel, Johnathon G.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2016-01-01

    Gordonia phages Bowser and Schwabeltier are newly isolated phages infecting Gordonia terrae 3612. Bowser and Schwabeltier have similar siphoviral morphologies and their genomes are related to each other, but not to other phages. Their lysis cassettes are atypically situated among virion tail genes, and Bowser encodes two tyrosine integrases. PMID:27516498

  15. Genome Sequence of Gordonia Phage BetterKatz

    PubMed Central

    Berryman, Emily N.; Forrest, Kaitlyn M.; McHale, Lilliana; Wertz, Anthony T.; Zhuang, Zenas; Kasturiarachi, Naomi S.; Pressimone, Catherine A.; Schiebel, Johnathon G.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Montgomery, Matthew T.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2016-01-01

    BetterKatz is a bacteriophage isolated from a soil sample collected in Pittsburgh, Pennsylvania using the host Gordonia terrae 3612. BetterKatz’s genome is 50,636 bp long and contains 75 predicted protein-coding genes, 35 of which have been assigned putative functions. BetterKatz is not closely related to other sequenced Gordonia phages. PMID:27516497

  16. Genome Sequence of Gordonia Phage BetterKatz.

    PubMed

    Pope, Welkin H; Berryman, Emily N; Forrest, Kaitlyn M; McHale, Lilliana; Wertz, Anthony T; Zhuang, Zenas; Kasturiarachi, Naomi S; Pressimone, Catherine A; Schiebel, Johnathon G; Furbee, Emily C; Grubb, Sarah R; Warner, Marcie H; Montgomery, Matthew T; Garlena, Rebecca A; Russell, Daniel A; Jacobs-Sera, Deborah; Hatfull, Graham F

    2016-01-01

    BetterKatz is a bacteriophage isolated from a soil sample collected in Pittsburgh, Pennsylvania using the host Gordonia terrae 3612. BetterKatz's genome is 50,636 bp long and contains 75 predicted protein-coding genes, 35 of which have been assigned putative functions. BetterKatz is not closely related to other sequenced Gordonia phages. PMID:27516497

  17. Cholesterol Degradation by Gordonia cholesterolivorans ▿ †

    PubMed Central

    Drzyzga, O.; Fernández de las Heras, L.; Morales, V.; Navarro Llorens, J. M.; Perera, J.

    2011-01-01

    This paper reports physiological and genetic data about the type strain Gordonia cholesterolivorans, a strain that is able to degrade steroid compounds containing a long carbon side chain such as cholesterol (C27), cholestenone (C27), ergosterol (C28), and stigmasterol (C29). The length of the carbon side chain appears to be of great importance for this bacterium, as the strain is unable to grow using steroids with a shorter or nonaliphatic carbon side chain such as cholic acid (C24), progesterone (C21), testosterone, androsterone, 4-androstene-3,17-dione (all C19), and further steroids. This study also demonstrates that the degradation of cholesterol is a quite common feature of the genus Gordonia by comparing Gordonia cholesterolivorans with some other species of this genus (e.g., G. sihwensis, G. hydrophobica, G. australis, and G. neofelifaecis). Pyrosequencing of the genome of G. cholesterolivorans led to the identification of two conventional cholesterol oxidase genes on an 8-kb and a 12.8-kb genomic fragment with genetic organizations that are quite unique as compared to the genomes of other cholesterol-degrading bacteria sequenced so far. The identified two putative cholesterol oxidases of G. cholesterolivorans are both intracellularly acting enzymes of the class I type. Whereas one of these two cholesterol oxidases (ChoOx-1) shows high identity with an oxidoreductase of the opportunistic pathogen G. bronchialis and is not transcribed during growth with cholesterol, the other one (ChoOx-2) appears phylogenetically closer to cholesterol oxidases from members of the genus Rhodococcus and is transcribed constitutively. By using targeted gene disruption, a G. cholesterolivorans ChoOx-2 gene mutant strain that was unable to grow with steroids was obtained. PMID:21622796

  18. Species by environment interactions affect pyrrolizidine alkaloid expression in Senecio jacobaea, Senecio aquaticus, and their hybrids.

    PubMed

    Kirk, Heather; Vrieling, Klaas; Van Der Meijden, Eddy; Klinkhamer, Peter G L

    2010-04-01

    We examined the effects of water and nutrient availability on the expression of the defense pyrrolizidine alkaloids (PAs) in Senecio jacobaea and S. aquaticus. Senecio jacobaea, and S. aquaticus are adapted to different natural habitats, characterized by differing abiotic conditions and different selection pressures from natural enemies. We tested if PA concentration and diversity are plastic over a range of water and nutrient treatments, and also whether such plasticity is dependent on plant species. We also tested the hypothesis that hybridization may contribute to PA diversity within plants, by comparing PA expression in parental species to that in artificially generated F(1) hybrids, and also in later generation natural hybrids between S. jacobaea and S. aquaticus. We showed that total PA concentration in roots and shoots is not dependent on species, but that species determines the pattern of PA diversification. Pyrrolizidine alkaloid diversity and concentration are both dependent on environmental factors. Hybrids produce a putatively novel PA, and this PA is conserved in natural hybrids, that are backcrossed to S. jacobaea. Natural hybrids that are backcrossed several times to S. jacobaea are with regard to PA diversity significantly different from S. jacobaea but not from S. aquaticus, while F(1) hybrids are in all cases more similar to S. jacobaea. These results collectively suggest that PA diversity is under the influence of natural selection. PMID:20309618

  19. Genome Sequences of Gordonia terrae Phages Benczkowski14 and Katyusha

    PubMed Central

    Benczkowski, Matthew S.; Green, Daryn E.; Hwang, Melina; Kennedy, Bryan; Kocak, Bradley; Kruczek, Ellen; Lin, Leon; Moretti, Matthew L.; Onelangsy, Faith L.; Mezghani, Nadia; Milliken, Katherine A.; Toner, Chelsea L.; Thompson, Paige K.; Ulbrich, Megan C.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Montgomery, Matthew T.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2016-01-01

    Bacteriophages Katyusha and Benczkowski14 are newly isolated phages that infect Gordonia terrae 3612. Both have siphoviral morphologies with isometric heads and long tails (500 nm). The genomes are 75,380 bp long and closely related, and the tape measure genes (9 kbp) are among the largest to be identified. PMID:27340062

  20. Genome Sequences of Gordonia terrae Phages Benczkowski14 and Katyusha.

    PubMed

    Pope, Welkin H; Benczkowski, Matthew S; Green, Daryn E; Hwang, Melina; Kennedy, Bryan; Kocak, Bradley; Kruczek, Ellen; Lin, Leon; Moretti, Matthew L; Onelangsy, Faith L; Mezghani, Nadia; Milliken, Katherine A; Toner, Chelsea L; Thompson, Paige K; Ulbrich, Megan C; Furbee, Emily C; Grubb, Sarah R; Warner, Marcie H; Montgomery, Matthew T; Garlena, Rebecca A; Russell, Daniel A; Jacobs-Sera, Deborah; Hatfull, Graham F

    2016-01-01

    Bacteriophages Katyusha and Benczkowski14 are newly isolated phages that infect Gordonia terrae 3612. Both have siphoviral morphologies with isometric heads and long tails (500 nm). The genomes are 75,380 bp long and closely related, and the tape measure genes (9 kbp) are among the largest to be identified. PMID:27340062

  1. Genome Sequences of Gordonia Phages Hotorobo, Woes, and Monty

    PubMed Central

    Davis, Jameson P.; O’Shea, Sirinya; Pfeiffer, Anastasia C.; Rich, Alexandra N.; Xue, Jason C.; Shedlock, Kathleen A.; Stanton, Ann-Catherine J.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Montgomery, Matthew T.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2016-01-01

    Hotorobo, Woes, and Monty are newly isolated bacteriophages of Gordonia terrae 3612. The three phages are related, and their genomes are similarly sized (76,972 bp, 73,752 bp, and 75,680 bp for Hotorobo, Woes, and Monty, respectively) and organized. They have extremely long tails and among the longest tape measure protein genes described to date. PMID:27516500

  2. Genome Sequences of Gordonia terrae Bacteriophages Phinally and Vivi2

    PubMed Central

    Anderson, Kaitlyn C.; Arora, Charu; Bortz, Michael E.; Burnet, George; Conover, David H.; D’Incau, Gina M.; Ghobrial, Jonathan A.; Jonas, Audrey L.; Migdal, Emily J.; Rote, Nicole L.; German, Brian A.; McDonnell, Jill E.; Mezghani, Nadia; Schafer, Claire E.; Thompson, Paige K.; Ulbrich, Megan C.; Yu, Victor J.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Montgomery, Matthew T.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2016-01-01

    Bacteriophages Phinally and Vivi2 were isolated from soil from Pittsburgh, Pennsylvania, USA, using host Gordonia terrae 3612. The Phinally and Vivi2 genomes are 59,265 bp and 59,337 bp, respectively, and share sequence similarity with each other and with GTE6. Fewer than 25% of the 87 to 89 putative genes have predictable functions. PMID:27540050

  3. Genome Sequences of Gordonia terrae Bacteriophages Phinally and Vivi2.

    PubMed

    Pope, Welkin H; Anderson, Kaitlyn C; Arora, Charu; Bortz, Michael E; Burnet, George; Conover, David H; D'Incau, Gina M; Ghobrial, Jonathan A; Jonas, Audrey L; Migdal, Emily J; Rote, Nicole L; German, Brian A; McDonnell, Jill E; Mezghani, Nadia; Schafer, Claire E; Thompson, Paige K; Ulbrich, Megan C; Yu, Victor J; Furbee, Emily C; Grubb, Sarah R; Warner, Marcie H; Montgomery, Matthew T; Garlena, Rebecca A; Russell, Daniel A; Jacobs-Sera, Deborah; Hatfull, Graham F

    2016-01-01

    Bacteriophages Phinally and Vivi2 were isolated from soil from Pittsburgh, Pennsylvania, USA, using host Gordonia terrae 3612. The Phinally and Vivi2 genomes are 59,265 bp and 59,337 bp, respectively, and share sequence similarity with each other and with GTE6. Fewer than 25% of the 87 to 89 putative genes have predictable functions. PMID:27540050

  4. Genome Sequences of Gordonia Phages Hotorobo, Woes, and Monty.

    PubMed

    Pope, Welkin H; Davis, Jameson P; O'Shea, Sirinya; Pfeiffer, Anastasia C; Rich, Alexandra N; Xue, Jason C; Shedlock, Kathleen A; Stanton, Ann-Catherine J; Furbee, Emily C; Grubb, Sarah R; Warner, Marcie H; Montgomery, Matthew T; Garlena, Rebecca A; Russell, Daniel A; Jacobs-Sera, Deborah; Hatfull, Graham F

    2016-01-01

    Hotorobo, Woes, and Monty are newly isolated bacteriophages of Gordonia terrae 3612. The three phages are related, and their genomes are similarly sized (76,972 bp, 73,752 bp, and 75,680 bp for Hotorobo, Woes, and Monty, respectively) and organized. They have extremely long tails and among the longest tape measure protein genes described to date. PMID:27516500

  5. Genome Sequences of Gordonia Phages BaxterFox, Kita, Nymphadora, and Yeezy.

    PubMed

    Pope, Welkin H; Bandla, Sharanya; Colbert, Alexandra K; Eichinger, Fiona G; Gamburg, Michelle B; Horiates, Stavroula G; Jamison, Jerrica M; Julian, Dana R; Moore, Whitney A; Murthy, Pranav; Powell, Meghan C; Smith, Sydney V; Mezghani, Nadia; Milliken, Katherine A; Thompson, Paige K; Toner, Chelsea L; Ulbrich, Megan C; Furbee, Emily C; Grubb, Sarah R; Warner, Marcie H; Montgomery, Matthew T; Garlena, Rebecca A; Russell, Daniel A; Jacobs-Sera, Deborah; Hatfull, Graham F

    2016-01-01

    Gordonia phages BaxterFox, Kita, Nymphadora, and Yeezy are newly characterized phages of Gordonia terrae, isolated from soil samples in Pittsburgh, Pennsylvania. These phages have genome lengths between 50,346 and 53,717 bp, and encode on average 84 predicted proteins. All have G+C content of 66.6%. PMID:27516501

  6. Genome Sequences of Gordonia Phages BaxterFox, Kita, Nymphadora, and Yeezy

    PubMed Central

    Bandla, Sharanya; Colbert, Alexandra K.; Eichinger, Fiona G.; Gamburg, Michelle B.; Horiates, Stavroula G.; Jamison, Jerrica M.; Julian, Dana R.; Moore, Whitney A.; Murthy, Pranav; Powell, Meghan C.; Smith, Sydney V.; Mezghani, Nadia; Milliken, Katherine A.; Thompson, Paige K.; Toner, Chelsea L.; Ulbrich, Megan C.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Montgomery, Matthew T.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2016-01-01

    Gordonia phages BaxterFox, Kita, Nymphadora, and Yeezy are newly characterized phages of Gordonia terrae, isolated from soil samples in Pittsburgh, Pennsylvania. These phages have genome lengths between 50,346 and 53,717 bp, and encode on average 84 predicted proteins. All have G+C content of 66.6%. PMID:27516501

  7. Complete genome sequence of Gordonia bronchialis type strain (3410T)

    SciTech Connect

    Ivanova, N; Sikorski, Johannes; Jando, Marlen; Lapidus, Alla L.; Nolan, Matt; Glavina Del Rio, Tijana; Tice, Hope; Copeland, A; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Saunders, Elizabeth H; Han, Cliff; Detter, J C; Brettin, Thomas S; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C

    2010-01-01

    Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a human-pathogenic organism that has been isolated from a large variety of human tissues. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Gordoniaceae. The 5,290,012 bp long genome with its 4,944 protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  8. Complete genome sequence of Gordonia bronchialis type strain (3410T)

    PubMed Central

    Ivanova, Natalia; Sikorski, Johannes; Jando, Marlen; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Chain, Patrick; Saunders, Elizabeth; Han, Cliff; Detter, John C.; Brettin, Thomas; Rohde, Manfred; Göker, Markus; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C.

    2010-01-01

    Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a human-pathogenic organism that has been isolated from a large variety of human tissues. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Gordoniaceae. The 5,290,012 bp long genome with its 4,944 protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304674

  9. Phylogenetic and phylogeographic evidence for a Pleistocene disjunction between Campanula jacobaea (Cape Verde Islands) and C. balfourii (Socotra).

    PubMed

    Alarcón, Marisa; Roquet, Cristina; García-Fernández, Alfredo; Vargas, Pablo; Aldasoro, Juan José

    2013-12-01

    Our understanding of processes that led to biogeographic disjunct patterns of plant lineages in Macaronesia, North Africa and Socotra remains poor. Here, we study a group of Campanula species distributed across these areas integrating morphological and reproductive traits with phylogenetic and phylogeographic data based on the obtention of sequences for 4 highly variable cpDNA regions and AFLP data. The phylogeny obtained shows a sister relationship between Campanula jacobaea (endemic to Cape Verde Islands) and C. balfourii (endemic to Socotra), thus revealing a striking disjunct pattern (8300 km). These species diverged around 1.0 Mya; AFLP and haplotype data suggest that no genetic interchange has occurred since then. Their closest taxon, C. hypocrateriformis, is endemic to SW Morocco. The archipelagos of Macaronesia and Socotra have probably acted as refugia for North-African species, leading to speciation through isolation. Although C. balfourii has a restricted distribution, its genetic variability suggests that its populations have suffered no bottlenecks. C. jacobaea is also genetically rich and its distribution across Cape Verde Islands seems to have been influenced by the NE-SW trade winds, which may also have favoured the admixture found among the populations of the three southern islands. Floral features of the morphologically hypervariable C. jacobaea were also measured to assess whether the taxon C. bravensis, described for some of the southeast populations of C. jacobaea, corresponds to a different evolutionary entity. We show that morphological variation in C. jacobaea does not correspond to any genetic or geographic group. PMID:23835079

  10. Gordonia didemni sp. nov. an actinomycete isolated from the marine ascidium Didemnum sp.

    PubMed

    de Menezes, Cláudia Beatriz Afonso; Afonso, Rafael Sanches; de Souza, Wallace Rafael; Parma, Márcia; de Melo, Itamar Soares; Zucchi, Tiago Domingues; Fantinatti-Garboggini, Fabiana

    2016-02-01

    A novel actinobacterium, designated isolate B204(T), was isolated from a marine ascidian Didemnum sp., collected from São Paulo, Brazil, and its taxonomic position established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological characteristics consistent with its classification in the genus Gordonia and formed a distinct phyletic line in the Gordonia 16S rRNA gene tree. It was closely related to Gordonia terrae DSM 43249(T) (99.9 % 16S rRNA gene sequence similarity) and Gordonia lacunae DSM 45085(T) (99.3 % 16S rRNA gene sequence similarity) but was distinguished from these strains by a moderate level of DNA-DNA relatedness (63.0 and 54.7 %) and discriminatory phenotypic properties. Based on the data obtained, the isolate B204(T) (=CBMAI 1069(T) = DSM 46679(T)) should therefore be classified as the type strain of a novel species of the genus Gordonia, for which the name Gordonia didemni sp. nov. is proposed. PMID:26678782

  11. Post-introduction evolution in the biological control agent Longitarsus jacobaeae (Coleoptera: Chrysomelidae).

    PubMed

    Szűcs, Marianna; Schaffner, Urs; Price, William J; Schwarzländer, Mark

    2012-12-01

    Rapid evolution has rarely been assessed in biological control systems despite the similarity with biological invasions, which are widely used as model systems. We assessed post-introduction climatic adaptation in a population of Longitarsus jacobaeae, a biological control agent of Jacobaea vulgaris, which originated from a low-elevation site in Italy and was introduced in the USA to a high-elevation site (Mt. Hood, Oregon) in the early 1980s. Life-history characteristics of beetle populations from Mt. Hood, from two low-elevation sites in Oregon (Italian origin) and from a high-elevation site from Switzerland were compared in common gardens. The performance of low- and high-elevation populations at a low- and a high-elevation site was evaluated using reciprocal transplants. The results revealed significant changes in aestival diapause and shifts in phenology in the Mt. Hood population, compared with the low-elevation populations. We found increased performance of the Mt. Hood population in its home environment compared with the low-elevation populations that it originated from. The results indicate that the beetles at Mt. Hood have adapted to the cooler conditions by life-history changes that conform to predictions based on theory and the phenology of the cold-adapted Swiss beetles. PMID:23346230

  12. Bacteriophages of wastewater foaming-associated filamentous Gordonia reduce host levels in raw activated sludge

    PubMed Central

    Liu, Mei; Gill, Jason J.; Young, Ry; Summer, Elizabeth J.

    2015-01-01

    Filamentous bacteria are a normal and necessary component of the activated sludge wastewater treatment process, but the overgrowth of filamentous bacteria results in foaming and bulking associated disruptions. Bacteriophages, or phages, were investigated for their potential to reduce the titer of foaming bacteria in a mixed-microbial activated sludge matrix. Foaming-associated filamentous bacteria were isolated from activated sludge of a commercial wastewater treatment plan and identified as Gordonia species by 16S rDNA sequencing. Four representative phages were isolated that target G. malaquae and two un-named Gordonia species isolates. Electron microscopy revealed the phages to be siphophages with long tails. Three of the phages - GordTnk2, Gmala1, and GordDuk1 - had very similar ~76 kb genomes, with >93% DNA identity. These genomes shared limited synteny with Rhodococcus equi phage ReqiDocB7 and Gordonia phage GTE7. In contrast, the genome of phage Gsput1 was smaller (43 kb) and was not similar enough to any known phage to be placed within an established phage type. Application of these four phages at MOIs of 5–15 significantly reduced Gordonia host levels in a wastewater sludge model by approximately 10-fold as compared to non-phage treated reactors. Phage control was observed for nine days after treatment. PMID:26349678

  13. A novel thermoalkaliphilic xylanase from Gordonia sp. is salt, solvent and surfactant tolerant.

    PubMed

    Kashyap, Radhika; Monika; Subudhi, Enketeswara

    2014-12-01

    Two aerobic bacterial consortia namely Con T and Con R were developed by enrichment technique from termite gut and cow dung respectively, using xylan as a sole carbon source. Molecular characterization of Con R based on 16S rRNA sequence analysis showed the presence of Pannonibacter sp. R-3 and Pseudoxanthomas sp. R-5. On the other hand, Con T showed the presence of Pseudoxanthomas sp. T-5, Cellulosimicrobium sp. T-21, and Gordonia sp. T-30. Being the maximum xylanase producer among the five isolates and being a novel xylanase producing bacterial genus, Gordonia sp. T-30 was selected. Xylanase produced by Gordonia sp. T-30 showed optimum activity at 60 °C and pH 9. Xylanase was 95% stable for 120 min at pH 9.0 and 98% stable at 60 °C for 90 min. Xylanase activity was stimulated in the presence of organic solvents such as petroleum ether, acetone, diethyl ether, n-hexane, and benzene. Detergent like cetyltrimethylammonium bromide and presence of NaCl also accelerated the xylanase function. Comparative evaluation was studied between sterilized and non-sterilized solid fermentation to produce xylanase by Gordonia sp. T-30 using various agricultural residues as growth substrate in cost effective manner. Industrially important features endowed by this xylanase make it a very promising candidate for food, feed, and fuel industry. PMID:24912946

  14. Draft Genome Sequence of Gordonia neofelifaecis NRRL B-59395, a Cholesterol-Degrading Actinomycete▿

    PubMed Central

    Ge, Fanglan; Li, Wei; Chen, Guiying; Liu, Yuchang; Zhang, Guangxiang; Yong, Bin; Wang, Qiong; Wang, Nan; Huang, Zhumei; Li, Weitian; Wang, Jing; Wu, Cheng; Xie, Qian; Liu, Gang

    2011-01-01

    We report a draft sequence of the genome of Gordonia neofelifaecis NRRL B-59395, a cholesterol-degrading actinomycete isolated from fresh feces of a clouded leopard (Neofelis nebulosa). As predicted, the reported genome contains several gene clusters for cholesterol degradation. This is the second available genome sequence of the family Gordoniaceae. PMID:21742880

  15. Sternal Osteomyelitis Caused by Gordonia bronchialis after Open-Heart Surgery

    PubMed Central

    Chang, Jeong-Hyun; Ji, Misuk; Hong, Hyo-Lim; Choi, Sang-Ho; Kim, Yang-Soo; Chung, Cheol-Hyun; Kim, Mi-Na

    2014-01-01

    We report the case of a deep sternal wound infection with sternal osteomyelitis caused by Gordonia bronchialis after open-heart surgery. The isolate was identified as a G. bronchialis by 16S rRNA and hsp65 gene sequencing, having initially been misidentified as a Rhodococcus by a commercial phenotypic identification system. PMID:25024874

  16. Genome Sequences of Gordonia terrae Phages Attis and SoilAssassin

    PubMed Central

    Biery, Daniel N.; Huff, Zachary T.; Huynh, Amy B.; McFadden, William M.; Mouat, Julia S.; Schneiderman, Scott E.; Song, Hannah; Szpak, Leah E.; Umbaugh, Melanie S.; German, Brian A.; McDonnell, Jill E.; Mezghani, Nadia; Schafer, Claire E.; Thompson, Paige K.; Ulbrich, Megan C.; Yu, Victor J.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Montgomery, Matthew T.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2016-01-01

    Attis and SoilAssassin are two closely related bacteriophages isolated on Gordonia terrae 3612 from separate soil samples in Pittsburgh, PA. The Attis and SoilAssassin genomes are 47,881 bp and 47,880 bp, respectively, and have 74 predicted protein-coding genes, including toxin-antitoxin systems, but no tRNAs. PMID:27365347

  17. Isolation and molecular characterization of a stationary phase promoter useful for gene expression in Gordonia.

    PubMed

    Singh, Pooja; Chachan, Sahil; Singhi, Divya; Srivastava, Preeti

    2016-10-10

    Gordonia are gram-positive bacteria belonging to Actinomycetes family with a wide variety of industrial and environmental applications. The genetic toolbox, however, is limited for manipulation of these organisms. In the present study, a new promoter has been isolated from Gordonia sp. IITR 100 and characterized in detail. The promoter was found to be functional in Escherichia coli. The minimal promoter was identified in a 166bp fragment by deletion mapping. The putative -35 and -10 hexamer showed four and five nucleotide matches respectively with the E. coli consensus sequence. Three direct repeats and an imperfect inverted repeat upstream to -35 were found. The isolated promoter was found to be six times stronger than the Pkan promoter observed by cloning lacZ downstream to each of them in a plasmid in E. coli. The β-galactosidase activity was maximum at stationary phase and found to be ~800MU for Gordonia sp. IITR 100 and E. coli. This is the first report of a stationary phase promoter isolated and characterized from Gordonia. PMID:27395430

  18. Genome Sequences of Gordonia Bacteriophages Obliviate, UmaThurman, and Guacamole.

    PubMed

    Pope, Welkin H; Akbar, Armaan F; Ayers, Taylor N; Belohoubek, Selena G; Chung, Connie F; Hartman, Allison C; Kayiti, Tejus; Kessler, Cecilia M; Koman, Philipp I; Kotovskiy, Grigoriy A; Morgan, Taylor M; Rohac, Rebecca M; Silva, Gabriela M; Willis, Charles E; Milliken, Katherine A; Shedlock, Kathleen A; Stanton, Ann-Catherine J; Toner, Chelsea L; Furbee, Emily C; Grubb, Sarah R; Warner, Marcie H; Montgomery, Matthew T; Garlena, Rebecca A; Russell, Daniel A; Jacobs-Sera, Deborah; Hatfull, Graham F

    2016-01-01

    We describe three newly isolated phages-Obliviate, UmaThurman, and Guacamole-that infect Gordonia terrae 3612. The three genomes are related to one another but are not closely related to other previously sequenced phages or prophages. The three phages are predicted to use integration-dependent immunity systems as described in several mycobacteriophages. PMID:27365348

  19. Genome Sequences of Gordonia Bacteriophages Obliviate, UmaThurman, and Guacamole

    PubMed Central

    Akbar, Armaan F.; Ayers, Taylor N.; Belohoubek, Selena G.; Chung, Connie F.; Hartman, Allison C.; Kayiti, Tejus; Kessler, Cecilia M.; Koman, Philipp I.; Kotovskiy, Grigoriy A.; Morgan, Taylor M.; Rohac, Rebecca M.; Silva, Gabriela M.; Willis, Charles E.; Milliken, Katherine A.; Shedlock, Kathleen A.; Stanton, Ann-Catherine J.; Toner, Chelsea L.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Montgomery, Matthew T.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2016-01-01

    We describe three newly isolated phages—Obliviate, UmaThurman, and Guacamole—that infect Gordonia terrae 3612. The three genomes are related to one another but are not closely related to other previously sequenced phages or prophages. The three phages are predicted to use integration-dependent immunity systems as described in several mycobacteriophages. PMID:27365348

  20. Parallel evolution in an invasive plant: effect of herbivores on competitive ability and regrowth of Jacobaea vulgaris.

    PubMed

    Lin, Tiantian; Klinkhamer, Peter G L; Vrieling, Klaas

    2015-07-01

    A shift in the composition of the herbivore guild in the invasive range is expected to select for plants with a higher competitive ability, a lower regrowth capacity and a lower investment in defence. We show here that parallel evolution took place in three geographically distinct invasive regions that differed significantly in climatic conditions. This makes it most likely that indeed the shifts in herbivore guilds were causal to the evolutionary changes. We studied competitive ability and regrowth of invasive and native Jacobaea vulgaris using an intraspecific competition set-up with and without herbivory. Without herbivores invasive genotypes have a higher competitive ability than native genotypes. The invasive genotypes were less preferred by the generalist Mamestra brassicae but more preferred by the specialist Tyria jacobaeae, consequently their competitive ability was significantly increased by the first and reduced by the latter. Invasive genotypes showed a lower regrowth ability in both herbivore treatments. PMID:25958781

  1. Arbuscular mycorrhizal colonization, plant chemistry, and aboveground herbivory on Senecio jacobaea

    NASA Astrophysics Data System (ADS)

    Reidinger, Stefan; Eschen, René; Gange, Alan C.; Finch, Paul; Bezemer, T. Martijn

    2012-01-01

    Arbuscular mycorrhizal fungi (AMF) can affect insect herbivores by changing plant growth and chemistry. However, many factors can influence the symbiotic relationship between plant and fungus, potentially obscuring experimental treatments and ecosystem impacts. In a field experiment, we assessed AMF colonization levels of individual ragwort ( Senecio jacobaea) plants growing in grassland plots that were originally sown with 15 or 4 plant species, or were unsown. We measured the concentrations of carbon, nitrogen and pyrrolizidine alkaloids (PAs), and assessed the presence of aboveground insect herbivores on the sampled plants. Total AMF colonization and colonization by arbuscules was lower in plots sown with 15 species than in plots sown with 4 species and unsown plots. AMF colonization was positively related to the cover of oxeye daisy ( Leucanthemum vulgare) and a positive relationship between colonization by arbuscules and the occurrence of a specialist seed-feeding fly ( Pegohylemyia seneciella) was found. The occurrence of stem-boring, leaf-mining and sap-sucking insects was not affected by AMF colonization. Total PA concentrations were negatively related to colonization levels by vesicles, but did not differ among the sowing treatments. No single factor explained the observed differences in AMF colonization among the sowing treatments or insect herbivore occurrence on S. jacobaea. However, correlations across the treatments suggest that some of the variation was due to the abundance of one plant species, which is known to stimulate AMF colonization of neighbouring plants, while AMF colonization was related to the occurrence of a specialist insect herbivore. Our results thus illustrate that in natural systems, the ecosystem impact of AMF through their influence on the occurrence of specialist insects can be recognised, but they also highlight the confounding effect of neighbouring plant species identity. Hence, our results emphasise the importance of field

  2. Draft Genome Sequence of Gordonia sihwensis Strain 9, a Branched Alkane-Degrading Bacterium

    PubMed Central

    Brown, Lisa M.; Gunasekera, Thusitha S.; Striebich, Richard C.

    2016-01-01

    Gordonia sihwensis strain 9 is a Gram-positive bacterium capable of efficient aerobic degradation of branched and normal alkanes. The draft genome of G. sihwensis S9 is 4.16 Mb in size, with 3,686 coding sequences and 68.1% G+C content. Alkane monooxygenase and P-450 cytochrome genes required for alkane degradation are predicted in G. sihwensis S9. PMID:27340079

  3. Chemical variation in Jacobaea vulgaris is influenced by the interaction of season and vegetation successional stage.

    PubMed

    Carvalho, Sabrina; Macel, Mirka; Mulder, Patrick P J; Skidmore, Andrew; van der Putten, Wim H

    2014-03-01

    Knowledge on spatio-temporal dynamics of plant primary and secondary chemistry under natural conditions is important to assess how plant defence varies in real field conditions. Plant primary and secondary chemistry is known to vary with both season and vegetation successional stage, however, in few studies these two sources of variation have been examined in combination. Here we examine variations in primary and secondary chemistry of Jacobaea vulgaris (Asteraceae) throughout the growing season in early, mid, and late stages of secondary succession following land abandonment using a well-established chronosequence in The Netherlands. We investigated primary and secondary chemistry of both leaves and flowers, in order to determine if patterns during seasonal (phenological) development may differ among successional stages. The chemical concentration of primary and secondary chemistry compounds in J. vulgaris varied throughout the season and was affected by vegetation succession stage. Concentrations of pyrrolizidine alkaloid (PA) tertiary-amines were highest in flowers during early Summer and in fields that had been abandoned ten to twenty years ago. PA N-oxide concentrations of both leaves and flowers, on the other hand increased with the progression of both season and succession. In Spring and early Summer chlorophyll concentrations were highest, especially in the oldest fields of the chronosequence. During phenological development, nitrogen concentration increased in flowers and decreased in leaves revealing allocation of nutrients from vegetative to reproductive plant parts throughout the growing season. The highest concentrations of N-oxides and chlorophylls were detected in older fields. Thus, our results suggest that variations in plant patterns of nutritional and defence compounds throughout the growing season are depending on successional context. PMID:24412324

  4. Gordonia bronchialis sternal wound infection in 3 patients following open heart surgery: intraoperative transmission from a healthcare worker.

    PubMed

    Wright, Shaneka N; Gerry, Joanna S; Busowski, Mary T; Klochko, Alena Y; McNulty, Steven G; Brown, Scott A; Sieger, Barry E; Ken Michaels, P; Wallace, Mark R

    2012-12-01

    We describe an investigation of 3 postoperative Gordonia bronchialis sternal infections. A nurse anesthetist was identified as the source of the outbreak, her scrubs likely becoming contaminated by her home washing machine. The outbreak ended after disposal of the implicated washing machine. Domestic laundering of surgical scrubs may need reevaluation. PMID:23143362

  5. Nosema tyriae n.sp. and Nosema sp., microsporidian parasites of Cinnabar moth Tyria jacobaeae.

    PubMed

    Canning, E U; Curry, A; Cheney, S A; Lafranchi-Tristem, N J; Kawakami, Y; Hatakeyama, Y; Iwano, H; Ishihara, R

    1999-07-01

    Nosema tyriae n.sp. was found in 63% of a population of Cinnabar moth larvae (Tyria jacobaeae). The infection was found in the gut wall, silk glands, and fat body and was probably generalized but appeared to be of low pathogenicity. Merogony and sporogony were by binary fission of diplokaryotic stages. Fresh spores were elongate, slightly pointed at the anterior end, and measured 4.7 x 2.0 microm. Ultrastructural features of special interest were 20-nm tubules connecting the surface of sporonts with host cell cytoplasm and, in the spores, a deeply domed polar sac, polaroplast consisting of closely packed longitudinally arranged membranes and loosely packed horizontally arranged membranes, and 10.5-14 coils of the polar tube in a single rank. The 16S rRNA genes of N. tyriae and Nosema bombycis from silkworms, Bombyx mori, differed by only six nucleotides and N. tyriae spores gave a moderately positive reaction with a monoclonal antibody raised to N. bombycis. N. tyriae was infective to B. mori but was less virulent than N. bombycis. However, no amplification product was obtained by PCR using N. tyriae DNA and primers considered to be specific for N. bombycis. Also, the spores of the two species are of entirely different shapes. A second diplokaryotic microsporidium, Nosema sp., found as a light infection in only one of the larvae had much smaller developmental stages and spores measuring 3.8 x 2.0 microm (fixed). Ultrastructurally it was distinguished by an abundance of dense membranes in cytoplasmic vesicles in both meronts and sporonts. Spores with up to 15 coils of the polar tube in irregular clusters or with about 12 coils in a single rank were observed in the tissues fixed from the one larva infected with this parasite. As this larva had been kept with N. tyriae-infected larvae for a few days before examination, it is possible that the two types of spores resulted from a double infection. PMID:10388544

  6. Effects of solution chemistry on antimicrobial activities of silver nanoparticles against Gordonia sp.

    PubMed

    Chen, Dong; Li, Xuan; Soule, Tanya; Yorio, Francis; Orr, Louisa

    2016-10-01

    Silver nanoparticles (NPs) are the largest and fastest growing category of nanotechnology-based medicines and consumer products. Silver can have great toxicity to some aquatic organisms and, as a biocidal agent, may also damage or alter the most abundant and vulnerable beneficial microorganisms in the environment, such as Gordonia sp. However, considering the complex chemical background of natural waters, silver NPs can have complicated interactions with background chemicals such as chloride, surfactants, and dissolved natural organic matters (NOM). The results of this study show that the average particle size and dispersivity of silver NPs and the surface characteristics play an important role in the toxicity of silver NPs. Aggregation was enhanced for silver NPs in 10mM NaNO3, but not much in 10mM NaCl due to reactions with chloride. However, the presence of 3mM sodium dodecyl sulfate (SDS) or 8mgC/L Suwannee River (SR) NOM appeared to reduce the aggregation of silver NPs. Regarding the bactericidal effect of silver NPs, solubility analysis suggests silver NPs inactivate Gordonia sp. differently from Ag(+) and/or a slow release of Ag(+) from silver NPs. When the silver NP concentration was raised from 7.3 to 29.2mg/L in DI water, the log inactivation rate of Gordonia sp. increased from 0.16±0.04 to 0.45±0.13. However, with 29.2mg/L silver NPs the log inactivation rate reached 1.40±0.26 in 3mM SDS. The presence of SRNOM mitigated the bactericidal efficacy of silver NPs due to surface coating/adsorption. On the other hand, 10mM NaCl reduced the log inactivation rate to 0.07±0.07 due to the formation of likely less toxic silver chloride species, such as AgCl, AgCl2(-), AgCl3(2-), and AgCl4(3-). PMID:27228306

  7. Characterization and Genomic Analysis of a Highly Efficient Dibutyl Phthalate-Degrading Bacterium Gordonia sp. Strain QH-12

    PubMed Central

    Jin, Decai; Kong, Xiao; Liu, Huijun; Wang, Xinxin; Deng, Ye; Jia, Minghong; Yu, Xiangyang

    2016-01-01

    A bacterial strain QH-12 isolated from activated sludge was identified as Gordonia sp. based on analysis of 16S rRNA gene sequence and was found to be capable of utilizing dibutyl phthalate (DBP) and other common phthalate esters (PAEs) as the sole carbon and energy source. The degradation kinetics of DBP under different concentrations by the strain QH-12 fit well with the modified Gompertz model (R2 > 0.98). However, strain QH-12 could not utilize the major intermediate product phthalate (phthalic acid; PA) as the sole carbon and energy source, and only a little amount of PA was detected. The QH-12 genome analysis revealed the presence of putative hydrolase/esterase genes involved in PAEs-degradation but no phthalic acid catabolic gene cluster was found, suggesting that a novel degradation pathway of PAEs was present in Gordonia sp. QH-12. This information will be valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs-degrading Gordonia sp. strains. PMID:27347943

  8. Characterization and Genomic Analysis of a Highly Efficient Dibutyl Phthalate-Degrading Bacterium Gordonia sp. Strain QH-12.

    PubMed

    Jin, Decai; Kong, Xiao; Liu, Huijun; Wang, Xinxin; Deng, Ye; Jia, Minghong; Yu, Xiangyang

    2016-01-01

    A bacterial strain QH-12 isolated from activated sludge was identified as Gordonia sp. based on analysis of 16S rRNA gene sequence and was found to be capable of utilizing dibutyl phthalate (DBP) and other common phthalate esters (PAEs) as the sole carbon and energy source. The degradation kinetics of DBP under different concentrations by the strain QH-12 fit well with the modified Gompertz model (R² > 0.98). However, strain QH-12 could not utilize the major intermediate product phthalate (phthalic acid; PA) as the sole carbon and energy source, and only a little amount of PA was detected. The QH-12 genome analysis revealed the presence of putative hydrolase/esterase genes involved in PAEs-degradation but no phthalic acid catabolic gene cluster was found, suggesting that a novel degradation pathway of PAEs was present in Gordonia sp. QH-12. This information will be valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs-degrading Gordonia sp. strains. PMID:27347943

  9. Lysis to Kill: Evaluation of the Lytic Abilities, and Genomics of Nine Bacteriophages Infective for Gordonia spp. and Their Potential Use in Activated Sludge Foam Biocontrol

    PubMed Central

    Dyson, Zoe A.; Tucci, Joseph; Seviour, Robert J.; Petrovski, Steve

    2015-01-01

    Nine bacteriophages (phages) infective for members of the genus Gordonia were isolated from wastewater and other natural water environments using standard enrichment techniques. The majority were broad host range phages targeting more than one Gordonia species. When their genomes were sequenced, they all emerged as double stranded DNA Siphoviridae phages, ranging from 17,562 to 103,424 bp in size, and containing between 27 and 127 genes, many of which were detailed for the first time. Many of these phage genomes diverged from the expected modular genome architecture of other characterized Siphoviridae phages and contained unusual lysis gene arrangements. Whole genome sequencing also revealed that infection with lytic phages does not appear to prevent spontaneous prophage induction in Gordonia malaquae lysogen strain BEN700. TEM sample preparation techniques were developed to view both attachment and replication stages of phage infection. PMID:26241321

  10. Genetic Analysis of Benzothiophene Biodesulfurization Pathway of Gordonia terrae Strain C-6

    PubMed Central

    Lian, Kehui; Zhang, Yue; Tian, Huimei; Ji, Kaihua; Li, Guoqiang

    2013-01-01

    Sulfur can be removed from benzothiophene (BT) by some bacteria without breaking carbon-carbon bonds. However, a clear mechanism for BT desulfurization and its genetic components have not been reported in literatures so far. In this study, we used comparative transcriptomics to study differential expression of genes in Gordonia terrae C-6 cultured with BT or sodium sulfate as the sole source of sulfur. We found that 135 genes were up-regulated with BT relative to sodium sulfate as the sole sulfur source. Many of these genes encode flavin-dependent monooxygenases, alkane sulfonate monooxygenases and desulfinase, which perform similar functions to those involved in the 4S pathway of dibenzothiophene (DBT) biodesulfurization. Three of the genes were found to be located in the same operon, designated bdsABC. Cell extracts of pET28a-bdsABC transfected E. coli Rosetta (DE3) converted BT to a phenolic compound, identified as o-hydroxystyrene. These results advance our understanding of enzymes involved in the BT biodesulfurization pathway. PMID:24367657

  11. Parental Ploidy Strongly Affects Offspring Fitness in Heteroploid Crosses among Three Cytotypes of Autopolyploid Jacobaea carniolica (Asteraceae)

    PubMed Central

    Sonnleitner, Michaela; Weis, Birgit; Flatscher, Ruth; García, Pedro Escobar; Suda, Jan; Krejčíková, Jana; Schneeweiss, Gerald M.; Winkler, Manuela; Schönswetter, Peter; Hülber, Karl

    2013-01-01

    Reproductive interactions among cytotypes in their contact zones determine whether these cytotypes can co-exist and form stable contact zones or not. In autopolyploids, heteroploid cross-compatibilities might depend on parental ploidy, but tests of this hypothesis in autopolyploid systems with more than two ploidies are lacking. Here, we study Jacobaea carniolica, which comprises diploid, tetraploid, and hexaploid individuals regularly forming contact zones. Seeds obtained from in situ cross-pollinations within and among cytotypes were subjected to DNA flow cytometry and greenhouse germination experiments. Hybrid fitness and parental effects on hybrid fitness were tested with regression models comparing fitness parameters of early life stages. Irrespective of the direction of crosses, seed viability and seedling survival in diploid-polyploid crosses were substantially lower than in tetraploid-hexaploid crosses. In contrast, seedling growth traits indicated neither transgressive character expression nor any selection against hybrid offspring. Congruent with a model of genome dosage effects, these traits differed between reciprocal crosses, especially of diploids and tetraploids, where trait values resembled those of the maternal parent. The strong effect of parental ploidy on offspring fitness in heteroploid crosses may cause contact zones involving exclusively polyploid cytotypes to be less stable over longer terms than those involving diploids and polyploids. PMID:24265735

  12. Involvement of an Alkane Hydroxylase System of Gordonia sp. Strain SoCg in Degradation of Solid n-Alkanes▿

    PubMed Central

    Lo Piccolo, Luca; De Pasquale, Claudio; Fodale, Roberta; Puglia, Anna Maria; Quatrini, Paola

    2011-01-01

    Enzymes involved in oxidation of long-chain n-alkanes are still not well known, especially those in Gram-positive bacteria. This work describes the alkane degradation system of the n-alkane degrader actinobacterium Gordonia sp. strain SoCg, which is able to grow on n-alkanes from dodecane (C12) to hexatriacontane (C36) as the sole C source. SoCg harbors in its chromosome a single alk locus carrying six open reading frames (ORFs), which shows 78 to 79% identity with the alkane hydroxylase (AH)-encoding systems of other alkane-degrading actinobacteria. Quantitative reverse transcription-PCR showed that the genes encoding AlkB (alkane 1-monooxygenase), RubA3 (rubredoxin), RubA4 (rubredoxin), and RubB (rubredoxin reductase) were induced by both n-hexadecane and n-triacontane, which were chosen as representative long-chain liquid and solid n-alkane molecules, respectively. Biotransformation of n-hexadecane into the corresponding 1-hexadecanol was detected by solid-phase microextraction coupled with gas chromatography-mass spectrometry (SPME/GC-MS) analysis. The Gordonia SoCg alkB was heterologously expressed in Escherichia coli BL21 and in Streptomyces coelicolor M145, and both hosts acquired the ability to transform n-hexadecane into 1-hexadecanol, but the corresponding long-chain alcohol was never detected on n-triacontane. However, the recombinant S. coelicolor M145-AH, expressing the Gordonia alkB gene, was able to grow on n-triacontane as the sole C source. A SoCg alkB disruption mutant that is completely unable to grow on n-triacontane was obtained, demonstrating the role of an AlkB-type AH system in degradation of solid n-alkanes. PMID:21183636

  13. Metabolism of toxic pyrrolizidine alkaloids from tansy ragwort (Senecio jacobaea) in ovine ruminal fluid under anaerobic conditions.

    PubMed Central

    Craig, A M; Latham, C J; Blythe, L L; Schmotzer, W B; O'Connor, O A

    1992-01-01

    The ability of ovine ruminal fluid to metabolize pyrrolizidine alkaloid (PA) from Senecio jacobaea under anaerobic conditions was evaluated. Four fistulated sheep fed PA served as individual sources of ruminal fluid, which was incubated in a defined minimal salts medium under two different anaerobic conditions, denitrifying and methanogenic. Anaerobic cultures amended with ovine ruminal fluids (20%), PA (100 micrograms/ml), and a defined minimal salts medium were monitored for a period of several days. These cultures revealed that while PA was not depleted in sterile, autoclaved controls or under denitrifying conditions, it was metabolized during periods of active methanogenesis under methanogenic conditions. In addition, samples of ruminal fluid were separated by differential centrifugation under anaerobic conditions, and the resultant supernatants were tested for their ability to metabolize PA as compared with those of the respective uncentrifuged control fluids. Uncentrifuged controls exhibited a PA depletion rate of -4.04 +/- 0.17 micrograms of PA per ml per h. Supernatants 1 (centrifuged at 41 x g for 2 min), 2 (centrifuged at 166 x g for 5 min), and 3 (centrifuged at 1,500 x g for 10 min) exhibited significantly slower depletion rates, with slopes of data representing -1.64 +/- 0.16, -1.44 +/- 0.16, and -1.48 +/- 0.16 micrograms of PA metabolized per ml per h, respectively, demonstrating no statistically significant difference among the supernatant cultures. Microscopic evaluations revealed that protozoa were present in the control whole ruminal fluid and to a lesser extent in supernatant 1, while supernatants 2 and 3 contained only bacteria.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1444382

  14. Biocatalytic desulfurization of diesel oil in an air-lift reactor with immobilized Gordonia nitida CYKS1 cells.

    PubMed

    Lee, In Su; Bae, Hee-Sung; Ryu, Hee Wook; Cho, Kyung-Suk; Chang, Yong Keun

    2005-01-01

    A new type of air-lift reactor with immobilized Gordonia nitida CYKS1 cells on a fibrous support was designed and used for the biocatalytic desulfurization (BDS) of diesel oil. Its performance was evaluated at different phase ratios of the oil to the aqueous medium (or oil phase fractions) and different sucrose concentrations. When the reaction mixture contained 10% diesel oil (v/v), 61-67% of sulfur was removed as the sulfur content decreased from 202-250 to 76-90 mg L(-1) in 72 h. The sulfur content did not decrease any further because the remaining sulfur compounds were recalcitrant to BDS. During the desulfurization, the strain CYKS1 consumed hydrocarbons in the diesel oil, mainly n-alkanes with 10-26 carbons, as carbon source even though an easily available carbon source, sucrose, was supplied. PMID:15932256

  15. Genome Sequences and Characterization of the Related Gordonia Phages GTE5 and GRU1 and Their Use as Potential Biocontrol Agents

    PubMed Central

    Tillett, Daniel; Seviour, Robert J.

    2012-01-01

    Activated sludge plants suffer frequently from the operational problem of stable foam formation on aerobic reactor surfaces, which can be difficult to prevent. Many foams are stabilized by mycolic acid-containing Actinobacteria, the mycolata. The in situ biocontrol of foaming using phages is an attractive strategy. We describe two polyvalent phages, GTE5 and GRU1, targeting Gordonia terrae and Gordonia rubrupertincta, respectively, isolated from activated sludge. Phage GRU1 also propagates on Nocardia nova. Both phages belong to the family Siphoviridae and have similar-size icosahedral heads that encapsulate double-stranded DNA genomes (∼65 kb). Their genome sequences are similar to each other but markedly different from those of other sequenced phages. Both are arranged in a modular fashion. These phages can reduce or eliminate foam formation by their host cells under laboratory conditions. PMID:22038604

  16. Role of nitrogen limitation in transformation of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) by Gordonia sp. strain KTR9.

    PubMed

    Indest, Karl J; Hancock, Dawn E; Jung, Carina M; Eberly, Jed O; Mohn, William W; Eltis, Lindsay D; Crocker, Fiona H

    2013-03-01

    The transcriptome of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine)-degrading strain Gordonia sp. strain KTR9 and its glnR mutant were studied as a function of nitrogen availability to further investigate the observed ammonium-mediated inhibition of RDX degradation. The results indicate that nitrogen availability is a major determinant of RDX degradation and xplA gene expression in KTR9. PMID:23275513

  17. Role of Nitrogen Limitation in Transformation of RDX (Hexahydro-1,3,5-Trinitro-1,3,5-Triazine) by Gordonia sp. Strain KTR9

    PubMed Central

    Hancock, Dawn E.; Jung, Carina M.; Eberly, Jed O.; Mohn, William W.; Eltis, Lindsay D.; Crocker, Fiona H.

    2013-01-01

    The transcriptome of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine)-degrading strain Gordonia sp. strain KTR9 and its glnR mutant were studied as a function of nitrogen availability to further investigate the observed ammonium-mediated inhibition of RDX degradation. The results indicate that nitrogen availability is a major determinant of RDX degradation and xplA gene expression in KTR9. PMID:23275513

  18. Gordonia Species as Emerging Causes of Continuous-Ambulatory-Peritoneal-Dialysis-Related Peritonitis Identified by 16S rRNA and secA1 Gene Sequencing and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry (MALDI-TOF MS)

    PubMed Central

    Lam, Jimmy Y. W.; Leung, Wai-Shing; Cheung, Ingrid; Chan, Jasper F. W.; Tse, Cindy W. S.; Lee, Rodney A.; Lau, Susanna K. P.

    2014-01-01

    We report here four cases of continuous ambulatory peritoneal dialysis-related peritonitis caused by three different species of Gordonia. The portal of entry was likely through Tenckhoff catheters. 16S rRNA and secA1 gene sequencing are so far the most reliable methods for the accurate identification of Gordonia species. PMID:25428146

  19. Characterization of the 101-Kilobase-Pair Megaplasmid pKB1, Isolated from the Rubber-Degrading Bacterium Gordonia westfalica Kb1

    PubMed Central

    Bröker, Daniel; Arenskötter, Matthias; Legatzki, Antje; Nies, Dietrich H.; Steinbüchel, Alexander

    2004-01-01

    The complete sequence of the circular 101,016-bp megaplasmid pKB1 from the cis-1,4-polyisoprene-degrading bacterium Gordonia westfalica Kb1, which represents the first described extrachromosomal DNA of a member of this genus, was determined. Plasmid pKB1 harbors 105 open reading frames. The predicted products of 46 of these are significantly related to proteins of known function. Plasmid pKB1 is organized into three functional regions that are flanked by insertion sequence (IS) elements: (i) a replication and putative partitioning region, (ii) a putative metabolic region, and (iii) a large putative conjugative transfer region, which is interrupted by an additional IS element. Southern hybridization experiments revealed the presence of another copy of this conjugational transfer region on the bacterial chromosome. The origin of replication (oriV) of pKB1 was identified and used for construction of Escherichia coli-Gordonia shuttle vectors, which was also suitable for several other Gordonia species and related genera. The metabolic region included the heavy-metal resistance gene cadA, encoding a P-type ATPase. Expression of cadA in E. coli mediated resistance to cadmium, but not to zinc, and decreased the cellular content of cadmium in this host. When G. westfalica strain Kb1 was cured of plasmid pKB1, the resulting derivative strains exhibited slightly decreased cadmium resistance. Furthermore, they had lost the ability to use isoprene rubber as a sole source of carbon and energy, suggesting that genes essential for rubber degradation are encoded by pKB1. PMID:14679241

  20. The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies.

    PubMed

    Doorduin, Leonie; Gravendeel, Barbara; Lammers, Youri; Ariyurek, Yavuz; Chin-A-Woeng, Thomas; Vrieling, Klaas

    2011-04-01

    Invasive individuals from the pest species Jacobaea vulgaris show different allocation patterns in defence and growth compared with native individuals. To examine if these changes are caused by fast evolution, it is necessary to identify native source populations and compare these with invasive populations. For this purpose, we are in need of intraspecific polymorphic markers. We therefore sequenced the complete chloroplast genomes of 12 native and 5 invasive individuals of J. vulgaris with next generation sequencing and discovered single-nucleotide polymorphisms (SNPs) and microsatellites. This is the first study in which the chloroplast genome of that many individuals within a single species was sequenced. Thirty-two SNPs and 34 microsatellite regions were found. For none of the individuals, differences were found between the inverted repeats. Furthermore, being the first chloroplast genome sequenced in the Senecioneae clade, we compared it with four other members of the Asteraceae family to identify new regions for phylogentic inference within this clade and also within the Asteraceae family. Five markers (ndhC-trnV, ndhC-atpE, rps18-rpl20, clpP and psbM-trnD) contained parsimony-informative characters higher than 2%. Finally, we compared two procedures of preparing chloroplast DNA for next generation sequencing. PMID:21444340

  1. The Complete Chloroplast Genome of 17 Individuals of Pest Species Jacobaea vulgaris: SNPs, Microsatellites and Barcoding Markers for Population and Phylogenetic Studies

    PubMed Central

    Doorduin, Leonie; Gravendeel, Barbara; Lammers, Youri; Ariyurek, Yavuz; Chin-A-Woeng, Thomas; Vrieling, Klaas

    2011-01-01

    Invasive individuals from the pest species Jacobaea vulgaris show different allocation patterns in defence and growth compared with native individuals. To examine if these changes are caused by fast evolution, it is necessary to identify native source populations and compare these with invasive populations. For this purpose, we are in need of intraspecific polymorphic markers. We therefore sequenced the complete chloroplast genomes of 12 native and 5 invasive individuals of J. vulgaris with next generation sequencing and discovered single-nucleotide polymorphisms (SNPs) and microsatellites. This is the first study in which the chloroplast genome of that many individuals within a single species was sequenced. Thirty-two SNPs and 34 microsatellite regions were found. For none of the individuals, differences were found between the inverted repeats. Furthermore, being the first chloroplast genome sequenced in the Senecioneae clade, we compared it with four other members of the Asteraceae family to identify new regions for phylogentic inference within this clade and also within the Asteraceae family. Five markers (ndhC-trnV, ndhC-atpE, rps18-rpl20, clpP and psbM-trnD) contained parsimony-informative characters higher than 2%. Finally, we compared two procedures of preparing chloroplast DNA for next generation sequencing. PMID:21444340

  2. Interaction of Operational and Physicochemical Factors Leading to Gordonia amarae-Like Foaming in an Incompletely Nitrifying Activated Sludge Plant

    PubMed Central

    Asvapathanagul, Pitiporn; Huang, Zhonghua; Gedalanga, Phillip B.; Baylor, Amber

    2012-01-01

    The overgrowth of Gordonia amarae-like bacteria in the mixed liquor of an incompletely nitrifying water reclamation plant was inversely correlated with temperature (r = −0.78; P < 0.005) and positively correlated with the solids retention time (SRT) obtained a week prior to sampling (r = 0.67; P < 0.005). Drops followed by spikes in the food-to-mass ratio (0.18 to 0.52) and biochemical oxygen demand concentrations in primary effluent (94 to 298 mg liter−1) occurred at the initiation of G. amarae-like bacterial growth. The total bacterial concentration did not increase as concentrations of G. amarae-like cells increased, but total bacterial cell concentrations fluctuated in a manner similar to that of G. amarae-like bacteria in the pseudo-steady state. The ammonium ion removal rate (percent) was inversely related to G. amarae-like cell concentrations during accelerated growth and washout phases. The dissolved oxygen concentration decreased as the G. amarae-like cell concentration decreased. The concentrations of G. amarae-like cells peaked (2.47 × 109 cells liter−1) approximately 1.5 months prior to foaming. Foaming occurred during the late pseudo-steady-state phase, when temperature declines reversed. These findings suggested that temperature changes triggered operational and physicochemical changes favorable to the growth of G. amarae-like bacteria. Fine-scale quantitative PCR (qPCR) monitoring at weekly intervals allowed a better understanding of the factors affecting this organism and indicated that frequent sampling was required to obtain statistical significance with factors changing as the concentrations of this organism increased. Furthermore, the early identification of G. amarae-like cells when they are confined to mixed liquor (107 cells liter−1) allows management strategies to prevent foaming. PMID:22983974

  3. Production of anti-Gordonia amarae mycolic acid polyclonal antibody for detection of mycolic acid-containing bacteria in activated sludge foam.

    PubMed

    Iwahori, K; Miyata, N; Takata, N; Morisada, S; Mochizuki, T

    2001-01-01

    Mycolic acid-containing actinomycetes (mycolata) are considered the causative agents of foaming of activated sludge and scum formation in activated sludge treatment plants. In this study, the production of anti-Gordonia amarae mycolic acid polyclonal antibodies was investigated. Rabbits were immunized with a conjugate of keyhole limpet hemocyanin and mycolic acids of G. amarae, which contained 48 to 56 carbon atoms (average, 52.0). Enzyme-linked immunosorbent assay (ELISA) demonstrated that the polyclonal antibodies could recognize cells of G. amarae ranging from 0.1 to 10 microg. The antibodies also reacted with other tested mycolata strains belonging to the genera Nocardia, Rhodococcus, Dietzia, Mycobacterium and Tsukamurella. However, reactivities against other gram-positive and gram-negative bacteria not containing mycolic acid were negligible or much lower. The results indicate that the anti-G. amarae mycolic acid antibodies show a reactivity selective for a group of mycolata involved in the foaming of activated sludge. PMID:16233121

  4. Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Nocardia, Rhodococcus, Kocuria, Gordonia, Tsukamurella, and Listeria Species

    PubMed Central

    Lee, Tai-Fen; Du, Shin-Hei; Teng, Shih-Hua; Liao, Chun-Hsing; Sheng, Wang-Hui; Teng, Lee-Jene

    2014-01-01

    We evaluated whether the Bruker Biotyper matrix-associated laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) system provides accurate species-level identifications of 147 isolates of aerobically growing Gram-positive rods (GPRs). The bacterial isolates included Nocardia (n = 74), Listeria (n = 39), Kocuria (n = 15), Rhodococcus (n = 10), Gordonia (n = 7), and Tsukamurella (n = 2) species, which had all been identified by conventional methods, molecular methods, or both. In total, 89.7% of Listeria monocytogenes, 80% of Rhodococcus species, 26.7% of Kocuria species, and 14.9% of Nocardia species (n = 11, all N. nova and N. otitidiscaviarum) were correctly identified to the species level (score values, ≥2.0). A clustering analysis of spectra generated by the Bruker Biotyper identified six clusters of Nocardia species, i.e., cluster 1 (N. cyriacigeorgica), cluster 2 (N. brasiliensis), cluster 3 (N. farcinica), cluster 4 (N. puris), cluster 5 (N. asiatica), and cluster 6 (N. beijingensis), based on the six peaks generated by ClinProTools with the genetic algorithm, i.e., m/z 2,774.477 (cluster 1), m/z 5,389.792 (cluster 2), m/z 6,505.720 (cluster 3), m/z 5,428.795 (cluster 4), m/z 6,525.326 (cluster 5), and m/z 16,085.216 (cluster 6). Two clusters of L. monocytogenes spectra were also found according to the five peaks, i.e., m/z 5,594.85, m/z 6,184.39, and m/z 11,187.31, for cluster 1 (serotype 1/2a) and m/z 5,601.21 and m/z 11,199.33 for cluster 2 (serotypes 1/2b and 4b). The Bruker Biotyper system was unable to accurately identify Nocardia (except for N. nova and N. otitidiscaviarum), Tsukamurella, or Gordonia species. Continuous expansion of the MALDI-TOF MS databases to include more GPRs is necessary. PMID:24759706

  5. Involvement of Two Latex-Clearing Proteins during Rubber Degradation and Insights into the Subsequent Degradation Pathway Revealed by the Genome Sequence of Gordonia polyisoprenivorans Strain VH2

    PubMed Central

    Hiessl, Sebastian; Schuldes, Jörg; Thürmer, Andrea; Halbsguth, Tobias; Bröker, Daniel; Angelov, Angel; Liebl, Wolfgang; Daniel, Rolf

    2012-01-01

    The increasing production of synthetic and natural poly(cis-1,4-isoprene) rubber leads to huge challenges in waste management. Only a few bacteria are known to degrade rubber, and little is known about the mechanism of microbial rubber degradation. The genome of Gordonia polyisoprenivorans strain VH2, which is one of the most effective rubber-degrading bacteria, was sequenced and annotated to elucidate the degradation pathway and other features of this actinomycete. The genome consists of a circular chromosome of 5,669,805 bp and a circular plasmid of 174,494 bp with average GC contents of 67.0% and 65.7%, respectively. It contains 5,110 putative protein-coding sequences, including many candidate genes responsible for rubber degradation and other biotechnically relevant pathways. Furthermore, we detected two homologues of a latex-clearing protein, which is supposed to be a key enzyme in rubber degradation. The deletion of these two genes for the first time revealed clear evidence that latex-clearing protein is essential for the microbial utilization of rubber. Based on the genome sequence, we predict a pathway for the microbial degradation of rubber which is supported by previous and current data on transposon mutagenesis, deletion mutants, applied comparative genomics, and literature search. PMID:22327575

  6. Substrate specificity of β-glucosidase from Gordonia terrae for ginsenosides and its application in the production of ginsenosides Rg₃, Rg₂, and Rh₁ from ginseng root extract.

    PubMed

    Shin, Kyung-Chul; Lee, Hye-Ji; Oh, Deok-Kun

    2015-05-01

    A β-glucosidase from Gordonia terrae was cloned and expressed in Escherichia coli. The recombinant enzyme with a specific activity of 16.4 U/mg for ginsenoside Rb1 was purified using His-trap chromatography. The purified enzyme specifically hydrolyzed the glucopyranosides at the C-20 position in protopanaxadiol (PPD)-type ginsenosides and hydrolyzed the glucopyranoside at the C-6 or C-20 position in protopanaxatriol (PPT)-type ginsenosides. The reaction conditions for the high-level production of Rg3 from Rb1 by the enzyme were pH 6.5, 30°C, 20 mg/ml enzyme, and 4 mg/ml Rb1. Under these conditions, G. terrae β-glucosidase completely converted Rb1 and Re to Rg3 and Rg2, respectively, after 2.5 and 8 h, respectively. Moreover, the enzyme converted Rg1 to Rh1 at 1 h with a molar conversion yield of 82%. The enzyme at 10 mg/ml produced 1.16 mg/ml Rg3, 1.47 mg/ml Rg2, and 1.17 mg/ml Rh1 from Rb1, Re, and Rg1, respectively, in 10% (w/v) ginseng root extract at pH 6.5 and 30°C after 33 h with molar conversion yields of 100%, 100%, and 77%, respectively. The combined molar conversion yield of Rg2, Rg3, and Rh1 from total ginsenosides in 10% (w/v) ginseng root extract was 68%. These above results suggest that this enzyme is useful for the production of ginsenosides Rg3, Rg2, and Rh1. PMID:25457989

  7. Mineralization of the Cyclic Nitramine Explosive Hexahydro-1,3,5-Trinitro-1,3,5-Triazine by Gordonia and Williamsia spp.

    PubMed Central

    Thompson, Karen T.; Crocker, Fiona H.; Fredrickson, Herbert L.

    2005-01-01

    Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a cyclic nitroamine explosive that is a major component in many military high-explosive formulations. In this study, two aerobic bacteria that are capable of using RDX as the sole source of carbon and nitrogen to support their growth were isolated from surface soil. These bacterial strains were identified by their fatty acid profiles and 16S ribosomal gene sequences as Williamsia sp. KTR4 and Gordonia sp. KTR9. The physiology of each strain was characterized with respect to the rates of RDX degradation and [U-14C]RDX mineralization when RDX was supplied as a sole carbon and nitrogen source in the presence and absence of competing carbon and nitrogen sources. Strains KTR4 and KTR9 degraded 180 μM RDX within 72 h when RDX served as the only added carbon and nitrogen source while growing to total protein concentrations of 18.6 and 16.5 μg/ml, respectively. Mineralization of [U-14C]RDX to 14CO2 was 30% by strain KTR4 and 27% by KTR9 when RDX was the only added source of carbon and nitrogen. The addition of (NH4)2SO4 greatly inhibited KTR9's degradation of RDX but had little effect on that of KTR4. These are the first two pure bacterial cultures isolated that are able to use RDX as a sole carbon and nitrogen source. These two genera possess different physiologies with respect to RDX mineralization, and each can serve as a useful microbiological model for the study of RDX biodegradation with regard to physiology, biochemistry, and genetics. PMID:16332812

  8. Characterization of the Genome of the Polyvalent Lytic Bacteriophage GTE2, Which Has Potential for Biocontrol of Gordonia-, Rhodococcus-, and Nocardia-Stabilized Foams in Activated Sludge Plants ▿ †

    PubMed Central

    Petrovski, Steve; Seviour, Robert J.; Tillett, Daniel

    2011-01-01

    Hydrophobic Actinobacteria are commonly associated with the stabilization of foams in activated sludge systems. One possible attractive approach to control these foam-stabilizing organisms is the use of specific bacteriophages. We describe the genome characterization of a novel polyvalent DNA phage, GTE2, isolated from activated sludge. This phage is lytic for Gordonia terrae, Rhodococcus globerulus, Rhodococcus erythropolis, Rhodococcus erythropolis, Nocardia otitidiscaviarum, and Nocardia brasiliensis. Phage GTE2 belongs to the family Siphoviridae, possessing a characteristic icosahedral head encapsulating a double-stranded DNA linear genome (45,530 bp) having 10-bp 3′-protruding cohesive ends. The genome sequence is 98% unique at the DNA level and contains 57 putative genes. The genome can be divided into two components, where the first is modular and encodes phage structural proteins and lysis genes. The second is not modular, and the genes harbored there are involved in DNA replication, repair, and metabolism. Some have no known function. GTE2 shows promising results in controlling stable foam production by its host bacteria under laboratory conditions, suggesting that it may prove useful in the field as a biocontrol agent. PMID:21498753

  9. The essential role of nitrogen limitation in expression of xplA and degradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in Gordonia sp. strain KTR9.

    PubMed

    Zhu, Song-Hua; Reuther, Jens; Liu, Jie; Crocker, Fiona H; Indest, Karl J; Eltis, Lindsay D; Mohn, William W

    2015-01-01

    Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a widely used explosive and a major soil and groundwater contaminant. Organisms such as Gordonia sp. KTR9, capable of degrading RDX and using it as an N source, may prove useful for bioremediation of contaminated sites. XplA is a cytochrome P450 monooxygenase responsible for RDX degradation. Expression of xplA in KTR9 was not induced by RDX but was strongly induced (50-fold) during N-limited growth. When glnR, encoding a regulatory protein affecting N assimilation in diverse Actinobacteria, was deleted from KTR9, the bacterium lost the ability to use nitrate, nitrite, and RDX as N sources. Deletion of glnR also abolished the inhibition of xplA expression by nitrite. Our results confirm the essential role of GlnR in regulating assimilation of nitrite, but there was no evidence for a direct role of GlnR in regulating XplA expression. Rather, the general availability of nitrogen repressed XplA expression. We conclude that the inability of the glnR mutant to use RDX as an N source was due to its inability to assimilate nitrite, an intermediate in the assimilation of nitrogen from RDX. Regulation of XplA does not seem adaptive for KTR9, but it is important for RDX bioremediation with KTR9 or similar bacteria. PMID:25142696

  10. Functional characterization of pGKT2, a 182-kilobase plasmid containing the xplAB genes, which are involved in the degradation of hexahydro-1,3,5-trinitro-1,3,5-triazine by Gordonia sp. strain KTR9.

    PubMed

    Indest, Karl J; Jung, Carina M; Chen, Hao-Ping; Hancock, Dawn; Florizone, Christine; Eltis, Lindsay D; Crocker, Fiona H

    2010-10-01

    Several microorganisms have been isolated that can transform hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), a cyclic nitramine explosive. To better characterize the microbial genes that facilitate this transformation, we sequenced and annotated a 182-kb plasmid, pGKT2, from the RDX-degrading strain Gordonia sp. KTR9. This plasmid carries xplA, encoding a protein sharing up to 99% amino acid sequence identity with characterized RDX-degrading cytochromes P450. Other genes that cluster with xplA are predicted to encode a glutamine synthase-XplB fusion protein, a second cytochrome P450, Cyp151C, and XplR, a GntR-type regulator. Rhodococcus jostii RHA1 expressing xplA from KTR9 degraded RDX but did not utilize RDX as a nitrogen source. Moreover, an Escherichia coli strain producing XplA degraded RDX but a strain producing Cyp151C did not. KTR9 strains cured of pGKT2 did not transform RDX. Physiological studies examining the effects of exogenous nitrogen sources on RDX degradation in strain KTR9 revealed that ammonium, nitrite, and nitrate each inhibited RDX degradation by up to 79%. Quantitative real-time PCR analysis of glnA-xplB, xplA, and xplR showed that transcript levels were 3.7-fold higher during growth on RDX than during growth on ammonium and that this upregulation was repressed in the presence of various inorganic nitrogen sources. Overall, the results indicate that RDX degradation by KTR9 is integrated with central nitrogen metabolism and that the uptake of RDX by bacterial cells does not require a dedicated transporter. PMID:20709853

  11. Functional Characterization of pGKT2, a 182-Kilobase Plasmid Containing the xplAB Genes, Which Are Involved in the Degradation of Hexahydro-1,3,5-Trinitro-1,3,5-Triazine by Gordonia sp. Strain KTR9 ▿

    PubMed Central

    Indest, Karl J.; Jung, Carina M.; Chen, Hao-Ping; Hancock, Dawn; Florizone, Christine; Eltis, Lindsay D.; Crocker, Fiona H.

    2010-01-01

    Several microorganisms have been isolated that can transform hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), a cyclic nitramine explosive. To better characterize the microbial genes that facilitate this transformation, we sequenced and annotated a 182-kb plasmid, pGKT2, from the RDX-degrading strain Gordonia sp. KTR9. This plasmid carries xplA, encoding a protein sharing up to 99% amino acid sequence identity with characterized RDX-degrading cytochromes P450. Other genes that cluster with xplA are predicted to encode a glutamine synthase-XplB fusion protein, a second cytochrome P450, Cyp151C, and XplR, a GntR-type regulator. Rhodococcus jostii RHA1 expressing xplA from KTR9 degraded RDX but did not utilize RDX as a nitrogen source. Moreover, an Escherichia coli strain producing XplA degraded RDX but a strain producing Cyp151C did not. KTR9 strains cured of pGKT2 did not transform RDX. Physiological studies examining the effects of exogenous nitrogen sources on RDX degradation in strain KTR9 revealed that ammonium, nitrite, and nitrate each inhibited RDX degradation by up to 79%. Quantitative real-time PCR analysis of glnA-xplB, xplA, and xplR showed that transcript levels were 3.7-fold higher during growth on RDX than during growth on ammonium and that this upregulation was repressed in the presence of various inorganic nitrogen sources. Overall, the results indicate that RDX degradation by KTR9 is integrated with central nitrogen metabolism and that the uptake of RDX by bacterial cells does not require a dedicated transporter. PMID:20709853

  12. Toxic pyrrolizidinalkaloids as undesired contaminants in food and feed: degradation of the PAs from Senecio jacobaea in silage.

    PubMed

    Becerra-Jiminez, J; Kuschak, M; Roeder, E; Wiedenfeld, H

    2013-07-01

    Pyrrolizidine alkaloids (PAs) can show a hazardous potential for men and animals. They can act as cancerogenic, mutagenic, teratogenic and fetotoxic agents. One pathway of a human intoxication is its occurence as contaminants in food and feed. Here, the contamination of cereals already led to severe and fatal intoxication episodes. Besides this, milk is of special concern as it is the main food for children which show a very high susceptibility for a PA intoxication. Milk can contain PAs in case the milk producing animals have access to contaminated feed. In this context it is of special interest whether the PA content of contaminated silage remains stable during the ensiling procedure or show a more or less high level of decomposition. We could show that ensiling will not lead to PA-free silage. PMID:23923650

  13. METABOLISM OF TOXIC PYRROLIZIDINE ALKALOIDS FROM TANSY RAGWORT, SENECIO JACOBAEA, IN BOVINE RUMINAL FLUID UNDER ANAEROBIC CONDITIONS. (R825689C006)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  14. Ecological differentiation, lack of hybrids involving diploids, and asymmetric gene flow between polyploids in narrow contact zones of Senecio carniolicus (syn. Jacobaea carniolica, Asteraceae)

    PubMed Central

    Hülber, Karl; Sonnleitner, Michaela; Suda, Jan; Krejčíková, Jana; Schönswetter, Peter; Schneeweiss, Gerald M; Winkler, Manuela

    2015-01-01

    Areas of immediate contact of different cytotypes offer a unique opportunity to study evolutionary dynamics within heteroploid species and to assess isolation mechanisms governing coexistence of cytotypes of different ploidy. The degree of reproductive isolation of cytotypes, that is, the frequency of heteroploid crosses and subsequent formation of viable and (partly) fertile hybrids, plays a crucial role for the long-term integrity of lineages in contact zones. Here, we assessed fine-scale distribution, spatial clustering, and ecological niches as well as patterns of gene flow in parental and hybrid cytotypes in zones of immediate contact of di-, tetra-, and hexaploid Senecio carniolicus (Asteraceae) in the Eastern Alps. Cytotypes were spatially separated also at the investigated microscale; the strongest spatial separation was observed for the fully interfertile tetra- and hexaploids. The three main cytotypes showed highly significant niche differences, which were, however, weaker than across their entire distribution ranges in the Eastern Alps. Individuals with intermediate ploidy levels were found neither in the diploid/tetraploid nor in the diploid/hexaploid contact zones indicating strong reproductive barriers. In contrast, pentaploid individuals were frequent in the tetraploid/hexaploid contact zone, albeit limited to a narrow strip in the immediate contact zone of their parental cytotypes. AFLP fingerprinting data revealed introgressive gene flow mediated by pentaploid hybrids from tetra- to hexaploid individuals, but not vice versa. The ecological niche of pentaploids differed significantly from that of tetraploids but not from hexaploids. PMID:25859328

  15. Ecological differentiation, lack of hybrids involving diploids, and asymmetric gene flow between polyploids in narrow contact zones of Senecio carniolicus (syn. Jacobaea carniolica, Asteraceae).

    PubMed

    Hülber, Karl; Sonnleitner, Michaela; Suda, Jan; Krejčíková, Jana; Schönswetter, Peter; Schneeweiss, Gerald M; Winkler, Manuela

    2015-03-01

    Areas of immediate contact of different cytotypes offer a unique opportunity to study evolutionary dynamics within heteroploid species and to assess isolation mechanisms governing coexistence of cytotypes of different ploidy. The degree of reproductive isolation of cytotypes, that is, the frequency of heteroploid crosses and subsequent formation of viable and (partly) fertile hybrids, plays a crucial role for the long-term integrity of lineages in contact zones. Here, we assessed fine-scale distribution, spatial clustering, and ecological niches as well as patterns of gene flow in parental and hybrid cytotypes in zones of immediate contact of di-, tetra-, and hexaploid Senecio carniolicus (Asteraceae) in the Eastern Alps. Cytotypes were spatially separated also at the investigated microscale; the strongest spatial separation was observed for the fully interfertile tetra- and hexaploids. The three main cytotypes showed highly significant niche differences, which were, however, weaker than across their entire distribution ranges in the Eastern Alps. Individuals with intermediate ploidy levels were found neither in the diploid/tetraploid nor in the diploid/hexaploid contact zones indicating strong reproductive barriers. In contrast, pentaploid individuals were frequent in the tetraploid/hexaploid contact zone, albeit limited to a narrow strip in the immediate contact zone of their parental cytotypes. AFLP fingerprinting data revealed introgressive gene flow mediated by pentaploid hybrids from tetra- to hexaploid individuals, but not vice versa. The ecological niche of pentaploids differed significantly from that of tetraploids but not from hexaploids. PMID:25859328

  16. BACILLUS THURINGIENSIS VAR. KURSTAKI AFFECTS A BENEFICIAL INSECT, THE CINNABAR MOTH (LEPIDOPTERA: ARCTIIDAE)

    EPA Science Inventory

    The microbial insecticide bacillus thuringiensis Berliner var. kurstaki is used to control forest pests in regions where tansy ragwort, Senecio jacobaea L. occurs. iological control of this noxious weed may be compromised if the cinnabar moth, Tyria jacobaeae (L), is susceptible ...

  17. Can a Pathogen Provide Insurance against Host Shifts by a Biological Control Organism?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The cinnabar moth (Tyria jacobaeae (L.), Lepidoptera: Arctiidae) is an icon in population ecology and biological control that has recently lost its shine based on evidence that (1) it is less effective than alternatives (such as the ragwort flea beetle Longitarsus jacobaeae (Waterhouse) (Coleoptera:...

  18. Plant pollinator interactions: comparison between an invasive and a native congeneric species

    NASA Astrophysics Data System (ADS)

    Vanparys, Valérie; Meerts, Pierre; Jacquemart, Anne-Laure

    2008-11-01

    Plant-pollinator interactions determine reproductive success for animal-pollinated species and, in the case of invasive plants, they are supposed to play an important role in invasive success. We compared the invasive Senecio inaequidens to its native congener S. jacobaea in terms of interactions with pollinators. Visitor guild, visitation rate, and seed set were compared over 3 years in three sites in Belgium. Floral display (capitula number and arrangement) and phenology were quantified, and visiting insects were individually censused, i.e. number of visited capitula and time per visited capitulum. As expected from capitula resemblance, visitor guilds of both species were very similar (proportional similarity = 0.94). Senecio inaequidens was visited by 33 species, versus 36 for S. jacobaea. For both species, main visitors were Diptera, especially Syrphidae, and Hymenoptera. Visitation rate averaged 0.13 visitor per capitulum per 10 min for S. inaequidens against 0.08 for S. jacobaea. However, insects visited more capitula per plant on S. jacobaea, due to high capitula density (886 m -2 versus 206 m -2 for S. inaequidens), which is likely to increase self-pollen deposition considerably. Seed set of S. jacobaea was lower than that of S. inaequidens. We suggest that floral display is the major factor explaining the differences in insect visitation and seed set between the two Senecio species.

  19. A polymicrobial outbreak of surgical site infections following cardiac surgery at a community hospital in Florida, 2011–2012

    PubMed Central

    Nguyen, Duc B.; Gupta, Neil; Abou-Daoud, Alison; KleKamp, Benjamin G.; Rhone, Chaz; Winston, Tiffany; Hedberg, Trevor; Scuteri, Ana; Evans, Charlotte; Jensen, Bette; Moulton-Meissner, Heather; Török, Thomas; Berríos-Torres, Sandra I.; Noble-Wang, Judith; Kallen, Alexander

    2015-01-01

    We describe an outbreak of 22 sternal surgical site infections following cardiac surgery, including 4 Gordonia infections. Possible operation room environmental contamination and suboptimal infection control practices regarding scrub attire may have contributed to the outbreak. PMID:24679572

  20. Locating and Activating Molecular ‘Time Bombs’: Induction of Mycolata Prophages

    PubMed Central

    Dyson, Zoe A.; Brown, Teagan L.; Farrar, Ben; Doyle, Stephen R.; Tucci, Joseph; Seviour, Robert J.; Petrovski, Steve

    2016-01-01

    Little is known about the prevalence, functionality and ecological roles of temperate phages for members of the mycolic acid producing bacteria, the Mycolata. While many lytic phages infective for these organisms have been isolated, and assessed for their suitability for use as biological control agents of activated sludge foaming, no studies have investigated how temperate phages might be induced for this purpose. Bioinformatic analysis using the PHAge Search Tool (PHAST) on Mycolata whole genome sequence data in GenBank for members of the genera Gordonia, Mycobacterium, Nocardia, Rhodococcus, and Tsukamurella revealed 83% contained putative prophage DNA sequences. Subsequent prophage inductions using mitomycin C were conducted on 17 Mycolata strains. This led to the isolation and genome characterization of three novel Caudovirales temperate phages, namely GAL1, GMA1, and TPA4, induced from Gordonia alkanivorans, Gordonia malaquae, and Tsukamurella paurometabola, respectively. All possessed highly distinctive dsDNA genome sequences. PMID:27487243

  1. Large animal hepatotoxic and nephrotoxic plants.

    PubMed

    Oladosu, L A; Case, A A

    1979-10-01

    The hepatotoxic and nephrotoxic plants of large domestic animals have been reviewed. The most important ones are those widely distributed as weeds over pastures, negelcted forests and grasslands, those used as ornamentals, the nitrate concentrating forage crops, and the cyanophoric plants. Crotolaria spp, the ragwort (Senecia jacobaea), the lantana spp. and heliotopum are common hepatoxic plants. Amaranthus retroflexus, Datura stramonium, Solanum rostratum, and the castor oil plant (Ricinus communis) are nephrotoxic plants. PMID:516370

  2. Genomic and transcriptomic studies of an RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine)-degrading actinobacterium.

    PubMed

    Chen, Hao-Ping; Zhu, Song-Hua; Casabon, Israël; Hallam, Steven J; Crocker, Fiona H; Mohn, William W; Indest, Karl J; Eltis, Lindsay D

    2012-11-01

    Whole-genome sequencing, transcriptomic analyses, and metabolic reconstruction were used to investigate Gordonia sp. strain KTR9's ability to catabolize a range of compounds, including explosives and steroids. Aspects of this mycolic acid-containing actinobacterium's catabolic potential were experimentally verified and compared with those of rhodococci and mycobacteria. PMID:22923396

  3. Genomic and Transcriptomic Studies of an RDX (Hexahydro-1,3,5-Trinitro-1,3,5-Triazine)-Degrading Actinobacterium

    PubMed Central

    Chen, Hao-Ping; Zhu, Song-Hua; Casabon, Israël; Hallam, Steven J.; Crocker, Fiona H.; Mohn, William W.

    2012-01-01

    Whole-genome sequencing, transcriptomic analyses, and metabolic reconstruction were used to investigate Gordonia sp. strain KTR9's ability to catabolize a range of compounds, including explosives and steroids. Aspects of this mycolic acid-containing actinobacterium's catabolic potential were experimentally verified and compared with those of rhodococci and mycobacteria. PMID:22923396

  4. Effect of pretreatment of rubber material on its biodegradability by various rubber degrading bacteria.

    PubMed

    Berekaa, M M; Linos, A; Reichelt, R; Keller, U; Steinbüchel, A

    2000-03-15

    The effect of pretreatment of several cis-1,4-polyisoprene containing rubbers on their biodegradability was examined. Tests were carried out with six recently isolated and characterized rubber degrading bacteria belonging to the genera Gordonia (strains Kb2, Kd2 and VH2), Mycobacterium, Micromonospora and Pseudomonas. All strains were able to use natural rubber (NR) as well as NR latex gloves as sole carbon source. Extraction of NR latex gloves by organic solvents resulted in an enhancement of growth for three of the selected strains. On the other hand, growth of Gordonia sp. (strain Kb2 and Kd2), Mycobacterium fortuitum NF4 and Micromonospora aurantiaca W2b on synthetic cis-1,4-polyisoprene did only occur after removal of the antioxidants, that are usually added during manufacture to prevent aging of the materials. Detailed degradation studies performed with Gordonia sp. Kb2 revealed an enhanced mineralization of pretreated NR latex gloves and mineralization of purified natural rubber (NR), indicating the actual mineralization of cis-1,4-polyisoprene rubber constituent even after removal of non-rubber constituent that may act as co-metabolic substrate and support microbial growth. Further analysis by scanning electron microscopy (SEM) clearly demonstrated the enhanced colonization efficiency of these bacteria towards pretreated NR latex gloves. Colonization was additionally visualized by staining of overgrown NR latex gloves with Schiff's reagent, and the purple color produced in the area of degradation was an evidence for the accumulation of aldehydes containing oligomers. Further enhancement of latex gloves degradation could be achieved after successive replacement of mineral salts medium during cultivation. Thereby, a rapid disintegration of untreated NR latex gloves material was accomplished by Gordonia sp. strain VH2. PMID:10713421

  5. Community structure and PAH ring-hydroxylating dioxygenase genes of a marine pyrene-degrading microbial consortium.

    PubMed

    Gallego, Sara; Vila, Joaquim; Tauler, Margalida; Nieto, José María; Breugelmans, Philip; Springael, Dirk; Grifoll, Magdalena

    2014-07-01

    Marine microbial consortium UBF, enriched from a beach polluted by the Prestige oil spill and highly efficient in degrading this heavy fuel, was subcultured in pyrene minimal medium. The pyrene-degrading subpopulation (UBF-Py) mineralized 31 % of pyrene without accumulation of partially oxidized intermediates indicating the cooperation of different microbial components in substrate mineralization. The microbial community composition was characterized by culture dependent and PCR based methods (PCR-DGGE and clone libraries). Molecular analyses showed a highly stable community composed by Alphaproteobacteria (84 %, Breoghania, Thalassospira, Paracoccus, and Martelella) and Actinobacteria (16 %, Gordonia). The members of Thalasosspira and Gordonia were not recovered as pure cultures, but five additional strains, not detected in the molecular analysis, that classified within the genera Novosphingobium, Sphingopyxis, Aurantimonas (Alphaproteobacteria), Alcanivorax (Gammaproteobacteria) and Micrococcus (Actinobacteria), were isolated. None of the isolates degraded pyrene or other PAHs in pure culture. PCR amplification of Gram-positive and Gram-negative dioxygenase genes did not produce results with any of the cultured strains. However, sequences related to the NidA3 pyrene dioxygenase present in mycobacterial strains were detected in UBF-Py consortium, suggesting the representative of Gordonia as the key pyrene degrader, which is consistent with a preeminent role of actinobacteria in pyrene removal in coastal environments affected by marine oil spills. PMID:24356981

  6. Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers

    PubMed Central

    Guo, Feng; Wang, Zhi-Ping; Yu, Ke; Zhang, T.

    2015-01-01

    Foaming of activated sludge (AS) causes adverse impacts on wastewater treatment operation and hygiene. In this study, we investigated the microbial communities of foam, foaming AS and non-foaming AS in a sewage treatment plant via deep-sequencing of the taxonomic marker genes 16S rRNA and mycobacterial rpoB and a metagenomic approach. In addition to Actinobacteria, many genera (e.g., Clostridium XI, Arcobacter, Flavobacterium) were more abundant in the foam than in the AS. On the other hand, deep-sequencing of rpoB did not detect any obligate pathogenic mycobacteria in the foam. We found that unknown factors other than the abundance of Gordonia sp. could determine the foaming process, because abundance of the same species was stable before and after a foaming event over six months. More interestingly, although the dominant Gordonia foam former was the closest with G. amarae, it was identified as an undescribed Gordonia species by referring to the 16S rRNA gene, gyrB and, most convincingly, the reconstructed draft genome from metagenomic reads. Our results, based on metagenomics and deep sequencing, reveal that foams are derived from diverse taxa, which expands previous understanding and provides new insight into the underlying complications of the foaming phenomenon in AS. PMID:25560234

  7. Mixed metazoan and bacterial infection of the gas bladder of the lined seahorse-a case report.

    PubMed

    Anderson, Paul A; Petty, Barbara D

    2013-03-01

    Five wild-caught Lined Seahorses Hippocampus erectus from an aquarium system presented with altered buoyancy and distended upper trunks. Radiography of one specimen revealed a reduced air volume in the gas bladder. Pneumocystocentesis revealed a brown exudate of numerous leukocytes, parasite ova, and Gram- and acid-fast-positive bacilli under wet mounts and stains. Necropsies revealed enlarged, friable kidneys and distended gas bladders containing copious purulent exudate, necrotic tissue, and adult digeneans Dictysarca virens. Bacterial isolates from exudate cultures grown on Lowenstein-Jensen medium were identified as Gordonia sp. and Mycobacterium poriferae by high-performance liquid chromatography and 16S ribosomal DNA sequencing. Histopathology demonstrated a histiocytic response in kidney and gas bladder exudate, inflammation of the gas bladder wall, and infection of the gas bladder lumen with parasite ova and acid-fast-positive and Gomori's methenamine silver-positive bacilli. Praziquantel is prescribed for digenean infections but dissolves incompletely in seawater and is toxic to this host. Eradication of intermediate host vectors is a management option. Treatment of Gordonia infection has not been addressed in nonhuman animals, and there is no known effective treatment for Mycobacterium spp. infection in fishes. This is the first case report of digenean infection of the gas bladder in a syngnathid, Gordonia sp. infection in a nonhuman animal, and M. poriferae infection in a fish. PMID:23343385

  8. Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers

    NASA Astrophysics Data System (ADS)

    Guo, Feng; Wang, Zhi-Ping; Yu, Ke; Zhang, T.

    2015-01-01

    Foaming of activated sludge (AS) causes adverse impacts on wastewater treatment operation and hygiene. In this study, we investigated the microbial communities of foam, foaming AS and non-foaming AS in a sewage treatment plant via deep-sequencing of the taxonomic marker genes 16S rRNA and mycobacterial rpoB and a metagenomic approach. In addition to Actinobacteria, many genera (e.g., Clostridium XI, Arcobacter, Flavobacterium) were more abundant in the foam than in the AS. On the other hand, deep-sequencing of rpoB did not detect any obligate pathogenic mycobacteria in the foam. We found that unknown factors other than the abundance of Gordonia sp. could determine the foaming process, because abundance of the same species was stable before and after a foaming event over six months. More interestingly, although the dominant Gordonia foam former was the closest with G. amarae, it was identified as an undescribed Gordonia species by referring to the 16S rRNA gene, gyrB and, most convincingly, the reconstructed draft genome from metagenomic reads. Our results, based on metagenomics and deep sequencing, reveal that foams are derived from diverse taxa, which expands previous understanding and provides new insight into the underlying complications of the foaming phenomenon in AS.

  9. Interspecific transfer of pyrrolizidine alkaloids: An unconsidered source of contaminations of phytopharmaceuticals and plant derived commodities.

    PubMed

    Nowak, Melanie; Wittke, Carina; Lederer, Ines; Klier, Bernhard; Kleinwächter, Maik; Selmar, Dirk

    2016-12-15

    Many plant derived commodities contain traces of toxic pyrrolizidine alkaloids (PAs). The main source of these contaminations seems to be the accidental co-harvest of PA-containing weeds. Yet, based on the insights of the newly described phenomenon of the horizontal transfer of natural products, it is very likely that the PA-contaminations may also be due to an uptake of the alkaloids from the soil, previously being leached out from rotting PA-plants. The transfer of PAs was investigated using various herbs, which had been mulched with dried plant material from Senecio jacobaea. All of the acceptor plants exhibited marked concentrations of PAs. The extent and the composition of the imported PAs was dependent on the acceptor plant species. These results demonstrate that PAs indeed are leached out from dried Senecio material into the soil and confirm their uptake by the roots of the acceptor plants and the translocation into the leaves. PMID:27451168

  10. An evaluation of acetone extracts from six plants in the Ames mutagenicity test.

    PubMed

    White, R D; Krumperman, P H; Cheeke, P R; Buhler, D R

    1983-01-01

    Acetone extracts from six plants were evaluated for mutagenic activity with the Salmonella/mammalian-microsome mutagenicity test (Ames) utilizing tester strains TA98 and TA100 and in the presence and absence of induced rat liver microsomes. Extracts from alfalfa (Medicago sativa), lettuce (Lactuca sativa) and thread-leaf groundsel (Senecio longilobus) produced only negative responses. Comfrey (Symphytum officinale) and tansy ragwort (Senecio jacobaea) extracts produced toxic responses that were abolished in the presence of the microsomal bioactivation system. Bracken (Pteridium aquilinum) and tansy ragwort extracts produced positive responses following bioactivation with the liver microsomal system. The results suggest that the Ames mutagenicity test may be of some value in initial evaluations for potential toxic effects of plants consumed by animals and man. PMID:6836587

  11. Changes in plant defense chemistry (pyrrolizidine alkaloids) revealed through high-resolution spectroscopy

    NASA Astrophysics Data System (ADS)

    Carvalho, Sabrina; Macel, Mirka; Schlerf, Martin; Moghaddam, Fatemeh Eghbali; Mulder, Patrick P. J.; Skidmore, Andrew K.; van der Putten, Wim H.

    2013-06-01

    Plant toxic biochemicals play an important role in defense against natural enemies and often are toxic to humans and livestock. Hyperspectral reflectance is an established method for primary chemical detection and could be further used to determine plant toxicity in the field. In order to make a first step for pyrrolizidine alkaloids detection (toxic defense compound against mammals and many insects) we studied how such spectral data can estimate plant defense chemistry under controlled conditions. In a greenhouse, we grew three related plant species that defend against generalist herbivores through pyrrolizidine alkaloids: Jacobaea vulgaris, Jacobaea erucifolia and Senecio inaequidens, and analyzed the relation between spectral measurements and chemical concentrations using multivariate statistics. Nutrient addition enhanced tertiary-amine pyrrolizidine alkaloids contents of J. vulgaris and J. erucifolia and decreased N-oxide contents in S. inaequidens and J. vulgaris. Pyrrolizidine alkaloids could be predicted with a moderate accuracy. Pyrrolizidine alkaloid forms tertiary-amines and epoxides were predicted with 63% and 56% of the variation explained, respectively. The most relevant spectral regions selected for prediction were associated with electron transitions and Csbnd H, Osbnd H, and Nsbnd H bonds in the 1530 and 2100 nm regions. Given the relatively low concentration in pyrrolizidine alkaloids concentration (in the order of mg g-1) and resultant predictions, it is promising that pyrrolizidine alkaloids interact with incident light. Further studies should be considered to determine if such a non-destructive method may predict changes in PA concentration in relation to plant natural enemies. Spectroscopy may be used to study plant defenses in intact plant tissues, and may provide managers of toxic plants, food industry and multitrophic-interaction researchers with faster and larger monitoring possibilities.

  12. Flavin-dependent monooxygenases as a detoxification mechanism in insects: new insights from the arctiids (lepidoptera).

    PubMed

    Sehlmeyer, Sven; Wang, Linzhu; Langel, Dorothee; Heckel, David G; Mohagheghi, Hoda; Petschenka, Georg; Ober, Dietrich

    2010-01-01

    Insects experience a wide array of chemical pressures from plant allelochemicals and pesticides and have developed several effective counterstrategies to cope with such toxins. Among these, cytochrome P450 monooxygenases are crucial in plant-insect interactions. Flavin-dependent monooxygenases (FMOs) seem not to play a central role in xenobiotic detoxification in insects, in contrast to mammals. However, the previously identified senecionine N-oxygenase of the arctiid moth Tyria jacobaeae (Lepidoptera) indicates that FMOs have been recruited during the adaptation of this insect to plants that accumulate toxic pyrrolizidine alkaloids. Identification of related FMO-like sequences of various arctiids and other Lepidoptera and their combination with expressed sequence tag (EST) data and sequences emerging from the Bombyx mori genome project show that FMOs in Lepidoptera form a gene family with three members (FMO1 to FMO3). Phylogenetic analyses suggest that FMO3 is only distantly related to lepidopteran FMO1 and FMO2 that originated from a more recent gene duplication event. Within the FMO1 gene cluster, an additional gene duplication early in the arctiid lineage provided the basis for the evolution of the highly specific biochemical, physiological, and behavioral adaptations of these butterflies to pyrrolizidine-alkaloid-producing plants. The genes encoding pyrrolizidine-alkaloid-N-oxygenizing enzymes (PNOs) are transcribed in the fat body and the head of the larvae. An N-terminal signal peptide mediates the transport of the soluble proteins into the hemolymph where PNOs efficiently convert pro-toxic pyrrolizidine alkaloids into their non-toxic N-oxide derivatives. Heterologous expression of a PNO of the generalist arctiid Grammia geneura produced an N-oxygenizing enzyme that shows noticeably expanded substrate specificity compared with the related enzyme of the specialist Tyria jacobaeae. The data about the evolution of FMOs within lepidopteran insects and the

  13. Metabolic versatility of Gram-positive microbial isolates from contaminated river sediments.

    PubMed

    Narancic, Tanja; Djokic, Lidija; Kenny, Shane T; O'Connor, Kevin E; Radulovic, Vanja; Nikodinovic-Runic, Jasmina; Vasiljevic, Branka

    2012-05-15

    Gram-positive bacteria from river sediments affected by the proximity of a petrochemical industrial site were isolated and characterized with respect to their ability to degrade a wide range of aromatic compounds. In this study we identified metabolically diverse Gram-positive bacteria capable of growth on wide range aromatic compounds in the presence of heavy metals and with the ability to accumulate biopolymers. Thirty-four isolates that were able to use 9 or more common aromatic pollutants, such as benzene, biphenyl, naphthalene etc. as a sole source of carbon and energy included members of Bacillus, Arthrobacter, Rhodococcus, Gordonia, Streptomyces, and Staphylococcus genus. Rhodococcus sp. TN105, Gordonia sp. TN103 and Arthrobacter sp. TN221 were identified as novel strains. Nine isolates were able to grow in the presence of one or more metals (mercury, cadmium, nickel) at high concentration (100mM). Seven isolates could degrade 15 different aromatic compounds and could grow in the presence of one or more heavy metals. Two of these isolates were resistant to multiple antibiotics including erythromycin and nalidixic acid. One third of isolates could accumulate at least one biopolymer. Twelve isolates (mainly Bacillus sp. and Arthrobacter sp.) accumulated polyphosphate, 3 Bacillus sp. accumulated polyhydroxybutyrate, while 4 isolates could accumulate exopolysaccharides. PMID:22421345

  14. Evaluation of microbial transport during aerobic bioaugmentation of an RDX-contaminated aquifer.

    PubMed

    Crocker, Fiona H; Indest, Karl J; Jung, Carina M; Hancock, Dawn E; Fuller, Mark E; Hatzinger, Paul B; Vainberg, Simon; Istok, Jonathan D; Wilson, Edward; Michalsen, Mandy M

    2015-11-01

    In situ bioaugmentation with aerobic hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)-degrading bacteria is being considered for treatment of explosives-contaminated groundwater at Umatilla Chemical Depot, Oregon (UMCD). Two forced-gradient bacterial transport tests of site groundwater containing chloride or bromide tracer and either a mixed culture of Gordonia sp. KTR9 (xplA (+)Km(R)), Rhodococcus jostii RHA1 (pGKT2 transconjugant; xplA (+)Km(R)) and Pseudomonas fluorescens I-C (xenB (+)), or a single culture of Gordonia sp. KTR9 (xplA (+); i.e. wild-type) were conducted at UMCD. Groundwater monitoring evaluated cell viability and migration in the injection well and downgradient monitoring wells. Enhanced degradation of RDX was not evaluated in these demonstrations. Quantitative PCR analysis of xplA, the kanamycin resistance gene (aph), and xenB indicated that the mixed culture was transported at least 3 m within 2 h of injection. During a subsequent field injection of bioaugmented groundwater, strain KTR9 (wild-type) migrated up to 23-m downgradient of the injection well within 3 days. Thus, the three RDX-degrading strains were effectively introduced and transported within the UMCD aquifer. This demonstration represents an innovative application of bioaugmentation to potentially enhance RDX biodegradation in aerobic aquifers. PMID:26438043

  15. The influence of bioaugmentation and biosurfactant addition on bioremediation efficiency of diesel-oil contaminated soil: feasibility during field studies.

    PubMed

    Szulc, Alicja; Ambrożewicz, Damian; Sydow, Mateusz; Ławniczak, Łukasz; Piotrowska-Cyplik, Agnieszka; Marecik, Roman; Chrzanowski, Łukasz

    2014-01-01

    The study focused on assessing the influence of bioaugmentation and addition of rhamnolipids on diesel oil biodegradation efficiency during field studies. Initial laboratory studies (measurement of emitted CO2 and dehydrogenase activity) were carried out in order to select the consortium for bioaugmentation as well as to evaluate the most appropriate concentration of rhamnolipids. The selected consortium consisted of following bacterial taxa: Aeromonas hydrophila, Alcaligenes xylosoxidans, Gordonia sp., Pseudomonas fluorescens, Pseudomonas putida, Rhodococcus equi, Stenotrophomonas maltophilia, Xanthomonas sp. It was established that the application of rhamnolipids at 150 mg/kg of soil was most appropriate in terms of dehydrogenase activity. Based on the obtained results, four treatment methods were designed and tested during 365 days of field studies: I) natural attenuation; II) addition of rhamnolipids; III) bioaugmentation; IV) bioaugmentation and addition of rhamnolipids. It was observed that bioaugmentation contributed to the highest diesel oil biodegradation efficiency, whereas the addition of rhamnolipids did not notably influence the treatment process. PMID:24291585

  16. A full-scale study of mixing and foaming in egg-shaped anaerobic digesters.

    PubMed

    Subramanian, Bhargavi; Miot, Alexandre; Jones, Bonnie; Klibert, Corey; Pagilla, Krishna R

    2015-09-01

    Seasonal foaming in full-scale egg-shaped digesters (ESD) at the Oceanside Water Pollution Control Plant was investigated over a two-year period. The causes and contributors of anaerobic digestion (AD) foaming, namely, Gordonia amarae filaments and mixing effects were evaluated in these ESDs. The seasonal presence of high levels of G. amarae as a primary cause and excessive induced mixing as an important contributor of AD foaming has been established. The induced mixing frequency in the ESDs was gradually reduced and eventually shut off in a series of controlled experimental phases. Total solids and temperature profiles indicated that reducing mixing frequency did not significantly impact digester performance or disrupt the homogeneity of digester contents, although it did reduce the occurrence of foam in the digesters. Excessive induced mixing, a contributor to foaming, increased foam events at G. amarae thresholds above 10(6)intersections/mg VSS in the mixed liquor. PMID:26080103

  17. Lateral Transfer of Genes for Hexahydro-1,3,5-Trinitro-1,3,5-Triazine (RDX) Degradation▿ †

    PubMed Central

    Andeer, Peter F.; Stahl, David A.; Bruce, Neil C.; Strand, Stuart E.

    2009-01-01

    Recent studies demonstrated that degradation of the military explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by species of Rhodococcus, Gordonia, and Williamsia is mediated by a novel cytochrome P450 with a fused flavodoxin reductase domain (XplA) in conjunction with a flavodoxin reductase (XplB). Pulse field gel analysis was used to localize xplA to extrachromosomal elements in a Rhodococcus sp. and distantly related Microbacterium sp. strain MA1. Comparison of Rhodococcus rhodochrous 11Y and Microbacterium plasmid sequences in the vicinity of xplB and xplA showed near identity (6,710 of 6,721 bp). Sequencing of the associated 52.2-kb region of the Microbacterium plasmid pMA1 revealed flanking insertion sequence elements and additional genes implicated in RDX uptake and degradation. PMID:19270122

  18. Identification and location of symbionts associated with potato psyllid (Bactericera cockerelli) lifestages.

    PubMed

    Hail, Daymon; Dowd, Scot E; Bextine, Blake

    2012-02-01

    The potato psyllid (Bactericera cockerelli, Sulc) is an invasive pest of solenaceous plants including potatoes (Solanum tuberosum L.)and tomatoes (Solanum lycopersicum L.). The insect transmits the phytopathogen Candidatus Liberibacter solanacearum, which has been identified as the causal agent of Zebra Chip in potatoes. The microbiome of the potato psyllid provides knowledge of the insect's bacterial makeup which enables researchers to develop targeted biological control strategies. In this study, the microbes associated with four B. cockerelli life stages were evaluated by 16S bTEFAP pyrosequencing. The sequences were compared with a 16S-rDNA database derived from NCBI's GenBank. Some bacteria identified are initial discoveries. Species of Wolbachia, Rhizobium, Gordonia, Mycobacterium, Xanthomonas and others were also detected and an assessment of the microbiome associated with B. cockerelli was established. PMID:22525064

  19. Identification and antimicrobial activity of actinobacteria from soils in southern Thailand.

    PubMed

    Sripreechasak, P; Tanasupawat, S; Matsumoto, A; Inahashi, Y; Suwanborirux, K; Takahashi, Y

    2013-03-01

    The aim of this research was to study on the identification and antimicrobial activity of actinobacteria from six soil samples collected around Krung Ching waterfall, Nakhon Si Thammarat province, the southern part of Thailand. Thirty-one isolates of actinobacteria were isolated using the dilution plating method on modified starch casein nitrate agar plates and potato starch-glycerol agar plates. On the primary screening, 9 isolates exhibited the antimicrobial activity against Bacillus subtilis, 8 isolates against Kocuria rhizophila, 6 isolates against Mucor racemosus, 2 isolates against Escherichia coli and Candida albicans and 5 isolates against Xanthomonas campestris pv. oryzae. All the isolates were identified based on their morphological and cultural characteristics including the 16S rRNA gene sequence analysis. Eighteen isolates were identified as Streptomyces, 8 isolates as Nocardia, 2 isolates as Kitasatospora, one of each isolate as Amycolatopsis, Rhodococcus and Gordonia. PMID:23665707

  20. Diversity of actinomycetes isolated from subseafloor sediments after prolonged low-temperature storage.

    PubMed

    Ulanova, Dana; Goo, Kian-Sim

    2015-05-01

    Subseafloor sediments present an untapped source of novel bacterial species with industrially important bioactivities. Subseafloor core samples collected during the Integrated Ocean Drilling Program Expeditions 315, 316, and 331 and stored in Kochi Core Center at -80 °C for 1 to 4 years were used for cultivation-based study of viable actinomycetes. In total, more than 100 actinomycete-like colonies were isolated from two deep-frozen subseafloor sediment samples. Isolated actinomycetes showed close similarity to known Actinotalea, Dietzia, Gordonia, Isoptericola, Microbacterium, Nocardia, Rhodococcus, Pseudonocardia, Streptomyces, and Tsukamurella species and were halotolerant. Bioactivity assays revealed that two of the isolates were producing potent antibacterial compound(s) and one isolate was having antifungal activity. Our study demonstrated that deep-frozen subseafloor core samples could be a potential source of viable actinomycetes, which may be used in drug discovery. PMID:25381631

  1. Bacteria Present in Comadia redtenbacheri Larvae (Lepidoptera: Cossidae).

    PubMed

    Hernández-Flores, L; Llanderal-Cázares, C; Guzmán-Franco, A W; Aranda-Ocampo, S

    2015-09-01

    The external and internal culturable bacterial community present in the larvae of Comadia redtenbacheri Hammerschmidt, an edible insect, was studied. Characterization of the isolates determined the existence of 18 morphotypes and phylogenetic analysis of the 16S rRNA gene revealed the existence of Paenibacillus sp., Bacillus safensis, Pseudomonas sp., Bacillus pseudomycoides, Corynebacterium variabile, Enterococcus sp., Gordonia sp., Acinetobacter calcoaceticus, Arthrobacter sp., Micrococcus sp., and Bacillus cereus. Greater diversity of bacteria was found in those larvae obtained from vendors than in those directly taken from Agave plants in nature. Many of the larvae obtained from vendors presented signs of potential disease, and after the analysis, results showed a greater bacterial community compared with the larvae with a healthy appearance. This indicates that bacterial flora can vary in accordance with how the larvae are handled during extraction, collection, and transport. PMID:26336239

  2. Biodegradation of cis-1,4-Polyisoprene Rubbers by Distinct Actinomycetes: Microbial Strategies and Detailed Surface Analysis

    PubMed Central

    Linos, Alexandros; Berekaa, Mahmoud M.; Reichelt, Rudolf; Keller, Ulrike; Schmitt, Jürgen; Flemming, Hans-Curt; Kroppenstedt, Reiner M.; Steinbüchel, Alexander

    2000-01-01

    Several actinomycetes isolated from nature were able to use both natural rubber (NR) and synthetic cis-1,4-polyisoprene rubber (IR) as a sole source of carbon. According to their degradation behavior, they were divided into two groups. Representatives of the first group grew only in direct contact to the rubber substrate and led to considerable disintegration of the material during cultivation. The second group consisted of weaker rubber decomposers that did not grow adhesively, as indicated by the formation of clear zones (translucent halos) around bacterial colonies after cultivation on NR dispersed in mineral agar. Taxonomic analysis of four selected strains based on 16S rRNA similarity examinations revealed two Gordonia sp. strains, VH2 and Kb2, and one Mycobacterium fortuitum strain, NF4, belonging to the first group as well as one Micromonospora aurantiaca strain, W2b, belonging to the second group. Schiff's reagent staining tests performed for each of the strains indicated colonization of the rubber surface, formation of a bacterial biofilm, and occurrence of compounds containing aldehyde groups during cultivation with NR latex gloves. Detailed analysis by means of scanning electron microscopy yielded further evidence for the two different microbial strategies and clarified the colonization efficiency. Thereby, strains VH2, Kb2, and NF4 directly adhered to and merged into the rubber material, while strain W2b produced mycelial corridors, especially on the surface of IR. Fourier transform infrared spectroscopy comprising the attenuated total reflectance technique was applied on NR latex gloves overgrown by cells of the Gordonia strains, which were the strongest rubber decomposers. Spectra demonstrated the decrease in number of cis-1,4 double bonds, the formation of carbonyl groups, and the change of the overall chemical environment, indicating that an oxidative attack at the double bond is the first metabolic step of the biodegradation process. PMID:10742254

  3. Evolving while invading: rapid adaptive evolution in juvenile development time for a biological control organism colonizing a high-elevation environment.

    PubMed

    McEvoy, Peter B; Higgs, Kimberley M; Coombs, Eric M; Karaçetin, Evrim; Ann Starcevich, Leigh

    2012-07-01

    We report evidence of adaptive evolution in juvenile development time on a decadal timescale for the cinnabar moth Tyria jacobaeae (Lepidoptera: Arctiidae) colonizing new habitats and hosts from the Willamette Valley to the Coast Range and Cascades Mountains in Oregon. Four lines of evidence reveal shorter egg to pupa juvenile development times evolved in the mountains, where cooler temperatures shorten the growing season: (i) field observations showed that the mountain populations have shorter phenological development; (ii) a common garden experiment revealed genetic determination of phenotypic differences in juvenile development time between Willamette Valley and mountain populations correlated with the growing season; (iii) a laboratory experiment rearing offspring from parental crosses within and between Willamette Valley and Cascades populations demonstrated polygenic inheritance, high heritability, and genetic determination of phenotypic differences in development times; and (iv) statistical tests that exclude random processes (founder effect, genetic drift) in favor of natural selection as explanations for observed differences in phenology. These results support the hypothesis that rapid adaptation to the cooler mountain climate occurred in populations established from populations in the warmer valley climate. Our findings should motivate regulators to require evaluation of evolutionary potential of candidate biological control organisms prior to release. PMID:22949927

  4. The effect of nutrients on pyrrolizidine alkaloids in Senecio plants and their interactions with herbivores and pathogens.

    PubMed

    Hol, W H G

    2011-03-01

    The aim of this review is to combine the knowledge of studies on effects of nutrients on pyrrolizidine alkaloids (PAs) in Senecio with those studies of effects of PAs on herbivores and pathogens in order to predict the effects that nutrients may have on herbivores and pathogens via changes in PAs. We discuss whether these predictions match with the outcome of studies where the effect of nutrients on herbivores and insects were measured. PA concentrations in S. jacobaea, S. vulgaris and S. aquaticus were mostly reduced by NPK fertilization, with genotype-specific effects occurring. Plant organs varied in their response to increased fertilization; PA concentrations in flowers remained constant, while shoot and roots were mostly negatively affected. Biomass change is probably largely responsible for the change in concentrations. Nutrients affect both the variety and the levels of PAs in the plant. The reduced PA concentrations after NPK fertilization was expected to benefit herbivores, but no or negative responses from insect herbivores were observed. Apparently other changes in the plant after fertilization are overriding the effect of PAs. Pathogens do seem to benefit from the lower PA concentrations after fertilization; they were more detrimental to fertilized plants than to unfertilized control plants. Future studies should include the effect of each element of nutrients separately and in combinations in order to gain more insight in the effect of specific nutrients on PA content in Senecio plants. PMID:21475405

  5. The complete chloroplast genome sequence of Aster spathulifolius (Asteraceae); genomic features and relationship with Asteraceae.

    PubMed

    Choi, Kyoung Su; Park, SeonJoo

    2015-11-10

    Aster spathulifolius, a member of the Asteraceae family, is distributed along the coast of Japan and Korea. This plant is used for medicinal and ornamental purposes. The complete chloroplast (cp) genome of A. sphathulifolius consists of 149,473 bp that include a pair of inverted repeats of 24,751 bp separated by a large single copy region of 81,998 bp and a small single copy region of 17,973 bp. The chloroplast genome contains 78 coding genes, four rRNA genes and 29 tRNA genes. When compared to other cpDNA sequences of Asteraceae, A. spathulifolius showed the closest relationship with Jacobaea vulgaris, and its atpB gene was found to be a pseudogene, unlike J. vulgaris. Furthermore, evaluation of the gene compositions of J. vulgaris, Helianthus annuus, Guizotia abyssinica and A. spathulifolius revealed that 13.6-kb showed inversion from ndhF to rps15, unlike Lactuca of Asteraceae. Comparison of the synonymous (Ks) and nonsynonymous (Ka) substitution rates with J. vulgaris revealed that synonymous genes related to a small subunit of the ribosome showed the highest value (0.1558), while nonsynonymous rates of genes related to ATP synthase genes were highest (0.0118). These findings revealed that substitution has occurred at similar rates in most genes, and the substitution rates suggested that most genes is a purified selection. PMID:26164759

  6. Hyperspectral reflectance of leaves and flowers of an outbreak species discriminates season and successional stage of vegetation

    NASA Astrophysics Data System (ADS)

    Carvalho, Sabrina; Schlerf, Martin; van der Putten, Wim H.; Skidmore, Andrew K.

    2013-10-01

    Spectral reflectance can be used to assess large-scale performances of plants in the field based on plant nutrient balance as well as composition of defence compounds. However, plant chemical composition is known to vary with season - due to its phenology - and it may even depend on the succession stage of its habitat. Here we investigate (i) how spectral reflectance could be used to discriminate successional and phenological stages of Jacobaea vulgaris in both leaf and flower organs and (ii) if chemical content estimation by reflectance is flower or leaf dependent. We used J. vulgaris, which is a natural outbreak plant species on abandoned arable fields in north-western Europe and studied this species in a chronosequence representing successional development during time since abandonment. The chemical content and reflectance between 400 and 2500 nm wavelengths of flowers and leaves were measured throughout the season in fields of different successional ages. The data were analyzed with multivariate statistics for temporal discrimination and estimation of chemical contents in both leaf and flower organs. Two main effects were revealed by spectral reflectance measurements: (i) both flower and leaf spectra show successional and seasonal changes, but the pattern is complex and organ specific (ii) flower head pyrrolizidine alkaloids, which are involved in plant defence against herbivores, can be detected through hyperspectral reflectance.We conclude that spectral reflectance of both leaves and flowers can provide information on plant performance during season and successional stages. As a result, remote sensing studies of plant performance in complex field situations will benefit from considering hyperspectral reflectance of different plant organs. This approach may enable more detailed studies on the link between spectral information and plant defence dynamics both aboveground and belowground.

  7. Linking operation parameters and environmental variables to population dynamics of Mycolata in a membrane bioreactor.

    PubMed

    Maza-Márquez, P; Gómez-Silván, C; Gómez, M A; González-López, J; Martínez-Toledo, M V; Rodelas, B

    2015-03-01

    The community structure and population dynamics of Mycolata were monitored in a full-scale membrane bioreactor during four experimental phases under changing operating and environmental conditions, by means of temperature-gradient gel electrophoresis of partial 16S-rRNA genes amplified from community DNA and RNA templates (total and active populations). Non-metric multidimensional scaling and BIO-ENV analyses demonstrated that population dynamics were mostly explained (30-32%) by changes in the input of nutrients in the influent water and the accumulation of biomass in the bioreactors, while the influence of hydraulic and solid retention times, temperature and F/M ratio was minor. Significant correlations were observed between particular Mycolata phylotypes and one or more variables, contributing information for the prediction of their abundance and activity under changing conditions. Fingerprinting and multivariate analyses demonstrated that two foaming episodes, recorded at temperatures <20°C, were connected to the increase of the relative abundance of Mycolata unrelated to Gordonia amarae. PMID:25621724

  8. Antimicrobial Activity of Heterotrophic Bacterial Communities from the Marine Sponge Erylus discophorus (Astrophorida, Geodiidae)

    PubMed Central

    Graça, Ana Patrícia; Bondoso, Joana; Gaspar, Helena; Xavier, Joana R.; Monteiro, Maria Cândida; de la Cruz, Mercedes; Oves-Costales, Daniel; Vicente, Francisca; Lage, Olga Maria

    2013-01-01

    Heterotrophic bacteria associated with two specimens of the marine sponge Erylus discophorus were screened for their capacity to produce bioactive compounds against a panel of human pathogens (Staphylococcus aureus wild type and methicillin-resistant S. aureus (MRSA), Bacillus subtilis, Pseudomonas aeruginosa, Acinetobacter baumanii, Candida albicans and Aspergillus fumigatus), fish pathogen (Aliivibrio fischeri) and environmentally relevant bacteria (Vibrio harveyi). The sponges were collected in Berlengas Islands, Portugal. Of the 212 isolated heterotrophic bacteria belonging to Alpha- and Gammaproteobacteria, Actinobacteria and Firmicutes, 31% produced antimicrobial metabolites. Bioactivity was found against both Gram positive and Gram negative and clinically and environmentally relevant target microorganisms. Bioactivity was found mainly against B. subtilis and some bioactivity against S. aureus MRSA, V. harveyi and A. fisheri. No antifungal activity was detected. The three most bioactive genera were Pseudovibrio (47.0%), Vibrio (22.7%) and Bacillus (7.6%). Other less bioactive genera were Labrenzia, Acinetobacter, Microbulbifer, Pseudomonas, Gordonia, Microbacterium, Micrococcus and Mycobacterium, Paenibacillus and Staphylococcus. The search of polyketide I synthases (PKS-I) and nonribosomal peptide synthetases (NRPSs) genes in 59 of the bioactive bacteria suggested the presence of PKS-I in 12 strains, NRPS in 3 strains and both genes in 3 strains. Our results show the potential of the bacterial community associated with Erylus discophorus sponges as producers of bioactive compounds. PMID:24236081

  9. Role of Nocardia in Activated Sludge

    PubMed Central

    Bafghi, Mehdi Fatahi; Yousefi, Nader

    2016-01-01

    Activated sludge process is a biological process that is widely used in the domestic and industrial wastewater treatment in over the world. The foam formation is often reported in wastewater treatment plants which are related to this process. Some operational problems can be created by foaming, such as effluent quality deteriorates, the creation of malodorous, increased time requirements in order to plant maintenance, and in extreme cases, hazardous working conditions resulting from foam spilling out of the aeration basin and as well as increased in operational costs. There are different ways to overcome this problem, such as reduce air flows into the aeration basin, reduction in the grease and oil content of the wastewater, surface and return activated sludge (RAS) chlorination, anoxic and anaerobic selectors, solid retention time (SRT) control and antifoams and organic polymer addition. On the other hand, rapid and accurate identification of the foam causes is in the first step to control bulking and foaming. Foam problem is often created by filamentous bacteria, such as Nocardia and Gordonia species. This bacterium has a role important in activated sludge. PMID:27418874

  10. Corrosion behavior of carbon steel in the presence of two novel iron-oxidizing bacteria isolated from sewage treatment plants.

    PubMed

    Ashassi-Sorkhabi, H; Moradi-Haghighi, M; Zarrini, G; Javaherdashti, R

    2012-02-01

    In this work, two novel iron oxidizing bacteria (IOB), namely Gordonia sp. MZ-89 and Enterobacter sp. M01101, were isolated from sewage treatment plants and identified by biochemical and molecular methods. Then, microbially influenced corrosion (MIC) of carbon steel in the presence of these bacteria was investigated. The electrochemical techniques such as potentiodynamic polarization measurements and electrochemical impedance spectroscopy (EIS) were used to measure the corrosion rate and observe the corrosion mechanism. The results showed that the existence of these microorganisms decreased the corrosion potential and enhanced the corrosion rate. Scanning electron microscopy (SEM) images revealed the ground boundary attacks and pitting on carbon steel samples in the presence of these bacteria after polarization. Corrosion scales were identified with X-ray diffraction (XRD). It was demonstrated that these bacteria can greatly affect the crystalline phase of corrosion products that also confirmed by SEM results. It was inferred that these bacteria were responsible for the corrosion of carbon steel, especially in the form of localized corrosion. PMID:21695454

  11. 2-Butanol and butanone production in Saccharomyces cerevisiae through combination of a B12 dependent dehydratase and a secondary alcohol dehydrogenase using a TEV-based expression system.

    PubMed

    Ghiaci, Payam; Norbeck, Joakim; Larsson, Christer

    2014-01-01

    2-Butanol and its chemical precursor butanone (methyl ethyl ketone--MEK) are chemicals with potential uses as biofuels and biocommodity chemicals. In order to produce 2-butanol, we have demonstrated the utility of using a TEV-protease based expression system to achieve equimolar expression of the individual subunits of the two protein complexes involved in the B12-dependent dehydratase step (from the pdu-operon of Lactobacillus reuteri), which catalyze the conversion of meso-2,3-butanediol to butanone. We have furthermore identified a NADH dependent secondary alcohol dehydrogenase (Sadh from Gordonia sp.) able to catalyze the subsequent conversion of butanone to 2-butanol. A final concentration of 4±0.2 mg/L 2-butanol and 2±0.1 mg/L of butanone was found. A key factor for the production of 2-butanol was the availability of NADH, which was achieved by growing cells lacking the GPD1 and GPD2 isogenes under anaerobic conditions. PMID:25054226

  12. Role of Nocardia in Activated Sludge.

    PubMed

    Bafghi, Mehdi Fatahi; Yousefi, Nader

    2016-05-01

    Activated sludge process is a biological process that is widely used in the domestic and industrial wastewater treatment in over the world. The foam formation is often reported in wastewater treatment plants which are related to this process. Some operational problems can be created by foaming, such as effluent quality deteriorates, the creation of malodorous, increased time requirements in order to plant maintenance, and in extreme cases, hazardous working conditions resulting from foam spilling out of the aeration basin and as well as increased in operational costs. There are different ways to overcome this problem, such as reduce air flows into the aeration basin, reduction in the grease and oil content of the wastewater, surface and return activated sludge (RAS) chlorination, anoxic and anaerobic selectors, solid retention time (SRT) control and antifoams and organic polymer addition. On the other hand, rapid and accurate identification of the foam causes is in the first step to control bulking and foaming. Foam problem is often created by filamentous bacteria, such as Nocardia and Gordonia species. This bacterium has a role important in activated sludge. PMID:27418874

  13. Diversity and Antimicrobial Activities of Actinobacteria Isolated from Tropical Mangrove Sediments in Malaysia

    PubMed Central

    Lee, Learn-Han; Zainal, Nurullhudda; Azman, Adzzie-Shazleen; Eng, Shu-Kee; Goh, Bey-Hing; Yin, Wai-Fong; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan

    2014-01-01

    The aim of this study was to isolate and identify Actinobacteria from Malaysia mangrove forest and screen them for production of antimicrobial secondary metabolites. Eighty-seven isolates were isolated from soil samples collected at 4 different sites. This is the first report to describe the isolation of Streptomyces, Mycobacterium, Leifsonia, Microbacterium, Sinomonas, Nocardia, Terrabacter, Streptacidiphilus, Micromonospora, Gordonia, and Nocardioides from mangrove in east coast of Malaysia. Of 87 isolates, at least 5 isolates are considered as putative novel taxa. Nine Streptomyces sp. isolates were producing potent antimicrobial secondary metabolites, indicating that Streptomyces isolates are providing high quality metabolites for drug discovery purposes. The discovery of a novel species, Streptomyces pluripotens sp. nov. MUSC 135T that produced potent secondary metabolites inhibiting the growth of MRSA, had provided promising metabolites for drug discovery research. The biosynthetic potential of 87 isolates was investigated by the detection of polyketide synthetase (PKS) and nonribosomal polyketide synthetase (NRPS) genes, the hallmarks of secondary metabolites production. Results showed that many isolates were positive for PKS-I (19.5%), PKS-II (42.5%), and NRPS (5.7%) genes, indicating that mangrove Actinobacteria have significant biosynthetic potential. Our results highlighted that mangrove environment represented a rich reservoir for isolation of Actinobacteria, which are potential sources for discovery of antimicrobial secondary metabolites. PMID:25162061

  14. Laboratory evaluation of bioaugmentation for aerobic treatment of RDX in groundwater.

    PubMed

    Fuller, Mark E; Hatzinger, Paul B; Condee, Charles W; Andaya, Christina; Vainberg, Simon; Michalsen, Mandy M; Crocker, Fiona H; Indest, Karl J; Jung, Carina M; Eaton, Hillary; Istok, Jonathan D

    2015-02-01

    The potential for bioaugmentation with aerobic explosive degrading bacteria to remediate hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) contaminated aquifers was demonstrated. Repacked aquifer sediment columns were used to examine the transport and RDX degradation capacity of the known RDX degrading bacterial strains Gordonia sp. KTR9 (modified with a kanamycin resistance gene) Pseudomonas fluorescens I-C, and a kanamycin resistant transconjugate Rhodococcus jostii RHA1 pGKT2:Km+. All three strains were transported through the columns and eluted ahead of the conservative bromide tracer, although the total breakthrough varied by strain. The introduced cells responded to biostimulation with fructose (18 mg L(-1), 0.1 mM) by degrading dissolved RDX (0.5 mg L(-1), 2.3 µM). The strains retained RDX-degrading activity for at least 6 months following periods of starvation when no fructose was supplied to the column. Post-experiment analysis of the soil indicated that the residual cells were distributed along the length of the column. When the strains were grown to densities relevant for field-scale application, the cells remained viable and able to degrade RDX for at least 3 months when stored at 4 °C. These results indicate that bioaugmentation may be a viable option for treating RDX in large dilute aerobic plumes. PMID:25503243

  15. Antioxidant capacities and total phenolic contents of 56 wild fruits from South China.

    PubMed

    Fu, Li; Xu, Bo-Tao; Xu, Xiang-Rong; Qin, Xin-Sheng; Gan, Ren-You; Li, Hua-Bin

    2010-01-01

    In order to identify wild fruits possessing high nutraceutical potential, the antioxidant activities of 56 wild fruits from South China were systematically evaluated. The fat-soluble components were extracted with tetrahydrofuran, and the water-soluble ones were extracted with a 50:3.7:46.3 (v/v) methanol-acetic acid-water mixture. The antioxidant capacities of the extracts were evaluated using the ferric reducing antioxidant power (FRAP) and Trolox equivalent antioxidant capacity (TEAC) assays, and their total phenolic contents were measured by the Folin-Ciocalteu method. Most of these wild fruits were analyzed for the first time for their antioxidant activities. Generally, these fruits had high antioxidant capacities and total phenolic contents. A significant correlation between the FRAP value and the TEAC value suggested that antioxidant components in these wild fruits were capable of reducing oxidants and scavenging free radicals. A high correlation between antioxidant capacity and total phenolic content indicated that phenolic compounds could be the main contributors to the measured antioxidant activity. The results showed that fruits of Eucalyptus robusta, Eurya nitida, Melastoma sanguineum, Melaleuca leucadendron, Lagerstroemia indica, Caryota mitis, Lagerstroemia speciosa and Gordonia axillaris possessed the highest antioxidant capacities and total phenolic contents among those tested, and could be potential rich sources of natural antioxidants and functional foods. The results obtained are very helpful for the full utilization of these wild fruits. PMID:21116229

  16. Culturable diversity and antimicrobial activity of Actinobacteria from marine sediments in Valparaíso bay, Chile

    PubMed Central

    Claverías, Fernanda P.; Undabarrena, Agustina; González, Myriam; Seeger, Michael; Cámara, Beatriz

    2015-01-01

    Marine-derived Actinobacteria are a source of a broad variety of secondary metabolites with diverse biological activities, such as antibiotics and antitumorals; many of which have been developed for clinical use. Rare Actinobacteria represent an untapped source of new bioactive compounds that have been scarcely recognized. In this study, rare Actinobacteria from marine sediments were isolated from the Valparaíso bay, Chile, and their potential to produce antibacterial compounds was evaluated. Different culture conditions and selective media that select the growth of Actinobacteria were used leading to the isolation of 68 bacterial strains. Comparative analysis of the 16S rRNA gene sequences led to identifying isolates that belong to the phylum Actinobacteria with genetic affiliations to 17 genera: Aeromicrobium, Agrococcus, Arthrobacter, Brachybacterium, Corynebacterium, Dietzia, Flaviflexus, Gordonia, Isoptericola, Janibacter, Microbacterium, Mycobacterium, Ornithinimicrobium, Pseudonocardia, Rhodococcus, Streptomyces, and Tessaracoccus. Also, one isolate could not be consistently classified and formed a novel phylogenetic branch related to the Nocardiopsaceae family. The antimicrobial activity of these isolates was evaluated, demonstrating the capability of specific novel isolates to inhibit the growth of Gram-positive and Gram-negative bacteria. In conclusion, this study shows a rich biodiversity of culturable Actinobacteria, associated to marine sediments from Valparaíso bay, highlighting novel rare Actinobacteria, and their potential for the production of biologically active compounds. PMID:26284034

  17. Bioremediation of hydrocarbons contaminating sewage effluent using man-made biofilms: effects of some variables.

    PubMed

    Al-Mailem, D M; Kansour, M K; Radwan, S S

    2014-11-01

    Biofilm samples were established on glass slides by submerging them in oil-free and oil-containing sewage effluent for a month. In batch cultures, such biofilms were effective in removing crude oil, pure n-hexadecane, and pure phenanthrene contaminating sewage effluent. The amounts of the removed hydrocarbons increased with increasing biofilm surface area exposed to the effluent. On the other hand, addition of the reducing agent thioglycollate dramatically inhibited the hydrocarbon bioremediation potential of the biofilms. The same biofilm samples removed contaminating hydrocarbons effectively in three successive batch bioremediation cycles but started to become less effective in the cycles thereafter, apparently due to mechanical biofilm loss during successive transfers. As major hydrocarbonoclastic bacteria, the biofilms harbored species belonging to the genera Pseudomonas, Microvirga, Zavarzinia, Mycobacterium, Microbacterium, Stenotrophomonas, Gordonia, Bosea, Sphingobium, Brachybacterium, and others. The nitrogen fixer Azospirillum brasilense and the microalga Ochromonas distigma were also present; they seemed to enrich the biofilms, with nitrogenous compounds and molecular oxygen, respectively, which are known to enhance microbiological hydrocarbon degradation. It was concluded that man-made biofilms based upon sewage microflora are promising tools for bioremediation of hydrocarbons contaminating sewage effluent. PMID:25146193

  18. 2-Butanol and Butanone Production in Saccharomyces cerevisiae through Combination of a B12 Dependent Dehydratase and a Secondary Alcohol Dehydrogenase Using a TEV-Based Expression System

    PubMed Central

    Ghiaci, Payam; Norbeck, Joakim; Larsson, Christer

    2014-01-01

    2-Butanol and its chemical precursor butanone (methyl ethyl ketone – MEK) are chemicals with potential uses as biofuels and biocommodity chemicals. In order to produce 2-butanol, we have demonstrated the utility of using a TEV-protease based expression system to achieve equimolar expression of the individual subunits of the two protein complexes involved in the B12-dependent dehydratase step (from the pdu-operon of Lactobacillus reuterii), which catalyze the conversion of meso-2,3-butanediol to butanone. We have furthermore identified a NADH dependent secondary alcohol dehydrogenase (Sadh from Gordonia sp.) able to catalyze the subsequent conversion of butanone to 2-butanol. A final concentration of 4±0.2 mg/L 2-butanol and 2±0.1 mg/L of butanone was found. A key factor for the production of 2-butanol was the availability of NADH, which was achieved by growing cells lacking the GPD1 and GPD2 isogenes under anaerobic conditions. PMID:25054226

  19. Microbial succession in response to pollutants in batch-enrichment culture.

    PubMed

    Jiao, Shuo; Chen, Weimin; Wang, Entao; Wang, Junman; Liu, Zhenshan; Li, Yining; Wei, Gehong

    2016-01-01

    As a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl2. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl2 affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments. PMID:26905741

  20. Dynamics of the Fouling Layer Microbial Community in a Membrane Bioreactor

    PubMed Central

    Ziegler, Anja S.; McIlroy, Simon J.; Larsen, Poul; Albertsen, Mads; Hansen, Aviaja A.; Heinen, Nicolas; Nielsen, Per Halkjær

    2016-01-01

    Membrane fouling presents the greatest challenge to the application of membrane bioreactor (MBR) technology. Formation of biofilms on the membrane surface is the suggested cause, yet little is known of the composition or dynamics of the microbial community responsible. To gain an insight into this important question, we applied 16S rRNA gene amplicon sequencing with a curated taxonomy and fluorescent in situ hybridization to monitor the community of a pilot-scale MBR carrying out enhanced biological nitrogen and phosphorus removal with municipal wastewater. In order to track the dynamics of the fouling process, we concurrently investigated the communities of the biofilm, MBR bulk sludge, and the conventional activated sludge system used to seed the MBR system over several weeks from start-up. As the biofilm matured the initially abundant betaproteobacterial genera Limnohabitans, Hydrogenophaga and Malikia were succeeded by filamentous Chloroflexi and Gordonia as the abundant species. This study indicates that, although putative pioneer species appear, the biofilm became increasingly similar to the bulk community with time. This suggests that the microbial population in bulk water will largely determine the community structure of the mature biofilm. PMID:27399199

  1. Molecular Identification of Mycobacterium Species of Public Health Importance in Cattle in Zimbabwe by 16S rRNA Gene Sequencing

    PubMed Central

    Padya, Leah; Chin'ombe, Nyasha; Magwenzi, Marcelyn; Mbanga, Joshua; Ruhanya, Vurayai; Nziramasanga, Pasipanodya

    2015-01-01

    Mycobacterium species are naturally found in the environment as well as in domestic animals such as cattle. So far, more than 150 species of Mycobacterium, some of which are pathogenic, have been identified. Laboratory isolation, detection and identification of Mycobacterium species are therefore critical if human and animal infections are to be controlled. The objective of this study was to identify Mycobacterium species isolated in cattle in Zimbabwe using 16S ribosomal RNA gene amplification and sequencing. A total of 134 cow dung samples were collected throughout Zimbabwe and mycobacteria were isolated by culture. Only 49 culture isolates that were found to be acid-fast bacilli positive by Ziehl-Neelsen staining. The 16S rRNA gene was successfully amplified by PCR in 41 (84%) of the samples. There was no amplification in 8 (16%) of the samples. Out of the 41 samples that showed amplification, 26 (63%) had strong PCR bands and were selected for DNA sequencing. Analysis of the DNA sequences showed that 7 (27%) belonged to Mycobacterium neoaurum, 6 (23%) belonged to Mycobacterium fortuitum, 3 (12%) to Mycobacterium goodii, 2 (1%) to Mycobacterium arupense, 2 (1%) to Mycobacterium peregrinum or M. septicum and 1 isolate (0.04%) to Mycobacterium elephantis. There were 5 (19%) isolates that were non-mycobacteria and identified as Gordonia terrae, a close relative of Mycobacterium. The study therefore provided a molecular basis for detection and identification of Mycobacterium species in animals and humans. PMID:26668660

  2. Microbial succession in response to pollutants in batch-enrichment culture

    PubMed Central

    Jiao, Shuo; Chen, Weimin; Wang, Entao; Wang, Junman; Liu, Zhenshan; Li, Yining; Wei, Gehong

    2016-01-01

    As a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl2. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl2 affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments. PMID:26905741

  3. Population Dynamics of Bulking and Foaming Bacteria in a Full-scale Wastewater Treatment Plant over Five Years

    NASA Astrophysics Data System (ADS)

    Jiang, Xiao-Tao; Guo, Feng; Zhang, Tong

    2016-04-01

    Bulking and foaming are two notorious problems in activated sludge wastewater treatment plants (WWTPs), which are mainly associated with the excessive growth of bulking and foaming bacteria (BFB). However, studies on affecting factors of BFB in full-scale WWTPs are still limited. In this study, data sets of high-throughput sequencing (HTS) of 16S V3–V4 amplicons of 58 monthly activated sludge samples from a municipal WWTP was re-analyzed to investigate the BFB dynamics and further to study the determinative factors. The population of BFB occupied 0.6~36% (averagely 8.5% ± 7.3%) of the total bacteria and showed seasonal variations with higher abundance in winter-spring than summer-autumn. Pair-wise correlation analysis and canonical correlation analysis (CCA) showed that Gordonia sp. was positively correlated with NO2-N and negatively correlated with NO3-N, and Nostocodia limicola II Tetraspharea sp. was negatively correlated with temperature and positively correlated with NH3-N in activated sludge. Bacteria species correlated with BFB could be clustered into two negatively related modules. Moreover, with intensive time series sampling, the dominant BFB could be accurately modeled with environmental interaction network, i.e. environmental parameters and biotic interactions between BFB and related bacteria, indicating that abiotic and biotic factors were both crucial to the dynamics of BFB.

  4. Enrichment of aliphatic, alicyclic and aromatic acids by oil-degrading bacteria isolated from the rhizosphere of plants growing in oil-contaminated soil from Kazakhstan.

    PubMed

    Mikolasch, Annett; Omirbekova, Anel; Schumann, Peter; Reinhard, Anne; Sheikhany, Halah; Berzhanova, Ramza; Mukasheva, Togzhan; Schauer, Frieder

    2015-05-01

    Three microbial strains were isolated from the rhizosphere of alfalfa (Medicago sativa), grass mixture (Festuca rubra, 75 %; Lolium perenne, 20 %; Poa pratensis, 10 %), and rape (Brassica napus) on the basis of their high capacity to use crude oil as the sole carbon and energy source. These isolates used an unusually wide spectrum of hydrocarbons as substrates (more than 80), including n-alkanes with chain lengths ranging from C12 to C32, monomethyl- and monoethyl-substituted alkanes (C12-C23), n-alkylcyclo alkanes with alkyl chain lengths from 4 to 18 carbon atoms, as well as substituted monoaromatic and diaromatic hydrocarbons. These three strains were identified as Gordonia rubripertincta and Rhodococcus sp. SBUG 1968. During their transformation of this wide range of hydrocarbon substrates, a very large number of aliphatic, alicyclic, and aromatic acids was detected, 44 of them were identified by GC/MS analyses, and 4 of them are described as metabolites for the first time. Inoculation of plant seeds with these highly potent bacteria had a beneficial effect on shoot and root development of plants which were grown on oil-contaminated sand. PMID:25592733

  5. Population Dynamics of Bulking and Foaming Bacteria in a Full-scale Wastewater Treatment Plant over Five Years

    PubMed Central

    Jiang, Xiao-Tao; Guo, Feng; Zhang, Tong

    2016-01-01

    Bulking and foaming are two notorious problems in activated sludge wastewater treatment plants (WWTPs), which are mainly associated with the excessive growth of bulking and foaming bacteria (BFB). However, studies on affecting factors of BFB in full-scale WWTPs are still limited. In this study, data sets of high-throughput sequencing (HTS) of 16S V3–V4 amplicons of 58 monthly activated sludge samples from a municipal WWTP was re-analyzed to investigate the BFB dynamics and further to study the determinative factors. The population of BFB occupied 0.6~36% (averagely 8.5% ± 7.3%) of the total bacteria and showed seasonal variations with higher abundance in winter-spring than summer-autumn. Pair-wise correlation analysis and canonical correlation analysis (CCA) showed that Gordonia sp. was positively correlated with NO2-N and negatively correlated with NO3-N, and Nostocodia limicola II Tetraspharea sp. was negatively correlated with temperature and positively correlated with NH3-N in activated sludge. Bacteria species correlated with BFB could be clustered into two negatively related modules. Moreover, with intensive time series sampling, the dominant BFB could be accurately modeled with environmental interaction network, i.e. environmental parameters and biotic interactions between BFB and related bacteria, indicating that abiotic and biotic factors were both crucial to the dynamics of BFB. PMID:27064107

  6. Dynamics of the Fouling Layer Microbial Community in a Membrane Bioreactor.

    PubMed

    Ziegler, Anja S; McIlroy, Simon J; Larsen, Poul; Albertsen, Mads; Hansen, Aviaja A; Heinen, Nicolas; Nielsen, Per Halkjær

    2016-01-01

    Membrane fouling presents the greatest challenge to the application of membrane bioreactor (MBR) technology. Formation of biofilms on the membrane surface is the suggested cause, yet little is known of the composition or dynamics of the microbial community responsible. To gain an insight into this important question, we applied 16S rRNA gene amplicon sequencing with a curated taxonomy and fluorescent in situ hybridization to monitor the community of a pilot-scale MBR carrying out enhanced biological nitrogen and phosphorus removal with municipal wastewater. In order to track the dynamics of the fouling process, we concurrently investigated the communities of the biofilm, MBR bulk sludge, and the conventional activated sludge system used to seed the MBR system over several weeks from start-up. As the biofilm matured the initially abundant betaproteobacterial genera Limnohabitans, Hydrogenophaga and Malikia were succeeded by filamentous Chloroflexi and Gordonia as the abundant species. This study indicates that, although putative pioneer species appear, the biofilm became increasingly similar to the bulk community with time. This suggests that the microbial population in bulk water will largely determine the community structure of the mature biofilm. PMID:27399199

  7. Antimicrobial activity of heterotrophic bacterial communities from the marine sponge Erylus discophorus (Astrophorida, Geodiidae).

    PubMed

    Graça, Ana Patrícia; Bondoso, Joana; Gaspar, Helena; Xavier, Joana R; Monteiro, Maria Cândida; de la Cruz, Mercedes; Oves-Costales, Daniel; Vicente, Francisca; Lage, Olga Maria

    2013-01-01

    Heterotrophic bacteria associated with two specimens of the marine sponge Erylus discophorus were screened for their capacity to produce bioactive compounds against a panel of human pathogens (Staphylococcus aureus wild type and methicillin-resistant S. aureus (MRSA), Bacillus subtilis, Pseudomonas aeruginosa, Acinetobacter baumanii, Candida albicans and Aspergillus fumigatus), fish pathogen (Aliivibrio fischeri) and environmentally relevant bacteria (Vibrio harveyi). The sponges were collected in Berlengas Islands, Portugal. Of the 212 isolated heterotrophic bacteria belonging to Alpha- and Gammaproteobacteria, Actinobacteria and Firmicutes, 31% produced antimicrobial metabolites. Bioactivity was found against both Gram positive and Gram negative and clinically and environmentally relevant target microorganisms. Bioactivity was found mainly against B. subtilis and some bioactivity against S. aureus MRSA, V. harveyi and A. fisheri. No antifungal activity was detected. The three most bioactive genera were Pseudovibrio (47.0%), Vibrio (22.7%) and Bacillus (7.6%). Other less bioactive genera were Labrenzia, Acinetobacter, Microbulbifer, Pseudomonas, Gordonia, Microbacterium, Micrococcus and Mycobacterium, Paenibacillus and Staphylococcus. The search of polyketide I synthases (PKS-I) and nonribosomal peptide synthetases (NRPSs) genes in 59 of the bioactive bacteria suggested the presence of PKS-I in 12 strains, NRPS in 3 strains and both genes in 3 strains. Our results show the potential of the bacterial community associated with Erylus discophorus sponges as producers of bioactive compounds. PMID:24236081

  8. Cells of the connective tissue differentiate and migrate into pollen sacs

    NASA Astrophysics Data System (ADS)

    Iqbal, M. C. M.; Wijesekara, Kolitha B.

    2002-01-01

    In angiosperms, archesporial cells in the anther primordium undergo meiosis to form haploid pollen, the sole occupants of anther sacs. Anther sacs are held together by a matrix of parenchyma cells, the connective tissue. Cells of the connective tissue are not known to differentiate. We report the differentiation of parenchyma cells in the connective tissue of two Gordonia species into pollen-like structures (described as pseudopollen), which migrate into the anther sacs before dehiscence. Pollen and pseudopollen were distinguishable by morphology and staining. Pollen were tricolpate to spherical while pseudopollen were less rigid and transparent with a ribbed surface. Both types were different in size, shape, staining and surface architecture. The ratio of the number of pseudopollen to pollen was 1:3. During ontogeny in the connective tissue, neither cell division nor tetrad formation was observed and hence pseudopollen were presumed to be diploid. Only normal pollen germinated on a germination medium. Fixed preparations in time seemed to indicate that pseudopollen migrate from the connective tissue into the anther sac.

  9. Hoyosella altamirensis gen. nov., sp. nov., a new member of the order Actinomycetales isolated from a cave biofilm.

    PubMed

    Jurado, Valme; Kroppenstedt, Reiner M; Saiz-Jimenez, Cesáreo; Klenk, Hans-Peter; Mouniée, Delphine; Laiz, Leonila; Couble, Andrée; Pötter, Gabriele; Boiron, Patrick; Rodríguez-Nava, Verónica

    2009-12-01

    A novel actinomycete, strain OFN S31(T), was isolated from a complex biofilm in the Altamira Cave, Spain. A polyphasic study was carried out to clarify the taxonomic position of this strain. Phylogenetic analysis with 16S rRNA gene sequences of representatives of the genera Corynebacterium, Dietzia, Gordonia, Millisia, Mycobacterium, Nocardia, Rhodococcus, Segniliparus, Skermania, Tsukamurella and Williamsia indicated that strain OFN S31(T) formed a distinct taxon in the 16S rRNA gene tree that was more closely associated with the Mycobacterium clade. The type strain of Mycobacterium fallax was the closest relative of strain OFN S31(T) (95.6 % similarity). The cell wall contained meso-diaminopimelic acid, arabinose and galactose, which are characteristic components of cell-wall chemotype IV of actinomycetes. The sugars of the peptidoglycan were acetylated. The polar lipid pattern was composed of phosphatidylinositol, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain OFN S31(T) is characterized by the absence of mycelium and mycolic acids. Strain OFN S31(T) had MK-8 as the major menaquinone. The DNA G+C content was 49.3 mol%, the lowest found among all taxa included in the suborder Corynebacterineae. Based on morphological, chemotaxonomic, phenotypic and genetic characteristics, strain OFN S31(T) is considered to represent a novel species of a new genus, for which the name Hoyosella altamirensis gen. nov., sp. nov. is proposed. The type strain of Hoyosella altamirensis is strain OFN S31(T) (=CIP 109864(T) =DSM 45258(T)). PMID:19643882

  10. [Microbial composition of the activated sludges of the Moscow wastewater treatment plants].

    PubMed

    Kallistova, A Iu; Pimenov, N V; Kozlov, M N; Nikolaev, Iu A; Dorofeev, A G; Aseeva, V G; Grachev, V A; Men'ko, E V; Berestovskaia, Iu Iu; Nozhevnikova, A N; Kevbrina, M V

    2014-01-01

    The contribution of the major technologically important microbial groups (ammonium- and nitrite-oxidizing, phosphate-accumulating, foam-inducing, and anammox bacteria, as well as planctomycetes and methanogenic archaea) was characterized for the aeration tanks of the Moscow wastewater treatment facilities. FISH investigation revealed that aerobic sludges were eubacterial communities; the metabolically active archaea contributed insignificantly. Stage II nitrifying microorganisms and planctomycetes were significant constituents of the bacterial component of activated sludge, with Nitrobacter spp. being the dominant nitrifier. No metabolically active anammox bacteria were revealed in the sludge from aeration tanks. The sludge from the aeration tanks using different wastewater treatment technologies were found to differ in characteristics. Abundance of the nitrifying and phosphate-accumulating bacteria in the sludges generally correlated with microbial activity, in microcosms and with efficiency of nitrogen and phosphorus removal from wastewater. The highest microbial numbers and activity were found in the sludges of the tanks operating according to the technologies developed in the universities of Hanover and Cape Town. The activated sludge from the Novokur yanovo facilities, where abundant growth of filamentous bacteria resulted in foam formation, exhibited the lowest activity The group of foaming bacteria included Gordonia spp. and Acinetobacter spp., utilizing petroleum and motor oils, Sphaerotilus spp. utilizing unsaturated fatty acids, and Candidatus 'Microthrix parvicella'. Thus, the data on abundance and composition of metabolically active microorganisms obtained by FISH may be used for the technological control of wastewater treatment. PMID:25844473

  11. The isolation of microorganisms capable of phenol degradation.

    PubMed

    Przybulewska, Krystyna; Wieczorek, Andrzej; Nowak, Andrzej; Pochrzaszcz, Magdalena

    2006-01-01

    The results of a study on the composition of microflora settling the pilot biofilter bed that purifies the exhausting gases from a cable factory's coil-wire varnishing division are presented in this study. The ability of isolated bacterial strains to biodegrade phenol was also evaluated using culture media of various compositions. Phenol was introduced into the medium at the following concentrations: 0.25, 0.5, 0.75 and 1 g x dm(-3). In addition, air in desiccators, where micro-organisms grew, was saturated with phenol. The isolated microorganisms were graded by the phenol decomposition rate using gas chromatography. The beds of biofilters utilized in industry appeared to be the source of microorganisms capable of degrading phenol. The most active were: Rhodococcus rhodochrous, Gordonia sputi, Pseudomonas putida. Their mixture showed higher degradation activity than the particular isolates. Isolated and identified bacteria metabolized phenol at high rate (about 14 to 42 g x m(-3) x h(-3)). PMID:16878606

  12. Role of proton pump of mitochondria-rich cells for active transport of chloride ions in toad skin epithelium.

    PubMed Central

    Larsen, E H; Willumsen, N J; Christoffersen, B C

    1992-01-01

    1. Active Cl- currents were studied in short-circuited toad skin epithelium in which the passive voltage-activated Cl- current is zero. Under visual control double-barrelled microelectrodes were used for impaling principal cells from the serosal side, or for measuring the pH profile in the solution bathing the apical border. 2. The net inward (active) 36Cl- flux of 27 +/- 8 pmol s-1 cm-2 (16) (mean +/- S.E.M (number of observation)) was abolished by 2 mM-CN- (6.3 +/- 3.5 pmol s-1 cm-2 (8)). The active flux was maintained in the absence of active Na+ transport when the latter was eliminated by either 100 microM-mucosal amiloride, replacement of mucosal Na+ with K+, or by 3 mM-serosal ouabain. 3. In Ringer solution buffered by 24 mM-HCO3- -5% CO2 mucosal amiloride reversed the short circuit current (ISC). The outward ISC was maintained when gluconate replaced mucosal Cl-, and it was reversibly reduced in CO2-free 5 mM-Tris-buffered Ringer solution (pH = 7.40) or by the proton pump inhibitor oligomycin. These observations indicate that the source of the outward ISC is an apical proton pump. 4. Amiloride caused principal cells to hyperpolarize from a basolateral membrane potential, Vb, of -73 +/- 3 (22) to -93 +/- 1 mV (26), and superfusion with CO2-free Tris-buffered Ringer solution induced a further hyperpolarization (Vb = -101 +/- 1 mV (26)) which could be blocked by Ba2+. The CO2-sensitive current changes were null at Vb = EK (potassium reversal potential, -106 +/- 2 mV (55)) implying that they are carried by K+ channels in the basolateral membrane. Such a response cannot account for the inhibition of the outward ISC which by default seems to be located to mitochondria-rich (MR) cells. 5. In the absence of mucosal Cl- a pH gradient was built up above MR cells with pH = 7.02 +/- 0.04 (42) and pH increasing to 7.37 +/- 0.02 (10) above principal cells (pH = 7.40 in bulk solution buffered by 0.1 mM-Tris). This observation localizes a proton pump to the apical membrane of MR cells. Using the integrated diffusion equation it was shown that the measured external pH gradient would account within an order of magnitude for measured currents. 6. Standing gradients of protons were eliminated in the presence of mucosal Cl- suggesting that active uptake of Cl- is associated with the exit of base equivalents across the apical membrane of MR cells.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:1331423

  13. Characterization and evaluation of metformin-loaded solid lipid nanoparticles for celluar and mitochondrial uptake.

    PubMed

    Xu, Qiang; Zhu, Tao; Yi, Chaoli; Shen, Qi

    2016-01-01

    Considered a popular drug for diabetes in recent years, metformin was determined to have a moderate anti-tumor effect, particularly in breast cancer. In this study, the anticancer mechanism of metformin was verified by preparing solid lipid nanoparticles (SLNs) and chitosan-modified solid lipid nanoparticles (CSLNs) containing metformin and then estimating the potential of these SLNs for uptake in cells and mitochondria. Metformin-SLNs were prepared using an emulsification and low-temperature solidification method. The mean particle size, zeta potential, entrapment efficiency, and loading efficiency of metformin-SLNs and metformin chitosan-modified SLNs were 102.3 ± 4.16 and 200.1 ± 17.69 nm, -21.25 ± 4.89 and 50.6 ± 4.09 mv, 26.25 ± 2.59% and 33.6 ± 2.21%, and 1.74 ± 0.16% and 1.46 ± 0.10%, respectively. TEM images showed that both the nanoparticles had spherical morphologies with no aggregation. Results of cellular and mitochondrial uptake showed that the metformin-SLNs were easier to uptake in cells and mitochondria than the pure drug group (that was the control group without SLN structure modification). The findings of this research provide a basis for conducting further studies on the anticancer mechanism of metformin. PMID:26288997

  14. Screening of novel yeast inulinases and further application to bioprocesses.

    PubMed

    Paixão, Susana M; Teixeira, Pedro D; Silva, Tiago P; Teixeira, Alexandra V; Alves, Luís

    2013-09-25

    Inulin is a carbohydrate composed of linear chains of β-2,1-linked D-fructofuranose molecules terminated by a glucose residue through a sucrose-type linkage at the reducing end. Jerusalem artichoke (JA) is one of the most interesting materials among unconventional and renewable raw materials, with levels of inulin reaching 50-80% of dry matter. Inulin or inulin-rich materials can be actively hydrolyzed by microbial inulinases to produce glucose and fructose syrups that can be used in bioprocesses. In this study, several microbial strains were isolated and their ability to inulinase biosynthesis was evaluated. The novel yeast strain Talf1, identified as Zygosaccharomyces bailii, was the best inulinase producer, attaining 8.67 U/ml of inulinase activity when JA juice was used as the inducer substrate. Z. bailii strain Talf1 and/or its enzymatic crude extract were further applied for bioethanol production and biodesulfurization (BDS) processes, using inulin and JA juice as carbon source. In a consolidated bioprocessing for ethanol production from 200 g/l inulin, Z. bailii strain Talf1 was able to produce 67 g/l of ethanol. This ethanol yield was improved in a simultaneous saccharification and fermentation (SSF) process, with the ethanologenic yeast Saccharomyces cerevisiae CCMI 885 and the Talf1 inulinases, achieving a production of 78 g/l ethanol. However, the highest ethanol yield (∼48%) was obtained in a SSF process from JA juice (∼130 g/l fermentable sugars), where the S. cerevisiae produced 63 g/l ethanol. Relatively to the dibenzothiophene BDS tests, the Gordonia alkanivorans strain 1B achieved a desulfurization rate of 4.8 μM/h within a SSF process using Talf1 inulinases and JA juice, highlighting the potential of JA as a less expensive alternative carbon source. These results showed the high potential of Z. bailii strain Talf1 inulinases as a versatile tool for bioprocesses using inulin-rich materials. PMID:23419675

  15. Simultaneously saccharification and fermentation approach as a tool for enhanced fossil fuels biodesulfurization.

    PubMed

    Paixão, Susana M; Arez, Bruno F; Roseiro, José C; Alves, Luís

    2016-11-01

    Biodesulfurization can be a complementary technology to the hydrodesulfurization, the commonly physical-chemical process used for sulfur removal from crude oil. The desulfurizing bacterium Gordonia alkanivorans strain 1B as a fructophilic microorganism requires fructose as C-source. In this context, the main goal of this work was the optimization of a simultaneous saccharification and fermentation (SSF) approach using the Zygosaccharomyces bailii strain Talf1 crude enzymes with invertase activity and sucrose as a cheaper fructose-rich commercial C-source (50% fructose) towards dibenzothiophene (DBT) desulfurization by strain 1B. The determination of optimal conditions, for both sucrose hydrolysis and DBT desulfurization was carried out through two sequential experimental uniform designs according to the Doehlert distribution for two factors: pH (5.5-7.5) and temperature (28-38 °C), with the enzyme load of 1.16 U/g/L; and enzyme load (0-4 U/g/L) and temperature (28-38 °C), with pH at 7.5. Based on 2-hydroxybiphenyl production, the analysis of the response surfaces obtained pointed out for pH 7.5, 32 °C and 1.8 U/g/L as optimal conditions. Further optimized SSF of sucrose during the DBT desulfurization process permitted to attain a 4-fold enhanced biodesulfurization. This study opens a new focus of research through the exploitation of sustainable low cost sucrose-rich feedstocks towards a more economical viable bioprocess scale-up. PMID:27505164

  16. Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils.

    PubMed

    Woo, Hannah L; Hazen, Terry C; Simmons, Blake A; DeAngelis, Kristen M

    2014-02-01

    Lignocellulolytic bacteria have promised to be a fruitful source of new enzymes for next-generation lignocellulosic biofuel production. Puerto Rican tropical forest soils were targeted because the resident microbes decompose biomass quickly and to near-completion. Isolates were initially screened based on growth on cellulose or lignin in minimal media. 75 Isolates were further tested for the following lignocellulolytic enzyme activities: phenol oxidase, peroxidase, β-d-glucosidase, cellobiohydrolase, β-xylopyranosidase, chitinase, CMCase, and xylanase. Cellulose-derived isolates possessed elevated β-d-glucosidase, CMCase, and cellobiohydrolase activity but depressed phenol oxidase and peroxidase activity, while the contrary was true of lignin isolates, suggesting that these bacteria are specialized to subsist on cellulose or lignin. Cellobiohydrolase and phenol oxidase activity rates could classify lignin and cellulose isolates with 61% accuracy, which demonstrates the utility of model degradation assays. Based on 16S rRNA gene sequencing, all isolates belonged to phyla dominant in the Puerto Rican soils, Proteobacteria, Firmicutes, and Actinobacteria, suggesting that many dominant taxa are capable of the rapid lignocellulose degradation characteristic of these soils. The isolated genera Aquitalea, Bacillus, Burkholderia, Cupriavidus, Gordonia, and Paenibacillus represent rarely or never before studied lignolytic or cellulolytic species and were undetected by metagenomic analysis of the soils. The study revealed a relationship between phylogeny and lignocellulose-degrading potential, supported by Kruskal-Wallis statistics which showed that enzyme activities of cultivated phyla and genera were different enough to be considered representatives of distinct populations. This can better inform future experiments and enzyme discovery efforts. PMID:24238986

  17. Sequence-Based Identification of Aerobic Actinomycetes

    PubMed Central

    Patel, Jean Baldus; Wallace, Richard J.; Brown-Elliott, Barbara A.; Taylor, Tony; Imperatrice, Carol; Leonard, Deborah G. B.; Wilson, Rebecca W.; Mann, Linda; Jost, Kenneth C.; Nachamkin, Irving

    2004-01-01

    We investigated the utility of 500-bp 16S rRNA gene sequencing for identifying clinically significant species of aerobic actinomycetes. A total of 28 reference strains and 71 clinical isolates that included members of the genera Streptomyces, Gordonia, and Tsukamurella and 10 taxa of Nocardia were studied. Methods of nonsequencing analyses included growth and biochemical analysis, PCR-restriction enzyme analysis of the 439-bp Telenti fragment of the 65 hsp gene, susceptibility testing, and, for selected isolates, high-performance liquid chromatography. Many of the isolates were included in prior taxonomic studies. Sequencing of Nocardia species revealed that members of the group were generally most closely related to the American Type Culture Collection (ATCC) type strains. However, the sequences of Nocardia transvalensis, N. otitidiscaviarum, and N. nova isolates were highly variable; and it is likely that each of these species contains multiple species. We propose that these three species be designated complexes until they are more taxonomically defined. The sequences of several taxa did not match any recognized species. Among other aerobic actinomycetes, each group most closely resembled the associated reference strain, but with some divergence. The study demonstrates the ability of partial 16S rRNA gene sequencing to identify members of the aerobic actinomycetes, but the study also shows that a high degree of sequence divergence exists within many species and that many taxa within the Nocardia spp. are unnamed at present. A major unresolved issue is the type strain of N. asteroides, as the present one (ATCC 19247), chosen before the availability of molecular analysis, does not represent any of the common taxa associated with clinical nocardiosis. PMID:15184431

  18. Analysis of the xplAB-containing gene cluster involved in the bacterial degradation of the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine.

    PubMed

    Chong, Chun Shiong; Sabir, Dana Khdr; Lorenz, Astrid; Bontemps, Cyril; Andeer, Peter; Stahl, David A; Strand, Stuart E; Rylott, Elizabeth L; Bruce, Neil C

    2014-11-01

    Repeated use of the explosive compound hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) on military land has resulted in significant soil and groundwater pollution. Rates of degradation of RDX in the environment are low, and accumulated RDX, which the U.S. Environmental Protection Agency has determined is a possible human carcinogen, is now threatening drinking water supplies. RDX-degrading microorganisms have been isolated from RDX-contaminated land; however, despite the presence of these species in contaminated soils, RDX pollution persists. To further understand this problem, we studied RDX-degrading species belonging to four different genera (Rhodococcus, Microbacterium, Gordonia, and Williamsia) isolated from geographically distinct locations and established that the xplA and xplB (xplAB) genes, which encode a cytochrome P450 and a flavodoxin redox partner, respectively, are nearly identical in all these species. Together, the xplAB system catalyzes the reductive denitration of RDX and subsequent ring cleavage under aerobic and anaerobic conditions. In addition to xplAB, the Rhodococcus species studied here share a 14-kb region flanking xplAB; thus, it appears likely that the RDX-metabolizing ability was transferred as a genomic island within a transposable element. The conservation and transfer of xplAB-flanking genes suggest a role in RDX metabolism. We therefore independently knocked out genes within this cluster in the RDX-degrading species Rhodococcus rhodochrous 11Y. Analysis of the resulting mutants revealed that XplA is essential for RDX degradation and that XplB is not the sole contributor of reducing equivalents to XplA. While XplA expression is induced under nitrogen-limiting conditions and further enhanced by the presence of RDX, MarR is not regulated by RDX. PMID:25128343

  19. Antibiotic resistance genes and human bacterial pathogens: Co-occurrence, removal, and enrichment in municipal sewage sludge digesters.

    PubMed

    Ju, Feng; Li, Bing; Ma, Liping; Wang, Yubo; Huang, Danping; Zhang, Tong

    2016-03-15

    Understanding which/how antibiotic resistance genes (ARGs) contribute to increased acquisition of resistance by pathogens in aquatic environments are challenges of profound significance. We explored the co-occurrence and removal versus enrichment of ARGs and human bacterial pathogens (HBPs) in municipal sewage sludge digesters. We combined metagenomic detection of a wide spectrum of 323 ARGs and 83 HBPs with a correlation-based statistical approach and charted a network of their co-occurrence relationships. The results indicate that most ARGs and a minor proportion of HBPs (mainly Collinsella aerofaciens, Streptococcus salivarius and Gordonia bronchialis) could not be removed by anaerobic digestion, revealing a biological risk of post-digestion sludge in disseminating antibiotic resistance and pathogenicity. Moreover, preferential co-occurrence patterns were evident within one ARG type (e.g., multidrug, beta-lactam, and aminoglycoside) and between two different ARG types (i.e., aminoglycoside and beta-lactam), possibly implicating co-effects of antibiotic selection pressure and co-resistance on shaping antibiotic resistome in sewage sludge. Unlike beta-lactam resistance genes, ARGs of multidrug and macrolide-lincosamide-streptogramin tended to co-occur more with HBPs. Strikingly, we presented evidence that the most straightforward biological origin of an ARG-species co-occurring event is a hosting relationship. Furthermore, a significant and robust HBP-species co-occurrence correlation provides a proper scenario for nominating HBP indicators (e.g., Bifidobacterium spp. are perfect indicators of C. aerofaciens; r = 0.92-0.99 and P-values < 0.01). Combined, this study demonstrates a creative and effective network-based metagenomic approach for exploring ARG hosts and HBP indicators and assessing ARGs acquisition by HBPs in human-impacted environments where ARGs and HBPs may co-thrive. PMID:26773390

  20. Analysis of the xplAB-Containing Gene Cluster Involved in the Bacterial Degradation of the Explosive Hexahydro-1,3,5-Trinitro-1,3,5-Triazine

    PubMed Central

    Chong, Chun Shiong; Sabir, Dana Khdr; Lorenz, Astrid; Bontemps, Cyril; Andeer, Peter; Stahl, David A.; Strand, Stuart E.; Rylott, Elizabeth L.

    2014-01-01

    Repeated use of the explosive compound hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) on military land has resulted in significant soil and groundwater pollution. Rates of degradation of RDX in the environment are low, and accumulated RDX, which the U.S. Environmental Protection Agency has determined is a possible human carcinogen, is now threatening drinking water supplies. RDX-degrading microorganisms have been isolated from RDX-contaminated land; however, despite the presence of these species in contaminated soils, RDX pollution persists. To further understand this problem, we studied RDX-degrading species belonging to four different genera (Rhodococcus, Microbacterium, Gordonia, and Williamsia) isolated from geographically distinct locations and established that the xplA and xplB (xplAB) genes, which encode a cytochrome P450 and a flavodoxin redox partner, respectively, are nearly identical in all these species. Together, the xplAB system catalyzes the reductive denitration of RDX and subsequent ring cleavage under aerobic and anaerobic conditions. In addition to xplAB, the Rhodococcus species studied here share a 14-kb region flanking xplAB; thus, it appears likely that the RDX-metabolizing ability was transferred as a genomic island within a transposable element. The conservation and transfer of xplAB-flanking genes suggest a role in RDX metabolism. We therefore independently knocked out genes within this cluster in the RDX-degrading species Rhodococcus rhodochrous 11Y. Analysis of the resulting mutants revealed that XplA is essential for RDX degradation and that XplB is not the sole contributor of reducing equivalents to XplA. While XplA expression is induced under nitrogen-limiting conditions and further enhanced by the presence of RDX, MarR is not regulated by RDX. PMID:25128343

  1. Butyric Acid- and Dimethyl Disulfide-Assimilating Microorganisms in a Biofilter Treating Air Emissions from a Livestock Facility▿

    PubMed Central

    Kristiansen, Anja; Lindholst, Sabine; Feilberg, Anders; Nielsen, Per H.; Neufeld, Josh D.; Nielsen, Jeppe L.

    2011-01-01

    Biofiltration has proven an efficient tool for the elimination of volatile organic compounds (VOCs) and ammonia from livestock facilities, thereby reducing nuisance odors and ammonia emissions to the local environment. The active microbial communities comprising these filter biofilms have not been well characterized. In this study, a trickle biofilter treating air from a pig facility was investigated and proved efficient in removing carboxylic acids (>70% reduction), mainly attributed to the primary filter section within which reduced organic sulfur compounds were also depleted (up to 50%). The secondary filter eliminated several aromatic compounds: phenol (81%), p-cresol (89%), 4-ethylphenol (68%), indole (48%), and skatole (69%). The active butyric acid degrading bacterial community of an air filter sample was identified by DNA stable-isotope probing (DNA-SIP) and microautoradiography, combined with fluorescence in situ hybridization (MAR-FISH). The predominant 16S rRNA gene sequences from a clone library derived from “heavy” DNA from [13C4]butyric acid incubations were Microbacterium, Gordonia, Dietzia, Rhodococcus, Propionibacterium, and Janibacter, all from the Actinobacteria. Actinobacteria were confirmed and quantified by MAR-FISH as being the major bacterial phylum assimilating butyric acid along with several Burkholderiales-related Betaproteobacteria. The active bacterial community assimilating dimethyl disulfide (DMDS) was characterized by DNA-SIP and MAR-FISH and found to be associated with the Actinobacteria, along with a few representatives of Flavobacteria and Sphingobacteria. Interestingly, ammonia-oxidizing Betaproteobacteria were also implicated in DMDS degradation, as were fungi. Thus, multiple isotope-based methods provided complementary data, enabling high-resolution identification and quantitative assessments of odor-eliminating Actinobacteria-dominated populations of these biofilter environments. PMID:22003018

  2. Effect of tree species and end seal on attractiveness and utility of cut bolts to the redbay ambrosia beetle and granulate ambrosia beetle (coleoptera: Curculionidae: Scolytinae).

    PubMed

    Mayfield, A E; Hanula, J L

    2012-04-01

    The redbay ambrosia beetle, Xyleborus glabratus Eichhoff, is a non-native invasive pest and vector of the fungus that causes laurel wilt disease in certain trees of the family Lauraceae. This study assessed the relative attractiveness and suitability of cut bolts of several tree species to X. glabratus. In 2009, female X. glabratus were equally attracted to traps baited with swampbay (Persea palustris (Rafinesque) Sargent) and camphortree (Cinnamomum camphora (L.) J. Presl), which were more attractive than avocado (Persea americana Miller), lancewood (Ocotea coriacea (Swartz) Britton), and sweetbay (Magnolia virginiana L.). These species were more attractive than loblolly bay (Gordonia lasianthus (L.) J. Ellis). X. glabratus entrance hole density and emergence from caged bolts were highest on swampbay and camphortree. In 2010, swampbay was significantly more attractive to X. glabratus than sassafras (Sassafras albidum (Nuttall) Nees), yellow poplar (Liriodendron tulipifera L.), and eastern redbud (Cercis canadensis L.). Sassafras bolts end sealed with a liquid wax-and-water emulsion were more attractive to X. glabratus than end-sealed bolts of yellow poplar and redbud. Relative to unsealed bolts, end seal decreased X. glabratus entrance hole density on swampbay and decreased granulate ambrosia beetle (Xylosandrus crassiusculus (Motschulsky)) trap catch, entrance hole density, and adult emergence from swampbay. X. crassiusculus was not attracted to sassafras, yellow poplar, and redbud and was not more attracted to manuka oil than to unbaited traps. Sassafras was more attractive to X. glabratus than previously reported and supported reproducing populations of the insect. End sealing bolts with a wax-and-water emulsion may not be optimal for attracting and rearing ambrosia beetles in small logs. PMID:22606816

  3. Genome-wide bioinformatics analysis of steroid metabolism-associated genes in Nocardioides simplex VKM Ac-2033D.

    PubMed

    Shtratnikova, Victoria Y; Schelkunov, Mikhail I; Fokina, Victoria V; Pekov, Yury A; Ivashina, Tanya; Donova, Marina V

    2016-08-01

    Actinobacteria comprise diverse groups of bacteria capable of full degradation, or modification of different steroid compounds. Steroid catabolism has been characterized best for the representatives of suborder Corynebacterineae, such as Mycobacteria, Rhodococcus and Gordonia, with high content of mycolic acids in the cell envelope, while it is poorly understood for other steroid-transforming actinobacteria, such as representatives of Nocardioides genus belonging to suborder Propionibacterineae. Nocardioides simplex VKM Ac-2033D is an important biotechnological strain which is known for its ability to introduce ∆(1)-double bond in various 1(2)-saturated 3-ketosteroids, and perform convertion of 3β-hydroxy-5-ene steroids to 3-oxo-4-ene steroids, hydrolysis of acetylated steroids, reduction of carbonyl groups at C-17 and C-20 of androstanes and pregnanes, respectively. The strain is also capable of utilizing cholesterol and phytosterol as carbon and energy sources. In this study, a comprehensive bioinformatics genome-wide screening was carried out to predict genes related to steroid metabolism in this organism, their clustering and possible regulation. The predicted operon structure and number of candidate gene copies paralogs have been estimated. Binding sites of steroid catabolism regulators KstR and KstR2 specified for N. simplex VKM Ac-2033D have been calculated de novo. Most of the candidate genes grouped within three main clusters, one of the predicted clusters having no analogs in other actinobacteria studied so far. The results offer a base for further functional studies, expand the understanding of steroid catabolism by actinobacteria, and will contribute to modifying of metabolic pathways in order to generate effective biocatalysts capable of producing valuable bioactive steroids. PMID:26832142

  4. Latex Clearing Protein (Lcp) of Streptomyces sp. Strain K30 Is a b-Type Cytochrome and Differs from Rubber Oxygenase A (RoxA) in Its Biophysical Properties

    PubMed Central

    Birke, Jakob; Röther, Wolf

    2015-01-01

    Specific polyisoprene-cleaving activities of 1.5 U/mg and 4.6 U/mg were determined for purified Strep-tagged latex clearing protein (Lcp) of Streptomyces sp. strain K30 at 23°C and 37°C, respectively. Metal analysis revealed the presence of approximately one atom of iron per Lcp molecule. Copper, which had been identified in Lcp1VH2 of Gordonia polyisoprenivorans previously, was below the detection limit in LcpK30. Heme was identified as a cofactor in purified LcpK30 by (i) detection of characteristic α-, β-, and γ (Soret)-bands at 562 nm, 532 nm, and 430 nm in the visible spectrum after chemical reduction, (ii) detection of an acetone-extractable porphyrin molecule, (iii) determination of a heme b-type-specific absorption maximum (556 nm) after chemical conversion of the heme group to a bipyridyl-heme complex, and (iv) detection of a b-heme-specific m/z value of 616.2 via mass spectrometry. Spectroscopic analysis showed that purified Lcp as isolated contains an oxidized heme-Fe3+ that is free of bound dioxygen. This is in contrast to the rubber oxygenase RoxA, a c-type heme-containing polyisoprene-cleaving enzyme present in Gram-negative rubber degraders, in which the covalently bound heme firmly binds a dioxygen molecule. LcpK30 also differed from RoxA in the lengths of the rubber degradation cleavage products and in having a higher melting point of 61.5°C (RoxA, 54.3°C). In summary, RoxA and Lcp both are equipped with a heme cofactor and catalyze an oxidative C-C cleavage reaction but differ in the heme subgroup type and in several biochemical and biophysical properties. These findings suggest differences in the catalytic reaction mechanisms. PMID:25819959

  5. Dibenzothiophene desulfurization capability and evolutionary divergence of newly isolated bacteria.

    PubMed

    Akhtar, Nasrin; Ghauri, Muhammad A; Akhtar, Kalsoom

    2016-08-01

    Metabolically microorganisms are diverse, and they are capable of transforming almost every known group of chemical compounds present in coal and oil in various forms. In this milieu, one of the important microbial metabolic processes is the biodesulfurization [cleavage of carbon-sulfur (C-S) bond] of thiophenic compounds, such as dibenzothiophene (DBT), which is the most abundant form of organic sulfur present in fossil fuels. In the current study, ten newly isolated bacterial isolates, designated as species of genera Gordonia, Amycolatopsis, Microbacterium and Mycobacterium, were enriched from different samples in the presence of DBT as a sole source of organic sulfur. The HPLC analysis of the DBT grown cultures indicated the consumption of DBT and accumulation of 2-hydroxybiphenyl (2-HBP). Detection of 2-HBP, a marker metabolite of 4S (sulfoxide-sulfone-sulfinate-sulfate) pathway, suggested that the newly isolated strains harbored metabolic activity for DBT desulfurization through the cleavage of C-S bond. The maximum 2-HBP formation rate was 3.5 µmol/g dry cell weight (DCW)/h. The phylogenetic analysis of the new isolates showed that they had diverse distribution within the phylogenetic tree and formed distinct clusters, suggesting that they might represent strains of already reported species or they were altogether new species. Estimates of evolutionary divergence showed high level of nucleotide divergence between the isolates within the same genus. The new isolates were able to use a range of heterocyclic sulfur compounds, thus making them suitable candidates for a robust biodesulfurization system for fossil fuels. PMID:26973057

  6. Evaluation of Biostimulation and Bioaugmentation To Stimulate Hexahydro-1,3,5-trinitro-1,3,5,-triazine Degradation in an Aerobic Groundwater Aquifer.

    PubMed

    Michalsen, Mandy M; King, Aaron S; Rule, Rebecca A; Fuller, Mark E; Hatzinger, Paul B; Condee, Charles W; Crocker, Fiona H; Indest, Karl J; Jung, Carina M; Istok, Jack D

    2016-07-19

    Hexahydro-1,3,5-trinitro-1,3,5,-triazine (RDX) is a toxic and mobile groundwater contaminant common to military sites. This study compared in situ RDX degradation rates following bioaugmentation with Gordonia sp. strain KTR9 (henceforth KTR9) to rates under biostimulation conditions in an RDX-contaminated aquifer in Umatilla, OR. Bioaugmentation was achieved by injecting site groundwater (6000 L) amended with KTR9 cells (10(8) cells mL(-1)) and low carbon substrate concentrations (<1 mM fructose) into site wells. Biostimulation (no added cells) was performed by injecting groundwater amended with low (<1 mM fructose) or high (>15 mM fructose) carbon substrate concentrations in an effort to stimulate aerobic or anaerobic microbial activity, respectively. Single-well push-pull tests were conducted to measure RDX degradation rates for each treatment. Average rate coefficients were 1.2 day(-1) for bioaugmentation and 0.7 day(-1) for high carbon biostimulation; rate coefficients for low carbon biostimulation were not significantly different from zero (p values ≥0.060). Our results suggest that bioaugmentation with KTR9 is a feasible strategy for in situ biodegradation of RDX and, at this site, is capable of achieving RDX concentration reductions comparable to those obtained by high carbon biostimulation while requiring ~97% less fructose. Bioaugmentation has potential to minimize substrate quantities and associated costs, as well as secondary groundwater quality impacts associated with anaerobic biostimulation processes (e.g., hydrogen sulfide, methane production) during full-scale RDX remediation. PMID:27301804

  7. Bacterial community structure in treated sewage sludge with mesophilic and thermophilic anaerobic digestion.

    PubMed

    Stiborova, Hana; Wolfram, Jan; Demnerova, Katerina; Macek, Tomas; Uhlik, Ondrej

    2015-11-01

    Stabilized sewage sludge is applied to agricultural fields and farmland due to its high organic matter content. The aim of this study was to investigate the effects of two types of sludge stabilization, mesophilic anaerobic digestion (MAD) and thermophilic anaerobic digestion (TAD), on bacterial communities in sludge, including the presence of pathogenic microorganisms. Bacterial community structure and phylogenetic diversity were analyzed in four sewage sludge samples from the Czech Republic. Analysis of 16S ribosomal RNA (rRNA) genes showed that investigated sludge samples harbor diverse bacterial populations with only a few taxa present across all samples. Bacterial diversity was higher in sludge samples after MAD versus TAD treatment, and communities in MAD-treated sludge shared the highest genetic similarities. In all samples, the bacterial community was dominated by reads affiliated with Proteobacteria. The sludge after TAD treatment had considerably higher number of reads of thermotolerant/thermophilic taxa, such as the phyla Deinococcus-Thermus and Thermotogae or the genus Coprothermobacter. Only one operational taxonomic unit (OTU), which clustered with Rhodanobacter, was detected in all communities at a relative abundance >1 %. All of the communities were screened for the presence of 16S rRNA gene sequences of pathogenic bacteria using a database of 122 pathogenic species and ≥98 % identity threshold. The abundance of such sequences ranged between 0.23 and 1.57 % of the total community, with lower numbers present after the TAD treatment, indicating its higher hygienization efficiency. Sequences clustering with nontuberculous mycobacteria were present in all samples. Other detected sequences of pathogenic bacteria included Streptomyces somaliensis, Acinetobacter calcoaceticus, Alcaligenes faecalis, Gordonia spp., Legionella anisa, Bordetella bronchiseptica, Enterobacter aerogenes, Brucella melitensis, and Staphylococcus aureus. PMID:25921720

  8. Variation of the Linkage of Root Function with Root Branch Order

    PubMed Central

    Chen, Zhengxia; Zeng, Hui

    2013-01-01

    Mounting evidence has shown strong linkage of root function with root branch order. However, it is not known whether this linkage is consistent in different species. Here, root anatomic traits of the first five branch order were examined in five species differing in plant phylogeny and growth form in tropical and subtropical forests of south China. In Paramichelia baillonii, one tree species in Magnoliaceae, the intact cortex as well as mycorrhizal colonization existed even in the fifth-order root suggesting the preservation of absorption function in the higher-order roots. In contrast, dramatic decreases of cortex thickness and mycorrhizal colonization were observed from lower- to higher-order roots in three other tree species, Cunninghamia lanceolata, Acacia auriculiformis and Gordonia axillaries, which indicate the loss of absorption function. In a fern, Dicranopteris dichotoma, there were several cortex layers with prominently thickened cell wall and no mycorrhizal colonization in the third- and fourth-order roots, also demonstrating the loss of absorptive function in higher-order roots. Cluster analysis using these anatomic traits showed a different classification of root branch order in P. baillonii from other four species. As for the conduit diameter-density relationship in higher-order roots, the mechanism underpinning this relationship in P. baillonii was different from that in other species. In lower-order roots, different patterns of coefficient of variance for conduit diameter and density provided further evidence for the two types of linkage of root function with root branch order. These linkages corresponding to two types of ephemeral root modules have important implication in the prediction of terrestrial carbon cycling, although we caution that this study was pseudo-replicated. Future studies by sampling more species can test the generality of these two types of linkage. PMID:23451168

  9. Production and characterization of a novel yeast extracellular invertase activity towards improved dibenzothiophene biodesulfurization.

    PubMed

    Arez, Bruno F; Alves, Luís; Paixão, Susana M

    2014-11-01

    The main goal of this work was the production and characterization of a novel invertase activity from Zygosaccharomyces bailii strain Talf1 for further application to biodesulfurization (BDS) in order to expand the exploitable alternative carbon sources to renewable sucrose-rich feedstock. The maximum invertase activity (163 U ml(-1)) was achieved after 7 days of Z. bailii strain Talf1 cultivation at pH 5.5-6.0, 25 °C, and 150 rpm in Yeast Malt Broth with 25 % Jerusalem artichoke pulp as inducer substrate. The optimum pH and temperature for the crude enzyme activity were 5.5 and 50 °C, respectively, and moreover, high stability was observed at 30 °C for pH 5.5-6.5. The application of Talf1 crude invertase extract (1 %) to a BDS process by Gordonia alkanivorans strain 1B at 30 °C and pH 7.5 was carried out through a simultaneous saccharification and fermentation (SSF) approach in which 10 g l(-1) sucrose and 250 μM dibenzothiophene were used as sole carbon and sulfur sources, respectively. Growth and desulfurization profiles were evaluated and compared with those of BDS without invertase addition. Despite its lower stability at pH 7.5 (loss of activity within 24 h), Talf1 invertase was able to catalyze the full hydrolysis of 10 g l(-1) sucrose in culture medium into invert sugar, contributing to a faster uptake of the monosaccharides by strain 1B during BDS. In SSF approach, the desulfurizing bacterium increased its μmax from 0.035 to 0.070 h(-1) and attained a 2-hydroxybiphenyl productivity of 5.80 μM/h in about 3 days instead of 7 days, corresponding to an improvement of 2.6-fold in relation to the productivity obtained in BDS process without invertase addition. PMID:25163885

  10. Re-characterization of mono-2-ethylhexyl phthalate hydrolase belonging to the serine hydrolase family.

    PubMed

    Iwata, Makoto; Imaoka, Takuya; Nishiyama, Takashi; Fujii, Takao

    2016-08-01

    A novel bacterium assimilating di-2-ethylhexyl phthalate as a sole carbon source was isolated, and identified as a Rhodococcus species and the strain was named EG-5. The strain has a mono-2-ethylhexyl phthalate (MEHP) hydrolase (EG-5 MehpH), which exhibits some different enzymatic features when compared with the previously reported MEHP hydrolase (P8219 MehpH) from Gordonia sp. These differences include different pH optimum activity, maximal reaction temperature and heat stability. The Km and Vmax values of EG-5 MehpH were significantly higher than those of P8219 MehpH. The primary structure of EG-5 MehpH showed the highest sequence identity to that of P8219 MehpH (39%) among hydrolases. The phylogenetic tree suggested that EG-5 MehpH and P8219 MehpH were categorized in different groups of the novel MEHP hydrolase family. Mutation of a conserved R(109) residue of EG-5 MehpH to a hydrophobic residue resulted in a dramatic reduction in the Vmax value towards MEHP without affecting the Km value. These results indicate that this residue may neutralize the negative charge of a carboxylate anion of MEHP, and thus inhibit the catalytic nucleophile from attacking the ester bond. In other words, the R residue blocks inhibition from the carboxylate anion of MEHP. Recently, registered hypothetical proteins exhibiting 98% or 99% identities for EG-5 MehpH or for P8219 MehpH were found from some pathogens belonging to Actinomycetes. The protein may have other activities besides MEHP hydrolysis and function in other physiological reactions in some Actinomycetes. PMID:26868518

  11. Rational approaches to improving the isolation of endophytic actinobacteria from Australian native trees.

    PubMed

    Kaewkla, Onuma; Franco, Christopher M M

    2013-02-01

    In recent years, new actinobacterial species have been isolated as endophytes of plants and shrubs and are sought after both for their role as potential producers of new drug candidates for the pharmaceutical industry and as biocontrol inoculants for sustainable agriculture. Molecular-based approaches to the study of microbial ecology generally reveal a broader microbial diversity than can be obtained by cultivation methods. This study aimed to improve the success of isolating individual members of the actinobacterial population as pure cultures as well as improving the ability to characterise the large numbers obtained in pure culture. To achieve this objective, our study successfully employed rational and holistic approaches including the use of isolation media with low concentrations of nutrients normally available to the microorganism in the plant, plating larger quantities of plant sample, incubating isolation plates for up to 16 weeks, excising colonies when they are visible and choosing Australian endemic trees as the source of the actinobacteria. A hierarchy of polyphasic methods based on culture morphology, amplified 16S rRNA gene restriction analysis and limited sequencing was used to classify all 576 actinobacterial isolates from leaf, stem and root samples of two eucalypts: a Grey Box and Red Gum, a native apricot tree and a native pine tree. The classification revealed that, in addition to 413 Streptomyces spp., isolates belonged to 16 other actinobacterial genera: Actinomadura (two strains), Actinomycetospora (six), Actinopolymorpha (two), Amycolatopsis (six), Gordonia (one), Kribbella (25), Micromonospora (six), Nocardia (ten), Nocardioides (11), Nocardiopsis (one), Nonomuraea (one), Polymorphospora (two), Promicromonospora (51), Pseudonocardia (36), Williamsia (two) and a novel genus Flindersiella (one). In order to prove novelty, 12 strains were characterised fully to the species level based on polyphasic taxonomy. One strain represented a novel

  12. Expression and characterization of an N-oxygenase from Rhodococcus jostii RHAI.

    PubMed

    Indest, Karl J; Eberly, Jed O; Hancock, Dawn E

    2015-01-01

    Nitro group-containing natural products are rare in nature. There are few examples of N-oxygenases, enzymes that incorporate atmospheric oxygen into primary and secondary amines, characterized in the literature. N-oxygenases have yet to be characterized from the Corynebacterineae, a metabolically diverse group of organisms that includes the genera Rhodococcus, Gordonia, and Mycobacterium. A preliminary in silico search for N-oxygenase AurF gene orthologs revealed multiple protein candidates present in the genome of the Actinomycete Rhodococcus jostii RHAI (RHAI_ro06104). Towards the goal of identifying novel biocatalysts with potential utility for the biosynthesis of nitroaromatics, AurF ortholog RHAI_ro6104 was cloned, expressed and purified in E. coli and amine and nitro containing phenol substrates tested for activity. RHAI-ro06104 showed the highest activity with 4-aminophenol, producing a Vmax of 18.76 μM s(-1) and a Km of 15.29 mM and demonstrated significant activities with 2-aminophenol and 2-amino-5-methylphenol, producing a Vmax of 12.86 and 12.72 μM s(-1) with a Km of 8.34 and 2.81 mM, respectively. These findings are consistent with a substrate range observed in other N-oxygenases, which seem to accommodate substrates that lack halogenated substitutions and side groups directly flanking the amine group. Attempts to identify modulators of RHAI-ro06104 gene activity demonstrated that aromatic amino acids inhibit expression by almost 50%. PMID:26782651

  13. Population dynamics of filamentous bacteria identified in Polish full-scale wastewater treatment plants with nutrients removal.

    PubMed

    Miłobędzka, A; Muszyński, A

    2015-01-01

    A comprehensive study of the identity and population dynamics of filamentous bacteria in five Polish full-scale municipal wastewater treatment plants (WWTPs) with nutrients removal had been carried out for 2 years. A quantitative culture-independent, molecular method - fluorescence in situ hybridization - was applied to evaluate the structure of different filamentous bacteria populations and their temporal variations. Activated sludge was examined for the abundance of 11 groups of filamentous bacteria. On average, filaments constituted 28% of all bacteria. All samples presented a low diversity of probe-defined filamentous bacteria, usually with significant domination of Chloroflexi (with distinction to types 1851, 0803 and others) and/or Microthrix (14% and 7% of EUBmix, respectively). Haliscomenobacter hydrossis, Mycolata, Skermania piniformis and TM7 were less abundant, whereas Curvibacter, Thiothrix/021N and family Gordonia have not been detected in any of the samples. The tested WWTPs showed similarity among species found and differences in their abundance. The composition of filamentous populations was rather stable in each plant and similar to those found in other European countries. Little differences between plants were shown by multivariate analysis of variance in terms of Chloroflexi and Microthrix. No significant general correlations have been found with Pearson product-moment correlation coefficient and Spearman's rank correlation coefficient. Medium correlation strength between the presence of different filaments was recorded only for Microthrix and Skermania piniformis. Deleterious effect on settling properties of sludge (measured as sludge volume index) was found only for abundance of Microthrix; a strong linear correlation was recorded between them. However, no other correlations with wastewater and operational data were revealed. PMID:25768213

  14. Engineering of Corynebacterium glutamicum to utilize methyl acetate, a potential feedstock derived by carbonylation of methanol with CO.

    PubMed

    Choo, Seungjung; Um, Youngsoon; Han, Sung Ok; Woo, Han Min

    2016-04-20

    The possibilities to utilize one-carbon substrates (C1) like CO, methane and methanol have been explored as a cheap alternative feedstock in the biotechnology. For the first time, methyl acetate (MeOAc), which can be formed from carbonylation of methanol with CO, was demonstrated to be an alternative carbon source for the cell growth of Corynebacterium glutamicum as a model microbial cell factory. To do so, a carboxyl esterase activity was necessary to hydrolyze MeOAc to methanol and acetate. Although the wild-type has an unknown esterase activity to MeOAc, the activity was not high enough to grow from 270mM MeOAc as sole carbon source, reaching OD600 of 5.28±0.2 in 32h. Based on the literatures studied for the esterase, we chose three esterases (MekB of Pseudomonas veronii MEK700, AcmB of Gordonia sp. Strain TY-5, and Est of Pyrobaculum calidifontis VA1) and cloned into the wild-type. As a result, the recombinant C. glutamicum expressing the highly active MekB esterase (28.6±0.77U/mg protein) showed complete degradation of MeOAc and utilization of acetate, resulting in OD600 of 16.5±0.02at 24h. In addition, the recombinant strain exhibited the rapid degradation of MeOAc to methanol and acetate in 2h under anaerobic condition. Therefore, MeOAc can be used as another C1-derived carbon source in the biotechnology. PMID:26970052

  15. Bacterial communities associated with biofouling materials used in bench-scale hydrocarbon bioremediation.

    PubMed

    Al-Mailem, Dina; Kansour, Mayada; Radwan, Samir

    2015-03-01

    Biofouling material samples from the Arabian (Persian) Gulf, used as inocula in batch cultures, brought about crude oil and pure-hydrocarbon removal in a mineral medium. Without any added nitrogen fertilizers, the hydrocarbon-removal values were between about 10 and 50 %. Fertilization with NaNO3 alone or together with a mixture of the vitamins thiamine, pyridoxine, vitamin B12, biotin, riboflavin, and folic acid increased the hydrocarbon-removal values, to reach 90 %. Biofouling material samples harbored total bacteria in the magnitude of 10(7) cells g(-1), about 25 % of which were hydrocarbonoclastic. These numbers were enhanced by NaNO3 and vitamin amendment. The culture-independent analysis of the total bacterioflora revealed the predominance of the gammaproteobacterial genera Marinobacter, Acinetobacter, and Alcanivorax, the Flavobacteriia, Flavobacterium, Gaetbulibacter, and Owenweeksia, and the Alphaproteobacteria Tistrella, Zavarzinia, and others. Most of those bacteria are hydrocarbonoclastic. Culture-dependent analysis of hydrocarbonoclastic bacteria revealed that Marinobacter hydrocarbonoclasticus, Dietzia maris, and Gordonia bronchialis predominated in the fouling materials. In addition, each material had several more-specific hydrocarbonoclastic species, whose frequencies were enhanced by NaNO3 and vitamin fertilization. The same samples of fouling materials were used in four successive crude-oil-removal cycles without any dramatic loss of their hydrocarbon-removal potential nor of their associated hydrocarbonoclastic bacteria. In the fifth cycle, the oil-removal value was reduced by about 50 % in only one of the studied samples. This highlights how firmly biofouling materials were immobilizing the hydrocarbonoclastic bacteria. PMID:25249052

  16. Latex Clearing Protein (Lcp) of Streptomyces sp. Strain K30 Is a b-Type Cytochrome and Differs from Rubber Oxygenase A (RoxA) in Its Biophysical Properties.

    PubMed

    Birke, Jakob; Röther, Wolf; Jendrossek, Dieter

    2015-06-01

    Specific polyisoprene-cleaving activities of 1.5 U/mg and 4.6 U/mg were determined for purified Strep-tagged latex clearing protein (Lcp) of Streptomyces sp. strain K30 at 23 °C and 37 °C, respectively. Metal analysis revealed the presence of approximately one atom of iron per Lcp molecule. Copper, which had been identified in Lcp1VH2 of Gordonia polyisoprenivorans previously, was below the detection limit in LcpK30. Heme was identified as a cofactor in purified LcpK30 by (i) detection of characteristic α-, β-, and γ (Soret)-bands at 562 nm, 532 nm, and 430 nm in the visible spectrum after chemical reduction, (ii) detection of an acetone-extractable porphyrin molecule, (iii) determination of a heme b-type-specific absorption maximum (556 nm) after chemical conversion of the heme group to a bipyridyl-heme complex, and (iv) detection of a b-heme-specific m/z value of 616.2 via mass spectrometry. Spectroscopic analysis showed that purified Lcp as isolated contains an oxidized heme-Fe(3+) that is free of bound dioxygen. This is in contrast to the rubber oxygenase RoxA, a c-type heme-containing polyisoprene-cleaving enzyme present in Gram-negative rubber degraders, in which the covalently bound heme firmly binds a dioxygen molecule. LcpK30 also differed from RoxA in the lengths of the rubber degradation cleavage products and in having a higher melting point of 61.5 °C (RoxA, 54.3 °C). In summary, RoxA and Lcp both are equipped with a heme cofactor and catalyze an oxidative C-C cleavage reaction but differ in the heme subgroup type and in several biochemical and biophysical properties. These findings suggest differences in the catalytic reaction mechanisms. PMID:25819959

  17. Radiography of magnetically-driven implosions of initially solid beryllium cylindrical shells for equation-of-state studies at the Z pulsed-power facility

    NASA Astrophysics Data System (ADS)

    McBride, Ryan

    2011-06-01

    The Z accelerator delivers approximately 4-MV, 26-MA electrical pulses with adjustable current rise times of 100--600 ns, as well as adjustable pulse waveforms. The magnetic pressure produced is used for various applications, including magnetically-driven implosions. The Z-Beamlet Laser (ZBL) is a pulsed (0.3-1.5 ns), multi-kJ, TW-class Nd:glass laser system that provides x-ray radiography capabilities for Z experiments. This talk focuses primarily on the radiography diagnostic used to study the magnetically-driven implosions of initially solid cylindrical shells (also referred to as ``liners''). Specifically, we discuss the 6.151-keV monochromatic backlighting system and its use in obtaining radiographs of imploding beryllium (Be) liners. The high transmission efficiency of 6.151-keV photons in Be allowed us to obtain radiographs with finite transmission throughout the radial extent of the imploding liners. Abel inverting these data, we have obtained time-resolved measurements of the imploding liner's density as a function of both axial and radial location throughout the field of view. These data are allowing us to study magneto-Rayleigh-Taylor (MRT) growth for inertial-confinement-fusion applications, as well as compression-wave propagation for equation-of-state studies (see talks by R.L. Lemke and M.R. Martin). Additionally, Z's pulse-shaping capabilities have enabled us to obtain data for both shock- and quasi-isentropically-compressed Be. Example data from MRT, shock-compression, and quasi-isentropic-compression experiments will be shown. We will also discuss planned upgrades to 25-keV radiography that will allow us to study materials with opacities beyond that of beryllium. This work was done in collaboration with R.W. Lemke, M.R. Martin, J.-P. Davis, M.D. Knudson, D.B. Sinars, S.A. Slutz, C.A. Jennings, M.E. Cuneo, D.G. Flicker, and M.C. Herrmann. Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed-Martin company, for the US

  18. Host Galaxies of Luminous Type 2 Quasars at z ~ 0.5

    NASA Astrophysics Data System (ADS)

    Liu, Xin; Zakamska, Nadia L.; Greene, Jenny E.; Strauss, Michael A.; Krolik, Julian H.; Heckman, Timothy M.

    2009-09-01

    We present deep Gemini GMOS optical spectroscopy of nine luminous quasars at redshifts z ~ 0.5, drawn from the Sloan Digital Sky Survey type 2 quasar sample. Our targets were selected to have high intrinsic luminosities (MV < -26 mag) as indicated by the [O III] λ5007 Å emission-line luminosity (L [O III]). Our sample has a median black hole mass of ~108.8 M sun inferred assuming the local M BH-σ* relation and a median Eddington ratio of ~0.7, using stellar velocity dispersions σ* measured from the G band. We estimate the contamination of the stellar continuum from scattered quasar light based on the strength of broad Hβ, and provide an empirical calibration of the contamination as a function of L [O III]; the scattered-light fraction is ~30% of L 5100 for objects with L [O III] = 109.5 L sun. Population synthesis indicates that young poststarburst populations (<0.1 Gyr) are prevalent in luminous type 2 quasars, in addition to a relatively old population (>1 Gyr) which dominates the stellar mass. Broad emission complexes around He II λ4686 Å with luminosities up to 108.3 L sun are unambiguously detected in three out of the nine targets, indicative of Wolf-Rayet (WR) populations. Population synthesis shows that ~5 Myr poststarburst populations contribute substantially to the luminosities (>50% of L 5100) of all three objects with WR detections. We find two objects with double cores and four with close companions. Our results may suggest that luminous type 2 quasars trace an early stage of galaxy interaction, perhaps responsible for both the quasar and the starburst activity. Based, in part, on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the NSF on behalf of the Gemini partnership: the National Science Foundation (United States), the Science and Technology Facilities Council (United Kingdom), the National Research Council (Canada

  19. Electrical conductivity and streaming potential coefficient in a moderately alkaline lava series

    NASA Astrophysics Data System (ADS)

    Perrier, Frédéric; Froidefond, Thierry

    2003-05-01

    Coupled hydraulic and electrical problems are being investigated with renewed interest in geophysical applications. In this study, electrical conductivity and streaming potential coefficient (SPC) have been measured in the laboratory for crushed oceanite, hawaite, and trachyte samples from an almost complete moderately alkaline lava series from the Mururoa atoll (French Polynesia). For pH varying from 7 to 9.5 and ionic strength varying from 0.1 to 100 mmol/l, despite the closely related mineralogy of the rocks, contrasted results are obtained for the surface conductivity as defined by Revil and Glover: 0.10±0.07 mS/m, 8.3±0.2 mS/m and 1.05±0.16 mS/m for oceanite, hawaite, and trachyte, respectively, and for the inferred ζ potential: -6.6±0.3 mV, -26.3±0.5 mV, and -14.6±0.3 mV, respectively. The higher values obtained with hawaite suggest that electrical properties are controlled by secondary and accessory minerals such as clay minerals and zeolites resulting from low-temperature seawater alteration, rather than by the magmatic differentiation. Furthermore, a synthesis of results obtained with 20 rock samples indicates that signatures of the alteration process may emerge from the study of the ζ potential as a function of surface conductivity. The results with the lava series can be used to derive estimates of the scaling of basalt resistivity and associated SPC as a function of permeability. For permeability values smaller than 10 -15 m 2, the value of the SPC can be dramatically affected by the value of the surface conductivity. At least in the brittle crust, a better knowledge of the contributions of clay minerals and zeolites to surface conduction is therefore needed, both for the interpretation of electrical conductivity profiles and for the estimation of electrical variations associated with groundwater flow, as could be produced for example during volcanic or tectonic cycles.

  20. Characterization of two diesel fuel degrading microbial consortia enriched from a non acclimated, complex source of microorganisms

    PubMed Central

    2010-01-01

    Background The bioremediation of soils impacted by diesel fuels is very often limited by the lack of indigenous microflora with the required broad substrate specificity. In such cases, the soil inoculation with cultures with the desired catabolic capabilities (bioaugmentation) is an essential option. The use of consortia of microorganisms obtained from rich sources of microbes (e.g., sludges, composts, manure) via enrichment (i.e., serial growth transfers) on the polluting hydrocarbons would provide bioremediation enhancements more robust and reproducible than those achieved with specialized pure cultures or tailored combinations (co-cultures) of them, together with none or minor risks of soil loading with unrelated or pathogenic allocthonous microorganisms. Results In this work, two microbial consortia, i.e., ENZ-G1 and ENZ-G2, were enriched from ENZYVEBA (a complex commercial source of microorganisms) on Diesel (G1) and HiQ Diesel (G2), respectively, and characterized in terms of microbial composition and hydrocarbon biodegradation capability and specificity. ENZ-G1 and ENZ-G2 exhibited a comparable and remarkable biodegradation capability and specificity towards n-C10 to n-C24 linear paraffins by removing about 90% of 1 g l-1 of diesel fuel applied after 10 days of aerobic shaken flask batch culture incubation at 30°C. Cultivation dependent and independent approaches evidenced that both consortia consist of bacteria belonging to the genera Chryseobacterium, Acinetobacter, Psudomonas, Stenotrophomonas, Alcaligenes and Gordonia along with the fungus Trametes gibbosa. However, only the fungus was found to grow and remarkably biodegrade G1 and G2 hydrocarbons under the same conditions. The biodegradation activity and specificity and the microbial composition of ENZ-G1 and ENZ-G2 did not significantly change after cryopreservation and storage at -20°C for several months. Conclusions ENZ-G1 and ENZ-G2 are very similar highly enriched consortia of bacteria and a

  1. A comparison of bacterial populations in enhanced biological phosphorus removal processes using membrane filtration or gravity sedimentation for solids-liquid separation.

    PubMed

    Hall, Eric R; Monti, Alessandro; Mohn, William W

    2010-05-01

    In an earlier phase of this study, we compared the performances of pilot scale treatment systems operated in either a conventional enhanced biological phosphorus removal (CEBPR) mode, or a membrane enhanced biological phosphorus removal (MEBPR) mode. In the present investigation, we characterized the bacterial community populations in these processes during parallel operation with the same municipal wastewater feed. The objectives of the study were (1) to assess the similarity of the bacterial communities supported in the two systems over time, (2) to determine if distinct bacterial populations are associated with the MEBPR and CEBPR processes, and (3) to relate the dynamics of the community composition to changes in treatment process configuration and to treatment process performance. The characteristics of the bacterial populations were first investigated with ribosomal intergenic spacer analysis, or RISA. To further understand the bacterial population dynamics, important RISA phylotypes were isolated and identified through 16S RNA gene sequencing. The parallel MEBPR and CEBPR systems developed bacterial communities that were distinct. The CEBPR community appeared to exhibit greater diversity, and this may have been the primary reason why the CEBPR treatment train demonstrated superior functional stability relative to the MEBPR counterpart. Moreover, the more diverse bacterial population apparent in the CEBPR system was observed to be more dynamic than that of the MEBPR process. Several RISA bands were found to be characteristic of either the membrane or conventional biological system. In particular, the MEBPR configuration appeared to be selective for the slow-growing organism Magnospira bakii and for the foam-associated Microthrix parvicella and Gordonia sp., while gravity separation led to the washout of M. parvicella. In both pilot trains, sequence analysis confirmed the presence of EBPR-related organisms such as Accumulibacter phosphatis. The survey of the

  2. Automated pattern recognition to support geological mapping and exploration target generation - A case study from southern Namibia

    NASA Astrophysics Data System (ADS)

    Eberle, Detlef; Hutchins, David; Das, Sonali; Majumdar, Anandamayee; Paasche, Hendrik

    2015-06-01

    This paper demonstrates a methodology for the automatic joint interpretation of high resolution airborne geophysical and space-borne remote sensing data to support geological mapping in a largely automated, fast and objective manner. At the request of the Geological Survey of Namibia (GSN), part of the Gordonia Subprovince of the Namaqua Metamorphic Belt situated in southern Namibia was selected for this study. All data - covering an area of 120 km by 100 km in size - were gridded, with a spacing of adjacent data points of only 200 m. The data points were coincident for all data sets. Published criteria were used to characterize the airborne magnetic data and to establish a set of attributes suitable for the recognition of linear features and their pattern within the study area. This multi-attribute analysis of the airborne magnetic data provided the magnetic lineament pattern of the study area. To obtain a (pseudo-) lithology map of the area, the high resolution airborne gamma-ray data were integrated with selected Landsat band data using unsupervised fuzzy partitioning clustering. The outcome of this unsupervised clustering is a classified (zonal) map which in terms of the power of spatial resolution is superior to any regional geological mapping. The classified zones are then assigned geological/geophysical parameters and attributes known from the study area, e.g. lithology, physical rock properties, age, chemical composition, geophysical field characteristics, etc. This information is obtained from the examination of archived geological reports, borehole logs, any kind of existing geological/geophysical data and maps as well as ground truth controls where deemed necessary. To obtain a confidence measure validating the unsupervised fuzzy clustering results and receive a quality criterion of the classified zones, stepwise linear discriminant analysis was chosen. Only a small percentage (8%) of the samples was misclassified by discriminant analysis when compared

  3. American black bears and bee yard depredation at Okefenokee Swamp, Georgia

    USGS Publications Warehouse

    Clark, J.D.; Dobey, S.; Masters, D.V.; Scheick, B.K.; Pelton, M.R.; Sunquist, M.E.

    2005-01-01

    We studied American black bears (Ursus americanus), on the northwest periphery of Okefenokee Swamp in southeast Georgia, to assess landowner attitudes toward bears, estimate the extent of damage to commercial honey bee operations by bears, and evaluate methods to reduce bear depredations to apiaries. We collected 8,351 black bear radiolocations and identified 51 bee yards on our study area. Twenty-seven of 43 home ranges contained ≥1 bee yard, averaging 11.3 and 5.1 bee yards/home range of males (n = 7) and females (n = 20), respectively. From 1996 to 1998, we documented 7 instances of bears raiding bee yards within our study area and 6 instances in adjacent areas. All but 1 of the 13 raided yards were enclosed by electric fencing. In the 12 cases of damage to electrically fenced yards, however, the fences were not active because of depleted batteries. Based on compositional analysis, bear use of areas 800–1,400 m from bee yards was disproportionately greater than use 0–800 m from bee yards. Bears disproportionately used bay (red bay: Persea borbonia, loblolly bay: Gordonia lasianthus, and southern magnolia: Magnolia virginia), gum (water tupelo: Nyssa aquatic and black gum: N. sylvatica), and cypress (Taxodium spp.) and loblolly bay habitats, however, compared with slash pine (Pinus elliottii) or pine–oak (Quercus spp.), where bee yards usually were placed. The distribution of bear radiolocations likely reflected the use of those swamp and riparian areas, rather than avoidance of bee yards. Distances to streams from damaged bee yards (x̄ = 1,750 m) were less than from undamaged yards (x̄ = 4,442 m), and damaged bee yards were closer to unimproved roads (x̄ = 134 m) than were undamaged bee yards (x̄ = 802 m). Our analysis suggests that bee yard placement away from bear travel routes (such as streams and unimproved roads) can reduce bear depredation problems. Our results strongly indicate that working electric fences are effective deterrents to bear

  4. Gasoline Biodesulfurization DE-FC07-97ID13570 FINAL REPORT

    SciTech Connect

    Pienkos, Philip T.

    2002-01-15

    Nine strains were identified to grow with gasoline as sole sulfur source. Two different genes were cloned from Gordonia terrae KGB1 and tested for the ability to support gasoline BDS. The first of these, fmoA, was cloned by screening a KGB1 gene library for the ability to convert indole to indigo (a sulfur-regulated capability in KGB1). The fmoA gene was overexpressed in a gasoline tolerant strain of Pseudomonas putida PpG1 and the recombinant strain was shown to convert thiophene to a dimer of thiophene sulfoxide at rates nearly two orders of magnitude higher than KGB1 could catalyze the reaction. Despite this high activity the recombinant PpG1 was unable to demonstrate any activity against gasoline either in shake flask or in bench-scale gasoline BDS bioreactor. A second gene (toeA) was cloned from KGB1 and shown to support growth of Rhodococcus erythropolis JB55 on gasoline. The toeA gene was also identified in another gasoline strain T. wratislaviensis EMT4, and was identified as a homolog of dszA from R. erythropolis IGTS8. Expression of this gene in JB55 supported conversion of DBTO2 (the natural substrate for DszA) to HPBS, but activity against gasoline was low and BDS results were inconsistent. It appeared that activity was directed against C2- and C3-thiophenes. Efforts to increase gene expression by plasmid manipulation, by addition of flavin reductase genes, or by expression in PpG1 were unsuccessful. The DszC protein (DBT monooxygenase) from IGTS8 has very little activity against the sulfur compounds in gasoline, but a mutant enzyme with a substitution of phenylalanine for valine at position 261 was shown to have an altered substrate range. This alteration resulted in increased activity against gasoline, with activity towards mainly C3- and C4-thiophenes and benzothiophene. A mutant library of dszB was constructed by RACHITT (W. C. Coco et al., DNA shuffling method for generating highly recombined genes and evolved enzymes. 2001. Nature Biotech. 19

  5. Rhodococcus biphenylivorans sp. nov., a polychlorinated biphenyl-degrading bacterium.

    PubMed

    Su, Xiaomei; Liu, Yindong; Hashmi, Muhammad Zaffar; Hu, Jinxing; Ding, Linxian; Wu, Min; Shen, Chaofeng

    2015-01-01

    A Gram-positive, aerobic, non-motile and rod-coccus shaped novel actinobacterial strain, designated as TG9(T), was isolated from a polychlorinated biphenyl (PCB)-contaminated sediment in Taizhou city, Zhejiang province, eastern China. The isolate was observed to grow at 10-45 °C (optimum 28-32 °C), pH 5.0-11.0 (optimum pH 7.0-8.0) and with 0-9.0 % (w/v) NaCl (optimum 0-3.0 %). Comparison of the 16S rRNA gene sequences of strain TG9(T) and other members of the genus Rhodococcus showed that strain TG9(T) shared highest similarities with Rhodococcus pyridinivorans DSM 44555(T) (99.4 %), R. rhodochrous DSM 43241(T) (99.2 %), R. gordoniae DSM 44689(T) (99.2 %) and R. artemisiae DSM 45380(T) (98.2 %). However, low levels of DNA-DNA relatedness (15-48 %), which are below the 70 % limit for prokaryotic species identification, were obtained by DNA-DNA hybridization. Strain TG9(T) was found to contain meso-diaminopimelic acid as the diagnostic diamino acid and arabinose and galactose in the whole-cell hydrolysate. Mycolic acids were found to be present. The major fatty acids were identified as C16:0, C16:1 ω7c and/or iso-C15:0 2-OH, 10-methyl C18:0 and C18:1 ω9c. The only menaquinone detected was MK-8 (H2). The major polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, glycolipid and traces of some unknown lipids. The genomic DNA G+C content of strain TG9(T) was determined to be 62.8 %. The combined phenotypic and genotypic data show that the strain represents a novel species of the genus Rhodococcus for which the name Rhodococcus biphenylivorans sp. nov. is proposed, with the type strain TG9(T) (=CGMCC 1.12975(T) = KCTC 29673(T) = MCCC 1K00286(T)). PMID:25315102

  6. Uppermost Pleistocene Sea-Level Transgression across a Last Glacial Maximum Mixed Carbonate/Siliciclastic Coastline, Modern Gulf of Papua Shelf Break in the Northern Ashmore Trough

    NASA Astrophysics Data System (ADS)

    Mallarino, G.; Francis, J. M.; Droxler, A. W.; Opdyke, B. N.; Bentley, S. J.; Dickens, G. R.; Peterson, L. C.

    2004-12-01

    This research focuses on the analyses of an 8.5 m-long piston core, MV26-0403-73JPC, recovered during a Spring 2004 R/V Melville cruise, in the Gulf of Papua. The core was taken at 138 m of water depth on the modern shelf break of the northern Ashmore Trough. Sediments in the core represent a deepening upward sequence deposited in a mixed carbonate/siliciclastic setting during the time interval from 17,680 ± 370 to 10,980 ± 360 calendar years BP based on six calibrated 14C dates. Four main units are identified based upon the downcore sedimentologic, mineralogic, and micropaleontologic variations. The lowermost Unit D (8.5 to 6.0 mbsf) is approximately 17.5-17 cal. kyr BP in age and consists of a fining upward sequence ranging from bioclastic gravel with abundant ooids to fine sand with other coated grains, bioclasts, and angular quartz grains. The carbonate content of Unit D average 80% whereas the < 63 μ m fraction is rich in quartz. The benthic foraminiferal assemblage is dominated by Calcarina spp. indicative of a shallow water open marine environment. The overlying Unit C, (6.5 to 3.0 mbsf) consists of silty sand with increased quartz and lower carbonate contents (15%-40%). The age of the top is approximately 16.5 cal. kyr BP. Unit B (3.0 to 0.5 mbsf), which spans the interval up to 12 cal. kyr BP, records an important transition marked by the disappearance of coated grains, an increase of the silt-mud fraction, and the appearance of planktonic foraminifers. The uppermost 0.5 m, Unit A, mostly indurated and ranging in age from 12 to 11 cal. kyr BP, consists of bioclastic packstone-wackestone with Halimeda segments, red algae, more abundant planktonic foraminifers, and quartz grains. The carbonate content increases to 75% and high-Mg calcite and quartz are the main components of the fine fraction. Calcarinids become a minor component among the benthic foraminifers whereas Amphistegina spp. (flattened form) dominates, pointing to an outer shelf depositional