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Sample records for gordonia jacobaea mv-26

  1. 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

  2. [Senecio jacobaea: deceiving beauty. Senecio jacobaea poisoning].

    PubMed

    Vos, J H; Geerts, A A J; Borgers, J W; Mars, M H; Muskens, J A M; van Wuijckhuise-Sjouke, L A

    2002-12-15

    In a cattle herd problems were noticed during 1.5 years, characterised by emaciation and loss of milk production with lower fat- and protein%, tenesmus, central nervous symptoms (aggression, circling and blindness), diarrhoea, eczema solare and death. Clinical, laboratory and post mortem examinations did not reveal a specific cause at first. An intoxication was suspected based on the clinical symptoms, the course of the disease in sick animals and severe liver cirrhosis found in a sudden death cow: The animals were fed grassilage derived from an air force base on which an overwhelming amount of tansy ragwort (Senecio jacobaea) was present. On subsequent microscopic examination of the livers of 11 slaughtered clinically healthy animals all of these showed fibrosis in varying extension. Cirrhosis and fibrosis of the liver and the clinical symptoms are all features of chronic pyrrolyzidine alkaloidosis. Tansy ragwort poisoning has not been diagnosed in the Netherlands for years. The rise in cases is due to more extensive use of land.

  3. Complete Genome Sequence of Gordonia terrae 3612

    PubMed Central

    Russell, Daniel A.; Guerrero Bustamante, Carlos A.; Garlena, Rebecca A.

    2016-01-01

    Here, we report the complete genome sequence of Gordonia terrae 3612, also known by the strain designations ATCC 25594, NRRL B-16283, and NBRC 100016. The genome sequence reveals it to be free of prophage and clustered regularly interspaced short palindromic repeats (CRISPRs), and it is an effective host for the isolation and characterization of Gordonia bacteriophages. PMID:27688316

  4. Complete Genome Sequence of Gordonia terrae 3612.

    PubMed

    Russell, Daniel A; Guerrero Bustamante, Carlos A; Garlena, Rebecca A; Hatfull, Graham F

    2016-01-01

    Here, we report the complete genome sequence of Gordonia terrae 3612, also known by the strain designations ATCC 25594, NRRL B-16283, and NBRC 100016. The genome sequence reveals it to be free of prophage and clustered regularly interspaced short palindromic repeats (CRISPRs), and it is an effective host for the isolation and characterization of Gordonia bacteriophages. PMID:27688316

  5. 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

  6. Genome Sequence of Gordonia Bacteriophage Lucky10.

    PubMed

    Pope, Welkin H; 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. Genome Sequences of Gordonia Phages Bowser and Schwabeltier.

    PubMed

    Montgomery, Matthew T; Pope, Welkin H; 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

  14. 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

  15. Hybrid vigor in the biological control agent, Longitarsus jacobaeae

    PubMed Central

    Szűcs, Marianna; Eigenbrode, Sanford D; Schwarzländer, Mark; Schaffner, Urs

    2012-01-01

    Hybridization is an important evolutionary mechanism that can increase the fitness and adaptive potential of populations. A growing body of evidence supports its importance as a key factor contributing to rapid evolution in invasive species, but the effects of hybridization have rarely been assessed in intentionally introduced biological control agents. We investigated hybrids between a Swiss and an Italian population of the beetle, Longitarsus jacobaeae, a biological control agent of Jacobaea vulgaris, by reciprocally crossing individuals in the laboratory. Phenological traits of F1 and F2 hybrid lineages showed intermediate values relative to their parental populations, with some maternal influence. Fitness of the F2 generation, measured as lifetime fecundity, was higher than that of the Italian parent in one of the lineages and higher than that of either parent in the other hybrid lineage. The increased fecundity of hybrids may benefit tansy ragwort biological control by increasing the establishment success and facilitating a more rapid population buildup in the early generations. Even though the long-term consequences of hybridization in this and other systems are hard to predict, intentional hybridization may be a useful tool in biological control strategies as it would promote similar microevolutionary processes operating in numerous targeted invasive species. PMID:22949924

  16. 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

    2016-08-18

    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.

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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.

  6. Draft Genome Sequence of Gordonia sp. Strain UCD-TK1 (Phylum Actinobacteria)

    PubMed Central

    Koenigsaecker, Tynisha M.; Coil, David A.

    2016-01-01

    Here, we present the draft genome of Gordonia sp. strain UCD-TK1. The assembly contains 5,470,576 bp in 98 contigs. This strain was isolated from a disinfected ambulatory surgery center. PMID:27738036

  7. Pyrrolizidine alkaloid composition influences cinnabar moth oviposition preferences in Jacobaea hybrids.

    PubMed

    Cheng, Dandan; van der Meijden, Eddy; Mulder, Patrick P J; Vrieling, Klaas; Klinkhamer, Peter G L

    2013-03-01

    Plants produce a variety of secondary metabolites (PSMs) that may be selective against herbivores. Yet, specialist herbivores may use PSMs as cues for host recognition, oviposition, and feeding stimulation, or for their own defense against parasites and predators. This summarizes a dual role of PSMs: deter generalists but attract specialists. It is not clear yet whether specialist herbivores are a selective force in the evolution of PSM diversity. A prerequisite for such a selective force would be that the preference and/or performance of specialists is influenced by PSMs. To investigate these questions, we conducted an oviposition experiment with cinnabar moths (Tyria jacobaeae) and plants from an artificial hybrid family of Jacobaea vulgaris and Jacobaea aquatica. The cinnabar moth is a specialist herbivore of J. vulgaris and is adapted to pyrrolizidine alkaloids (PAs), defensive PSMs of these plants. The number of eggs and egg batches oviposited by the moths were dependent on plant genotype and positively correlated to concentrations of tertiary amines of jacobine-like PAs and some otosenine-like PAs. The other PAs did not correlate with oviposition preference. Results suggest that host plant PAs influence cinnabar moth oviposition preference, and that this insect is a potential selective factor against a high concentration of some individual PAs, especially those that are also involved in resistance against generalist herbivores. PMID:23435642

  8. 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

  9. Chemical composition of the essential oil of Jacobaea maritima (L.) Pelser & Meijden and Jacobaea maritima subsp. bicolor (Willd.) B. Nord. & Greuter (Asteraceae) collected wild in Croatia and Sicily, respectively.

    PubMed

    Maggio, Antonella; Venditti, Alessandro; Senatore, Felice; Bruno, Maurizio; Formisano, Carmen

    2015-01-01

    In this study, the chemical compositions of the essential oils from aerial parts (JmA) and radices (JmR) of Jacobaea maritima (L.) Pelser & Meijden, collected in Croatia, and of Jacobaea maritima subsp. bicolor (Willd.) B. Nord. & Greuter, collected in Sicily, were evaluated by using gas chromatography and gas chromatography-mass spectrometry. The main components of the essential oil from J. maritima, both in JmA and JmR, were pentacosane (15.7%), heptacosane (13.1%) and nonacosane (8.1%) whereas the essential oil from J. maritima subsp. bicolor was characterised by the presence of hexadecanoic acid (14.6%), caryophyllene oxide (9.3%) and hexahydrofarnesylacetone (6.5%). The comparison of the essential oil with other studied oils of the genus Jacobaea is discussed.

  10. Isolation and application of Gordonia sp. JC11 for removal of boat lubricants.

    PubMed

    Chanthamalee, Jirapat; Luepromchai, Ekawan

    2012-01-01

    Boat lubricants are continuously released into the marine environment and thereby cause chronic oil pollution. This study aims to isolate lubricant-degrading microorganisms from Thai coastal areas as well as to apply a selected strain for removal of boat lubricants. Ten microorganisms in the genera of Gordonia, Microbacterium, Acinetobacter, Pseudomonas, Brucella, Enterococcus and Candida were initially isolated by crude oil enrichment culture techniques. The lubricant-removal activity of these isolates was investigated with mineral-based lubricants that had been manufactured for the 4-stroke diesel engines of fishing boats. Gordonia sp. JC11, the most effective strain was able to degrade 25-55% of 1,000 mg L(-1) total hydrocarbons in six tested lubricants, while only 0-15% of the lubricants was abiotically removed. The bacterium had many characteristics that promoted lubricant degradation such as hydrocarbon utilization ability, emulsification activity and cell surface hydrophobicity. For bioaugmentation treatment of lubricant contaminated seawater, the inoculum of Gordonia sp. JC11 was prepared by immobilizing the bacterium on polyurethane foam (PUF). PUF-immobilized Gordonia sp. JC11 was able to remove 42-56% of 100-1,000 mg L(-1) waste lubricant No. 2 within 5 days. This lubricant removal efficiency was higher than those of free cells and PUF without bacterial cells. The bioaugmentation treatment significantly increased the number of lubricant-degrading microorganisms in the fishery port seawater microcosm and resulted in rapid removal of waste lubricant No. 2.

  11. Draft genome sequence of Gordonia neofelifaecis NRRL B-59395, a cholesterol-degrading actinomycete.

    PubMed

    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

    2011-09-01

    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.

  12. 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

    2016-06-30

    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.

  13. 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

  14. 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

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

    PubMed

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

    2015-09-09

    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.

  16. Genome Sequences of Gordonia terrae Phages Attis and SoilAssassin.

    PubMed

    Pope, Welkin H; 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. 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

  18. 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

  19. 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.

  20. 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

  1. 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

  2. Benzo[b]thiophene desulfurization by Gordonia rubropertinctus strain T08.

    PubMed

    Matsui, T; Onaka, T; Maruhashi, K; Kurane, R

    2001-10-01

    A benzothiophene-desulfurizing bacterium which has a novel desulfurization pathway was isolated and identified as Gordonia rubropertinctus strain T08. Gas chromatography/mass spectroscopy analysis of the ethyl acetate extract of the culture broth detected benzothiophene sulfoxide, benzothiophene sulfone, benzo[e][1,2]oxathiin S-oxide (BT-sultine), benzo[e][1,2]oxathiin S,S-dioxide (BT-sultone), o-hydroxystyrene, and 2-coumaranone, but not 2-(2'-hydroxyphenyl)ethan-1-al, which has been reported to be a desulfurized product of mesophilic nocardioforms.

  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.

  4. 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

  5. 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-).

  6. Testing the generalist-specialist dilemma: the role of pyrrolizidine alkaloids in resistance to invertebrate herbivores in Jacobaea species.

    PubMed

    Wei, Xianqin; Vrieling, Klaas; Mulder, Patrick P J; Klinkhamer, Peter G L

    2015-02-01

    Plants produce a diversity of secondary metabolites (SMs) to protect them from generalist herbivores. On the other hand, specialist herbivores use SMs for host plant recognition, feeding and oviposition cues, and even sequester SMs for their own defense. Therefore, plants are assumed to face an evolutionary dilemma stemming from the contrasting effects of generalist and specialist herbivores on SMs. To test this hypothesis, bioassays were performed with F2 hybrids from Jacobaea species segregating for their pyrrolizidine alkaloids (PAs), using a specialist flea beetle (Longitarsus jacobaeae) and a generalist slug (Deroceras invadens). Our study demonstrated that while slug feeding damage was negatively correlated with the concentration of total PAs and that of senecionine-like PAs, flea beetle feeding damage was not affected by PAs. It was positively correlated though, with leaf fresh weight. The generalist slug was deterred by senecionine-like PAs but the specialist flea beetle was adapted to PAs in its host plant. Testing other herbivores in the same plant system, it was observed that the egg number of the specialist cinnabar moth was positively correlated with jacobine-like PAs, while the silver damage of generalist thrips was negatively correlated with senecionine- and jacobine-like PAs, and the pupae number of generalist leaf miner was negatively correlated with otosenine-like PAs. Therefore, while the specialist herbivores showed no correlation whatsoever with PA concentration, the generalist herbivores all showed a negative correlation with at least one type of PA. We concluded that the generalist herbivores were deterred by different structural groups of PAs while the specialist herbivores were attracted or adapted to PAs in its host plants.

  7. Testing the generalist-specialist dilemma: the role of pyrrolizidine alkaloids in resistance to invertebrate herbivores in Jacobaea species.

    PubMed

    Wei, Xianqin; Vrieling, Klaas; Mulder, Patrick P J; Klinkhamer, Peter G L

    2015-02-01

    Plants produce a diversity of secondary metabolites (SMs) to protect them from generalist herbivores. On the other hand, specialist herbivores use SMs for host plant recognition, feeding and oviposition cues, and even sequester SMs for their own defense. Therefore, plants are assumed to face an evolutionary dilemma stemming from the contrasting effects of generalist and specialist herbivores on SMs. To test this hypothesis, bioassays were performed with F2 hybrids from Jacobaea species segregating for their pyrrolizidine alkaloids (PAs), using a specialist flea beetle (Longitarsus jacobaeae) and a generalist slug (Deroceras invadens). Our study demonstrated that while slug feeding damage was negatively correlated with the concentration of total PAs and that of senecionine-like PAs, flea beetle feeding damage was not affected by PAs. It was positively correlated though, with leaf fresh weight. The generalist slug was deterred by senecionine-like PAs but the specialist flea beetle was adapted to PAs in its host plant. Testing other herbivores in the same plant system, it was observed that the egg number of the specialist cinnabar moth was positively correlated with jacobine-like PAs, while the silver damage of generalist thrips was negatively correlated with senecionine- and jacobine-like PAs, and the pupae number of generalist leaf miner was negatively correlated with otosenine-like PAs. Therefore, while the specialist herbivores showed no correlation whatsoever with PA concentration, the generalist herbivores all showed a negative correlation with at least one type of PA. We concluded that the generalist herbivores were deterred by different structural groups of PAs while the specialist herbivores were attracted or adapted to PAs in its host plants. PMID:25666592

  8. Isolation of carotenoid-deficient mutant from alkylated dibenzothiophene desulfurizing nocardioform bacteria, Gordonia sp. TM414.

    PubMed

    Matsui, Toru; Maruhashi, Kenji

    2004-02-01

    The dibenzothiophene-desulfurizing nocardioform bacteria, Gordonia sp. TM414, was isolated from oil-contaminated soil. To avoid coloration of the oil layer after the desulfurization reaction, which could decrease the quality of the oil, two colorless knock-out mutants, TPc and TPd, were isolated by using a broad-host-range transposon complex. Genomic sequence analysis revealed that the same gene was disrupted in these mutants and that the transposon-inserted gene was assigned as the gene for phytoene desaturase, crt I. The crt I mutants also showed desulfurization activity comparable to that of the parent strain in a model-oil/aqueous bi-phasic reaction, suggesting that the carotenoid production is not responsible for the bi-phasic desulfurization reaction that requires hydrophobic substrate incorporation from the organic phase.

  9. 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

  10. 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

  11. 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

  12. Identification of gene expression profiles in the actinomycete Gordonia neofelifaecis grown with different steroids.

    PubMed

    Li, Wenjing; Ge, Fanglan; Zhang, Qingyan; Ren, Yao; Yuan, Jiadai; He, Junzhong; Li, Wei; Chen, Guiying; Zhang, Guangxiang; Zhuang, Yong; Xu, Li

    2014-06-01

    Gordonia neofelifaecis NRRL B-59395 was initially isolated from the fresh feces of a clouded leopard based on its ability to degrade cholesterol. The transcriptome profiles of G. neofelifaecis NRRL B-59395 grown with cholesterol, androstenedione (AD), and pyruvic acid were compared by RNA-Seq. The sterol catabolic genes are highly conserved in G. neofelifaecis, Rhodococcus jostii RHA1, and Mycobacterium tuberculosis. The RNA-Seq results indicated that the genes involved in the sterol side chain cleavage were exclusively induced by cholesterol, while the genes involved in the degradation of rings A/B and C/D were up-regulated by both cholesterol and AD. It appears that the induction mechanisms for the genes responsible for side chain cleavage and those for degradation of rings are different. There are approximately 21 genes encoding transporter proteins that are differentially expressed in cholesterol or AD compared with pyruvic acid. The genes camABCD and camM encode two systems that take up cholate, and they have been shown to be cholesterol- and AD-inducible. The potential biological functions of other differentially expressed genes are also discussed. These results will promote the functional characterization of the sterol catabolic genes and also provide important clues in understanding the mechanisms of their gene expression, and they may help us understand the mechanism underlying microbial cholesterol catabolism.

  13. 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

  14. Effects of root herbivory on pyrrolizidine alkaloid content and aboveground plant-herbivore-parasitoid interactions in Jacobaea vulgaris.

    PubMed

    Kostenko, Olga; Mulder, Patrick P J; Bezemer, T Martijn

    2013-01-01

    The importance of root herbivory is increasingly recognized in ecological studies, and the effects of root herbivory on plant growth, chemistry, and performance of aboveground herbivores have been relatively well studied. However, how belowground herbivory by root feeding insects affects aboveground parasitoid development is largely unknown. In this study, we examined the effects of root herbivory by wireworms (Agriotes lineatus) on the expression of primary and secondary compounds in the leaves and roots of ragwort (Jacobaea vulgaris). We also studied the effects of root herbivory on the performance of a generalist aboveground herbivore, Mamestra brassicae and its parasitoid Microplitis mediator. In contrast to what most other studies have reported, root herbivory in J. vulgaris had a strong negative effect on the total concentration of pyrrolizidine alkaloids (PAs) in shoot tissues. The composition of PAs in the shoots also changed after root herbivory. In particular, the concentration of less toxic N-oxide PAs decreased. There was no significant effect of root herbivory on PA composition and concentration in the roots. Although the concentration of PA in the leaves decreased, M. brassicae tended to grow slower on the plants exposed to root herbivory. Parasitoid performance was not affected by root herbivory, but parasitoids developed faster when the concentration of jacobine-type PAs in the foliage was higher. These results point at a putative role of individual PAs in multitrophic interactions and emphasize that generalizations about aboveground-belowground effects should be made with great caution.

  15. 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

  16. Human Dermatitis After Skin Exposure to Jacobaea vulgaris and Spectrum of Health Hazards Induced by This Plant to Humans and Livestock.

    PubMed

    Pietkiewicz, Paweł; Gornowicz-Porowska, Justyna; Bowszyc-Dmochowska, Monika; Dmochowski, Marian

    2015-01-01

    Jacobaea vulgaris is a biennial or perennial herb, reaching up to 200 cm, with pinnatifid leaves and numerous yellow flowerheads borne in flat-topped corymbs. The blooming season starts in June and lasts till September. The weed prefers waysides, railway embankments, pastures, and wastelands. While considered an indigenous herb of Europe and Western Asia, it is also widely found in North and South Americas, South Africa, India, Siberia, New Zealand, and Australia, where it poses a serious threat for agriculture and local ecosystems in the absence of natural insects and pathogen species. Although the plant was utilized in Early Modern Europe as a medicine for various purposes, it contains numerous harmful ingredients. Sesquiterpene lactones (STLs) are responsible for allergic dermatitis and phototoxic properties of the sap, while pyrrolizidine alkaloids (PAs) pose a serious threat to livestock after ingestion. Jacobaea vulgaris has been regarded as a noxious weed since the 19th century. In the present day, its eradication from pastures is regulated by law in many countries. Nevertheless, migrant workers might not be conscious that this weed is dangerous. In the summer of 2012, a young migrant male farm worker was seen in the University Dermatology Out-Patient Clinic in Poznan due to acute blistering Jacobaea vulgaris-induced dermatitis clinically resembling dermatitis herpetiformis (cutaneous manifestation of gluten intolerance). The biological/chemical/mechanical control of the plant in farmlands, as well as education at an early age about poisonous and injurious herbs, is advisable for preventing potentially serious health hazards, particularly to urban dwellers accidentally exposed to those plants at their urban stands.

  17. 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

  18. Influence of the carbon source on Gordonia alkanivorans strain 1B resistance to 2-hydroxybiphenyl toxicity.

    PubMed

    Teixeira, Alexandra V; Paixão, Susana M; da Silva, Teresa Lopes; Alves, Luís

    2014-06-01

    The viability of bacteria plays a critical role in the enhancement of fossil fuels biodesulfurization efficiency since cells are exposed to toxic compounds such as 2-hydroxybiphenyl (2-HBP), the end product of dibenzothiophene (DBT) biodesulfurization. The goal of this work was to study the influence of the carbon source on the resistance of Gordonia alkanivorans strain 1B to 2-HBP. The physiological response of this bacterium, pre-grown in glucose or fructose, to 2-HBP was evaluated using two approaches: a growth inhibition toxicity test and flow cytometry. The results obtained from the growth inhibition bioassays showed that the carbon source has an influence on the sensitivity of strain 1B growing cells to 2-HBP. The highest IC50 value was obtained for the assay using fructose as carbon source in both inoculum growth and test medium (IC50-48 h = 0.464 mM). Relatively to the evaluation of 2-HBP effect on the physiological state of resting cells by flow cytometry, the results showed that concentrations of 2-HBP >1 mM generated significant loss of cell viability. The higher the 2-HBP concentration, the higher the toxicity effect on cells and the faster the loss of cell viability. In overall, the flow cytometry results highlighted that strain 1B resting cells grown in glucose-SO4 or glucose-DBT are physiologically less resistant to 2-HBP than resting cells grown in fructose-SO4 or fructose-DBT, respectively.

  19. Etiological Misidentification by Routine Biochemical Tests of Bacteremia Caused by Gordonia terrae Infection in the Course of an Episode of Acute Cholecystitis

    PubMed Central

    Gil-Sande, E.; Brun-Otero, M.; Campo-Cerecedo, F.; Esteban, E.; Aguilar, L.; García-de-Lomas, J.

    2006-01-01

    Gordonia terrae has been reported to be a rare cause of bacteremia. We report the first case of bacteremia associated with acute cholecystitis. Commercial biochemical testing was not able to identify the strain at the genus level, classifying it instead as Rhodococcus sp. Definitive identification was obtained by sequencing of the 16S rRNA gene. PMID:16825404

  20. Isolation and preliminary characterization of a respiratory nitrate reductase from hydrocarbon-degrading bacterium Gordonia alkanivorans S7.

    PubMed

    Romanowska, Irena; Kwapisz, Ewa; Mitka, Magdalena; Bielecki, Stanisław

    2010-06-01

    Gordonia alkanivorans S7 is an efficient degrader of fuel oil hydrocarbons that can simultaneously utilize oxygen and nitrate as electron acceptors. The respiratory nitrate reductase (Nar) from this organism has been isolated using ion exchange chromatography and gel filtration, and then preliminarily characterized. PAGE, SDS-PAGE and gel filtration chromatography revealed that Nar consisted of three subunits of 103, 53 and 25 kDa. The enzyme was optimally active at pH 7.9 and 40 degrees C. K(m) values for NO(3)(-) (110 microM) and for ClO(3)(-) (138 microM) were determined for a reduced viologen as an electron donor. The purified Nar did not use NADH as the electron donor to reduce nitrate or chlorate. Azide was a strong inhibitor of its activity. Our results imply that enzyme isolated from G. alkanivorans S7 is a respiratory membrane-bound nitrate reductase. This is the first report of purification of a nitrate reductase from Gordonia species.

  1. 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

  2. Consumption of poisonous plants (Senecio jacobaea, Symphytum officinale, Pteridium aquilinum, Hypericum perforatum) by rats: chronic toxicity, mineral metabolism, and hepatic drug-metabolizing enzymes.

    PubMed

    Garrett, B J; Cheeke, P R; Miranda, C L; Goeger, D E; Buhler, D R

    1982-02-01

    Effect of dietary tancy ragwort (Senecio jacobaea), comfrey (Symphytum officinale), bracken (Pteridium aquilinum) and alfalfa (Medicago sativa) on hepatic drug-metabolizing enzymes in rats were measured. Tansy ragwort and bracken increased (P less than 0.05) the activity of glutathione transferase and epoxide hydrolase. Comfrey and alfalfa increased (P less than 0.05) the activity of aminopyrine N-demethylase. Feeding bracken or St. John's wort (Hypericum perforatum) in conjunction with tansy ragwort did not influence chronic toxicity of tansy ragwort as assessed by rat survival time. Dietary tansy ragwort resulted in increased (P less than 0.05) hepatic copper levels; the other plants did not affect copper levels. The results do not suggest any major interaction in the toxicity of tansy ragwort with bracken or St. John's wort. PMID:7080084

  3. Fructophilic behaviour of Gordonia alkanivorans strain 1B during dibenzothiophene desulfurization process.

    PubMed

    Alves, Luís; Paixão, Susana M

    2014-01-25

    Biodesulfurization (BDS) aims at the removal of recalcitrant sulfur from fossil fuels at mild operating conditions with the aid of microorganisms. These microorganisms can remove sulfur from dibenzothiphene (DBT), a model compound, or other polycyclic aromatic used as sulfur source, making BDS an easy and environmental friendly process. Gordonia alkanivorans strain 1B has been described as a desulfurizing bacterium, able to desulfurize DBT to 2-hydroxybiphenyl (2-HBP), the final product of the 4S pathway, using d-glucose as carbon source. However, both cell growth and desulfurization can be largely affected by the nutrient composition of the growth medium, due to cofactor requirements of many enzymes involved in the BDS biochemical pathway. In this study, the main goal was to investigate the influence of several sugars, as carbon source, on the growth and DBT desulfurization ability of G. alkanivorans strain 1B. The results of desulfurization tests showed that the lowest values for the growth rate (0.025 hour(-1)) and for the overall 2-HBP production rate (1.80 μm/hour) by the strain 1B were obtained in glucose grown cultures. When using sucrose, the growth rate increase exhibited by strain 1B led to a higher biomass productivity, which induced a slightly increase in the 2-HBP production rate (1.91 μm/hour), conversely in terms of 2-HBP specific production rate (q2-HBP) the value obtained was markedly lower (0.718 μmol/g/hour in sucrose versus 1.22 μmol/g/hour in glucose). When a mixture of glucose and fructose was used as carbon source, strain 1B reached a value of q2-HBP=1.90 μmol/g/hour, close to that in fructose (q2-HBP=2.12 μmol/g/hour). The highest values for both cell growth (μ=0.091 hour(-1)) and 2-HPB production (9.29μm/hour) were obtained when strain 1B was desulfurizing DBT in the presence of fructose as the only carbon source, indicating a fructophilic behaviour by this bacterium. This fact is in agreement with the highest value of biomass

  4. 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.

  5. 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

  6. Enhancement of dibenzothiophene desulfurization by Gordonia alkanivorans strain 1B using sugar beet molasses as alternative carbon source.

    PubMed

    Alves, Luís; Paixão, Susana M

    2014-03-01

    There are several problems limiting an industrial application of fossil fuel biodesulfurization, and one of them is the cost of culture media used to grow the microorganisms involved in the process. In this context, the utilization of alternative carbon sources resulting from agro-industrial by-products could be a strategy to reduce the investment in the operating expenses of a future industrial application. Recently, Gordonia alkanivorans 1B was described as a fructophilic desulfurizing bacterium, and this characteristic opens a new interest in alternative carbon sources rich in fructose. Thus, the goal of this study was to evaluate the utilization of sugar beet molasses (SBM) in the dibenzothiophene (DBT) desulfurization process using strain 1B. SBM firstly treated with 0.25% BaCl2 (w/v) was used after sucrose acidic hydrolysis or in a simultaneous saccharification and fermentation process with a Zygosaccharomyces bailii Talf1 invertase (1%), showing promising results. In optimal conditions, strain 1B presented a μ max of 0.0795 h(-1), and all DBT was converted to 2-hydroxybiphenyl (250 μM) within 48 h with a maximum production rate of 7.78 μM h(-1). Our results showed the high potential of SBM to be used in a future industrial fossil fuel biodesulfurization process using strain 1B.

  7. 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

  8. The effects of putative lipase and wax ester synthase/acyl-CoA:diacylglycerol acyltransferase gene knockouts on triacylglycerol accumulation in Gordonia sp. KTR9.

    PubMed

    Indest, Karl J; Eberly, Jed O; Ringelberg, David B; Hancock, Dawn E

    2015-02-01

    Previously, we demonstrated triacylglycerol (TAG) accumulation and the in vivo ability to catalyze esters from exogenous short chain alcohol sources in Gordonia sp. strain KTR9. In this study, we investigated the effects that putative lipase (KTR9_0186) and wax ester synthase/acyl-CoA:diacylglycerol acyltransferase (WS/DGAT; KTR9_3844) gene knockouts had on TAG accumulation. Gene disruption of KTR9_0186 resulted in a twofold increase in TAG content in nitrogen starved cells. Lipase mutants subjected to carbon starvation, following nitrogen starvation, retained 75 % more TAGs and retained pigmentation. Transcriptome expression data confirmed the deletion of KTR9_0186 and identified the up-regulation of key genes involved in fatty acid degradation, a likely compensatory mechanism for reduced TAG mobilization. In vitro assays with purified KTR9_3844 demonstrated WS/DGAT activity with short chain alcohols and C16 and C18 fatty acid Co-As. Collectively, these results indicate that Gordonia sp. KTR9 has a suitable tractable genetic background for TAG production as well as the enzymatic capacity to catalyze fatty acid esters from short chain alcohols.

  9. Oil spill remediation by using the remediation agent JE1058BS that contains a biosurfactant produced by Gordonia sp. strain JE-1058.

    PubMed

    Saeki, Hisashi; Sasaki, Masaru; Komatsu, Koei; Miura, Akira; Matsuda, Hitoshi

    2009-01-01

    A remediation agent containing a biosurfactant was prepared by spray drying the sterilized culture broth of Gordonia sp. strain JE-1058, and the agent was designated as JE1058BS. On subjection to the baffled flask test developed by the United States Environmental Protection Agency, JE1058BS showed a strong potential to be applied as an oil spill dispersant even in the absence of a solvent. It also proved to be an effective bioremediation agent for the remediation of oil spills at sea. The addition of JE1058BS to seawater stimulated the degradation of weathered crude oil (ANS 521) via the activity of the indigenous marine bacteria. Its addition also stimulated the removal of crude oil from the surface of contaminated sea sand. These results indicate that biosurfactant-containing JE1058BS has a strong potential to be applied as a remediation agent for the clean-up of oil spills at sea and on shorelines.

  10. 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

  11. 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

  12. 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

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

    2012-04-01

    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.

  13. 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.

  14. 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.

  15. Transgressive segregation of primary and secondary metabolites in F(2) hybrids between Jacobaea aquatica and J. vulgaris.

    PubMed

    Kirk, Heather; Cheng, Dandan; Choi, Young Hae; Vrieling, Klaas; Klinkhamer, Peter G L

    2012-04-01

    Hybridization between plant species can have a number of biological consequences; interspecific hybridization has been tied to speciation events, biological invasions, and diversification at the level of genes, metabolites, and phenotypes. This study aims to provide evidence of transgressive segregation in the expression of primary and secondary metabolites in hybrids between Jacobaeavulgaris and J. aquaticus using an NMR-based metabolomic profiling approach. A number of F(2) hybrid genotypes exhibited metabolomic profiles that were outside the range encompassed by parental species. Expression of a number of primary and secondary metabolites, including jacaronone analogues, chlorogenic acid, sucrose, glucose, malic acid, and two amino acids was extreme in some F(2) hybrid genotypes compared to parental genotypes, and citric acid was expressed in highest concentrations in J. vulgaris. Metabolomic profiling based on NMR is a useful tool for quantifying genetically controlled differences between major primary and secondary metabolites among plant genotypes. Interspecific plant hybrids in general, and specifically hybrids between J. vulgaris and J. aquatica, will be useful for disentangling the ecological role of suites of primary and secondary metabolites in plants, because interspecific hybridization generates extreme metabolomic diversity compared to that normally observed between parental genotypes.

  16. 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

  17. 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.

  18. 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...

  19. 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

  20. 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:...

  1. 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.

  2. Locating and Activating Molecular 'Time Bombs': Induction of Mycolata Prophages.

    PubMed

    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.

  3. Locating and Activating Molecular 'Time Bombs': Induction of Mycolata Prophages.

    PubMed

    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

  4. 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

  5. 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.

  6. Relative importance of fertiliser addition to plants and exclusion of predators for aphid growth in the field.

    PubMed

    Müller, Christine B; Fellowes, Mark D E; Godfray, H Charles J

    2005-04-01

    Herbivore dynamics and community structure are influenced both by plant quality and the actions of natural enemies. A factorial experiment manipulating both higher and lower trophic levels was designed to explore the determinants of colony growth of the aphid Aphis jacobaeae, a specialist herbivore on ragwort Senecio jacobaea. Potential plant quality was manipulated by regular addition of NPK-fertiliser and predator pressure was reduced by interception traps; the experiment was carried out at two sites. The size and persistence of aphid colonies were measured. Fertiliser addition affected plant growth in only one site, but never had a measurable effect on aphid colony growth. In both habitats the action of insect predators dominated, imposing strong and negative effects on aphid colony performance. Ants were left unmanipulated in both sites and their performance on the aphid colonies did not significantly differ between sites or between treatments. Our results suggest that, at least for aphid herbivores on S. jacobaea, the action of generalist insect predators appears to be the dominant factor affecting colony performance and can under certain conditions even improve plant productivity. PMID:15756583

  7. Evaporative light scattering detection of pyrrolizidine alkaloids.

    PubMed

    Schaneberg, Brian T; Molyneux, Russell J; Khan, Ikhlas A

    2004-01-01

    A reverse-phase high-performance liquid chromatography method utilizing evaporative light scattering detection (ELSD) has been developed for the simultaneous detection of hepatotoxic pyrrolizidine alkaloids with and without chromophores, namely, riddelliine, riddelliine N-oxide, senecionine, senecionine N-oxide, seneciphylline, retrorsine, integerrimine, lasiocarpine and heliotrine. Pyrrolizidine alkaloids were detected in five plant extracts (Senecio spartioides, S. douglasii var. longilobus, S. jacobaea, S. intergerrimus var. exaltatus and Symphytum officinale). The detection of heliotrine (which does not contain a chromophore) was much improved by ELSD compared with photodiode array detection. PMID:14979525

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. Effects of antibacterial agents on in vitro ovine ruminal biotransformation of the hepatotoxic pyrrolizidine alkaloid jacobine.

    PubMed

    Wachenheim, D E; Blythe, L L; Craig, A M

    1992-08-01

    Ingestion of pyrrolizidine alkaloids, naturally occurring plant toxins, causes illness and death in a number of animal species. Senecio jacobaea pyrrolizidine alkaloids cause significant economic losses due to livestock poisoning, particularly in the Pacific Northwest. Some sheep are resistant to pyrrolizidine alkaloid poisoning, because ovine ruminal biotransformation detoxifies free pyrrolizidine alkaloids in digesta. Antibacterial agents modify ruminal fermentation. Pretreatment with antibacterial agents may account for some animal variability in resistance to pyrrolizidine alkaloid toxicosis, and antibacterial agents can also be used for characterizing ruminal pyrrolizidine alkaloid-biotransforming microflora. The objective of this study was to evaluate the effects of antibacterial agents on biotransformation of a predominant S. jacobaea pyrrolizidine alkaloid, jacobine, in ovine ruminal contents. Ovine ruminal jacobine biotransformation was tested in vitro with 20 independent antibacterial agents. Low amounts of rifampin and erythromycin prevented jacobine biotransformation. Chlortetracycline, lasalocid, monensin, penicillin G, and tetracycline were slightly less effective at inhibiting jacobine biotransformation. Bacitracin, crystal violet, kanamycin, and neomycin were moderately inhibitory against jacobine biotransformation. Brilliant green, chloramphenicol, gramicidin, nalidixic acid, polymyxin B SO4, sodium azide, streptomycin, sulfisoxazole, and vancomycin had little to no effect on jacobine biotransformation. The antibiotics that were most effective at inhibiting biotransformation were those that are active against gram-positive bacteria. Therefore, gram-positive bacteria are most likely critical members of the jacobine-biotransforming consortia.

  13. 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

  14. Clinical manifestations of tansy ragwort poisoning.

    PubMed

    Pearson, E G

    1977-05-01

    The clinical signs of tansy ragwort poisoning are variable and in 5 cases included diarrhea, tenesmus, ascites, bloody feces, icterus, paresis, CNS involvement, rectal prolapse, poor appetite and weight loss. It is thus apparent that the disease can be confused clinically with many others, and tansy ragwort poisoning should be considered in animals exhibiting ascites, diarrhea and rectal prolapse. Several cases of tansy ragwort (Senecio jacobaea) poisoning occurring from 1969 to 1976 are reported to illustrate the numerous clinical pictures that might confront a practitioner. The disease is sporadic in this area. The poisonous principles in tansy ragwort are pyrrolizidine alkaloids, which cause gradual alteration and necrosis of liver cells with replacement by fibrous tissue. The development of signs in all of these cases could be attributed to failure of one or more liver functions.

  15. 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.

  16. Flavin-Dependent Monooxygenases as a Detoxification Mechanism in Insects: New Insights from the Arctiids (Lepidoptera)

    PubMed Central

    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

  17. 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

  18. 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.

  19. Isolation and characterization of a novel bacteriophage against Mycobacterium avium subspecies paratuberculosis.

    PubMed

    Basra, Simone; Anany, Hany; Brovko, Lioubov; Kropinski, Andrew M; Griffiths, Mansel W

    2014-10-01

    Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne's disease, has a doubling time of 24 hours, making rapid detection very difficult. Mycobacteriophages can be used in the detection of disease-causing mycobacteria such as MAP. Isolation and sequencing the genomes of lytic MAP bacteriophages are important preliminary steps towards designing phage-based rapid detection assays for this bacterium. A simple optimized protocol was developed to allow reproducible production of confluent growth of MAP on plates within four to six weeks of incubation at 30 °C. This protocol was applied to the screening of environmental and fecal samples for bacteriophages inhibiting the growth of MAP. As a result, a lytic phage, vB_MapS_FF47, was isolated from bovine feces. FF47 contains a double-stranded DNA genome ~48 kb in length with 73 protein coding sequences. It does not carry temperate or known virulence genes. This phage was shown to be most closely related to Mycobacterium phage Muddy, isolated in South Africa, and Gordonia phage GTE2; however, it could not infect any of the tested Gordonia, Rhodococcus, or Nocardia spp. that GTE2 could. The protocols that were developed for growth and phage isolation have potential applications in a high-throughput screening for compounds inhibiting the growth of MAP. This work describes the first time that a phage was isolated against M. paratuberculosis.

  20. Phylogenetic diversity of actinobacteria associated with soft coral Alcyonium gracllimum and stony coral Tubastraea coccinea in the East China Sea.

    PubMed

    Yang, Shan; Sun, Wei; Tang, Cen; Jin, Liling; Zhang, Fengli; Li, Zhiyong

    2013-07-01

    Actinobacteria are widely distributed in the marine environment. To date, few studies have been performed to explore the coral-associated Actinobacteria, and little is known about the diversity of coral-associated Actinobacteria. In this study, the actinobacterial diversity associated with one soft coral Alcyonium gracllimum and one stony coral Tubastraea coccinea collected from the East China Sea was investigated using both culture-independent and culture-dependent approaches. A total of 19 actinobacterial genera were detected in these two corals, among which nine genera (Corynebacterium, Dietzia, Gordonia, Kocuria, Microbacterium, Micrococcus, Mycobacterium, Streptomyces, and Candidatus Microthrix) were common, three genera (Cellulomonas, Dermatophilus, and Janibacter) were unique to the soft coral, and seven genera (Brevibacterium, Dermacoccus, Leucobacter, Micromonospora, Nocardioides, Rhodococcus, and Serinicoccus) were unique to the stony coral. This finding suggested that highly diverse Actinobacteria were associated with different types of corals. In particular, five actinobacterial genera (Cellulomonas, Dermacoccus, Gordonia, Serinicoccus, and Candidatus Microthrix) were recovered from corals for the first time, extending the known diversity of coral-associated Actinobacteria. This study shows that soft and stony corals host diverse Actinobacteria and can serve as a new source of marine actinomycetes. PMID:23503990

  1. Possible involvement of an extracellular superoxide dismutase (SodA) as a radical scavenger in poly(cis-1,4-isoprene) degradation.

    PubMed

    Schulte, Carina; Arenskötter, Matthias; Berekaa, Mahmoud M; Arenskötter, Quyen; Priefert, Horst; Steinbüchel, Alexander

    2008-12-01

    Gordonia westfalica Kb1 and Gordonia polyisoprenivorans VH2 induce the formation of an extracellular superoxide dismutase (SOD) during poly(cis-1,4-isoprene) degradation. To investigate the function of this enzyme in G. polyisoprenivorans VH2, the sodA gene was disrupted. The mutants exhibited reduced growth in liquid mineral salt media containing poly(cis-1,4-isoprene) as the sole carbon and energy source, and no SOD activity was detectable in the supernatants of the cultures. Growth experiments revealed that SodA activity is required for optimal growth on poly(cis-1,4-isoprene), whereas this enzyme has no effect on aerobic growth in the presence of water-soluble substrates like succinate, acetate, and propionate. This was detected by activity staining, and proof of expression was by antibody detection of SOD. When SodA from G. westfalica Kb1 was heterologously expressed in the sodA sodB double mutant Escherichia coli QC779, the recombinant mutant exhibited increased resistance to paraquat, thereby indicating the functionality of the G. westfalica Kb1 SodA and indirectly protection of G. westfalica cells by SodA from oxidative damage. Both sodA from G. polyisoprenivorans VH2 and sodA from G. westfalica Kb1 coded for polypeptides comprising 209 amino acids and having approximately 90% and 70% identical amino acids, respectively, to the SodA from Mycobacterium smegmatis strain MC(2) 155 and Micrococcus luteus NCTC 2665. As revealed by activity staining experiments with the wild type and the disruption mutant of G. polyisoprenivorans, this bacterium harbors only one active SOD belonging to the manganese family. The N-terminal sequences of the extracellular SodA proteins of both Gordonia species showed no evidence of leader peptides for the mature proteins, like the intracellular SodA protein of G. polyisoprenivorans VH2, which was purified under native conditions from the cells. In G. westfalica Kb1 and G. polyisoprenivorans VH2, SodA probably provides protection

  2. Toxicity evaluation of 2-hydroxybiphenyl and other compounds involved in studies of fossil fuels biodesulphurisation.

    PubMed

    Alves, L; Paixão, S M

    2011-10-01

    The acute toxicity of some compounds used in fossil fuels biodesulphurisation studies, on the respiration activity, was evaluated by Gordonia alkanivorans and Rhodococcus erythropolis. Moreover, the effect of 2-hydroxybiphenyl on cell growth of both strains was also determined, using batch (chronic bioassays) and continuous cultures. The IC₅₀ values obtained showed the toxicity of all the compounds tested to both strains, specially the high toxicity of 2-HBP. These results were confirmed by the chronic toxicity data. The toxicity data sets highlight for a higher sensitivity to the toxicant by the strain presenting a lower growth rate, due to a lower cells number in contact with the toxicant. Thus, microorganisms exhibiting faster generation times could be more resistant to 2-HBP accumulation during a BDS process. The physiological response of both strains to 2-HBP pulse in a steady-state continuous culture shows their potential to be used in a future fossil fuel BDS process.

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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

  9. Comparing arbuscular mycorrhizal communities of individual plants in a grassland biodiversity experiment.

    PubMed

    van de Voorde, Tess F J; van der Putten, Wim H; Gamper, Hannes A; Hol, W H Gera; Bezemer, T Martijn

    2010-05-01

    Plants differ greatly in the soil organisms colonizing their roots. However, how soil organism assemblages of individual plant roots can be influenced by plant community properties remains poorly understood. We determined the composition of arbuscular mycorrhizal fungi (AMF) in Jacobaea vulgaris plants, using terminal restriction fragment length polymorphism (T-RFLP). The plants were collected from an experimental field site with sown and unsown plant communities. Natural colonization was allowed for 10 yr in sown and unsown plots. Unsown plant communities were more diverse and spatially heterogeneous than sown ones. Arbuscular mycorrhizal fungi diversity did not differ between sown and unsown plant communities, but there was higher AMF assemblage dissimilarity between individual plants in the unsown plant communities. When we grew J. vulgaris in field soil that was homogenized after collection in order to rule out spatial variation, no differences in AMF dissimilarity between sown and unsown plots were found. Our study shows that experimental manipulation of plant communities in the field, and hence plant community assembly history, can influence the AMF communities of individual plants growing in those plant communities. This awareness is important when interpreting results from field surveys and experimental ecological studies in relation to plant-symbiont interactions.

  10. Disentangling above- and belowground neighbor effects on the growth, chemistry, and arthropod community on a focal plant.

    PubMed

    Kos, Martine; Bukovinszky, Tibor; Mulder, Patrick P J; Bezemeri, T Martijn

    2015-01-01

    Neighboring plants can influence arthropods on a focal plant, and this can result in associational resistance or associational susceptibility. These effects can be mediated by above- and belowground interactions between the neighbor and focal plant, but determining the relative contribution of the above- and belowground effects remains an open challenge. We performed a common garden experiment with a design that enabled us to disentangle the above- and belowground effects of five different plant species on the growth and chemistry of the focal plant ragwort (Jacobaea vulgaris), and the arthropod community associated with this plant. Aboveground effects of different neighboring plant species were more important for the growth and quality of J. vulgaris and for the arthropod abundance on this plant than belowground effects of neighbors. This remained true when only indirect neighbor effects (via affecting the biomass or quality of the focal plant) were considered. The aboveground neighbor effects on arthropod abundance on the focal plant were strongly negative. However, the magnitude of the effect depended on the identity of the neighboring species, and herbivore abundance on the focal plant was higher when surrounded by conspecific than when surrounded by heterospecific plants. We also observed interactions between above- and belowground neighbor effects, indicating that these effects may be nonadditive. We conclude that above- and belowground associational effects are not equally strong, and that neighbor effects on plant-arthropod interactions occur predominantly aboveground.

  11. Long-term effects of sowing high or low diverse seed mixtures on plant and gastropod diversity

    NASA Astrophysics Data System (ADS)

    Dedov, Ivailo; Stoyanov, Ivailo L.; Penev, Lyubomir; Harvey, Jeffrey A.; Van der Putten, Wim H.; Bezemer, T. Martijn

    2006-09-01

    A number of studies have reported that consumers affect a range of community-level processes, and in turn their diversity and abundance is influenced by the structure and diversity of the plant community. Although gastropods are important generalist herbivores in many environments, few studies have examined the effects of plant species richness and plant community structure on gastropods. This study investigated gastropod species richness and interactions with various above-ground parameters of the vegetation on an experimental field with four plant treatments: low and high diversity of sown later succession plant species, natural colonization at the start of the experiment and natural colonization after 3 years of continued agricultural practice. The investigated gastropod assemblage contained only seven species and was highly dominated by two of them. Both in pitfalls and with hand-sorting the number of species collected per plot was highest in plots with natural plant colonization. Multivariate analysis revealed that overall gastropod abundance was positively associated with plant height and percentage cover of plants, and negatively with percentage grass cover. The same pattern holds for one of the dominant species-complex ( Cochlicopa lubrica/ lubricella). The other dominant gastropod species ( Deroceras reticulatum) was more abundant in samples with higher percentages of moss cover and higher plant diversity, while less abundant at samples with higher plant cover, indicating that the gastropod species preferences may matter more than just their response to plant diversity. Two plant-gastropod species-level associations were observed: Senecio jacobaea with D. reticulatum and Tanacetum vulgare with Cochlicopa spp. The present study also demonstrated that pitfall-traps are suitable for collecting terrestrial gastropods, at least for species-poor grassland habitats.

  12. 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.

  13. Quantification of pyrrolizidine alkaloids in North American plants and honey by LC-MS: single laboratory validation.

    PubMed

    Mudge, Elizabeth M; Jones, A Maxwell P; Brown, Paula N

    2015-01-01

    Pyrrolizidine alkaloids (PAs) are a class of naturally occurring compounds produced by many flowering plants around the World. Their presence as contaminants in food systems has become a significant concern in recent years. For example, PAs are often found as contaminants in honey through pollen transfer. A validated method was developed for the quantification of four pyrrolizidine alkaloids and one pyrrolizidine alkaloid N-oxide in plants and honey grown and produced in British Columbia. The method was optimised for extraction efficiency from the plant materials and then subjected to a single-laboratory validation to assess repeatability, accuracy, selectivity, LOD, LOQ and method linearity. The PA content in plants ranged from1.0 to 307.8 µg/g with repeatability precision between 3.8 and 20.8% RSD. HorRat values were within acceptable limits and ranged from 0.62 to 1.63 for plant material and 0.56-1.82 for honey samples. Method accuracy was determined through spike studies with recoveries ranging from 84.6 to 108.2% from the raw material negative control and from 82.1-106.0 % for the pyrrolizidine alkaloids in corn syrup. Based on the findings in this single-laboratory validation, this method is suitable for the quantitation of lycopsamine, senecionine, senecionine N-oxide, heliosupine and echimidine in common comfrey (Symphytum officinale), tansy ragwort (Senecio jacobaea), blueweed (Echium vulgare) and hound's tongue (Cynoglossum officinale) and for PA quantitation in honey and found that PA contaminants were present at low levels in BC honey. PMID:26482059

  14. Quantification of pyrrolizidine alkaloids in North American plants and honey by LC-MS: single laboratory validation.

    PubMed

    Mudge, Elizabeth M; Jones, A Maxwell P; Brown, Paula N

    2015-01-01

    Pyrrolizidine alkaloids (PAs) are a class of naturally occurring compounds produced by many flowering plants around the World. Their presence as contaminants in food systems has become a significant concern in recent years. For example, PAs are often found as contaminants in honey through pollen transfer. A validated method was developed for the quantification of four pyrrolizidine alkaloids and one pyrrolizidine alkaloid N-oxide in plants and honey grown and produced in British Columbia. The method was optimised for extraction efficiency from the plant materials and then subjected to a single-laboratory validation to assess repeatability, accuracy, selectivity, LOD, LOQ and method linearity. The PA content in plants ranged from1.0 to 307.8 µg/g with repeatability precision between 3.8 and 20.8% RSD. HorRat values were within acceptable limits and ranged from 0.62 to 1.63 for plant material and 0.56-1.82 for honey samples. Method accuracy was determined through spike studies with recoveries ranging from 84.6 to 108.2% from the raw material negative control and from 82.1-106.0 % for the pyrrolizidine alkaloids in corn syrup. Based on the findings in this single-laboratory validation, this method is suitable for the quantitation of lycopsamine, senecionine, senecionine N-oxide, heliosupine and echimidine in common comfrey (Symphytum officinale), tansy ragwort (Senecio jacobaea), blueweed (Echium vulgare) and hound's tongue (Cynoglossum officinale) and for PA quantitation in honey and found that PA contaminants were present at low levels in BC honey.

  15. 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.

  16. 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

  17. 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.

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

    PubMed

    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

  19. Immunomagnetic separation of scum-forming bacteria using polyclonal antibody that recognizes mycolic acids.

    PubMed

    Morisada, S; Miyata, N; Iwahori, K

    2002-10-01

    Mycolic acid-containing bacteria (mycolata) are thought to be involved in scum formation in aeration basins of activated sludge plants due to their ability to produce biosurfactants and their cell surface hydrophobicity. To isolate these bacteria, immunomagnetic separation (IMS) using an anti-mycolic acid polyclonal antibody was investigated. IMS that targeted Gordonia amarae SC1 exhibited a 100% recovery at 5x10(3) CFU ml(-1). At cell concentration of 7.8x10(6) CFU ml(-1), the recovery was lowered, but 80% of cells were still captured. Effect of bead concentrations on the recovery of SC1 at 10(6) CFU ml(-1) was examined. The results showed that addition of more than 6-7x10(6) beads for 1x10(6) CFU reached a maximum recovery (83%). Furthermore, the IMS procedure optimized with SC1 cells was tested with another mycolata. The results suggested that variation of the recovery for each mycolata is dependent on the specificity of the polyclonal antibody and that mycolata which are recognized by the antibody can be recovered by this procedure. PMID:12133606

  20. Microbial degradation of the multiply branched alkane 2,6,10,15,19, 23-hexamethyltetracosane (Squalane) by Mycobacterium fortuitum and Mycobacterium ratisbonense.

    PubMed

    Berekaa, M M; Steinbüchel, A

    2000-10-01

    Among several bacterial species belonging to the general Gordonia, Mycobacterium, Micromonospora, Pseudomonas, and Rhodococcus, only two mycobacterial isolates, Mycobacterium fortuitum strain NF4 and the new isolate Mycobacterium ratisbonense strain SD4, which was isolated from a sewage treatment plant, were capable of utilizing the multiply branched hydrocarbon squalane (2,6,10,15,19, 23-hexamethyltetracosane) and its analogous unsaturated hydrocarbon squalene as the sole carbon source for growth. Detailed degradation studies and high-pressure liquid chromatography analysis showed a clear decrease of the concentrations of squalane and squalene during biomass increase. These results were supported by resting-cell experiments using strain SD4 and squalane or squalene as the substrate. The degradation of acyclic isoprenoids and alkanes as well as of acids derived from these compounds was also investigated. Inhibition of squalane and squalene degradation by acrylic acid indicated the possible involvement of beta-oxidation in the degradation route. To our knowledge, this is the first report demonstrating the biodegradation of squalane by using defined axenic cultures.

  1. 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

  2. Biotechnological methods for chalcone reduction using whole cells of Lactobacillus, Rhodococcus and Rhodotorula strains as a way to produce new derivatives.

    PubMed

    Stompor, Monika; Kałużny, Mateusz; Żarowska, Barbara

    2016-10-01

    Microbial strains of the genera Dietzia, Micrococcus, Pseudomonas, Rhodococcus, Gordonia, Streptomyces, Pseudomonas, Bacillus, Penicillium, Rhodotorula and Lactobacillus were screened for the ability to convert chalcones. Synthesis of chalcones was performed by the Claisen-Schmidt reaction. There were three groups of chalcones obtained as the products, which included the derivatives containing 4-substituted chalcone, 2'-hydroxychalcone and 4'-methoxychalcone. The B ring of the chalcones was substituted in the para position with different groups, such as halide, hydroxyl, nitro, methyl, ethyl and ethoxy one. The structure-activity relationship of the tested chalcones in biotransformation processes was studied. It has been proven that Gram-positive bacterial strains Rhodococcus and Lactobacillus catalyzed reduction of C=C bond in the chalcones to give respective dihydrochalcones. The strain Rhodotorula rubra AM 82 transformed chalcones into dihydrochalcones and respective secondary alcohols. These results suggest that the probiotic strain of Lactobacillus can be used for biotransformations of chalcones, which has not been described before. The structure of new metabolites 14a and 15b were established as 4-ethoxy-4'-methoxydihydrochalcone and 3-(4-bromophenyl)-1-(4'-O-methylphenyl)-2-propan-1-ol, respectively, which was confirmed by (1)H NMR and (13)C NMR analysis.

  3. Physiological, numerical and molecular characterization of alkyl ether-utilizing rhodococci.

    PubMed

    Kim, Yong-Hak; Engesser, Karl-Heinrich; Kim, Sang-Jong

    2007-06-01

    Twenty-seven Gram-positive strains were characterized physiologically and numerically and classified them into four groups according to their specific activities for utilization of linear alkyl ethers (AEs), cyclic AEs, monoalkoxybenzenes and 1,4-diethoxybenzene. The comparative analysis of the 16S ribosomal RNA gene and 16S-23S intergenic spacer region showed that they belonged to the genera Rhodococcus and Gordonia. Alkyl ether-utilizing rhodococci appeared to involve various and diverse cytochromes P450 of the families CYP116 (25 positive strains from 27), CYP153 (5/27), CYP249 (1/27) and a new family P450RR1 (27/27). The presence of P450RR1 was strongly related to the specific activity for utilization of 2-methoxyphenol and 2-ethoxyphenol. In addition, 26 of 27 strains contained multiple alkB genes coding for probable non-haem iron containing alkane monooxygenases and hydroxylases. Similar DNA fragments coding for a tetrahydrofuran monooxygenase A subunit (ThmA) were found in all cyclic AE-utilizing strains and nearly identical DNA fragments coding for likely orthologues of a propane monooxygenase A subunit (PrmA) in all linear AE-utilizing strains. The substrate availability in the degradation of aryl AEs, cyclic AEs and linear AEs agreed with the molecular probing of the respective genes encoding cytochrome P450RR1, ThmA and PrmA.

  4. 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

  5. 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

  6. 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

  7. 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

  8. Real-time PCR for rapidly detecting aniline-degrading bacteria in activated sludge.

    PubMed

    Kayashima, Takakazu; Suzuki, Hisako; Maeda, Toshinari; Ogawa, Hiroaki I

    2013-05-01

    We developed a detection method that uses quantitative real-time PCR (qPCR) and the TaqMan system to easily and rapidly assess the population of aniline-degrading bacteria in activated sludge prior to conducting a biodegradability test on a chemical compound. A primer and probe set for qPCR was designed by a multiple alignment of conserved amino acid sequences encoding the large (α) subunit of aniline dioxygenase. PCR amplification tests showed that the designed primer and probe set targeted aniline-degrading strains such as Acidovorax sp., Gordonia sp., Rhodococcus sp., and Pseudomonas putida, thereby suggesting that the developed method can detect a wide variety of aniline-degrading bacteria. There was a strong correlation between the relative copy number of the α-aniline dioxygenase gene in activated sludge obtained with the developed qPCR method and the number of aniline-degrading bacteria measured by the Most Probable Number method, which is the conventional method, and a good correlation with the lag time of the BOD curve for aniline degradation produced by the biodegradability test in activated sludge samples collected from eight different wastewater treatment plants in Japan. The developed method will be valuable for the rapid and accurate evaluation of the activity of inocula prior to conducting a ready biodegradability test.

  9. 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

  10. 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.

  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 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

  12. Microbial Degradation of the Multiply Branched Alkane 2,6,10,15,19,23-Hexamethyltetracosane (Squalane) by Mycobacterium fortuitum and Mycobacterium ratisbonense

    PubMed Central

    Berekaa, Mahmoud M.; Steinbüchel, Alexander

    2000-01-01

    Among several bacterial species belonging to the general Gordonia, Mycobacterium, Micromonospora, Pseudomonas, and Rhodococcus, only two mycobacterial isolates, Mycobacterium fortuitum strain NF4 and the new isolate Mycobacterium ratisbonense strain SD4, which was isolated from a sewage treatment plant, were capable of utilizing the multiply branched hydrocarbon squalane (2,6,10,15,19,23-hexamethyltetracosane) and its analogous unsaturated hydrocarbon squalene as the sole carbon source for growth. Detailed degradation studies and high-pressure liquid chromatography analysis showed a clear decrease of the concentrations of squalane and squalene during biomass increase. These results were supported by resting-cell experiments using strain SD4 and squalane or squalene as the substrate. The degradation of acyclic isoprenoids and alkanes as well as of acids derived from these compounds was also investigated. Inhibition of squalane and squalene degradation by acrylic acid indicated the possible involvement of β-oxidation in the degradation route. To our knowledge, this is the first report demonstrating the biodegradation of squalane by using defined axenic cultures. PMID:11010899

  13. Ex situ bioremediation of oil-contaminated soil.

    PubMed

    Lin, Ta-Chen; Pan, Po-Tsen; Cheng, Sheng-Shung

    2010-04-15

    An innovative bioprocess method, Systematic Environmental Molecular Bioremediation Technology (SEMBT) that combines bioaugmentation and biostimulation with a molecular monitoring microarray biochip, was developed as an integrated bioremediation technology to treat S- and T-series biopiles by using the landfarming operation and reseeding process to enhance the bioremediation efficiency. After 28 days of the bioremediation process, diesel oil (TPH(C10-C28)) and fuel oil (TPH(C10-C40)) were degraded up to approximately 70% and 63% respectively in the S-series biopiles. When the bioaugmentation and biostimulation were applied in the beginning of bioremediation, the microbial concentration increased from approximately 10(5) to 10(6) CFU/g dry soil along with the TPH biodegradation. Analysis of microbial diversity in the contaminated soils by microarray biochips revealed that Acinetobacter sp. and Pseudomonas aeruginosa were the predominant groups in indigenous consortia, while the augmented consortia were Gordonia alkanivorans and Rhodococcus erythropolis in both series of biopiles during bioremediation. Microbial respiration as influenced by the microbial activity reflected directly the active microbial population and indirectly the biodegradation of TPH. Field experimental results showed that the residual TPH concentration in the complex biopile was reduced to less than 500 mg TPH/kg dry soil. The above results demonstrated that the SEMBT technology is a feasible alternative to bioremediate the oil-contaminated soil.

  14. 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

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

    PubMed

    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.

  16. 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.

  17. 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.

  18. Lipoarabinomannans: from structure to biosynthesis.

    PubMed

    Nigou, Jérôme; Gilleron, Martine; Puzo, Germain

    2003-01-01

    Mycobacterium tuberculosis, the causative agent of tuberculosis, is one of the most effective human pathogens and the molecular basis of its virulence remains poorly understood. Here, we review our current knowledge about the structure and biosynthesis of the mycobacterial cell-wall lipoglycans, lipoarabinomannans (LAM). LAM are ubiquitous of mycobacteria and appear as the most potent non-peptidic molecules to modulate the host immune response. Nevertheless, LAM structure differs according to the mycobacterial species and three types of LAM have been described: mannose-capped LAM (ManLAM), phospho-myo-inositol-capped LAM (PILAM) and non-capped LAM (AraLAM). The type of capping is a major structural feature determining the ability of LAM to modulate the immune response. ManLAM, found in slow-growing mycobacteria, such as M. tuberculosis, have been demonstrated to be powerful anti-inflammatory molecules and emerge as key virulence factors that may be relevant drug targets. LAM-like molecules are not only confined to mycobacteria but are also present in actinomycetes (including the genera Rhodococcus, Corynebacterium or Gordonia). This offers the possibility of comparative studies that should help in deciphering the structure-function relationships and biosynthesis of these complex molecules in the future.

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

    PubMed

    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.

  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. 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

  2. Biotechnological methods for chalcone reduction using whole cells of Lactobacillus, Rhodococcus and Rhodotorula strains as a way to produce new derivatives.

    PubMed

    Stompor, Monika; Kałużny, Mateusz; Żarowska, Barbara

    2016-10-01

    Microbial strains of the genera Dietzia, Micrococcus, Pseudomonas, Rhodococcus, Gordonia, Streptomyces, Pseudomonas, Bacillus, Penicillium, Rhodotorula and Lactobacillus were screened for the ability to convert chalcones. Synthesis of chalcones was performed by the Claisen-Schmidt reaction. There were three groups of chalcones obtained as the products, which included the derivatives containing 4-substituted chalcone, 2'-hydroxychalcone and 4'-methoxychalcone. The B ring of the chalcones was substituted in the para position with different groups, such as halide, hydroxyl, nitro, methyl, ethyl and ethoxy one. The structure-activity relationship of the tested chalcones in biotransformation processes was studied. It has been proven that Gram-positive bacterial strains Rhodococcus and Lactobacillus catalyzed reduction of C=C bond in the chalcones to give respective dihydrochalcones. The strain Rhodotorula rubra AM 82 transformed chalcones into dihydrochalcones and respective secondary alcohols. These results suggest that the probiotic strain of Lactobacillus can be used for biotransformations of chalcones, which has not been described before. The structure of new metabolites 14a and 15b were established as 4-ethoxy-4'-methoxydihydrochalcone and 3-(4-bromophenyl)-1-(4'-O-methylphenyl)-2-propan-1-ol, respectively, which was confirmed by (1)H NMR and (13)C NMR analysis. PMID:27209040

  3. Screening for exopolysaccharide-producing bacteria from sub-tropical polluted groundwater.

    PubMed

    Fusconi, R; Godinho, M J L

    2002-05-01

    A selection of exopolysaccharide (EPS)--producing bacterial strains was conducted in groundwater adjacent to an old controlled landfill in the City of São Carlos (São Paulo, Brazil). The strains were isolated in P and E media under aerobic and microacrophilic conditions at 25 degrees C. A total of 26 strains were isolated and based on the mucoid mode of the colonies, 6 were selected and their morphological, physiological and biochemical aspects were characterized. All strains presented pigmentation, ranging from yellow to orange and from pink to salmon, with a shiny glistening aspect in all tested media. Strains Lb, Lc and Lg, which excelled the others with regard to the mucoid mode of the colonies, were selected to be cultured in E medium with alternate sucrose and glucose as carbon sources in anaerobiosis at 25 degrees C to analyze the production of EPS. Strains Lc and Lg were classified as being of order Actinomycelates, suborder Corynebacterineae. Lg strain was identified as Gordonia polyisoprenivorans and Lc strain did not correspond to a known description and therefore a more detailed study is under preparation. Considering all ecological aspects and the metabolic potential associated with the microorganisms of the environment studied, as well as the capacity to produce pigment and EPS, and the presence of G. polyisoprenivorans, a rubber degrader bacterium, the potential of the groundwater analyzed is evident as a source of microorganisms to be utilized in studies related to environmental remediation.

  4. Culture-dependent and culture-independent diversity of Actinobacteria associated with the marine sponge Hymeniacidon perleve from the South China Sea.

    PubMed

    Sun, Wei; Dai, Shikun; Jiang, Shumei; Wang, Guanghua; Liu, Guohui; Wu, Houbo; Li, Xiang

    2010-06-01

    In this report, the diversity of Actinobacteria associated with the marine sponge Hymeniacidon perleve collected from a remote island of the South China Sea was investigated employing classical cultivation and characterization, 16S rDNA library construction, 16S rDNA-restriction fragment length polymorphism (rDNA-RFLP) and phylogenetic analysis. A total of 184 strains were isolated using seven different media and 24 isolates were selected according to their morphological characteristics for phylogenetic analysis on the basis of their 16S rRNA gene sequences. Results showed that the 24 isolates were assigned to six genera including Salinispora, Gordonia, Mycobacterium, Nocardia, Rhodococcus and Streptomyces. This is the first report that Salinispora is present in a marine sponge from the South China Sea. Subsequently, 26 rDNA clones were selected from 191 clones in an Actinobacteria-specific 16S rDNA library of the H. perleve sample, using the RFLP technique for sequencing and phylogenetic analysis. In total, 26 phylotypes were clustered in eight known genera of Actinobacteria including Mycobacterium, Amycolatopsis, Arthrobacter, Brevibacterium, Microlunatus, Nocardioides, Pseudonocardia and Streptomyces. This study contributes to our understanding of actinobacterial diversity in the marine sponge H. perleve from the South China Sea.

  5. 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

  6. 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.

  7. Latex Clearing Protein—an Oxygenase Cleaving Poly(cis-1,4-Isoprene) Rubber at the cis Double Bonds

    PubMed Central

    Hiessl, Sebastian; Böse, Dietrich; Oetermann, Sylvia; Eggers, Jessica; Pietruszka, Jörg

    2014-01-01

    Gordonia polyisoprenivorans strain VH2, a potent rubber-degrading actinomycete, harbors two latex clearing proteins (Lcps), which are known to be essential for the microbial degradation of rubber. However, biochemical information on the exact role of this protein in the degradation of polyisoprene was lacking. In this study, the gene encoding Lcp1VH2 was heterologously expressed in strains of Escherichia coli, the corresponding protein was purified, and its role in rubber degradation was examined by measurement of oxygen consumption as well as by chromatographic and spectroscopic methods. It turned out that active Lcp1VH2 is a monomer and is responsible for the oxidative cleavage of poly(cis-1,4-isoprene) in synthetic as well as in natural rubber by the addition of oxygen (O2) to the cis double bonds. The resulting oligomers possess repetitive isoprene units with aldehyde (CHO-CH2—) and ketone (—CH2-CO-CH3) functional groups at the termini. Two fractions with average isoprene contents of 18 and 10, respectively, were isolated, thus indicating an endocleavage mechanism. The activity of Lcp1VH2 was determined by applying a polarographic assay. Alkenes, acyclic terpenes, or other rubber-like polymers, such as poly(cis-1,4-butadiene) or poly(trans-1,4-isoprene), are not oxidatively cleaved by Lcp1VH2. The pH and temperature optima of the enzyme are at pH 7 and 30°C, respectively. Furthermore, it was demonstrated that active Lcp1VH2 is a Cu(II)-containing oxygenase that exhibits a conserved domain of unknown function which cannot be detected in any other hitherto-characterized enzyme. The results presented here indicate that this domain might represent a new protein family of oxygenases. PMID:24928880

  8. 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.

  9. Degradation of various alkyl ethers by alkyl ether-degrading Actinobacteria isolated from activated sludge of a mixed wastewater treatment.

    PubMed

    Kim, Yong-Hak; Cha, Chang-Jun; Engesser, Karl-Heinrich; Kim, Sang-Jong

    2008-11-01

    Various substrate specificity groups of alkyl ether (AE)-degrading Actinobacteria coexisted in activated sewage sludge of a mixed wastewater treatment. There were substrate niche overlaps including diethyl ether between linear AE- and cyclic AE-degrading strains and phenetole between monoalkoxybenzene- and linear AE-degrading strains. Representatives of each group showed different substrate specificities and degradation pathways for the preferred substrates. Determining the rates of initial reactions and the initial metabolite(s) from whole cell biotransformation helped us to get information about the degradation pathways. Rhodococcus sp. strain DEE5311 and Rhodococcus rhodochrous strain 117 both were able to degrade anisole and phenetole through aromatic 2-monooxygenation to form 2-alkoxyphenols. In contrast, diethyl ether-oxidizing strain DEE5311 capable of degrading a broad range of linear AE, dibenzyl ether and monoalkoxybenzenes initially transformed anisole and phenetole to phenol via direct O-dealkylation. Compared to this, cyclic AE-degrading Rhodococcus sp. strain THF100 preferred tetrahydrofuran (265 ± 35 nmol min(-1)mg(-1) protein) to diethyl ether (<30), but it cannot oxidize bulkier AE than diethyl ether. Otherwise, 1,4-diethoxybenzene-degrading Rhodococcus sp. strain DEOB100 and Gordonia sp. strain DEOB200 transformed 1,3-/1,4-dialkoxybenzenes to 3-/4-alkoxyphenols by similar manners in the order of rates (nmol min(-1) mg(-1) protein): 1,4-diethoxybenzene (11.1 vs. 3.9)>1,4-dimethoxybenzene (1.6 vs. 2.6)>1,3-dimethoxybenzene (0.6 vs. 0.6). This study suggests that the AE-degrading Actinobacteria can orchestrate various substrate specificity responses to the degradation of various categories of AE pollutants in activated sludge communities.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. Latex clearing protein-an oxygenase cleaving poly(cis-1,4-isoprene) rubber at the cis double bonds.

    PubMed

    Hiessl, Sebastian; Böse, Dietrich; Oetermann, Sylvia; Eggers, Jessica; Pietruszka, Jörg; Steinbüchel, Alexander

    2014-09-01

    Gordonia polyisoprenivorans strain VH2, a potent rubber-degrading actinomycete, harbors two latex clearing proteins (Lcps), which are known to be essential for the microbial degradation of rubber. However, biochemical information on the exact role of this protein in the degradation of polyisoprene was lacking. In this study, the gene encoding Lcp1VH2 was heterologously expressed in strains of Escherichia coli, the corresponding protein was purified, and its role in rubber degradation was examined by measurement of oxygen consumption as well as by chromatographic and spectroscopic methods. It turned out that active Lcp1VH2 is a monomer and is responsible for the oxidative cleavage of poly(cis-1,4-isoprene) in synthetic as well as in natural rubber by the addition of oxygen (O2) to the cis double bonds. The resulting oligomers possess repetitive isoprene units with aldehyde (CHO-CH2-) and ketone (-CH2-CO-CH3) functional groups at the termini. Two fractions with average isoprene contents of 18 and 10, respectively, were isolated, thus indicating an endocleavage mechanism. The activity of Lcp1VH2 was determined by applying a polarographic assay. Alkenes, acyclic terpenes, or other rubber-like polymers, such as poly(cis-1,4-butadiene) or poly(trans-1,4-isoprene), are not oxidatively cleaved by Lcp1VH2. The pH and temperature optima of the enzyme are at pH 7 and 30°C, respectively. Furthermore, it was demonstrated that active Lcp1VH2 is a Cu(II)-containing oxygenase that exhibits a conserved domain of unknown function which cannot be detected in any other hitherto-characterized enzyme. The results presented here indicate that this domain might represent a new protein family of oxygenases.

  15. High level multiple antibiotic resistance among fish surface associated bacterial populations in non-aquaculture freshwater environment.

    PubMed

    Ozaktas, Tugba; Taskin, Bilgin; Gozen, Ayse G

    2012-12-01

    Freshwater fish, Alburnus alburnus (bleak), were captured from Lake Mogan, situated in Ankara, during spring. The surface mucus of the fish was collected and associated bacteria were cultured and isolated. By sequencing PCR-amplified 16S RNA encoding genes, the isolates were identified as members of 12 different genera: Acinetobacter, Aeromonas, Bacillus, Brevundimonas, Gordonia, Kocuria, Microbacterium, Mycobacterium, Pseudomonas, Rhodococcus, and Staphylococcus, in addition to one strain that was unidentified. The mucus-dwelling bacterial isolates were tested for resistance against ampicillin, kanamycin, streptomycin and chloramphenicol. About 95% of the isolates were found to be resistant to ampicillin, 93% to chloramphenicol, and 88% to kanamycin and streptomycin. A Microbacterium oxydans and the unidentified environmental isolate were resistant to all four antibiotics tested at very high levels (>1600 μg/ml ampicillin and streptomycin; >1120 μg/ml kanamycin; >960 μg/ml chloramphenicol). Only a Kocuria sp. was sensitive to all four antibiotics at the lowest concentrations tested (3.10 μg/ml ampicillin and streptomycin; 2.15 μg/ml kanamycin; 1.85 μg/ml chloramphenicol). The rest of the isolates showed different resistance levels. Plasmid isolations were carried out to determine if the multiple antibiotic resistance could be attributed to the presence of plasmids. However, no plasmid was detected in any of the isolates. The resistance appeared to be mediated by chromosome-associated functions. This study indicated that multiple antibiotic resistance at moderate to high levels is common among the current phenotypes of the fish mucus-dwelling bacterial populations in this temperate, shallow lake which has not been subjected to any aquaculturing so far but under anthropogenic effect being in a recreational area. PMID:23039919

  16. 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.

  17. Constitutive Expression of the Cytochrome P450 EthABCD Monooxygenase System Enables Degradation of Synthetic Dialkyl Ethers in Aquincola tertiaricarbonis L108

    PubMed Central

    Schuster, Judith; Purswani, Jessica; Breuer, Uta; Pozo, Clementina; Harms, Hauke; Müller, Roland H.

    2013-01-01

    In Rhodococcus ruber IFP 2001, Rhodococcus zopfii IFP 2005, and Gordonia sp. strain IFP 2009, the cytochrome P450 monooxygenase EthABCD catalyzes hydroxylation of methoxy and ethoxy residues in the fuel oxygenates methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE), and tert-amyl methyl ether (TAME). The expression of the IS3-type transposase-flanked eth genes is ETBE dependent and controlled by the regulator EthR (C. Malandain et al., FEMS Microbiol. Ecol. 72:289–296, 2010). In contrast, we demonstrated by reverse transcription-quantitative PCR (RT-qPCR) that the betaproteobacterium Aquincola tertiaricarbonis L108, which possesses the ethABCD genes but lacks ethR, constitutively expresses the P450 system at high levels even when growing on nonether substrates, such as glucose. The mutant strain A. tertiaricarbonis L10, which is unable to degrade dialkyl ethers, resulted from a transposition event mediated by a rolling-circle IS91-type element flanking the eth gene cluster in the wild-type strain L108. The constitutive expression of Eth monooxygenase is likely initiated by the housekeeping sigma factor σ70, as indicated by the presence in strain L108 of characteristic −10 and −35 binding sites upstream of ethA which are lacking in strain IFP 2001. This enables efficient degradation of diethyl ether, diisopropyl ether, MTBE, ETBE, TAME, and tert-amyl ethyl ether (TAEE) without any lag phase in strain L108. However, ethers with larger residues, n-hexyl methyl ether, tetrahydrofuran, and alkyl aryl ethers, were not attacked by the Eth system at significant rates in resting-cell experiments, indicating that the residue in the ether molecule which is not hydroxylated also contributes to the determination of substrate specificity. PMID:23354715

  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 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

  19. 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

  20. 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

  1. 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

  2. Gene structure and regulation of alkane monooxygenases in propane-utilizing Mycobacterium sp. TY-6 and Pseudonocardia sp. TY-7.

    PubMed

    Kotani, Tetsuya; Kawashima, Yui; Yurimoto, Hiroya; Kato, Nobuo; Sakai, Yasuyoshi

    2006-09-01

    Mycobacterium sp. TY-6 and Pseudonocardia sp. TY-7 were isolated from soil samples as propane-utilizing bacteria and were found to be able to utilize various gaseous and liquid n-alkanes as carbon and energy sources. One gene cluster, M-prmABCD, and two gene clusters, P-prm1ABCD and P-prm2ABCD, were cloned from the genomes of Mycobacterium sp. TY-6 and Pseudonocardia sp. TY-7, respectively. These gene clusters are homologous to the gene cluster encoding the multicomponent propane monooxygenase (prmABCD) of Gordonia sp. TY-5. The expression of prm gene clusters in Mycobacterium sp. TY-6 and Pseudonocardia sp. TY-7 was shown to be induced by gaseous n-alkanes (C2-C4) except methane, suggesting that the products of these genes are involved in gaseous n-alkane oxidation. Homologous genes for an alkane hydroxylase system (alk system) involved in liquid n-alkane oxidation were also cloned from the genomic DNA of Mycobacterium sp. TY-6. The alk gene cluster was transcribed in response to liquid n-alkanes (C11-C15). These results indicate that Mycobacterium sp. TY-6 has two distinct gene clusters for multicomponent monooxygenases involved in alkane oxidation. Whole-cell reactions revealed that propane is oxidized to 1-propanol through terminal oxidation in Mycobacterium sp. TY-6 and that propane is oxidized to 1-propanol and 2-propanol through both terminal and subterminal oxidations in Pseudonocardia sp. TY-7. This study reveals the diversity of propane metabolism present in microorganisms. PMID:17046531

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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

  11. Pyrrolizidine alkaloids in honey: comparison of analytical methods.

    PubMed

    Kempf, M; Wittig, M; Reinhard, A; von der Ohe, K; Blacquière, T; Raezke, K-P; Michel, R; Schreier, P; Beuerle, T

    2011-03-01

    Pyrrolizidine alkaloids (PAs) are a structurally diverse group of toxicologically relevant secondary plant metabolites. Currently, two analytical methods are used to determine PA content in honey. To achieve reasonably high sensitivity and selectivity, mass spectrometry detection is demanded. One method is an HPLC-ESI-MS-MS approach, the other a sum parameter method utilising HRGC-EI-MS operated in the selected ion monitoring mode (SIM). To date, no fully validated or standardised method exists to measure the PA content in honey. To establish an LC-MS method, several hundred standard pollen analysis results of raw honey were analysed. Possible PA plants were identified and typical commercially available marker PA-N-oxides (PANOs). Three distinct honey sets were analysed with both methods. Set A consisted of pure Echium honey (61-80% Echium pollen). Echium is an attractive bee plant. It is quite common in all temperate zones worldwide and is one of the major reasons for PA contamination in honey. Although only echimidine/echimidine-N-oxide were available as reference for the LC-MS target approach, the results for both analytical techniques matched very well (n = 8; PA content ranging from 311 to 520 µg kg(-1)). The second batch (B) consisted of a set of randomly picked raw honeys, mostly originating from Eupatorium spp. (0-15%), another common PA plant, usually characterised by the occurrence of lycopsamine-type PA. Again, the results showed good consistency in terms of PA-positive samples and quantification results (n = 8; ranging from 0 to 625 µg kg(-1) retronecine equivalents). The last set (C) was obtained by consciously placing beehives in areas with a high abundance of Jacobaea vulgaris (ragwort) from the Veluwe region (the Netherlands). J. vulgaris increasingly invades countrysides in Central Europe, especially areas with reduced farming or sites with natural restorations. Honey from two seasons (2007 and 2008) was sampled. While only trace amounts of

  12. 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

  13. [Recent progress in taxonomic studies on pathogenic nocardia and usefulness of the bacteria for the studies on secondary metabolites and antibiotic resistant mechanisms].

    PubMed

    Mikami, Yuzuru

    2010-01-01

    The present taxonomic situation of pathogenic actinomycetes including Nocardia was clarified, and the impact of genomic sequence information of Nocardia farcinica IFM 10152 on taxonomic work is introduced. The number of cases of nocardiosis is on the rise along with the increasing number of immunocompromised patients in Japan. From 1999 to 2007, 718 strains of pathogenic actinomycetes were received for identification by Medical Mycology Research Center (MMRC), Chiba University. About 75% of these were classified into Nocardia, major species being N. farcinica, N. nova, and N. brasiliensis. Among the strains classified as Nocardia species, there were some unclassifiable strains and taxonomic studies on these led to the proposal of more than 18 new species, resulting in more than 1/4 of all Nocardia species having been proposed by our group. Recently a new Nocardia species, Nocardia mikamii was proposed by American researchers. A new phylogenetic analysis method using gryB and secA1 genes was proposed for the Nocardia and Gordonia strains.Our whole genome analysis of N. farcinica suggests that the bacterium has unique and characteristic gene profiles, and also suggests that N. farcinica is similar to Mycobacterium tuberculosis. N. farcinica also has siderophore (nocobactin) and mce genes which are similar to mycobactin (siderophore) of M. tuberculosis as virulence factors. Nocardia strains were found to be producers of new secondary metabolites including antifungal, antitumor and immunosuppressive activities.We reported novel antibiotic resistance mechanisms such as ribosylation, glucosylation, phosphorylation and degradation of rifampicin, phosphorylation of aminoglycosides, and glucosylation of macrolide antibiotics. Among rifampicin inactivation mechanisms, ribosylation was found to be through the Arr enzyme that catalyzes ADP-ribosylation of rifampicin in a fast-growing Mycobacterium smegmatis. This unique mechanism has also been reported as an antibiotic

  14. Palynology of latest Neogene (Middle Miocene to late Pliocene) strata in the Delmarva Peninsula of Maryland and Virginia

    USGS Publications Warehouse

    Sirkin, L.; Owens, J.P.

    1998-01-01

    Palynology of Miocene and Pliocene formations in the Delmarva Peninsula of Maryland and Virginia reveals a significant representation of exotic pollen interspersed in pollen assemblages that are otherwise comparable to those from the modern vegetation of the Mid-Alantic coastal plain region. The late Tertiary arboreal pollen (AP) assemblages are dominated by oak, hickory, pine, birch and alder with minor amounts of mid- and southern coastal tree taxa, as well as minor spruce and hemlock and a trace of fir. Nonarboreal pollen (NAP) include grass, sedge, composite and aquatic taxa. Exotic pollen in these assemblages represent plants now foreign to this region. They may be placed in three categories. First, there are extinct forms, such as Labrapollis, Plicatopollis, and Multiporopollenites, that can be traced from the Cretaceous or Early Tertiary into the Late Tertiary. The second group includes forms, such as Podocarpus, Engelhardtia, Pterocarya, Ephedra, Eucommia, Ulmus-Zelkova, Glyptostrobus, Palmae, and Cyathea, that are not found in this region today and not found in early Pleistocene sediments in the eastern United States. Many of these taxa are subtropical or greatly restricted in geographic range. A third group of exotics, mainly Cyrilla, Planera, Gordonia, Jussiaea, and Sapotacaea, including Minusops, are generally found south of the study area or have their northern limit here at this time. The lack of the extinct or distant exotics in early to mid-Pleistocene sediments in the mid-Atlantic coastal plain and the last appearance of Pterocarya, as the last exotic taxon in the early Pleistocene of western Europe, support the stratigraphic assignment of the Pliocene units. The number of exotic taxa diminish markedly between the Miocene pollen assemblages and those of the Late Pliocene. Climatic fluctuations characterize the Late Tertiary environments. The Miocene, for example, incorporates a warming trend between the upper, middle Miocene and the Manokin beds

  15. 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

  16. 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

  17. 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