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Sample records for gordonia jacobaea mv-26

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

    NASA Astrophysics Data System (ADS)

    Vrieling, Klaas

    2006-09-01

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

  2. Gordonia humi sp. nov., isolated from soil.

    PubMed

    Kämpfer, P; Young, Chiu-Chung; Chu, Jiunn-Nan; Frischmann, A; Busse, H-J; Arun, A B; Shen, Fo-Ting; Rekha, P D

    2011-01-01

    A Gram-stain-positive, non-endospore-forming actinobacterium (CC-12301(T)) was isolated from soil attached to a spawn used in the laboratory to grow the edible mushroom Agaricus brasiliensis. Based on 16S rRNA gene sequence similarities, strain CC-12301(T) was shown to belong to the genus Gordonia and was most closely related to the type strains of Gordonia hydrophobica (97.6 % similarity), Gordonia terrae (97.5 %), Gordonia amarae (97.5 %) and Gordonia malaquae (97.4 %). The quinone system was determined to consist predominantly of menaquinone MK-9(H(2)), minor amounts of MK-8(H(2)) and MK-7(H(2)). The polar lipid profile consisted of the major compounds diphosphatidylglycerol and phosphatidylethanolamine, moderate amounts of two phosphatidylinositol mannosides and phosphatidylinositol and minor amounts of phosphatidylglycerol, three unidentified glycolipids, two phosphoglycolipids and a phospholipid. Mycolic acids were present. These chemotaxonomic traits and the major fatty acids, which were C(16 : 1) cis9, C(16 : 0), C(18 : 1) and tuberculostearic acid (10-methyl C(18 : 0)), supported the affiliation of strain CC-12301(T) to the genus Gordonia. The results of physiological and biochemical tests allowed clear phenotypic differentiation of strain CC-12301(T) from the most closely related Gordonia species. Strain CC-12301(T) therefore represents a novel species, for which the name Gordonia humi sp. nov. is proposed, with the type strain CC-12301(T) (=DSM 45298(T) =CCM 7727(T)).

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

    PubMed

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

    2012-07-01

    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.

  4. 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

  5. Interplay between Senecio jacobaea and plant, soil, and aboveground insect community composition.

    PubMed

    Bezemer, T Martijn; Harvey, Jeffrey A; Kowalchuk, George A; Korpershoek, Hanna; van der Putten, Wim H

    2006-08-01

    To elucidate the factors that affect the performance of plants in their natural environment, it is essential to study interactions with other neighboring plants, as well as with above- and belowground higher trophic organisms. We used a long-term field experiment to study how local plant community diversity influenced colonization by the biennial composite Senecio jacobaea in its native range in The Netherlands in Europe. We tested the effect of sowing later-succession plant species (0, 4, or 15 species) on plant succession and S. jacobaea performance. Over a period of eight years, the percent cover of S. jacobaea was relatively low in communities sown with 15 or 4 later-succession plant species compared to plots that were not sown, but that were colonized naturally. However, after four years of high abundance, the density of S. jacobaea in unsown plots started to decline, and the size of the individual plants was smaller than in the plots sown with 15 or 4 plant species. In the unsown plots, densities of aboveground leaf-mining, flower-feeding, and stem-boring insects on S. jacobaea plants were lower than on plants in sown plots, and there was a strong positive relationship between plant size and levels of herbivory. In a greenhouse experiment, we grew S. jacobaea in sterilized soil inoculated with soil from the different sowing treatments of the field experiment. Biomass production was lower when S. jacobaea test plants were grown in soil from the unsown plots than in soil from the sown plots (4 or 15 species). Molecular analysis of the fungal and bacterial communities revealed that the composition of fungal communities in unsown plots differed significantly from those in sown plots, suggesting that soil fungi could have been involved in the relative growth reduction of S. jacobaea in the greenhouse bioassay. Our results show that, in its native habitat, the abundance of S. jacobaea depends on the initial composition of the plant community and that, on a scale of

  6. Complete Genome Sequences of 38 Gordonia sp. Bacteriophages

    PubMed Central

    Montgomery, Matthew T.; Bonilla, J. Alfred; Dejong, Randall; Garlena, Rebecca A.; Guerrero Bustamante, Carlos; Klyczek, Karen K.; Russell, Daniel A.; Wertz, John T.; Jacobs-Sera, Deborah; Hatfull, Graham F.

    2017-01-01

    ABSTRACT We report here the genome sequences of 38 newly isolated bacteriophages using Gordonia terrae 3612 (ATCC 25594) and Gordonia neofelifaecis NRRL59395 as bacterial hosts. All of the phages are double-stranded DNA (dsDNA) tail phages with siphoviral morphologies, with genome sizes ranging from 17,118 bp to 93,843 bp and spanning considerable nucleotide sequence diversity. PMID:28057748

  7. Gordonia iterans sp. nov., isolated from a patient with pneumonia.

    PubMed

    Kang, Ying-Qian; Ming, Hong; Gonoi, Tohru; Chen, Yuru; Cao, Yu; Wang, Yan-Yan; Cheng, Juan; Koga, Takeharu; Mikami, Yuzuru; Li, Wen-Jun

    2014-10-01

    A second novel clinical actinobacterial strain, designated IFM 10348(T), was isolated from the sputum of the same Japanese patient with bacterial pneumonia from whom the type strain of Gordonia araii had been isolated. The strains differed in phylogenetic position and drug-resistance profiles. The taxonomic position of strain IFM 10348(T) was clarified by phenotypic, chemotaxonomic and phylogenetic studies. Phylogenetic analyses based on 16S rRNA gene sequences clearly demonstrated that strain IFM 10348(T) occupied a distinct clade within the genus Gordonia and was related closely to Gordonia malaquae DSM 45064(T) and Gordonia hirsuta DSM 44140(T) (97.3 and 97.1% similarities, respectively). Strain IFM 10348(T) was also clearly differentiated from G. malaquae DSM 45064(T) and G. hirsuta DSM 44140(T) based on gyrB and secA1 gene sequence similarity values. Strain IFM 10348(T) had MK-9(H2) as the predominant menaquonine, contained meso-diaminopimelic acid, arabinose, galactose and glucosamine as cell-wall components, and contained C18:1ω9c, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16:0 as the major cellular fatty acids. Mycolic acids were present. The DNA G+C content of strain IFM 10348(T) was 68.0 mol%. DNA-DNA relatedness data coupled with the combination of genotypic and phenotypic data indicated that strain IFM 10348(T) represents a novel species of the genus Gordonia, for which the name Gordonia iterans sp. nov. is proposed. The type strain is IFM 10348(T) ( = CCTCC M2011245(T) = NCCB 100436(T)).

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. Bacteremia Caused by Gordonia bronchialis in a Patient with Sequestrated Lung

    PubMed Central

    Sng, Li-Hwei; Koh, T. H.; Toney, S. R.; Floyd, M.; Butler, W. R.; Tan, B. H.

    2004-01-01

    Gordonia species have been recognized as pathogens in immunocompromised and immunocompetent patients. We report the first case of bacteremia due to Gordonia bronchialis in a diabetic patient with a sequestrated lung. Species identification was confirmed with mycolic acid analysis by high-performance liquid chromatography and sequencing of the 16S rRNA gene. PMID:15184495

  13. 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

  14. 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

    2016-08-11

    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%. Copyright © 2016 Pope et al.

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

    PubMed Central

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

    2010-01-01

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

  16. 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.

  17. Reevaluating establishment and potential hybridization of different biotypes of the biological control agent Longitarsus jacobaeae using molecular tools

    USDA-ARS?s Scientific Manuscript database

    Evaluation of past and current biological control programs using molecular tools can clarify establishment success of agent biotypes, and can contribute to our understanding of best practice for natural enemy importations. The flea beetle, Longitarsus jacobaeae has been quite successful at controlli...

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

    PubMed Central

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

    2012-01-01

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

  19. Evolutionary recruitment of a flavin-dependent monooxygenase for the detoxification of host plant-acquired pyrrolizidine alkaloids in the alkaloid-defended arctiid moth Tyria jacobaeae

    PubMed Central

    Naumann, Claudia; Hartmann, Thomas; Ober, Dietrich

    2002-01-01

    Larvae of Tyria jacobaeae feed solely upon the pyrrolizidine alkaloid-containing plant Senecio jacobaea. Ingested pyrrolizidine alkaloids (PAs), which are toxic to unspecialized insects and vertebrates, are efficiently N-oxidized in the hemolymph of T. jacobaeae by senecionine N-oxygenase (SNO), a flavin-dependent monooxygenase (FMO) with a high substrate specificity for PAs. Peptide microsequences obtained from purified T. jacobaeae SNO were used to clone the corresponding cDNA, which was expressed in active form in Escherichia coli. T. jacobaeae SNO possesses a signal peptide characteristic of extracellular proteins, and it belongs to a large family of mainly FMO-like sequences of mostly unknown function, including two predicted Drosophila melanogaster gene products. The data indicate that the gene for T. jacobaeae SNO, highly specific for toxic pyrrolizidine alkaloids, was recruited from a preexisting insect-specific FMO gene family of hitherto unknown function. The enzyme allows the larvae to feed on PA-containing plants and to accumulate predation-deterrent PAs in the hemolymph. PMID:11972041

  20. Sternal wound infection caused by Gordonia bronchialis: identification by MALDI-TOF MS

    PubMed Central

    Rodriguez-Lozano, Jesús; Pérez-Llantada, Enrique; Agüero, Jesús; Rodríguez-Fernández, Ana; Ruiz de Alegria, Carlos; Martinez-Martinez, Luis

    2016-01-01

    Introduction: Gordonia spp. infections are uncommon. However, a few clinical cases have been reported in the literature, particularly those involving immunocompromised hosts. Advanced microbiology diagnosis techniques, such as matrix-assisted laser desorption ionization-time of flight MS (MALDI-TOF MS), have been recently introduced in clinical microbiology laboratories in order to improve microbial identification, resulting in better patient management. Case presentation: Here, we present a new clinical case of persistent wound infection caused by Gordonia bronchialis in a 64-year-old woman after a mitral valve replacement, using two MALDI-TOF-based systems for identifying this micro-organism. Conclusion: Both MALDI-TOF systems were able to identify Gordonia spp.; thus, providing a useful tool that overcomes the current limitations of phenotypic identification associated with this micro-organism. Although the technique validation deserves additional verification, our study provides guidance about MALDI-TOF as a fast and easy method for Gordonia spp. identification. PMID:28348789

  1. 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

  2. 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

  3. A Chinese patient with peritoneal dialysis-related peritonitis caused by Gordonia terrae: a case report.

    PubMed

    Hou, Chenrui; Yang, Yun; Li, Ziyang

    2017-02-28

    Gordonia terrae is a rare cause of clinical infections, with only 23 reported cases. We report the first case of peritoneal dialysis-related peritonitis caused by Gordonia terrae in mainland China. A 52-year-old man developed peritoneal dialysis-related peritonitis and received preliminary antibiotic treatment. After claiming that his symptoms had been resolved, the patient insisted on being discharged (despite our recommendations) and did not receive continued treatment after leaving the hospital. A telephone follow-up with the patient's relatives revealed that the patient died 3 months later. Routine testing did not identify the bacterial strain responsible for the infection, although matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identified the strain as Gordonia rubropertincta. However, a 16S rRNA sequence analysis using an isolate from the peritoneal fluid culture revealed that the responsible strain was actually Gordonia terrae. Similar to this case, all previously reported cases have involved a delayed diagnosis and initial treatment failure, and the definitive diagnosis required a 16S rRNA sequence analysis. Changes from an inappropriate antibiotic therapy to an appropriate one have relied on microbiological testing and were performed 7-32 days after the initial treatment. The findings from our case and the previously reported cases indicate that peritoneal dialysis-related peritonitis caused by Gordonia terrae can be difficult to identify and treat. It may be especially challenging to diagnose these cases in countries with limited diagnostic resources.

  4. Gordonia (nocardia) amarae foaming due to biosurfactant production.

    PubMed

    Pagilla, K R; Sood, A; Kim, H

    2002-01-01

    Gordonia amarae, a filamentous actinomycete, commonly found in foaming activated sludge wastewater treatment plants was investigated for its biosurfactant production capability. Soluble acetate and paringly soluble hexadecane were used as carbon sources for G. amarae growth and biosurfactant production in laboratory scale batch reactors. The lowest surface tension (critical micelle concentration, CMC) of the cell-free culture broth was 55 dynes/cm when 1,900 mg/L acetate was used as the sole carbon source. The lowest surface tension was less than 40 dynes/cm when either 1% (v/v) hexadecane or a mixture of 1% (v/v) hexadecane and 0.5% (w/v) acetate was used as the carbon source. The maximum biomass concentration (the stationary phase) was achieved after 4 days when acetate was used along with hexadecane, whereas it took about 8 days to achieve the stationary phase with hexadecane alone. The maximum biosurfactant production was 3 x CMC with hexadecane as the sole carbon source, and it was 5 x CMC with the mixture of hexadecane and acetate. Longer term growth studies (approximately 35 days of culture growth) indicated that G. amarae produces biosurfactant in order to solubilize hexadecane, and that adding acetate improves its biosurfactant production by providing readily degradable substrate for initial biomass growth. This research confirms that the foaming problems in activated sludge containing G. amarae in the activated sludge are due to the biosurfactant production by G. amarae when hydrophobic substrates such as hexadecane are present.

  5. In silico modeling and evaluation of Gordonia alkanivorans for biodesulfurization.

    PubMed

    Aggarwal, Shilpi; Karimi, I A; Ivan, Gregorius Reinaldi

    2013-10-01

    The genus Gordonia is well known for its catabolic diversity and ability to transform several compounds including the various recalcitrant polyaromatic sulfur heterocycles (PASHs) found in the fossil fuels. In fact, some strains offer the unique ability to desulfurize even benzothiophene (BT) and other thiophenic compounds, which most of the commonly studied rhodococci strains cannot. In this work, we present the first genome scale metabolic model for G. alkanivorans, a desulfurizing strain, to enable a holistic study of its metabolism and comparison with R. erythropolis. Our model consists of 881 unique metabolites and 922 reactions associated with 568 ORFs/genes and 544 unique enzymes. It successfully predicts the growth rates from experimental studies and quantitatively elucidates the pathways for the desulfurization of the commonly studied sulfur compounds, namely dibenzothiophene (DBT) and benzothiophene (BT). Using our model, we identify the minimal media for G. alkanivorans, and show the significant effect of carbon sources on desulfurization with ethanol as the best source. Our model shows that the sulfur-containing amino acids such as cysteine and methionine decrease desulfurization activity, and G. alkanivorans prefers BT over DBT as a sulfur source. It also suggests that this preference may be driven by the lower NADH requirements for BT metabolism rather than the higher affinity of the transport system for BT. Our in silico comparison of R. erythropolis and G. alkanivorans suggests the latter to be a better desulfurizing strain due to its versatility for both BT and DBT, higher desulfurization activity, and higher growth rate.

  6. Establishment of Tn5096-Based Transposon Mutagenesis in Gordonia polyisoprenivorans

    PubMed Central

    Banh, Quyen; Arenskötter, Matthias; Steinbüchel, Alexander

    2005-01-01

    The transposons Tn5, Tn10, Tn611, and Tn5096 were characterized regarding transposition in Gordonia polyisoprenivorans strain VH2. No insertional mutants were obtained employing Tn5 or Tn10. The thermosensitive plasmid pCG79 harboring Tn611 integrated into the chromosome of G. polyisoprenivorans; however, the insertional mutants were fairly unstable und reverted frequently to the wild-type phenotype. In contrast, various stable mutants were obtained employing Tn5096-mediated transposon mutagenesis. Auxotrophic mutants, mutants defective or deregulated in carotenoid biosynthesis, and mutants defective in utilization of rubber and/or highly branched isoprenoid hydrocarbons were obtained by integration of plasmid pMA5096 harboring Tn5096 as a whole into the genome. From about 25,000 isolated mutants, the insertion loci of pMA5096 were subsequently mapped in 20 independent mutants in genes which could be related to the above-mentioned metabolic pathways or to putative regulation proteins. Analyses of the genotypes of pMA5096-mediated mutants defective in biodegradation of poly(cis-1,4-isoprene) did not reveal homologues to recently identified genes coding for enzymes catalyzing the initial cleavage of poly(cis-1,4-isoprene). One rubber-negative mutant was disrupted in mcr, encoding an α-methylacyl-coenzyme A racemase. This mutant was defective in degradation of poly(cis-1,4-isoprene) and also of highly branched isoprenoid hydrocarbons. PMID:16151089

  7. Prevention of Gordonia and Nocardia Stabilized Foam Formation by Using Bacteriophage GTE7▿†

    PubMed Central

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

    2011-01-01

    Most activated sludge treatment plants suffer from the presence of foams on the surfaces of their aeration reactors. These are often stabilized by hydrophobic mycolic acid-synthesizing actinobacterial species. A polyvalent Siphoviridae phage, GTE7, which lysed several Gordonia and Nocardia species, is described here. Its genome has a modular structure similar to that described for Rhodococcus phage ReqiDocB7. In laboratory-scale experiments, we showed that GTE7 prevents stabilization of foams by these Gordonia and Nocardia species. PMID:21926218

  8. 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.

  9. 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

  10. Gordonia malaquae sp. nov., isolated from sludge of a wastewater treatment plant.

    PubMed

    Yassin, A F; Shen, Fo-Ting; Hupfer, H; Arun, A B; Lai, Wei-An; Rekha, P D; Young, Chiu Chung

    2007-05-01

    The taxonomic status of a bacterial isolate from the sludge of a wastewater treatment plant was characterized by using a polyphasic taxonomic approach. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV, short-chain mycolic acids that co-migrated with those extracted from members of the genus Gordonia, fatty acids C(16 : 0) and C(18 : 0) (found by pyrolysis gas chromatography) and a dihydrogenated menaquinone with nine isoprene units [MK-9(H2)] as the predominant menaquinone. The genus assignment was confirmed by 16S rRNA gene sequencing. Comparative analysis of the 16S rRNA gene sequence showed that the novel isolate constitutes a hitherto unknown subline within the genus Gordonia, displaying 95.9 to 97.6 % gene sequence similarity to the recognized species of the genus. The novel isolate was distinguished from the type strains of phylogenetically related species by using a set of phenotypic features. The genotypic and phenotypic data show that the new strain merits classification as a novel species of the genus Gordonia, for which the name Gordonia malaquae sp. nov. is proposed. The type strain is IMMIB WWCC-22(T) (=DSM 45064(T)=CCUG 53555(T)).

  11. 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

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

    PubMed

    Kashyap, Radhika; Monika; Subudhi, Enketeswara

    2014-12-01

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

  13. Surface-active compounds and their role in the access to hydrocarbons in Gordonia strains.

    PubMed

    Franzetti, Andrea; Bestetti, Giuseppina; Caredda, Paolo; La Colla, Paolo; Tamburini, Elena

    2008-02-01

    Three new bacterial strains (M22, BS25 and BS29) belonging to the Gordonia genus were isolated from a site chronically contaminated by diesel. Those Gordonia strains were able to grow using a wide range of straight and branched aliphatic hydrocarbons as carbon and energy sources and to produce at least two classes of surface-active compounds. Emulsifying agents were released in the culture medium when bacteria grew both on hydrocarbons and water-soluble substrates. Cell-bound biosurfactants, which reduce the surface tension, were produced on hydrocarbons; however, their production was significantly lower on water soluble substrates. The relationship of growth phase, surface-active compound production and cell-surface properties was analyzed in kinetic experiments on hydrocarbons. Gordonia sp. BS29 synthesized, and released extracellularly, bioemulsans during the exponential phase with n-hexadecane as carbon and energy source. The production of biosurfactants started in the exponential phase and their concentration increased during the following linear growth. Furthermore, the adhesion of bacterial cells to hydrocarbons decreased during growth. Our results led us to hypothesize a change in the mode by which Gordonia cells access the substrate during growth on hydrocarbons.

  14. 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.

  15. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships

    PubMed Central

    Pope, Welkin H.; Mavrich, Travis N.; Garlena, Rebecca A.; Guerrero-Bustamante, Carlos A.; Jacobs-Sera, Deborah; Montgomery, Matthew T.; Russell, Daniel A.; Warner, Marcie H.

    2017-01-01

    ABSTRACT The global bacteriophage population is large, dynamic, old, and highly diverse genetically. Many phages are tailed and contain double-stranded DNA, but these remain poorly characterized genomically. A collection of over 1,000 phages infecting Mycobacterium smegmatis reveals the diversity of phages of a common bacterial host, but their relationships to phages of phylogenetically proximal hosts are not known. Comparative sequence analysis of 79 phages isolated on Gordonia shows these also to be diverse and that the phages can be grouped into 14 clusters of related genomes, with an additional 14 phages that are “singletons” with no closely related genomes. One group of six phages is closely related to Cluster A mycobacteriophages, but the other Gordonia phages are distant relatives and share only 10% of their genes with the mycobacteriophages. The Gordonia phage genomes vary in genome length (17.1 to 103.4 kb), percentage of GC content (47 to 68.8%), and genome architecture and contain a variety of features not seen in other phage genomes. Like the mycobacteriophages, the highly mosaic Gordonia phages demonstrate a spectrum of genetic relationships. We show this is a general property of bacteriophages and suggest that any barriers to genetic exchange are soft and readily violable. PMID:28811342

  16. 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.

  17. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships.

    PubMed

    Pope, Welkin H; Mavrich, Travis N; Garlena, Rebecca A; Guerrero-Bustamante, Carlos A; Jacobs-Sera, Deborah; Montgomery, Matthew T; Russell, Daniel A; Warner, Marcie H; Hatfull, Graham F

    2017-08-15

    The global bacteriophage population is large, dynamic, old, and highly diverse genetically. Many phages are tailed and contain double-stranded DNA, but these remain poorly characterized genomically. A collection of over 1,000 phages infecting Mycobacterium smegmatis reveals the diversity of phages of a common bacterial host, but their relationships to phages of phylogenetically proximal hosts are not known. Comparative sequence analysis of 79 phages isolated on Gordonia shows these also to be diverse and that the phages can be grouped into 14 clusters of related genomes, with an additional 14 phages that are "singletons" with no closely related genomes. One group of six phages is closely related to Cluster A mycobacteriophages, but the other Gordonia phages are distant relatives and share only 10% of their genes with the mycobacteriophages. The Gordonia phage genomes vary in genome length (17.1 to 103.4 kb), percentage of GC content (47 to 68.8%), and genome architecture and contain a variety of features not seen in other phage genomes. Like the mycobacteriophages, the highly mosaic Gordonia phages demonstrate a spectrum of genetic relationships. We show this is a general property of bacteriophages and suggest that any barriers to genetic exchange are soft and readily violable.IMPORTANCE Despite the numerical dominance of bacteriophages in the biosphere, there is a dearth of complete genomic sequences. Current genomic information reveals that phages are highly diverse genomically and have mosaic architectures formed by extensive horizontal genetic exchange. Comparative analysis of 79 phages of Gordonia shows them to not only be highly diverse, but to present a spectrum of relatedness. Most are distantly related to phages of the phylogenetically proximal host Mycobacterium smegmatis, although one group of Gordonia phages is more closely related to mycobacteriophages than to the other Gordonia phages. Phage genome sequence space remains largely unexplored, but

  18. 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.

  19. 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

  20. 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.

  1. The genomes of the non-clearing-zone-forming and natural-rubber- degrading species Gordonia polyisoprenivorans and Gordonia westfalica harbor genes expressing Lcp activity in Streptomyces strains.

    PubMed

    Bröker, Daniel; Dietz, David; Arenskötter, Matthias; Steinbüchel, Alexander

    2008-04-01

    The latex-clearing protein (Lcp(K30)) from the rubber-degrading bacterium Streptomyces sp. strain K30 is involved in the cleavage of poly(cis-1,4-isoprene), yielding isoprenoid aldehydes and ketones. Lcp homologues have so far been detected in all investigated clearing-zone-forming rubber-degrading bacteria. Internal degenerated oligonucleotides derived from lcp genes of Streptomyces sp. strain K30 (lcp(K30)), Streptomyces coelicolor strain A3(2), and Nocardia farcinica strains IFM10152 and E1 were applied in PCR to investigate whether lcp homologues occur also in the non-clearing-zone-forming rubber-utilizing bacteria Gordonia polyisoprenivorans strains VH2 and Y2K, Gordonia alkanivorans strain 44187, and Gordonia westfalica strain Kb1, which grow adhesively on rubber. The 1,230- and 1,224-bp lcp-homologous genes from G. polyisoprenivorans strain VH2 (lcp(VH2)) and G. westfalica strain Kb1 (lcp(Kb1)) were obtained after screening genomic libraries by degenerated PCR amplification, and their translational products exhibited 50 and 52% amino acid identity, respectively, to Lcp(K30). Recombinant lcp(VH2) and lcp(Kb1) harboring cells of the non-rubber-degrading Streptomyces lividans strain TK23 were able to form clearing zones and aldehydes on latex overlay-agar plates, thus indicating that lcp(VH2) and lcp(Kb1) encode functionally active proteins. Analysis by gel permeation chromatography demonstrated lower polymer concentrations and molecular weights of the remaining polyisoprenoid molecules after incubation with these recombinant S. lividans strains. Reverse transcription-PCR analysis demonstrated that lcp(VH2) was transcribed in cells of G. polyisoprenivorans strain VH2 cultivated in the presence of poly(cis-1,4-isoprene) but not in the presence of sodium acetate. Anti-Lcp(K30) immunoglobulin Gs, which were raised in this study, were rather specific for Lcp(K30) and did not cross-react with Lcp(VH2) and Lcp(Kb1). A lcp(VH2) disruption mutant was still able to grow

  2. Novel Acetone Metabolism in a Propane-Utilizing Bacterium, Gordonia sp. Strain TY-5▿

    PubMed Central

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

    2007-01-01

    In the propane-utilizing bacterium Gordonia sp. strain TY-5, propane was shown to be oxidized to 2-propanol and then further oxidized to acetone. In this study, the subsequent metabolism of acetone was studied. Acetone-induced proteins were found in extracts of cells induced by acetone, and a gene cluster designated acmAB was cloned on the basis of the N-terminal amino acid sequences of acetone-induced proteins. The acmA and acmB genes encode a Baeyer-Villiger monooxygenase (BVMO) and esterase, respectively. The BVMO encoded by acmA was purified from acetone-induced cells of Gordonia sp. strain TY-5 and characterized. The BVMO exhibited NADPH-dependent oxidation activity for linear ketones (C3 to C10) and cyclic ketones (C4 to C8). Escherichia coli expressing the acmA gene oxidized acetone to methyl acetate, and E. coli expressing the acmB gene hydrolyzed methyl acetate. Northern blot analyses revealed that polycistronic transcription of the acmAB gene cluster was induced by propane, 2-propanol, and acetone. These results indicate that the acmAB gene products play an important role in the metabolism of acetone derived from propane oxidation and clarify the propane metabolism pathway of strain TY-5 (propane → 2-propanol → acetone → methyl acetate → acetic acid + methanol). This paper provides the first evidence for BVMO-dependent acetone metabolism. PMID:17071761

  3. 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.

  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-). Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Tuberculosis-like pneumonias by the aerobic actinomycetes Rhodococcus, Tsukamurella and Gordonia.

    PubMed

    Savini, Vincenzo; Fazii, Paolo; Favaro, Marco; Astolfi, Daniela; Polilli, Ennio; Pompilio, Arianna; Vannucci, Mariangela; D'Amario, Claudio; Di Bonaventura, Giovanni; Fontana, Carla; D'Antonio, Domenico

    2012-05-01

    The order Actinomycetales includes phylogenetically diverse but morphologically similar aerobic and anaerobic organisms, exhibiting filamentous branching structures which fragment into rods or coccoid forms. Lung pathogens of the order comprise Mycobacterium, Nocardia, Corynebacterium, Actinomyces, Kytococcus, Rothia, Williamsia, as well as Gordonia, Tsukamurella and Rhodococcus. Particularly, members of the last three genera are uncommon aerobic agents of lung cavitations and tuberculosis(TB)-like syndromes, that should be carefully considered in the aetiology of parenchymal lesions. Correct identification of such organisms is hard to obtain, but is crucial to provide patients with adequate diagnose and treatment. Then, this review aims to unearth their airway tropism, as well as their clinical impact as agents of lung disease. Copyright © 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  6. Carotenoids in a Corynebacterineae, Gordonia terrae AIST-1: carotenoid glucosyl mycoloyl esters.

    PubMed

    Takaichi, Shinichi; Maoka, Takashi; Akimoto, Naoshige; Carmona, Marvelisa L; Yamaoka, Yukiho

    2008-10-01

    We isolated a strain of Corynebacterineae from surface seawater from the Inland Sea of Japan. This strain, AIST-1, was determined to be a strain of Gordonia terrae based on its 16S rRNA gene sequence. The colony was red-colored, and the pigments were identified to be carotenoid derivatives. The structures of two major carotenoids were (2'S)-deoxymyxol 1'-glucoside, a dihydroxyl derivative of gamma-carotene with 12 conjugated double bonds, and (2'S)-4-ketodeoxymyxol 1'-glucoside. Their glucosyl acyl esters and mycoloyl esters were also identified. While these carotenoid moieties have been found in only a few other bacteria, the carotenoid mycoloyl esters are novel carotenoid derivatives. The type strain of G. terrae NBRC 10016T also contained the same carotenoids, but the composition of the two carotenoid glucosides was low and the total carotenoid content was less than one tenth of that of strain AIST-1.

  7. Characterization of Gordonia sp. strain CC-NAPH129-6 capable of naphthalene degradation.

    PubMed

    Lin, Chun-Liang; Shen, Fo-Ting; Tan, Chen-Chung; Huang, Chieh-Chen; Chen, Bang-Yuan; Arun, A B; Young, Chiu-Chung

    2012-07-25

    A naphthalene-degrading isolate able to utilize naphthalene as a sole carbon source was identified as Gordonia sp. CC-NAPH129-6. Here a detail characterization of the naphthalene catabolic genes present in this strain was conducted. In nar region four structural genes (narAa, narAb, narB, narC), two regulatory genes (narR1, narR2), a rubredoxin encoding gene (rub1) and a gene (orf7) with unknown function were obtained. When compared with most of the members within naphthalene-degrading Rhodococcus, these naphthalene catabolic genes in strain CC-NAPH129-6 were organized into an operon-like gene cluster and present in the same order. This naphthalene gene cluster located in a 97-kb small plasmid of strain CC-NAPH129-6, as can be seen from the PFGE and Southern blot hybridization data. Besides, a partial transposase sequence containing an IS element structure with 12-nt inverted repeat at both ends was found, which was flanked by direct repeats downstream the narC gene in strain CC-NAPH129-6. This novel transposase gene sequence was unlike to the transposase sequence found between narR2 and rub1 genes in Rhodococcus opacus R7. The comparative analyses of the naphthalene catabolic genes, 16S rRNA and gyrB gene present in strain CC-NAPH129-6 and naphthalene-degrading Rhodococcus species imply that the naphthalene catabolic genes in strain CC-NAPH129-6 might be horizontally transferred from Rhodococcus members. This is the first report demonstrating that naphthalene catabolic genes organized into an operon-like gene cluster in the genus Gordonia, and this might provide evidence of the importance of this actinobacterial lineage in the bioremediation of oil-contaminated soils. Copyright © 2011 Elsevier GmbH. All rights reserved.

  8. Synthesis of vanillic acid using whole cell nitrilase of wild and mutant Gordonia terrae.

    PubMed

    Bhalla, Tek Chand; Prashant; Kumari, Nisha; Kumar, Vijay; Kumar, Virender; Savitri

    2016-01-01

    The resting cells of Gordonia terrae mutant E9 having enhanced nitrilase activity were used for biotransformation of 4-hydroxy-3-methoxybenzonitrile into vanillic acid. The maximum conversion was observed in 0.1 M phosphate buffer (pH 8.0), using 60 mM substrate and 0.75 mgDCW resting cells in 1 mL reaction at 40 °C. Km of the whole cell nitrilase of wild and mutant strains of G. terrae for this substrate were 20 and 16.6 mM, and Vmax were 0.19 and 0.95 Umg(-1)(DCW), respectively. Fed batch reaction for transformation of 4-hydroxy-3-methoxybenzonitrile using whole cell nitrilase of wild G. terrae resulted in 2.36 g of vanillic acid in 5 h with a catalytic and volumetric productivity of 0.78 gg(-1)(DCW) h(-1) and 4.72 gL(-1)h(-1), respectively. The whole cell nitrilase of G. terrae mutant E9 resulted in higher catalytic and volumetric productivity, i.e., 1.68 gg(-1)DCW h(-1) and 10 gL(-1)h(-1). A total 5.04 g of vanillic acid with 99% purity were accumulated in 100 mL of reaction after 5 h.

  9. Biological devulcanization of ground natural rubber by Gordonia desulfuricans DSM 44462(T) strain.

    PubMed

    Tatangelo, Valeria; Mangili, Ivan; Caracino, Paola; Anzano, Manuela; Najmi, Ziba; Bestetti, Giuseppina; Collina, Elena; Franzetti, Andrea; Lasagni, Marina

    2016-10-01

    Due to the rapid increase of waste vulcanized rubber products, the development of low-cost, efficient, and selective devulcanization processes is needed. In this paper, the devulcanization ability of Gordonia desulfuricans DSM 44462(T) was evaluated by a design of experiments. The aim of the experimental design was to investigate the importance of parameters influencing the bacterial growth, such as the glucose concentration (C), dibenzothiophene concentration (DBT), and initial biomass (optical density, OD) in biodevulcanization process. The complex viscosity (η*) was chosen as experimental response for the experimental design. A multiple linear regression was used to model the relationship between the response and the process variables. In addition, the crosslink density and gel fraction were measured. Furthermore, the automated ribosomal intergenic spacer analysis (ARISA) as a microbiological method was performed to assess the persistence of the inoculated strain during the experiments. Reduced regression models were obtained considering only the significant variables and interactions. The glucose concentration C and OD variables and C-DBT and DBT-OD interactions resulted to the relevant parameters for the process. The fingerprinting showed the persistence of G. desulfuricans DSM 44462(T), despite the presence of other bacterial population after the VGNR sterilization. These results highlight the importance to support the physics analysis with microbiological analyses to evaluate the bacterial persistence during the treatment.

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

    PubMed Central

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

    2013-01-01

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

  11. Potential applications of surface active compounds by Gordonia sp. strain BS29 in soil remediation technologies.

    PubMed

    Franzetti, Andrea; Caredda, Paolo; Ruggeri, Claudio; La Colla, Paolo; Tamburini, Elena; Papacchini, Maddalena; Bestetti, Giuseppina

    2009-05-01

    A wide range of structurally different surface active compounds (SACs) is synthesised by many prokaryotic and eukaryotic microorganisms. Due to their properties, microbial SACs have been exploited in environmental remediation techniques. From a diesel-contaminated soil, we isolated the Gordonia sp. strain BS29 which extensively grows on aliphatic hydrocarbons and produces two different types of SACs: extracellular bioemulsans and cell-bound biosurfactants. The aim of this work was to evaluate the potential applications of the strain BS29 and its SACs in the following environmental technologies: bioremediation of soils contaminated by aliphatic and aromatic hydrocarbons, and washing of soils contaminated by crude oil, polycyclic aromatic hydrocarbons (PAHs) and heavy metals. Microcosm bioremediation experiments were carried out with soils contaminated by aliphatic hydrocarbons or PAHs, while batch soil washing experiments were carried out with soils contaminated by crude oil, PAHs or heavy metals. Bioremediation results showed that the BS29 bioemulsans are able to slightly enhance the biodegradation of recalcitrant branched hydrocarbons. On the other hand, we obtained the best results in soil washing of hydrocarbons. The BS29 bioemulsans effectively remove crude oil and PAHs from soil. Particularly, crude oil removal by BS29 bioemulsans is comparable to the rhamnolipid one in the same experimental conditions showing that the BS29 bioemulsans are promising washing agents for remediation of hydrocarbon-contaminated soils.

  12. 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

    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.

  13. 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

  14. Involvement of an alkane hydroxylase system of Gordonia sp. strain SoCg in degradation of solid n-alkanes.

    PubMed

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

    2011-02-01

    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 (C(12)) to hexatriacontane (C(36)) 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.

  15. Degradation of Di(2-Ethylhexyl) Phthalate by a Novel Gordonia alkanivorans Strain YC-RL2.

    PubMed

    Nahurira, Ruth; Ren, Lei; Song, Jinlong; Jia, Yang; Wang, Junhuan; Fan, Shuanghu; Wang, Haisheng; Yan, Yanchun

    2017-03-01

    One bacterial strain, YC-RL2, isolated from petroleum-contaminated soil, could utilize environmental hormone Di(2-Ethylhexyl) phthalate (DEHP) as a sole carbon source for growth. Strain YC-RL2 was identified as Gordonia alkanivorans by 16S rRNA gene analysis and Biolog tests. The effects of environmental factors which might affect the degrading process were optimized at 30 °C and pH 8.0. Strain YC-RL2 showed superior halotolerance and could tolerate up to 0-5% NaCl in trace element medium supplemented with DEHP, although the DEHP degradation rates slowed as NaCl concentration increased. It also showed an outstanding performance in a wide range of pH (6.0-11.0). Meanwhile, strain YC-RL2 was able to withstand high concentrations of DEHP (from 100 to 800 mg/L), and the degradation rates were all above 94%. The DEHP intermediates were detected by HPLC-MS, and the degradation pathway was deduced tentatively. DEHP was transformed into phthalic acid (PA) via mono (2-ethylhexyl) phthalate (MEHP), and PA was further utilized for growth via benzoic acid (BA). The enzyme expected to catalyze the hydrolysis of MEHP to PA was identified from strain YC-RL2. Further investigation found that the enzyme could catalyze the transformation of a wide range of monoalkyl phthalates to PA. This study is the first report about species G. alkanivorans which could degrade several kinds of phthalic acid esters (PAEs), and indicates its application potential for bioremediation of PAE-polluted sites.

  16. Improved identification of Gordonia, Rhodococcus and Tsukamurella species by 5'-end 16S rRNA gene sequencing.

    PubMed

    Wang, Tao; Kong, Fanrong; Chen, Sharon; Xiao, Meng; Sorrell, Tania; Wang, Xiaoyan; Wang, Shuo; Sintchenko, Vitali

    2011-01-01

    The identification of fastidious aerobic Actinomycetes such as Gordonia, Rhodococcus, and Tsukamurella has remained a challenge leading to clinically significant misclassifications. This study is intended to examine the feasibility of partial 5'-end 16S rRNA gene sequencing for the identification of Gordonia, Rhodococcus, and Tsukamurella, and defined potential reference sequences for species from each of these genera. The 16S rRNA gene sequence based identification algorithm for species identification was used and enhanced by aligning test sequences with reference sequences from the List of Prokaryotic Names with Standing in Nomenclature. Conventional PCR based 16S rRNA gene sequencing and the alignment of the isolate 16S rRNA gene sequence with reference sequences accurately identified 100% of clinical strains of aerobic Actinomycetes. While partial 16S rRNA gene sequences of reference type strains matched with the 16S rRNA gene sequences of 19 isolates in our data set, another 13 strains demonstrated a degree of polymorphism with a 1-4 bp difference in the regions of difference. 5'-end 606 bp 16S rRNA gene sequencing, coupled with the assignment of well defined reference sequences to clinically relevant species of bacteria, can be a useful strategy for improving the identification of clinically relevant aerobic Actinomycetes.

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

    PubMed Central

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

    2011-01-01

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

  18. Microwave-Assisted Extraction of Natural Antioxidants from the Exotic Gordonia axillaris Fruit: Optimization and Identification of Phenolic Compounds.

    PubMed

    Li, Ya; Li, Sha; Lin, Sheng-Jun; Zhang, Jiao-Jiao; Zhao, Cai-Ning; Li, Hua-Bin

    2017-09-06

    Our previous study reported that the fruit of Gordonia axillaris , an edible wild fruit, possessed strong antioxidant activity. In this study, a microwave-assisted extraction (MAE) method was established to extract antioxidants from the fruit of Gordonia axillaris . The influence of five parameters, including ethanol concentration, solvent/material ratio, extraction time, extraction temperature and microwave power, was investigated by single-factor experiments. Three factors, namely ethanol concentration, solvent/material ratio, extraction time, were found to exert a major influence on extraction efficacy, and were further studied by response surface methodology to investigate their interactions. Ethanol concentration of 36.89%, solvent/material ratio of 29.56 mL/g, extraction time of 71.04 min, temperature of 40 °C, and microwave power of 400 W were found to be the optimal condition. The TEAC value was 198.16 ± 5.47 µmol Trolox/g DW under the optimal conditions, which was in conformity to the predicted value (200.28 µmol Trolox/g DW). In addition, the MAE method was compared with two conventional methods (Soxhlet extraction and maceration extraction). Results showed that the antioxidant capacity of the extract obtained by MAE method was stronger than that obtained by maceration (168.67 ± 3.88 µmol Trolox/g DW) or Soxhlet extraction (114.09 ± 2.01 µmol Trolox/g DW). Finally, several phenolic compounds in the extract were identified and quantified by UPLC-MS/MS, which were rutin, gallic acid, protocatechuic acid, epicatechin, epicatechin gallate, 2-hydrocinnamic acid, p -coumaric acid, quercetin, chlorogenic acid and ferulic acid.

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

    PubMed Central

    Tillett, Daniel; Seviour, Robert J.

    2012-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  1. 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

  2. Characterization of Gordonia sp. strain F.5.25.8 capable of dibenzothiophene desulfurization and carbazole utilization.

    PubMed

    Santos, S C C; Alviano, D S; Alviano, C S; Pádula, M; Leitão, A C; Martins, O B; Ribeiro, C M S; Sassaki, M Y M; Matta, C P S; Bevilaqua, J; Sebastián, G V; Seldin, L

    2006-07-01

    A dibenzothiophene (DBT)-degrading bacterial strain able to utilize carbazole as the only source of nitrogen was identified as Gordonia sp. F.5.25.8 due to its 16S rRNA gene sequence and phenotypic characteristics. Gas chromatography (GC) and GC-mass spectroscopy analyses showed that strain F.5.25.8 transformed DBT into 2-hydroxybiphenyl (2-HBP). This strain was also able to grow using various organic sulfur or nitrogen compounds as the sole sulfur or nitrogen sources. Resting-cell studies indicated that desulfurization occurs either in cell-associated or in cell-free extracts of F.5.25.8. The biological responses of F.5.25.8 to a series of mutagens and environmental agents were also characterized. The results revealed that this strain is highly tolerant to DNA damage and also refractory to induced mutagenesis. Strain F.5.25.8 was also characterized genetically. Results showed that genes involved in desulfurization (dsz) are located in the chromosome, and PCR amplification was observed with primers dszA and dszB designed based on Rhodococcus genes. However, no amplification product was observed with the primer based on dszC.

  3. 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.

  4. Down-regulation of NF-κB signaling by Gordonia bronchialis prevents the activation of gut epithelial cells.

    PubMed

    Smaldini, Paola L; Stanford, John; Romanin, David E; Fossati, Carlos A; Docena, Guillermo H

    2014-08-01

    The immunomodulatory power of heat-killed Gordonia bronchialis was studied on gut epithelial cells activated with pro-inflammatory stimuli (flagellin, TNF-α or IL-1β). Light emission of luciferase-transfected epithelial cells and mRNA expression of IL-1β, TNF-α, IL-6, CCL20, IL-8 and MCP-1 were measured. NF-κB activation was assessed by immunofluorescence and immunoblotting, and induction of reactive oxygen species (ROS) was evaluated. In vivo inhibitory properties of G. bronchialis were studied with ligated intestinal loop assay and in a mouse model of food allergy. G. bronchialis promoted the down-regulation of the expression of CCL20 and IL-1β on activated epithelial cells in a dose-dependent manner. A concomitant blocking of nuclear p65 translocation with increased production of ROS was found. In vivo experiments confirmed the inhibition of CCL20 expression and the suppression of IgE sensitization and hypersensitivity symptoms in the food allergy mouse model. In conclusion, heat-killed G. bronchialis inhibited the activation of NF-κB pathway in human epithelial cells, and suppressed the expression of CCL20. These results indicate that G. bronchialis may be used to modulate the initial steps of innate immune activation, which further suppress the allergic sensitization. This approach may be exploited as a therapy for intestinal inflammation. © The Author(s) 2013 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  5. Interaction of operational and physicochemical factors leading to Gordonia amarae-like foaming in an incompletely nitrifying activated sludge plant.

    PubMed

    Asvapathanagul, Pitiporn; Huang, Zhonghua; Gedalanga, Phillip B; Baylor, Amber; Olson, Betty H

    2012-12-01

    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 × 10(9) 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 (10(7) cells liter(-1)) allows management strategies to prevent foaming.

  6. 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

  7. Carotenoid stabilized gold and silver nanoparticles derived from the Actinomycete Gordonia amicalis HS-11 as effective free radical scavengers.

    PubMed

    Sowani, Harshada; Mohite, Pallavi; Damale, Shailesh; Kulkarni, Mohan; Zinjarde, Smita

    2016-12-01

    The Actinomycete Gordonia amicalis HS-11 produced orange pigments when cultivated on n-hexadecane as the sole carbon source. When cells of this pigmented bacterium were incubated with 1mM chloroauric acid (HAuCl4) or silver nitrate (AgNO3), pH 9.0, at 25°C, gold and silver nanoparticles, respectively, were obtained in a cell associated manner. It was hypothesized that the pigments present in the cells may be mediating metal reduction reactions. After solvent extraction and High Performance Liquid Chromatography, two major pigments displaying UV-vis spectra characteristic of carotenoids were isolated. These were identified on the basis of Atmospheric Pressure Chemical Ionization Mass Spectrometry (APCI-MS) in the positive mode as 1'-OH-4-keto-γ-carotene (Carotenoid K) and 1'-OH-γ-carotene (Carotenoid B). The hydroxyl groups present in the carotenoids were eliminated under alkaline conditions and provided the reducing equivalents necessary for synthesizing nanoparticles. Cell associated and carotenoid stabilized nanoparticles were characterized by different analytical techniques. In vitro free radical scavenging activities of cells (control, gold and silver nanoparticle loaded), purified carotenoids and carotenoid stabilized gold and silver nanoparticles were evaluated. Silver nanoparticle loaded cells and carotenoid stabilized silver nanoparticles exhibited improved nitric oxide (NO) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging activities compared to their control and gold counterparts. This paper thus reports cell associated nanoparticle synthesis by G. amicalis, describes for the first time the role of carotenoid pigments in metal reduction processes and demonstrates enhanced free radical scavenging activities of the carotenoid stabilized nanoparticles. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Genomic and proteomic characterization of Gordonia sp. NB4-1Y in relation to 6 : 2 fluorotelomer sulfonate biodegradation.

    PubMed

    Van Hamme, Jonathan D; Bottos, Eric M; Bilbey, Nicholas J; Brewer, Sharon E

    2013-08-01

    Gordonia sp. strain NB4-1Y was isolated from vermicompost using bis-(3-pentafluorophenylpropyl)-sulfide as the sole added sulfur source and was found to have a broad capacity for metabolizing organosulfur compounds. NB4-1Y is closely related to G. desulfuricans and was found to metabolize 6 : 2 fluorotelomer sulfonate (6 : 2 FTS) to 5 : 3 fluorotelomer acid (5 : 3 acid) via 6 : 2 fluorotelomer acid (6 : 2 FTCA), 6 : 2 unsaturated fluorotelomer acid (6 : 2 FTUCA) and 5 : 3 unsaturated fluorotelomer acid (5 : 3 Uacid). Given that the molecular and biochemical basis for the microbial metabolism of poly- and per-fluorinated compounds has yet to be examined, we undertook to investigate 6 : 2 FTS metabolism in NB4-1Y. To this end, a whole-genome shotgun sequence was prepared and two-dimensional differential in-gel electrophoresis was used to compare proteomes of MgSO4- and 6 : 2 FTS-grown cells. Of the three putative alkanesulfonate monooxygenases, four nitrilotriacetate monooxygenases and one taurine dioxygenase located in the draft genome, two nitrilotriacetate monooxygenases were differentially expressed in the presence of 6 : 2 FTS. It is hypothesized that these two enzymes may be responsible for 6 : 2 FTS desulfonation. In addition, a differentially expressed putative double bond reductase may be involved in the reduction of 5 : 3 Uacid to 5 : 3 acid. Other proteins differentially expressed during 6 : 2 FTS metabolism included a sulfate ABC transporter ATP-binding protein and two alkyl hydroperoxide reductases. This work establishes a foundation for future studies on the molecular biology and biochemistry of poly- and per-fluorinated compound metabolism in bacteria.

  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. [Isolation and identification of a PAHs-degrading strain Gordonia sp. He4 and its dynamics during bioremediation of phenanthrene polluted soil].

    PubMed

    Liu, Lei; Li, Xi-Wu; Liu, Shuang-Jiang; Liu, Zhi-Pei

    2007-03-01

    A bacterial strain, He4, capable of degrading n-hexadecane and other polycyclic aromatic compounds was isolated from petroleum polluted soil. This strain was identified as Gordonia sp. He4 according to its morphology, physiological, biochemical properties and the analysis of its 16S rRNA gene sequence. Based on its 16S rRNA gene sequence, specific primers were designed and a competitor template was amplified by PCR. The dynamics of strain He4 in phenanthrene polluted soil was analyzed by colony forming unit (CFU) method and QC-PCR method. The results showed that partial of He4 become non-culturable and un-detectable by CFU method. But by using QC-PCR, the population density of strain He4 could be measured accurately.

  11. 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

  12. 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

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

    2014-07-01

    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. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  13. 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

  14. 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.

  15. Biodegradation of ethyl t-butyl ether (ETBE), methyl t-butyl ether (MTBE) and t-amyl methyl ether (TAME) by Gordonia terrae.

    PubMed

    Hernandez-Perez, G; Fayolle, F; Vandecasteele, J P

    2001-01-01

    Gordonia terrae strain IFP 2001 was selected from activated sludge for its capacity to grow on ethyl t-butyl ether (ETBE) as sole carbon and energy source. ETBE was stoichiometrically degraded to t-butyl alcohol (TBA) and the activity was inducible. A constitutive strain, G. terrae IFP 2007, derived from strain IFP 2001, was also selected. Methyl t-butyl ether (MTBE) and t-amyl methyl ether (TAME) were not used as carbon and energy sources by the two strains, but cometabolic degradation of MTBE and TAME was demonstrated, to TBA and t-amyl alcohol (TAA) respectively, in the presence of a carbon source such as ethanol. No two-carbon compound was detected during growth on ETBE, but formate was produced during cometabolic degradation of MTBE or TAME. A monooxygenase was involved in the degradation of ethers, because no degradation of ETBE was observed under anaerobic conditions and the presence of a cytochrome P-450 was demonstrated in G. terrae IFP 2001 after induction by cultivation on ETBE.

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

    PubMed Central

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

    2005-01-01

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

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

    PubMed

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

    2015-01-01

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

  18. Ecology and management of tansy ragwort (Senecio jacobaea L.)

    Treesearch

    Jim Jacobs; Sharlene Sing

    2009-01-01

    Tansy ragwort, a member of the Asteraceae taxonomic family, is a large biennial or short-lived perennial herb native to and widespread throughout Europe and Asia. Stems can grow to a height of 5.5 feet (1.75 meters), with the lower half simple and the upper half many-branched at the inflorescence. Reproductive stems produce up to 2,500 bright golden-yellow flowers....

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

    PubMed Central

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

    2010-01-01

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

  20. Biological control of tansy ragwort (Senecio jacobaeae, L.) by the Cinnabar moth, Tyria jacobaeae (CL) (Lepidoptera: Arctiidae), in the northern Rockies

    Treesearch

    G. P. Markin; J. L. Littlefield

    2008-01-01

    The control of tansy ragwort on the coast of western North America is a major success story for weed biological control. However, tansy ragwort is still expanding into the colder interior regions of the Pacific Northwest of the United States where previous efforts to establish the same complex of agents have failed. We have successfully established one of the...

  1. 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.

  2. 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.

  3. 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

  4. 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...

  5. 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...

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

    USDA-ARS?s Scientific Manuscript database

    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:...

  7. The effectiveness of management interventions used to control ragwort species.

    PubMed

    Roberts, P D; Pullin, A S

    2007-05-01

    Ragwort (Senecio jacobaea and S. aquaticus) causes major losses to agricultural revenue and induces livestock morbidity throughout parts of Europe, North America, and Australasia. The introduction of legislation in the U.K. and Australia has meant that landowners can be prosecuted if the plant spreads to adjacent land, which has led to an increase in activities attempting to control these species. Commonly used interventions include natural enemies, herbicide applications, manual and mechanical removal. Through the use of explicit systematic methodology involving comprehensive searches and detailed inclusion criteria, data from primary research are collated for each type of intervention. Meta-analyses show that 2,4-D, Asulam, Clopyralid, and MCPA are effective at reducing ragwort densities. However, when the datasets were analysed for their effectiveness against individual species, 2,4-D and MCPA were only effective against S. jacobaea, while Asulam was only effective against S. aquaticus. Natural enemies Longitarsus jacobaeae and a combination of L. jacobaeae and Tyria jacobaeae appear to have the potential to reduce S. jacobaea densities. Only applying T. jacobaeae does not appear to significantly reduce S. jacobaea densities, but does reduce the number of capitula per plant, seeds per capitula, viability of seeds, and dry weight of the plants. There is insufficient experimental evidence available to assess other interventions such as manual or mechanical removal. Further research into these types of interventions is recommended, as well as more detailed reporting of site characteristics and experimental design to allow full investigation of each intervention to explain possible reasons for variations in their effectiveness.

  8. 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.

  9. Beef herd poisoning due to ingestion of tansy ragwort in southwestern Ontario

    PubMed Central

    Walsh, Robert B.; Dingwell, Randy T.

    2007-01-01

    Deaths attributed to Senecio jacobaea were investigated. The animal presented was a mature bull that was lethargic and dragging its feet. The bull was euthanized and 3 other cows died. Significantly, this disease has not been documented in Ontario before, and clinical signs of icterus or hepatoencephalopathy were not observed. PMID:17824160

  10. Modelling the long term effects of an introduced herbivore on spread of an invasive tree

    USDA-ARS?s Scientific Manuscript database

    Melaleuca quinquenervia (Cav.) Blake (hereafter melaleuca) is an invasive tree from Australia that has spread over the freshwater ecosystems of southern Florida, displacing native vegetation such as slash pine (Pinus elliottii), pond cypress (Taxodium ascendens), and loblolly bay (Gordonia lasianthu...

  11. Quantifying filamentous microorganisms in activated sludge before, during, and after an incident of foaming by oligonucleotide probe hybridizations and antibody staining.

    PubMed

    Oerther, D B; de los Reyes, F L; de los Reyes, M F; Raskin, L

    2001-10-01

    Quantitative oligonucleotide probe hybridizations, immunostaining, and a simple foaming potential test were used to follow an incident of seasonal filamentous foaming at the Urbana-Champaign Sanitary District, Northeast Wastewater Treatment Plant. A positive correlation was observed between an increase in foaming potential and the appearance of foam on the surfaces of aeration basins and secondary clarifiers. In addition, during the occurrence of foaming, the mass and activity of Gordonia spp. increased as measured by fluorescence in situ hybridization, antibody staining, and quantitative membrane hybridization of RNA extracts. An increase in Gordonia spp. rRNA levels from 0.25 to 1.4% of total rRNA was observed using quantitative membrane hybridizations, whereas during the same period, the fraction of mixed liquor volatile suspended solids attributed to Gordonia spp. increased from 4% to more than 32% of the total mixed liquor volatile suspended solids. These results indicate that both the activity and biomass level of Gordonia spp. in activated sludge increased relative to the activity aid the biomass level of the complete microbial community during a seasonal occurrence of filamentous foaming. Thus, Gordonia spp. may represent a numerically dominant but metabolically limited fraction of the total biomass, and the role of Gordonia spp. in filamentous foaming may be linked more tightly to the physical presence of filamentous microorganisms than to the metabolic activity of the cells.

  12. 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

  13. 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.

  14. Removal Capacities of Polycyclic Aromatic Hydrocarbons (PAHs) by a Newly Isolated Strain from Oilfield Produced Water.

    PubMed

    Qi, Yi-Bin; Wang, Chen-Yu; Lv, Cheng-Yuan; Lun, Zeng-Min; Zheng, Cheng-Gang

    2017-02-22

    The polycyclic aromatic hydrocarbon (PAH)-degrading strain Q8 was isolated from oilfield produced water. According to the analysis of a biochemical test, 16S rRNA gene, house-keeping genes and DNA-DNA hybridization, strain Q8 was assigned to a novel species of the genus Gordonia. The strain could not only grow in mineral salt medium (MM) and utilize naphthalene and pyrene as its sole carbon source, but also degraded mixed naphthalene, phenanthrene, anthracene and pyrene. The degradation ratio of these four PAHs reached 100%, 95.4%, 73.8% and 53.4% respectively after being degraded by Q8 for seven days. A comparative experiment found that the PAHs degradation efficiency of Q8 is higher than that of Gordonia alkaliphila and Gordonia paraffinivorans, which have the capacities to remove PAHs. Fourier transform infrared spectra, saturate, aromatic, resin and asphaltene (SARA) and gas chromatography-mass spectrometry (GC-MS) analysis of crude oil degraded by Q8 were also studied. The results showed that Q8 could utilize n-alkanes and PAHs in crude oil. The relative proportions of the naphthalene series, phenanthrene series, thiophene series, fluorene series, chrysene series, C21-triaromatic steroid, pyrene, and benz(a)pyrene were reduced after being degraded by Q8. Gordonia sp. nov. Q8 had the capacity to remediate water and soil environments contaminated by PAHs or crude oil, and provided a feasible way for the bioremediation of PAHs and oil pollution.

  15. Fatty acid methyl ester (FAME) technology for monitoring biological foaming in activated sludge: full scale plant verification.

    PubMed

    Lee, J W; Cha, D K; Kim, I; Son, A; Ahn, K H

    2008-02-01

    Fatty acid methyl ester (FAME) technology was evaluated as a monitoring tool for quantification of Gordonia amarae in activated sludge systems. The fatty acid, 19:1 alcohol, which was identified as a unique fatty acid in G. amarae was not only confirmed to be present in foaming plant samples, but the quantity of the signature peak correlated closely with the degree of foaming. Foaming potential experiment provided a range of critical foaming levels that corresponded to G. amarae population. This range of critical Gordonia levels was correlated to the threshold signature FAME amount. Six full-scale wastewater treatment plants were selected based on a survey to participate in our full-scale study to evaluate the potential application of the FAME technique as the Gordonia monitoring tool. Greater amounts of signature FAME were extracted from the mixed liquor samples obtained from treatment plants experiencing Gordonia foaming problems. The amounts of signature FAME correlated well with the conventional filamentous counting technique. These results demonstrated that the relative abundance of the signature FAMEs can be used to quantitatively monitor the abundance of foam-causing microorganism in activated sludge.

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

    PubMed Central

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

    2012-01-01

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

  17. Removal Capacities of Polycyclic Aromatic Hydrocarbons (PAHs) by a Newly Isolated Strain from Oilfield Produced Water

    PubMed Central

    Qi, Yi-Bin; Wang, Chen-Yu; Lv, Cheng-Yuan; Lun, Zeng-Min; Zheng, Cheng-Gang

    2017-01-01

    The polycyclic aromatic hydrocarbon (PAH)-degrading strain Q8 was isolated from oilfield produced water. According to the analysis of a biochemical test, 16S rRNA gene, house-keeping genes and DNA–DNA hybridization, strain Q8 was assigned to a novel species of the genus Gordonia. The strain could not only grow in mineral salt medium (MM) and utilize naphthalene and pyrene as its sole carbon source, but also degraded mixed naphthalene, phenanthrene, anthracene and pyrene. The degradation ratio of these four PAHs reached 100%, 95.4%, 73.8% and 53.4% respectively after being degraded by Q8 for seven days. A comparative experiment found that the PAHs degradation efficiency of Q8 is higher than that of Gordonia alkaliphila and Gordonia paraffinivorans, which have the capacities to remove PAHs. Fourier transform infrared spectra, saturate, aromatic, resin and asphaltene (SARA) and gas chromatography–mass spectrometry (GC–MS) analysis of crude oil degraded by Q8 were also studied. The results showed that Q8 could utilize n-alkanes and PAHs in crude oil. The relative proportions of the naphthalene series, phenanthrene series, thiophene series, fluorene series, chrysene series, C21-triaromatic steroid, pyrene, and benz(a)pyrene were reduced after being degraded by Q8. Gordonia sp. nov. Q8 had the capacity to remediate water and soil environments contaminated by PAHs or crude oil, and provided a feasible way for the bioremediation of PAHs and oil pollution. PMID:28241412

  18. Horizontal gene transfer (HGT) as a mechanism of disseminating RDX-degrading activity among Actinomycete bacteria.

    PubMed

    Jung, C M; Crocker, F H; Eberly, J O; Indest, K J

    2011-06-01

    Hexahydro-1,3,5-trinitro-1,3,5,-triazine (RDX) is a cyclic nitramine explosive that is a major component in many high-explosive formulations and has been found as a contaminant of soil and groundwater. The RDX-degrading gene locus xplAB, located on pGKT2 in Gordonia sp. KTR9, is highly conserved among isolates from disparate geographical locations suggesting a horizontal gene transfer (HGT) event. It was our goal to determine whether Gordonia sp. KTR9 is capable of transferring pGKT2 and the associated RDX degradation ability to other bacteria. We demonstrate the successful conjugal transfer of pGKT2 from Gordonia sp. KTR9 to Gordonia polyisoprenivorans, Rhodococcus jostii RHA1 and Nocardia sp. TW2. Through growth and RDX degradation studies, it was demonstrated that pGKT2 conferred to transconjugants the ability to degrade and utilize RDX as a nitrogen source. The inhibitory effect of exogenous inorganic nitrogen sources on RDX degradation in transconjugant strains was found to be strain specific. Plasmid pGKT2 can be transferred by conjugation, along with the ability to degrade RDX, to related bacteria, providing evidence of at least one mechanism for the dissemination and persistence of xplAB in the environment. These results provide evidence of one mechanism for the environmental dissemination of xplAB and provide a framework for future field relevant bioremediation practices. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology. No claim to US Government works.

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

    PubMed

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

    2000-03-15

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

  20. 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

  1. 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.

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

    PubMed

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

    2014-07-01

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

  3. 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.

  4. Plant species introduced by foreigners according to folk tradition in Norway and some other European countries: xenophobic tales or not?

    PubMed

    Alm, Torbjørn

    2015-10-05

    In their quest to understand and interpret nature, people have frequently sought religious or divine origins for plant species and their characteristics. Less often, historical events or persons are involved. This study comprises eleven cases of the latter kind, all claiming that plant species have been introduced by foreigners or at least from foreign lands. Based on literature data and a few cases recorded during my own ethnobotanical field work, eleven European examples of pseudo-historical plant origins are presented here, including Cakile maritima, Cicuta virosa, Lathyrus japonicus, Leymus arenarius, Primula vulgaris, and Scopolia carniolica in Norway, Heracleum mantegazzianum and/or H. persicum in Denmark, Phoenix dactylifera and P. theophrastii in Greece, and Jacobaea vulgaris in Scotland. The only common trait in these stories is that foreigner or at least foreign lands are claimed as sources of the plant species. In most cases, the "historical" explanations given in folk tradition are demonstrably at odds with reality. In those cases that involve poisonous or potentially harmful species (Cicuta virosa, Heracleum mantegazzianum and/or H. persicum, Jacobaea vulgaris), or the "useless" Phoenix theophrastii, with its inedible fruits, the stories may be interpreted as xenophobic, blaming foreigners for introducing dangerous or worthless species. The remaining examples merely suggest a search for exotic and seemingly rational, if erroneous, origins for plant species and stands that people considered strange and unusual. The spreading vectors assumed in folk tradition are correct and well documented, e.g. ship cargos (including goods and packing materials), which are responsible for introducing ballast plants and other anthropochores, and wartime activities, introducing a broad range of species (polemochores). They do not, however, apply to the species included in this study, which are either indigenous plants or introduced ornamentals. The foreigners appearing

  5. 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.

  6. 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

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

    PubMed

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

    2010-05-03

    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

  8. Investigating differences in the ability of XplA/B-containing bacteria to degrade the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX).

    PubMed

    Sabir, Dana Khdr; Grosjean, Nicolas; Rylott, Elizabeth L; Bruce, Neil C

    2017-08-01

    The xenobiotic hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a toxic explosive and environmental pollutant. This study examines three bacterial species that degrade RDX, using it as a sole source of nitrogen for growth. Although isolated from diverse geographical locations, the species contain near identical copies of genes encoding the RDX-metabolising cytochrome P450, XplA and accompanying reductase, XplB. Sequence analysis indicates a single evolutionary origin for xplA and xplB as part of a genomic island, which has been distributed around the world via horizontal gene transfer. Despite the fact that xplA and xplB are highly conserved between species, Gordonia sp. KTR9 and Microbacterium sp. MA1 degrade RDX more slowly than Rhodococcus rhodochrous 11Y. Both Gordonia sp. KTR9 and Microbacterium sp. MA1 were found to contain single base-pair mutations in xplB which, following expression and purification, were found to encode inactive XplB protein. Additionally, the Gordonia sp. KTR9 XplB was fused to glutamine synthetase, which would be likely to sterically inhibit XplB activity. Although the glutamine synthetase is fused to XplB and truncated by 71 residues, it was found to be active. Glutamine synthetase has been implicated in the regulation of nitrogen levels; controlling nitrogen availability will be important for effective bioremediation of RDX. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Tsukamurella tyrosinosolvens intravascular catheter-related bacteremia in a haematology patient: a case report.

    PubMed

    Karunakaran, R; Halim, H A; Ng, K P; Hanifah, Y A; Chin, E; Jaafar, F L; Abubakar, S

    2011-11-01

    Tsukamurella spp. are a rare but important cause of intravascular catheter-related bacteremia in immunocompromised patients. The organism is an aerobic, Gram-positive, weakly acid-fast bacillus that is difficult to differentiate using standard laboratory methods from other aerobic actinomycetales such as Nocardia spp., Rhododoccus spp., Gordonia spp., and the rapid growing Mycobacterium spp. We report a case of Tsukamurella tyrosinosolvens catheter-related bacteremia in a 51-year-old haematology patient who responded to treatment with imipenem and subsequent line removal. 16srRNA sequencing allowed for the prompt identification of this organism.

  10. Six New Record Species of Whiteflies (Hemiptera: Aleyrodidae) Infesting Morus alba in China

    PubMed Central

    Wang, Ji-Rui; Song, Zao-Qin; Du, Yu-Zhou

    2014-01-01

    To determine the species of whiteflies occurring on mulberry, Morus alba L. (Rosales: Moraceae) in China, we collected samples in more than 87 sites in 16 provinces of China from 2008 to 2011. In total, 10 species, representing seven genera of the subfamily Aleyrodinae, were identified. Of these, six species are newly recorded on mulberry in China, namely, Aleuroclava ficicola Takahashi, Aleuroclava gordoniae (Takahashi), Aleurotrachelus camelliae (Kuwana), Bemisia afer (Priesner & Hosny), Bemisia tabaci Gennadius, and Pealius machili Takahashi. Information on the taxonomy, distribution, and host plants of the whitefly species found on mulberry in China, along with a brief description and illustrations of each species are provided. PMID:25368095

  11. Six new record species of whiteflies (Hemiptera: Aleyrodidae) infesting Morus alba in China.

    PubMed

    Wang, Ji-Rui; Song, Zao-Qin; Du, Yu-Zhou

    2014-01-01

    To determine the species of whiteflies occurring on mulberry, Morus alba L. (Rosales: Moraceae) in China, we collected samples in more than 87 sites in 16 provinces of China from 2008 to 2011. In total, 10 species, representing seven genera of the subfamily Aleyrodinae, were identified. Of these, six species are newly recorded on mulberry in China, namely, Aleuroclava ficicola Takahashi, Aleuroclava gordoniae (Takahashi), Aleurotrachelus camelliae (Kuwana), Bemisia afer (Priesner & Hosny), Bemisia tabaci Gennadius, and Pealius machili Takahashi. Information on the taxonomy, distribution, and host plants of the whitefly species found on mulberry in China, along with a brief description and illustrations of each species are provided.

  12. 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.

  13. 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.

  14. Characterisation of hexane-degrading microorganisms in a biofilter by stable isotope-based fatty acid analysis, FISH and cultivation.

    PubMed

    Friedrich, Michèle M; Lipski, André

    2010-01-01

    The hexane-degrading bacterial community of a biofilter was characterised by a combination of stable isotope-based phospholipid fatty acid analyses, fluorescence in situ hybridisation and cultivation. About 70 bacterial strains were isolated from a full-scale biofilter used for treatment of hexane containing waste gas of an oil mill. The isolation approach led to 16 bacterial groups, which were identified as members of the Alpha-, Beta- and Gammaproteobacteria, Actinobacteria and Firmicutes. Three groups showed good growth on hexane as the sole source of carbon. These groups were allocated to the genera Gordonia and Sphingomonas and to the Nevskia-branch of the Gammaproteobacteria. Actively degrading populations in the filter material were characterised by incubation of filter material samples with deuterated hexane and subsequent phospholipid fatty acid analysis. Significant labelling of the fatty acids 16:1 cis10, 18:1 cis9 and 18:0 10methyl affiliated the hexane-degrading activity of the biofilter with the isolates of the genus Gordonia. In vitro growth on hexane and in situ labelling of characteristic fatty acids confirmed the central role of these organisms in the hexane degradation within the full-scale biofilter.

  15. Identification and characterisation of isoprene-degrading bacteria in an estuarine environment.

    PubMed

    Johnston, Antonia; Crombie, Andrew T; El Khawand, Myriam; Sims, Leanne; Whited, Gregg M; McGenity, Terry J; Colin Murrell, J

    2017-09-01

    Approximately one-third of volatile organic compounds (VOCs) emitted to the atmosphere consists of isoprene, originating from the terrestrial and marine biosphere, with a profound effect on atmospheric chemistry. However, isoprene provides an abundant and largely unexplored source of carbon and energy for microbes. The potential for isoprene degradation in marine and estuarine samples from the Colne Estuary, UK, was investigated using DNA-Stable Isotope Probing (DNA-SIP). Analysis at two timepoints showed the development of communities dominated by Actinobacteria including members of the genera Mycobacterium, Rhodococcus, Microbacterium and Gordonia. Representative isolates, capable of growth on isoprene as sole carbon and energy source, were obtained from marine and estuarine locations, and isoprene-degrading strains of Gordonia and Mycobacterium were characterised physiologically and their genomes were sequenced. Genes predicted to be required for isoprene metabolism, including four-component isoprene monooxygenases (IsoMO), were identified and compared with previously characterised examples. Transcriptional and activity assays of strains growing on isoprene or alternative carbon sources showed that growth on isoprene is an inducible trait requiring a specific IsoMO. This study is the first to identify active isoprene degraders in estuarine and marine environments using DNA-SIP and to characterise marine isoprene-degrading bacteria at the physiological and molecular level. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  16. Interactions between Plant Metabolites Affect Herbivores: A Study with Pyrrolizidine Alkaloids and Chlorogenic Acid

    PubMed Central

    Liu, Xiaojie; Vrieling, Klaas; Klinkhamer, Peter G.L.

    2017-01-01

    The high structural diversity of plant metabolites suggests that interactions among them should be common. We investigated the effects of single metabolites and combinations of plant metabolites on insect herbivores. In particular we studied the interacting effects of pyrrolizidine alkaloid (PAs), and chlorogenic acid (CGA), on a generalist herbivore, Frankliniella occidentalis. We studied both the predominantly occurring PA N-oxides and the less frequent PA free bases. We found antagonistic effects between CGA and PA free bases on thrips mortality. In contrast PA N-oxides showed synergistic interactions with CGA. PA free bases caused a higher thrips mortality than PA N-oxides while the reverse was through for PAs in combination with CGA. Our results provide an explanation for the predominate storage of PA N-oxides in plants. We propose that antagonistic interactions represent a constraint on the accumulation of plant metabolites, as we found here for Jacobaea vulgaris. The results show that the bioactivity of a given metabolite is not merely dependent upon the amount and chemical structure of that metabolite, but also on the co-occurrence metabolites in, e.g., plant cells, tissues and organs. The significance of this study is beyond the concerns of the two specific groups tested here. The current study is one of the few studies so far that experimentally support the general conception that the interactions among plant metabolites are of great importance to plant-environment interactions. PMID:28611815

  17. Dietary pyrrolizidine (Senecio) alkaloids and tissue distribution of copper and vitamin A in broiler chickens.

    PubMed

    Huan, J; Cheeke, P R; Lowry, R R; Nakaue, H S; Snyder, S P; Whanger, P D

    1992-09-01

    The effect of feeding a diet containing 5% tansy ragwort (TR) (Senecio jacobaea), a poisonous plant containing pyrrolizidine alkaloids (PA), on the blood and liver levels of copper, zinc, iron and vitamin A in broiler chicks was examined. Serum and liver copper and liver iron concentrations were increased in chicks fed a diet with 5% TR, while serum and liver zinc and vitamin A decreased. When PA were removed from the diet, partial restoration of normal serum vitamin A level occurred, indicating that the ability to mobilize liver vitamin A is not irreversibly inhibited by PA. The decline in serum vitamin A occurred by 8 days of TR feeding with a concurrent decline in growth rate. When chicks were fed a diet high in vitamin A (25,000 IU/kg), followed by a basal diet containing TR, serum vitamin A levels were significantly (P < 0.01) decreased, while liver vitamin A level increased. This indicates that mobilization of previously stored vitamin A from the liver is impaired by PA. Prior feeding of a high vitamin A level resulted in protective effects against PA toxicity, as assessed by histopathology. This study shows that a dietary source of PA modifies metabolism and tissue distribution of minerals and vitamin A.

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

    PubMed

    Choi, Kyoung Su; Park, SeonJoo

    2015-11-10

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

  19. 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

  20. Possible Involvement of an Extracellular Superoxide Dismutase (SodA) as a Radical Scavenger in Poly(cis-1,4-Isoprene) Degradation▿

    PubMed Central

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

    2008-01-01

    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 MC2 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

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

    PubMed

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

    2015-09-01

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

  2. Thermal hydrolysis of secondary scum for control of biological foam.

    PubMed

    Jolis, Domènec; Marneri, Matina

    2006-08-01

    Thermal hydrolysis of secondary scum at 9 bars and 170 degrees C was shown to completely destroy Gordonia sp. cells and reduce its foaming potential, so that it can be recycled to headworks or sent to the solids-handling side of the plant without the risk of causing foaming problems in the activated sludge system and anaerobic digesters. This process shows promise for biological foam control in wastewater treatment plants where solids retention time control and selective wasting cannot be applied and/or selector installation is not possible. An initial cost comparison of thermal hydrolysis and several widely accepted foam-management strategies shows it to be competitive; however, optimization of operating pressure and temperature is necessary.

  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.

  4. Three of a Kind: Genetically Similar Tsukamurella Phages TIN2, TIN3, and TIN4.

    PubMed

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

    2015-10-01

    Three Tsukamurella phages, TIN2, TIN3, and TIN4, were isolated from activated sludge treatment plants located in Victoria, Australia, using conventional enrichment techniques. Illumina and 454 whole-genome sequencing of these Siphoviridae viruses revealed that they had similar genome sequences, ranging in size between 76,268 bp and 76,964 bp. All three phages shared 74% nucleotide sequence identity to the previously described Gordonia phage GTE7. Genome sequencing suggested that phage TIN3 had suffered a mutation in one of its lysis genes compared to the sequence of phage TIN4, to which it is genetically very similar. Mass spectroscopy data showed the unusual presence of a virion structural gene in the DNA replication module of phage TIN4, disrupting the characteristic modular genome architecture of Siphoviridae phages. All three phages appeared highly virulent on strains of Tsukamurella inchonensis and Tsukamurella paurometabola. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  5. Insights on the Effects of Heat Pretreatment, pH, and Calcium Salts on Isolation of Rare Actinobacteria from Karstic Caves.

    PubMed

    Fang, Bao-Zhu; Salam, Nimaichand; Han, Ming-Xian; Jiao, Jian-Yu; Cheng, Juan; Wei, Da-Qiao; Xiao, Min; Li, Wen-Jun

    2017-01-01

    The phylum Actinobacteria is one of the most ubiquitously present bacterial lineages on Earth. In the present study, we try to explore the diversity of cultivable rare Actinobacteria in Sigangli Cave, Yunnan, China by utilizing a combination of different sample pretreatments and under different culture conditions. Pretreating the samples under different conditions of heat, setting the isolation condition at different pHs, and supplementation of media with different calcium salts were found to be effective for isolation of diverse rare Actinobacteria. During our study, a total of 204 isolates affiliated to 30 genera of phylum Actinobacteria were cultured. Besides the dominant Streptomyces, rare Actinobacteria of the genera Actinocorallia, Actinomadura, Agromyces, Alloactinosynnema, Amycolatopsis, Beutenbergia, Cellulosimicrobium, Gordonia, Isoptericola, Jiangella, Knoellia, Kocuria, Krasilnikoviella, Kribbella, Microbacterium, Micromonospora, Mumia, Mycobacterium, Nocardia, Nocardioides, Nocardiopsis, Nonomuraea, Oerskovia, Pseudokineococcus, Pseudonocardia, Rhodococcus, Saccharothrix, Streptosporangium, and Tsukamurella were isolated from these cave samples.

  6. Insights on the Effects of Heat Pretreatment, pH, and Calcium Salts on Isolation of Rare Actinobacteria from Karstic Caves

    PubMed Central

    Fang, Bao-Zhu; Salam, Nimaichand; Han, Ming-Xian; Jiao, Jian-Yu; Cheng, Juan; Wei, Da-Qiao; Xiao, Min; Li, Wen-Jun

    2017-01-01

    The phylum Actinobacteria is one of the most ubiquitously present bacterial lineages on Earth. In the present study, we try to explore the diversity of cultivable rare Actinobacteria in Sigangli Cave, Yunnan, China by utilizing a combination of different sample pretreatments and under different culture conditions. Pretreating the samples under different conditions of heat, setting the isolation condition at different pHs, and supplementation of media with different calcium salts were found to be effective for isolation of diverse rare Actinobacteria. During our study, a total of 204 isolates affiliated to 30 genera of phylum Actinobacteria were cultured. Besides the dominant Streptomyces, rare Actinobacteria of the genera Actinocorallia, Actinomadura, Agromyces, Alloactinosynnema, Amycolatopsis, Beutenbergia, Cellulosimicrobium, Gordonia, Isoptericola, Jiangella, Knoellia, Kocuria, Krasilnikoviella, Kribbella, Microbacterium, Micromonospora, Mumia, Mycobacterium, Nocardia, Nocardioides, Nocardiopsis, Nonomuraea, Oerskovia, Pseudokineococcus, Pseudonocardia, Rhodococcus, Saccharothrix, Streptosporangium, and Tsukamurella were isolated from these cave samples. PMID:28848538

  7. Three of a Kind: Genetically Similar Tsukamurella Phages TIN2, TIN3, and TIN4

    PubMed Central

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

    2015-01-01

    Three Tsukamurella phages, TIN2, TIN3, and TIN4, were isolated from activated sludge treatment plants located in Victoria, Australia, using conventional enrichment techniques. Illumina and 454 whole-genome sequencing of these Siphoviridae viruses revealed that they had similar genome sequences, ranging in size between 76,268 bp and 76,964 bp. All three phages shared 74% nucleotide sequence identity to the previously described Gordonia phage GTE7. Genome sequencing suggested that phage TIN3 had suffered a mutation in one of its lysis genes compared to the sequence of phage TIN4, to which it is genetically very similar. Mass spectroscopy data showed the unusual presence of a virion structural gene in the DNA replication module of phage TIN4, disrupting the characteristic modular genome architecture of Siphoviridae phages. All three phages appeared highly virulent on strains of Tsukamurella inchonensis and Tsukamurella paurometabola. PMID:26187971

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

    PubMed Central

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

    2009-01-01

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

  9. Improved outcome of Trypanosoma cruzi infection in rats following treatment in early life with suspensions of heat-killed environmental Actinomycetales.

    PubMed

    Fontanella, G H; Pascutti, M F; Daurelio, L; Perez, A R; Nocito, A L; Wojdyla, D; Bottasso, O; Revelli, S S; Stanford, J L

    2007-04-30

    The well-established model of Chagas' disease in "l" rats was used to evaluate the effects of three injections of heat-killed Gordonia bronchialis, Rhodococcus coprophilus or saline on Trypanosoma cruzi parasitaemia and acute and chronic myocarditis, sequelae of the infection. Two vaccinating injections were given prior to challenge with T. cruzi, and the third, immunotherapeutic, injection was given 7 days after challenge. Treatment with either actinomycete significantly reduced acute parasitaemia (p<0.04), modified cellular infiltration during acute myocarditis and limited chronic myocarditis (p<0.03) in comparison with the saline-treated control animals. Immunological investigations showed that both bacterial preparations achieved their results through different mechanisms. The relevance of our findings to human Chagas' disease is discussed.

  10. [Microbial diversity in scorpion intestine (Buthus martensii Karsch)].

    PubMed

    Wang, Bao-Jun; Liu, Ying; Jiang, Jia-Tong; Liu, Bin; Liu, Shuang-Jiang

    2007-10-01

    Scorpion is an important officinal animal, and has a high nutritional value. In this study, the culture-independent and culture-dependent methods were used to investigate the microbial diversity in the scorpion's intestine. Results based on culture-independent method showed the bacteria to be related to alpha, beta, gamma-proteobacteria. Bacteria isolated by the culture-dependent method were high G + C, gram-positive bacteria. The genera Enterobacter, Serratia and Ochrobactrum were detected by both methods. To sum up the results from the two methods, the bacteria in scorpion intestine belong to 23 genera, which are Enterobacter, Serratia, Pseudomonas, Acinetobacter, Aeromonas, Citrobacter, Pedobacter, Delftia, Ralstonia, Ochrobactrum, Sphingomonas, Exiguobacterium, Gordonia, Nocardia, Rhodococcus, Janibacte, Kocuria, Micrococcus, Agromyces, Microbacterium, Agrococcus, Deinococcus, Ornithinimicrobium, and some uncultured species. The two methods have both advantages and shortcomings. However, when used simultaneously, they complement each other.

  11. Reclassification of Nocardia corynebacterioides Serrano et al. 1972 (Approved Lists 1980) as Rhodococcus corynebacterioides comb. nov.

    PubMed

    Yassin, A F; Schaal, K P

    2005-05-01

    The type strain of Nocardia corynebacterioides was the subject of a polyphasic taxonomic study. The 16S rRNA gene sequence was aligned with the sequences of representatives of the genera Corynebacterium, Dietzia, Gordonia, Mycobacterium, Nocardia, Rhodococcus, Skermania, Tsukamurella and Williamsia, and phylogenetic trees were constructed by using maximum-parsimony, maximum-likelihood and neighbour-joining methods. It was evident from the phylogenetic analysis that N. corynebacterioides represents a distinct phyletic line within the genus Rhodococcus. Menaquinone analysis showed that the organism contained dihydrogenated menaquinone with eight isoprene units, MK-8(H(2)), as the major isoprenologue. The genealogical evidence, together with chemotaxonomic and phenotypic data from this and previous studies, indicates that N. corynebacterioides DSM 20151(T) (= CIP 104510(T)) should be reclassified in the genus Rhodococcus as Rhodococcus corynebacterioides comb. nov.

  12. 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.

  13. 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.

  14. 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

  15. The two facies of pyrrolizidine alkaloids: the role of the tertiary amine and its N-oxide in chemical defense of insects with acquired plant alkaloids.

    PubMed

    Lindigkeit, R; Biller, A; Buch, M; Schiebel, H M; Boppré, M; Hartmann, T

    1997-05-01

    Larvae of Creatonotos transiens (Lepidoptera, Arctiidae) and Zonocerus variegatus (Orthoptera, Pyrgomorphidae) ingest 14C-labeled senecionine and its N-oxide with the same efficiency but sequester the two tracers exclusively as N-oxide. Larvae of the non-sequestering Spodoptera littoralis eliminate efficiently the ingested alkaloids. During feeding on the two alkaloidal forms transient levels of senecionine (but not of the N-oxide) are built up in the haemolymph of S. littoralis larvae. Based on these results, senecionine [18O]N-oxide was fed to C. transiens larvae and Z. variegatus adults. The senecionine N-oxide recovered from the haemolymph of the two insects shows an almost complete loss of 18O label, indicating reduction of the orally fed N-oxide in the guts, uptake of the tertiary alkaloid and its re-N-oxidation in the haemolymph. The enzyme responsible for N-oxidation is a soluble mixed function monooxygenase. It was isolated from the haemolymph of the sequestering arctiid Tyria jacobaeae and purified to electrophoretic homogeneity. The enzyme is a flavoprotein with a native Mr of 200000 and a subunit Mr of 51000. It shows a pH optimum at 7.0, has its maximal activity at a temperature of 40-45 degrees C and an isoelectric point at pH 4.9. The reaction is strictly NADPH-dependent (Km 1.3 microM). From 20 pyrrolizidine alkaloids so far tested as substrates, the enyzme N-oxidizes only alkaloids with structural elements which are essential for hepatotoxic and genotoxic pyrrolizidine alkaloids (i.e. 1,2-double bond, esterification of the allylic hydroxyl group, presence of a second free or esterified hydroxyl group at carbon 7). A great variety of related alkaloids and xenobiotics were tested as substrate, none was accepted. The Km values of senecionine, monocrotaline and heliotrine, representing the three main types of pyrrolizidine alkaloids, are 1.3 microM, 12.5 microM and 290 microM, respectively. The novel enzyme was named senecionine N-oxygenase (SNO). The

  16. 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.

  17. 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.

  18. Can plant resistance to specialist herbivores be explained by plant chemistry or resource use strategy?

    PubMed

    Kirk, Heather; Vrieling, Klaas; Pelser, Pieter B; Schaffner, Urs

    2012-04-01

    At both a macro- and micro-evolutionary level, selection of and performance on host plants by specialist herbivores are thought to be governed partially by host plant chemistry. Thus far, there is little evidence to suggest that specialists can detect small structural differences in secondary metabolites of their hosts, or that such differences affect host choice or performance of specialists. We tested whether phytochemical differences between closely related plant species are correlated with specialist host choice. We conducted no-choice feeding trials using 17 plant species of three genera of tribe Senecioneae (Jacobaea, Packera, and Senecio; Asteraceae) and a more distantly related species (Cynoglossum officinale; Boraginaceae) containing pyrrolizidine alkaloids (PAs), and four PA-sequestering specialist herbivores of the genus Longitarsus (Chrysomelidae). We also assessed whether variation in feeding by specialist herbivores is attributable to different resource use strategies of the tested plant species. Plant resource use strategy was quantified by measuring leaf dry matter content, which is related to both plant nutritive value and to plant investment in quantitative defences. We found no evidence that intra-generic differences in PA profiles affect feeding by specialist herbivores. Instead, our results indicate that decisions to begin feeding are related to plant resource use strategy, while decisions to continue feeding are not based on any plant characteristics measured in this study. These findings imply that PA composition does not significantly affect host choice by these specialist herbivores. Leaf dry matter content is somewhat phylogenetically conserved, indicating that plants may have difficulty altering resource use strategy in response to selection pressure by herbivores and other environmental factors on an evolutionary time scale.

  19. HST Data suggest proper motion for the optical counterpart of GRB 970228.

    NASA Astrophysics Data System (ADS)

    Caraveo, P. A.; Mignani, R. P.; Tavani, M.; Bignami, G. F.

    1997-10-01

    After a quarter of a century of γ-ray burst (GRB) astronomy, the Italian-Dutch satellite BeppoSAX on Feb 28^th^, 1997 detected a soft X-ray afterglow from GRB 970228 and positioned it accurately. This made possible the successful detection of an optical transient. Two public Hubble Space Telescope (HST) images of the GRB/optical transient region were taken on March 26^th^ and April 7^th^, 1997. They are analyzed here, with the purpose of understanding the nature of GRB 970228. We find that the position of the faint point-like object (m_v_~26) seen at the transient location changed by 0.40+/-0.10pixels in 12 days, corresponding to a proper motion of ~550mas/year. By comparison, four adjacent sources in the same field do not show any significant displacement, with astrometric residuals close to zero and average absolute displacements less than 0.09pixels. If confirmed, this result would strongly support the galactic nature of GRB 970228.

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

    PubMed

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

    2015-03-01

    The community structure and population dynamics of Mycolata were monitored in a full-scale membrane bioreactor during four experimental phases under changing operating and environmental conditions, by means of temperature-gradient gel electrophoresis of partial 16S-rRNA genes amplified from community DNA and RNA templates (total and active populations). Non-metric multidimensional scaling and BIO-ENV analyses demonstrated that population dynamics were mostly explained (30-32%) by changes in the input of nutrients in the influent water and the accumulation of biomass in the bioreactors, while the influence of hydraulic and solid retention times, temperature and F/M ratio was minor. Significant correlations were observed between particular Mycolata phylotypes and one or more variables, contributing information for the prediction of their abundance and activity under changing conditions. Fingerprinting and multivariate analyses demonstrated that two foaming episodes, recorded at temperatures <20°C, were connected to the increase of the relative abundance of Mycolata unrelated to Gordonia amarae. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. [Evaluation of API Coryne System, version 2.0, for diphteroid gram-positive rods identification with clinical relevance].

    PubMed

    Almuzara, M N; De Mier, C; Rodríguez, C R; Famiglietti, A M R; Vay, C A

    2006-01-01

    The ability of the API Coryne system, version 2.0, to identify 178 strains of gram-positive rods was evaluated. Seventy eight isolates belonged to genus Corynebacterium and one hundred to related genera, all strains were isolated from clinical samples at the Laboratory of Bacteriology, Hospital de Clínicas José de San Martin (UBA) between 1995 and 2004. The isolates were identified according to von Graevenitz and Funke's scheme. One hundred and sixty two out of 178 strains (91%) were correctly identified at genus and species level (IC95 = 85.6-94.6), in 44 of them (24.7%) additional tests were needed to final identification. Sixteen strains (9%) were not correctly identified (IC95 = 5.4-14.4); none of the 178 strains remained unidentified. The API Coryne system, version 2.0, is useful to identify the majority of Cory-nebacterium species with clinical relevance: Corynebacterium jeikeium, Corynebacterium urealyticum, Corynebacterium striatum, Corynebacterium pseudodiphtheriticum, Corynebacterium amycolatum and related species such as Arcanobacterium haemolyticum, Dermabacter hominis, Listeria monocytogenes, among others. Nevertheless for yellow-pigmented diphteroid gram-positive rods (Aureobacterium spp., Leifsonia aquatica, Microbacterium spp. and Cellulomonas spp.) and for acid fast gram-positive rods (Rhodococcus, Gordonia, Tsukamurella and Nocardia) the identification usefulness the system is limited.

  2. 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.

  3. Functional Gene-Guided Discovery of Type II Polyketides from Culturable Actinomycetes Associated with Soft Coral Scleronephthya sp

    PubMed Central

    Sun, Wei; Peng, Chongsheng; Zhao, Yunyu; Li, Zhiyong

    2012-01-01

    Compared with the actinomycetes in stone corals, the phylogenetic diversity of soft coral-associated culturable actinomycetes is essentially unexplored. Meanwhile, the knowledge of the natural products from coral-associated actinomycetes is very limited. In this study, thirty-two strains were isolated from the tissue of the soft coral Scleronephthya sp. in the East China Sea, which were grouped into eight genera by 16S rDNA phylogenetic analysis: Micromonospora, Gordonia, Mycobacterium, Nocardioides, Streptomyces, Cellulomonas, Dietzia and Rhodococcus. 6 Micromonospora strains and 4 Streptomyces strains were found to be with the potential for producing aromatic polyketides based on the analysis of KSα (ketoacyl-synthase) gene in the PKS II (type II polyketides synthase) gene cluster. Among the 6 Micromonospora strains, angucycline cyclase gene was amplified in 2 strains (A5-1 and A6-2), suggesting their potential in synthesizing angucyclines e.g. jadomycin. Under the guidance of functional gene prediction, one jadomycin B analogue (7b, 13-dihydro-7-O-methyl jadomycin B) was detected in the fermentation broth of Micromonospora sp. strain A5-1. This study highlights the phylogenetically diverse culturable actinomycetes associated with the tissue of soft coral Scleronephthya sp. and the potential of coral-derived actinomycetes especially Micromonospora in producing aromatic polyketides. PMID:22880121

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

    PubMed Central

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

    2014-01-01

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

  5. 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.

  6. Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters.

    PubMed

    Schorn, Michelle A; Alanjary, Mohammad M; Aguinaldo, Kristen; Korobeynikov, Anton; Podell, Sheila; Patin, Nastassia; Lincecum, Tommie; Jensen, Paul R; Ziemert, Nadine; Moore, Bradley S

    2016-12-01

    Traditional natural product discovery methods have nearly exhausted the accessible diversity of microbial chemicals, making new sources and techniques paramount in the search for new molecules. Marine actinomycete bacteria have recently come into the spotlight as fruitful producers of structurally diverse secondary metabolites, and remain relatively untapped. In this study, we sequenced 21 marine-derived actinomycete strains, rarely studied for their secondary metabolite potential and under-represented in current genomic databases. We found that genome size and phylogeny were good predictors of biosynthetic gene cluster diversity, with larger genomes rivalling the well-known marine producers in the Streptomyces and Salinispora genera. Genomes in the Micrococcineae suborder, however, had consistently the lowest number of biosynthetic gene clusters. By networking individual gene clusters into gene cluster families, we were able to computationally estimate the degree of novelty each genus contributed to the current sequence databases. Based on the similarity measures between all actinobacteria in the Joint Genome Institute's Atlas of Biosynthetic gene Clusters database, rare marine genera show a high degree of novelty and diversity, with Corynebacterium, Gordonia, Nocardiopsis, Saccharomonospora and Pseudonocardia genera representing the highest gene cluster diversity. This research validates that rare marine actinomycetes are important candidates for exploration, as they are relatively unstudied, and their relatives are historically rich in secondary metabolites.

  7. [Phylogenetic diversity of the culturable rare actinomycetes in marine sponge Hymeniacidon perlevis by improved isolation media].

    PubMed

    Xin, Yanjuan; Wu, Peichun; Deng, Maicun; Zhang, Wei

    2009-07-01

    Based on the molecular diversity information, seven actinomycete-selective culture media and isolation conditions were modified to isolate and cultivate diverse rare actinomycetes from Hymeniacidon perlevis. Modified, selective cultivation and enrichment media were used, with the addition of an elemental solution of simulating the elemental composition of marine sponge H. perlevis. Restriction Fragment Length Polymorphism (RFLP) analysis of 16S rDNA sequence was used to reveal the diversity of culturable rare actinomycetes. A total of 59 actinomycete strains were isolated from the marine sponge H. perlevis. A total of 27 representative actinomycetes were selected according to their morphological feature, color and pigments. They gave 15 different RFLP patterns after digesting their PCR products of 16s rDNA with Hha I. The results showed that these isolates belonged to 10 genera: Streptomyces, Nocardiopsis, Micromonospora, Cellulosimicrobium, Gordonia, Nocardia, Prauseria, Pseudonocardia , Saccharomonospora and Microbacterium. The modified isolation media and selective cultivation procedures are highly effective in the recovery of culturable actinomycetes from the marine sponge H. perlevis, resulting in the highest diversity of culturable rare actinomycetes from any sponges.

  8. Novel actinobacteria from marine sponges.

    PubMed

    Montalvo, Naomi F; Mohamed, Naglaa M; Enticknap, Julie J; Hill, Russell T

    2005-01-01

    Actinobacteria exclusively within the sub-class Acidimicrobidae were shown by 16S rDNA community analysis to be major components of the bacterial community associated with two sponge species in the genus Xestospongia. Four groups of Actinobacteria were identified in Xestospongia spp., with three of these four groups being found in both Xestospongia muta from Key Largo, Florida and Xestospongia testudinaria from Manado, Indonesia. This suggests that these groups are true symbionts in these sponges and may play a common role in both the Pacific and Atlantic sponge species. The fourth group was found only in X. testudinaria and was a novel assemblage distantly related to any previously sequenced actinobacterial clones. The only actinobacteria that were obtained in initial culturing attempts were Gordonia, Micrococcus and Brachybacterium spp., none of which were represented in the clone libraries. The closest cultured actinobacteria to all the Acidimicrobidae clones from Xestospongia spp. are 'Microthrix parvicella' and Acidimicrobium spp. Xestospongia spp. can now be targeted as source material from which to culture novel Acidimicrobidae to investigate their potential as producers of bioactive compounds. Isolation of sponge-associated Acidimicrobidae will also make it possible to elucidate their role as sponge symbionts.

  9. Role of Nocardia in Activated Sludge

    PubMed Central

    Bafghi, Mehdi Fatahi; Yousefi, Nader

    2016-01-01

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

  10. 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

    2016-04-11

    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.

  11. 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.

  12. Full-scale control of Mycolata foam by FEX-120 addition.

    PubMed

    Kragelund, C; Nilsson, B; Eskilsson, K; Bøgh, A M; Nielsen, P H

    2010-01-01

    Foaming incidents in activated sludge treatment plants are a worldwide problem and occur on a regular basis in both municipal and industrial activated sludge treatment plants. Foaming is most often caused by excessive growth of filamentous bacteria, especially the gram-positive ones affiliated within the Actinobacteria, e.g. the branched Mycolata or Candidatus Microthrix parvicella. Previous studies have shown that populations of Microthrix can be controlled by addition of certain polyaluminium compounds, but until now no effective chemicals have been identified to control other important foam formers such as the Mycolata. A new chemical (FilamentEx, FEX-120) was tested in full-scale in a Swedish wastewater treatment plant (WWTP) with immense foaming problems. In total, three different dosing events were carried out for more than 1 year. After only 8-17 weeks in each period, all foam had disappeared, and dosing of FEX-120 was stopped. Another 11 full-scale WWTPs in different countries were treated with FEX-120 because of severe Mycolata foaming on process tanks. In nine out of 11 plants, where the causative organisms were Gordonia or Skermania, a significant reduction of foam up to 100% was observed after treatment for approx. 10 weeks. In two WWTPs with unknown Mycolata organisms, no reduction was observed.

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

    PubMed Central

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

    2016-01-01

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

  14. Bioremediation of kerosene I: A case study in liquid media.

    PubMed

    Gouda, Mona K; Omar, Sanaa H; Chekroud, Zohra A; Nour Eldin, Hemdan M

    2007-11-01

    The ability of different local isolates in addition to some isolates from Germany to degrade kerosene in liquid medium was studied. The results showed that the percent of kerosene degradation varied among the different organisms and that 59-94% of kerosene was degraded after 21d. Two local isolates (Pseudomonas sp. AP and Pseudomonas sp. CK) and one German isolate (Gordonia sp. DM) were selected for this study. The addition of wheat bran, as co-substrate, stimulated the kerosene degradation by the two local strains, while glucose inhibited the degradation rate using the three organisms with different rates. Ammonium nitrate and urea was the best nitrogen sources. The use of superphosphate (as phosphorus source) in the presence of urea stimulates the degradation rate. It was also observed that the addition of 1% surfactants, like Triton X-100, Igepal, Tergitol, or Tween 20 and 80 enhanced the kerosene degradation. The degradation percent lied between 94% and 98%. The ability of the tested organisms to degrade kerosene concentration from 2% to 8% was evaluated. It was found that the three organisms degraded about 65-85% from 8% kerosene after 21d. The use of rice straw-immobilized cells reduced the time of degradation and enhanced the degradation ability of the organisms. The sodium dodecyl sulphate-polyacrylamide gel electrophoresis revealed the presence of a common protein band when the tested organisms were grown on kerosene.

  15. Identification and biodegradation potential of tropical aerobic hydrocarbon-degrading microorganisms.

    PubMed

    Chaillan, Frédéric; Le Flèche, Anne; Bury, Edith; Phantavong, Y-Hui; Grimont, Patrick; Saliot, Alain; Oudot, Jean

    2004-09-01

    Screening of aerobic culturable hydrocarbon (HC)-degrading microorganisms isolated from petroleum-polluted soils and cyanobacterial mats from Indonesia resulted in the collection of 33 distinct species. Eight bacteria, 21 fungi and 4 yeasts were identified to the specific level by molecular and phenotypic techniques. Bacterial strains belonged to the genera Gordonia, Brevibacterium, Aeromicrobium, Dietzia, Burkholderia and Mycobacterium. Four species are new and not yet described. Fungi belonged to Aspergillus, Penicillium, Fusarium, Amorphoteca, Neosartorya, Paecilomyces, Talaromyces and Graphium. Yeasts were Candida, Yarrowia and Pichia. All strains were cultivated axenically in synthetic liquid media with crude oil as sole carbon and energy source. After incubation, the detailed chemical composition of the residual oil was studied by gravimetric and gas-chromatographic techniques. Thirteen parameters for assessing the biodegradation potential were defined and computed for each strain. Maximum degradation was observed on the saturated HCs (n- and isoalkanes, isoprenoids), whereas aromatic HC degradation was lower and was related to the structural composition of the molecules. A principal components analysis (PCA) permitted grouping and classifying the strains as a function of their degradative capacities. It was shown that the most active strains produced polar metabolites which accumulated in the resins and asphaltene fractions. These fractions are highly resistant to microbial metabolism. No taxonomic trend could be defined between microbial phyla in terms of HC biodegradation activity.

  16. Diversity and antimicrobial activities of actinobacteria isolated from tropical mangrove sediments in Malaysia.

    PubMed

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

    2014-01-01

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

  17. 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. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Diversity of culturable nocardioform actinomycetes from wastewater treatment plants in Spain and their role in the biodegradability of aromatic compounds.

    PubMed

    Soler, Albert; García-Hernández, Jorge; Zornoza, Andrés; Alonso, José Luis

    2017-03-06

    Currently, municipal and industrial wastewater treatment plants (WWTPs) are mainly focusing on reduction of biological oxygen demand and on the removal of nutrients. However, there are microorganisms that interfere with the process. In this environment, there is a large diversity of microorganisms that have not been studied in detail and that could provide real and practical solutions to the foaming problems. Among such microorganisms, Gram-positive actinomycete bacteria are of special interest because they are known for producing secondary metabolites as well as chemically diverse compounds and for their capacity to degrade recalcitrant pollutants. Three different media were chosen to isolate actinomycetes from 28 WWTPs in Spain. A total of 189 activated sludge samples were collected; 126 strains were isolated and identified to belong to 1 suborder, i.e. Corynebacterineae, and 7 genera, i.e. Corynebacterium, Dietzia, Gordonia, Mycobacterium, Rhodococcus, Tsukamurella and Williamsia. Furthermore, 71 strains were capable of biodegrading at least 1 aromatic product, and that 27 of them amplified for catA gene. The results of this research help us understand the complexity of the foam-forming microbial populations in Spain and it shows that WWTPs can be a good source of microorganisms that can degrade phenol or naphthalene.

  19. Marine Actinobacteria as a source of compounds for phytopathogen control: An integrative metabolic-profiling / bioactivity and taxonomical approach

    PubMed Central

    Betancur, Luz A.; Naranjo-Gaybor, Sandra J.; Vinchira-Villarraga, Diana M.; Moreno-Sarmiento, Nubia C.; Maldonado, Luis A.; Suarez-Moreno, Zulma R.; Acosta-González, Alejandro; Padilla-Gonzalez, Gillermo F.; Puyana, Mónica; Castellanos, Leonardo; Ramos, Freddy A.

    2017-01-01

    Marine bacteria are considered as promising sources for the discovery of novel biologically active compounds. In this study, samples of sediment, invertebrate and algae were collected from the Providencia and Santa Catalina coral reef (Colombian Caribbean Sea) with the aim of isolating Actinobateria-like strain able to produce antimicrobial and quorum quenching compounds against pathogens. Several approaches were used to select actinobacterial isolates, obtaining 203 strains from all samples. According to their 16S rRNA gene sequencing, a total of 24 strains was classified within Actinobacteria represented by three genera: Streptomyces, Micromonospora, and Gordonia. In order to assess their metabolic profiles, the actinobacterial strains were grown in liquid cultures, and LC-MS-based analyses from ethyl acetate fractions were performed. Based on taxonomical classification, screening information of activity against phytopathogenic strains and quorum quenching activity, as well as metabolic profiling, six out of the 24 isolates were selected for follow-up with chemical isolation and structure identification analyses of putative metabolites involved in antimicrobial activities. PMID:28225766

  20. 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.

  1. 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.

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

    PubMed Central

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

    2016-01-01

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

  3. Identification of Species of Nontuberculous Mycobacteria Clinical Isolates from 8 Provinces of China

    PubMed Central

    Lian, Lulu; Jiang, Yi; Huang, Mingxiang; Tan, Yunhong; Zhang, Jingrui; Yu, Qin; Liu, Jiao; Dong, Haiyan; Lu, Bing

    2016-01-01

    Pulmonary diseases caused by nontuberculous mycobacteria (NTM) are increasing in incidence and prevalence worldwide. In this study, we identified NTM species of the clinical isolates from 8 provinces in China, in order to preliminarily provide some basic scientific data in the different species and distribution of NTM related to pulmonary disease in China. A total of 523 clinical isolates from patients with tuberculosis (TB) diagnosed clinically from 2005 to 2012 were identified to the species using conventional and molecular methods, including multilocus PCR, rpoB and hsp65 PCR-PRA, hsp65, rpoB, and 16S-23S internal transcribed spacer region sequencing. The isolates were identified into 3 bacterium genera, including NTM, Gordonia bronchialis, and Nocardia farcinica, and, for the 488 NTM isolates, 27 species were identified. For all the 27 species of NTM which were found to cause pulmonary infections in humans, the most prevalent species was M. intracellulare, followed by M. avium and M. abscessus. And seven other species were for the first time identified in patients with TB in China. NTM species identification is very important for distinguishing between tuberculosis and NTM pulmonary diseases, and the species diversity drives the creation of diverse and integrated identification methods with higher accuracy and efficacy. PMID:27882322

  4. A polyphasic approach for assessing the suitability of bioremediation for the treatment of hydrocarbon-impacted soil.

    PubMed

    Adetutu, Eric M; Smith, Renee J; Weber, John; Aleer, Sam; Mitchell, James G; Ball, Andrew S; Juhasz, Albert L

    2013-04-15

    Bioremediation strategies, though widely used for treating hydrocarbon-contaminated soil, suffer from lack of biodegradation endpoint accountability. To address this limitation, molecular approaches of alkB gene analysis and pyrosequencing were combined with chemical approaches of bioaccessibility and nutrient assays to assess contaminant degrading capacity and develop a strategy for endpoint biodegradation predictions. In long-term hydrocarbon-contaminated soil containing 10.3 g C10-C36 hydrocarbons kg(-1), 454 pyrosequencing detected the overrepresentation of potential hydrocarbon degrading genera such as Pseudomonas, Burkholderia, Mycobacterium and Gordonia whilst amplicons for PCR-DGGE were detected only with alkB primers targeting Pseudomonas. This indicated the presence of potential microbial hydrocarbon degradation capacity in the soil. Using non-exhaustive extraction methods of 1-propanol and HP-β-CD for hydrocarbon bioaccessibility assessment combined with biodegradation endpoint predictions with linear regression models, we estimated 33.7% and 46.7% hydrocarbon removal respectively. These predictions were validated in pilot scale studies using an enhanced natural attenuation strategy which resulted in a 46.4% reduction in soil hydrocarbon content after 320 days. When predicted biodegradation endpoints were compared to measured values, there was no significant difference (P=0.80) when hydrocarbon bioaccessibility was assessed with HP-β-CD. These results indicate that a combination of molecular and chemical techniques that inform microbial diversity, functionality and chemical bioaccessibility can be valuable tools for assessing the suitability of bioremediation strategies for hydrocarbon-contaminated soil.

  5. Widespread abundance of functional bacterial amyloid in mycolata and other gram-positive bacteria.

    PubMed

    Jordal, Peter Bruun; Dueholm, Morten Simonsen; Larsen, Poul; Petersen, Steen Vang; Enghild, Jan Johannes; Christiansen, Gunna; Højrup, Peter; Nielsen, Per Halkjaer; Otzen, Daniel Erik

    2009-06-01

    Until recently, extracellular functional bacterial amyloid (FuBA) has been detected and characterized in only a few bacterial species, including Escherichia coli, Salmonella, and the gram-positive organism Streptomyces coelicolor. Here we probed gram-positive bacteria with conformationally specific antibodies and revealed the existence of FuBA in 12 of 14 examined mycolata species, as well as six other distantly related species examined belonging to the phyla Actinobacteria and Firmicutes. Most of the bacteria produced extracellular fimbriae, sometimes copious amounts of them, and in two cases large extracellular fibrils were also produced. In three cases, FuBA was revealed only after extensive removal of extracellular material by saponification, indicating that there is integrated attachment within the cellular envelope. Spores of species in the genera Streptomyces, Bacillus, and Nocardia were all coated with amyloids. FuBA was purified from Gordonia amarae (from the cell envelope) and Geodermatophilus obscurus, and they had the morphology, tinctorial properties, and beta-rich structure typical of amyloid. The presence of approximately 9-nm-wide amyloids in the cell envelope of G. amarae was visualized by transmission electron microscopy analysis. We conclude that amyloid is widespread among gram-positive bacteria and may in many species constitute a hitherto overlooked integral part of the spore and the cellular envelope.

  6. Widespread Abundance of Functional Bacterial Amyloid in Mycolata and Other Gram-Positive Bacteria▿

    PubMed Central

    Jordal, Peter Bruun; Dueholm, Morten Simonsen; Larsen, Poul; Petersen, Steen Vang; Enghild, Jan Johannes; Christiansen, Gunna; Højrup, Peter; Nielsen, Per Halkjær; Otzen, Daniel Erik

    2009-01-01

    Until recently, extracellular functional bacterial amyloid (FuBA) has been detected and characterized in only a few bacterial species, including Escherichia coli, Salmonella, and the gram-positive organism Streptomyces coelicolor. Here we probed gram-positive bacteria with conformationally specific antibodies and revealed the existence of FuBA in 12 of 14 examined mycolata species, as well as six other distantly related species examined belonging to the phyla Actinobacteria and Firmicutes. Most of the bacteria produced extracellular fimbriae, sometimes copious amounts of them, and in two cases large extracellular fibrils were also produced. In three cases, FuBA was revealed only after extensive removal of extracellular material by saponification, indicating that there is integrated attachment within the cellular envelope. Spores of species in the genera Streptomyces, Bacillus, and Nocardia were all coated with amyloids. FuBA was purified from Gordonia amarae (from the cell envelope) and Geodermatophilus obscurus, and they had the morphology, tinctorial properties, and β-rich structure typical of amyloid. The presence of approximately 9-nm-wide amyloids in the cell envelope of G. amarae was visualized by transmission electron microscopy analysis. We conclude that amyloid is widespread among gram-positive bacteria and may in many species constitute a hitherto overlooked integral part of the spore and the cellular envelope. PMID:19395568

  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.

  8. 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.

  9. 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.

  10. Analysis of petroleum biodesulfurization in an airlift bioreactor using response surface methodology.

    PubMed

    Irani, Zahra Azimzadeh; Mehrnia, Mohammad Reza; Yazdian, Fatemeh; Soheily, Majid; Mohebali, Ghasemali; Rasekh, Behnam

    2011-11-01

    For the first time, growing cells of Gordonia alkanivorans RIPI90A were used for biodesulfurization (BDS) of diesel. This process was carried out in an internal airlift bioreactor. BDS parameters (oil/water phase ratio and initial sulfur concentration) were optimized in flasks using response surface methodology. Predicted results were found to be in good agreement with experimental results. Initial sulfur concentration had a remarkable effect on BDS process. Maximum removal of sulfur (21 mg/l) can be achieved at oil/water phase ratio of 25% (v/v) and initial sulfur concentration of 28 mg/l. Moreover, effect of superficial gas velocity (Ug) and working volume (v) on volumetric gas liquid mass transfer coefficient was studied in an airlift bioreactor for BDS of diesel. The best results were achieved at Ug and v of 2.5l/min and 6.6l, respectively. Subsequently, BDS of diesel was investigated in an airlift bioreactor under optimized conditions. Sulfur reduction after 30 h was 14 mg/l. Copyright © 2011 Elsevier Ltd. All rights reserved.

  11. Isolation and characterization of crude-oil-degrading bacteria from the Persian Gulf and the Caspian Sea.

    PubMed

    Hassanshahian, Mehdi; Emtiazi, Giti; Cappello, Simone

    2012-01-01

    Twenty-five crude-oil-degrading bacteria were isolated from oil-contaminated sites in the Persian Gulf and the Caspian Sea. Based on a high growth rate on crude oil and on hydrocarbon degradation ability, 11 strains were selected from the 25 isolated strains for further study. Determination of the nucleotide sequence of the 16S rRNA gene showed that these isolated strains belonged to genera Acinetobacter, Pseudomonas, Gordonia, Rhodococcus, Cobetia, Halomonas, Alcanivorax, Marinobacter and Microbacterium. Among the 11 isolates, strains BS (Acinetobacter calcoaceticus, 98%) and PG-12 (Alcanivorax dieselolei, 98%) were the most effective in degrading crude oil. Rate of crude-oil degradation of 82% (isolate BS) and 71% (isolate PG-12) were observed after 1 week of cultivation in mineral medium. These strains had high emulsification activity and biosurfactant production. GC-MS analysis showed that A. dieselolei PG-12 can degrade different alkanes in crude oil. Screening of the distribution of the alkane hydroxylase gene in 25 isolates in relation to the source of isolation indicated that the group (II) alkane hydroxylase is prevalent in the Caspian Sea, but in the Persian Gulf, the frequency of the group (III) alkane hydroxylase gene is greater than that of the group (II) alkane hydroxylase gene.

  12. 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.

  13. Selection and identification of bacterial strains with methyl-tert-butyl ether, ethyl-tert-butyl ether, and tert-amyl methyl ether degrading capacities.

    PubMed

    Purswani, Jessica; Pozo, Clementina; Rodríguez-Díaz, Marina; González-López, Jesús

    2008-11-01

    Nine bacterial strains isolated from two hydrocarbon-contaminated soils were selected because of their capacity for growth in culture media amended with 200 mg/L of one of the following gasoline oxygenates: Methyl-tert-butyl ether (MTBE), ethyl-tert-butyl ether (ETBE), and tert-amyl methyl ether (TAME). These strains were identified by amplification of their 16S rRNA gene, using fDl and rD1 primers, and were tested for their capacity to grow and biotransform these oxygenates in both mineral and cometabolic media. The isolates were classified as Bacillus simplex, Bacillus drentensis, Arthrobacter sp., Acinetobacter calcoaceticus, Acinetobacter sp., Gordonia amicalis (two strains), Nocardioides sp., and Rhodococcus ruber. Arthrobacter sp. (strain MG) and A. calcoaceticus (strain M10) consumed 100 (cometabolic medium) and 82 mg/L (mineral medium) of oxygenate TAME in 21 d, respectively, under aerobic conditions. Rhodococcus ruber (strain E10) was observed to use MTBE and ETBE as the sole carbon and energy source, whereas G. amicalis (strain T3) used TAME as the sole carbon and energy source for growth. All the bacterial strains transformed oxygenates better in the presence of an alternative carbon source (ethanol) with the exception of A. calcoaceticus (strain M10). The capacity of the selected strains to remove MTBE, ETBE, and TAME looks promising for application in bioremediation technologies.

  14. 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

  15. Petroleum oil removal by immobilized bacterial cells on polyurethane foam under different temperature conditions.

    PubMed

    Alessandrello, Mauricio J; Juárez Tomás, María S; Raimondo, Enzo E; Vullo, Diana L; Ferrero, Marcela A

    2017-09-15

    In this work, a mixed biofilm composed by Pseudomonas monteilii P26 and Gordonia sp. H19 was formed using polyurethane foam (PUF) as immobilization support, for crude oil removal from artificial sea water. Fresh immobilized cells and immobilized cells that were stored at 4°C for two months before use were assessed. The oil removal assays were carried out at microcosm scale at 4, 15 and 30°C. A viability loss of P. monteilii P26 was observed after the storage. The highest removal value (75%) was obtained at 30°C after 7days using fresh immobilized cells on PUF. Enhanced oil bioremoval was obtained at 4°C and 15°C with the previously stored immobilized cells compared to the fresh immobilized cells. Crude oil sorption on the different systems was responsible for the removal of 22-33% oil at the different temperatures. In conclusion, an economic tool for petroleum bioremediation is proposed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Effect of activated sludge properties and membrane operation conditions on fouling characteristics in membrane bioreactors.

    PubMed

    Choi, Hyeok; Zhang, Kai; Dionysiou, Dionysios D; Oerther, Daniel B; Sorial, George A

    2006-06-01

    Biofouling control is considered to be a major challenge in operating membrane bioreactors (MBRs) for the treatment of wastewater. This study examined the impact of biological, chemical, and physical properties of activated sludge on membrane filtration performance in laboratory-scale MBRs. Sludges with different microbial communities were produced using pseudo-continuous stirred-tank reactors and pseudo-plug flow reactors treating a synthetic paper mill wastewater. Various filtration resistances were used to investigate membrane fouling characteristics, and molecular biology tools targeting 16S ribosomal DNA gene sequences were used to identify predominant bacterial populations in the sludges or attached to the fouled membranes. Filtration experiments using axenic cultures of Escherichia coli, Acinetobacter calcoaceticus, and Gordonia amarae were also performed to better understand the initiation and development of biofouling. The results showed that the tendency of membranes to biofoul depended upon membrane operating conditions as well as the properties of the activated sludge in the MBR systems. Specific bacterial populations, which were not dominant in the activated sludges, were selectively accumulated on the membrane surface leading to the development of irreversible biofouling.

  17. 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. Copyright © 2011 Elsevier Ltd. All rights reserved.

  18. Isolation of cholesterol- and deoxycholate-degrading bacteria from soil samples: evidence of a common pathway.

    PubMed

    Merino, E; Barrientos, A; Rodríguez, J; Naharro, G; Luengo, J M; Olivera, E R

    2013-01-01

    Nineteen different steroid-degrading bacteria were isolated from soil samples by using selective media containing either cholesterol or deoxycholate as sole carbon source. Strains that assimilated cholesterol (17 COL strains) were gram-positive, belonging to the genera Gordonia, Tsukamurella, and Rhodococcus, and grew on media containing other steroids but were unable to use deoxycholate as sole carbon source. Surprisingly, some of the COL strains unable to grow using deoxycholate as sole carbon source were able to catabolize other bile salts (e.g., cholate). Conversely, strains able to grow using deoxycholate as the sole carbon source (two DOC isolates) were gram-negative, belonging to the genus Pseudomonas, and were unable to catabolize cholesterol and other sterols. COL and DOC were included into the corresponding taxonomic groups based on their morphology (cells and colonies), metabolic properties (kind of substrates that support bacterial growth), and genetic sequences (16S rDNA and rpoB). Additionally, different DOC21 Tn5 insertion mutants have been obtained. These mutants have been classified into two different groups: (1) those affected in the catabolism of bile salts but that, as wild type, can grow in other steroids and (2) those unable to grow in media containing any of the steroids tested. The identification of the insertion point of Tn5 in one of the mutants belonging to the second group (DOC21 Mut1) revealed that the gene knocked-out encodes an A-ring meta-cleavage dioxygenase needed for steroid catabolism.

  19. 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

  20. Successful immunotherapy of canine flea allergy with injected Actinomycetales preparations.

    PubMed

    Marro, Alicia; Pirles, Mónica; Schiaffino, Laura; Bin, Liliana; Dávila, Héctor; Bottasso, Oscar A; McIntyre, Graham; Ripley, Paul R; Stanford, Cynthia A; Stanford, John L

    2011-08-01

    Can heat-killed, borate-buffered suspensions of Gordonia bronchialis, Rhodococcus coprophilus or Tsukamurella inchonensis be used to treat canine flea allergy? Organisms cultured on Sauton's medium into stationary phase were autoclaved in borate-buffered saline and stored at 10 mg wet weight/ml. Intradermal injections of 0.1 ml containing 1 mg of bacilli were administered on the first and 20th days of the study. G. bronchialis and R. coprophilus were most effective in a pilot study of a small number of dogs with flea allergy. A larger number of affected dogs were then randomized to receive placebo or either of the two selected reagents. The extent and severity of allergic signs and symptoms were scored and blood samples were collected just before the first injection and 28 days after the second. Both selected reagents reduced the extent and severity of lesions (p < 0.001) and reduced scratching. Eosinophil numbers were reduced (p < 0.0001) between the first and second assessment. Injections of G. bronchialis or R. coprophilus effectively reduce the signs and symptoms of flea allergy in dogs.

  1. 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

  2. From oil spills to barley growth - oil-degrading soil bacteria and their promoting effects.

    PubMed

    Mikolasch, Annett; Reinhard, Anne; Alimbetova, Anna; Omirbekova, Anel; Pasler, Lisa; Schumann, Peter; Kabisch, Johannes; Mukasheva, Togzhan; Schauer, Frieder

    2016-11-01

    Heavy contamination of soils by crude oil is omnipresent in areas of oil recovery and exploitation. Bioremediation by indigenous plants in cooperation with hydrocarbon degrading microorganisms is an economically and ecologically feasible means to reclaim contaminated soils. To study the effects of indigenous soil bacteria capable of utilizing oil hydrocarbons on biomass production of plants growing in oil-contaminated soils eight bacterial strains were isolated from contaminated soils in Kazakhstan and characterized for their abilities to degrade oil components. Four of them, identified as species of Gordonia and Rhodococcus turned out to be effective degraders. They produced a variety of organic acids from oil components, of which 59 were identified and 7 of them are hitherto unknown acidic oil metabolites. One of them, Rhodococcus erythropolis SBUG 2054, utilized more than 140 oil components. Inoculating barley seeds together with different combinations of these bacterial strains restored normal growth of the plants on contaminated soils, demonstrating the power of this approach for bioremediation. Furthermore, we suggest that the plant promoting effect of these bacteria is not only due to the elimination of toxic oil hydrocarbons but possibly also to the accumulation of a variety of organic acids which modulate the barley's rhizosphere environment.

  3. 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

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

    PubMed

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

    2014-01-01

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

  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

    2016-02-24

    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.

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

    PubMed

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

    2016-01-01

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

  7. Clinical impact of the use of 16S rRNA sequencing method for the identification of "difficult-to-identify" bacteria in immunocompromised hosts.

    PubMed

    Bharadwaj, R; Swaminathan, S; Salimnia, H; Fairfax, M; Frey, A; Chandrasekar, P H

    2012-04-01

    Molecular method of 16S rRNA sequencing is reported to be helpful in the accurate identification of organisms with ambiguous phenotypic profiles. We analyzed the use of 16S rRNA sequencing method to identify clinically significant, "difficult-to-identify" bacteria recovered from clinical specimens, and evaluated its role in patient management and consequent clinical outcome. Among the 172 "difficult-to-identify" bacteria recovered over a 4-year period, 140 were gram-positive cocci or gram-negative bacilli; identification by 16S rRNA did not play a role in the management of patients infected with these bacteria. From 32 patients, 33 "difficult-to-identify" gram-positive bacilli were identified; the organisms were mycobacteria, Nocardia, Tsukamurella, Rhodococcus, and Gordonia. In 24 patients for whom clinical data were available, results from the 16S rRNA sequencing method led to treatment change in 14 immunocompromised patients (including 7 hematopoietic stem cell recipients and 1 liver transplant recipient). Therapy was modified in 9 patients, initiated in 3 patients, and discontinued in 2 patients. Most patients' therapy was switched to oral antibiotics with discontinuation of intravascular catheters, facilitating early hospital discharge. All 14 patients were alive 30 days after infection onset. The present study demonstrates the clinical application of 16S rRNA sequencing method to identify "difficult-to-identify" mycobacteria and other gram-positive bacilli in clinical specimens, particularly in immunocompromised hosts.

  8. Identification of Species of Nontuberculous Mycobacteria Clinical Isolates from 8 Provinces of China.

    PubMed

    Liu, Haican; Lian, Lulu; Jiang, Yi; Huang, Mingxiang; Tan, Yunhong; Zhao, Xiuqin; Zhang, Jingrui; Yu, Qin; Liu, Jiao; Dong, Haiyan; Lu, Bing; Wu, Yimou; Wan, Kanglin

    2016-01-01

    Pulmonary diseases caused by nontuberculous mycobacteria (NTM) are increasing in incidence and prevalence worldwide. In this study, we identified NTM species of the clinical isolates from 8 provinces in China, in order to preliminarily provide some basic scientific data in the different species and distribution of NTM related to pulmonary disease in China. A total of 523 clinical isolates from patients with tuberculosis (TB) diagnosed clinically from 2005 to 2012 were identified to the species using conventional and molecular methods, including multilocus PCR, rpoB and hsp65 PCR-PRA, hsp65, rpoB, and 16S-23S internal transcribed spacer region sequencing. The isolates were identified into 3 bacterium genera, including NTM, Gordonia bronchialis, and Nocardia farcinica, and, for the 488 NTM isolates, 27 species were identified. For all the 27 species of NTM which were found to cause pulmonary infections in humans, the most prevalent species was M. intracellulare, followed by M. avium and M. abscessus. And seven other species were for the first time identified in patients with TB in China. NTM species identification is very important for distinguishing between tuberculosis and NTM pulmonary diseases, and the species diversity drives the creation of diverse and integrated identification methods with higher accuracy and efficacy.

  9. 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.

  10. Marine Actinobacteria as a source of compounds for phytopathogen control: An integrative metabolic-profiling / bioactivity and taxonomical approach.

    PubMed

    Betancur, Luz A; Naranjo-Gaybor, Sandra J; Vinchira-Villarraga, Diana M; Moreno-Sarmiento, Nubia C; Maldonado, Luis A; Suarez-Moreno, Zulma R; Acosta-González, Alejandro; Padilla-Gonzalez, Gillermo F; Puyana, Mónica; Castellanos, Leonardo; Ramos, Freddy A

    2017-01-01

    Marine bacteria are considered as promising sources for the discovery of novel biologically active compounds. In this study, samples of sediment, invertebrate and algae were collected from the Providencia and Santa Catalina coral reef (Colombian Caribbean Sea) with the aim of isolating Actinobateria-like strain able to produce antimicrobial and quorum quenching compounds against pathogens. Several approaches were used to select actinobacterial isolates, obtaining 203 strains from all samples. According to their 16S rRNA gene sequencing, a total of 24 strains was classified within Actinobacteria represented by three genera: Streptomyces, Micromonospora, and Gordonia. In order to assess their metabolic profiles, the actinobacterial strains were grown in liquid cultures, and LC-MS-based analyses from ethyl acetate fractions were performed. Based on taxonomical classification, screening information of activity against phytopathogenic strains and quorum quenching activity, as well as metabolic profiling, six out of the 24 isolates were selected for follow-up with chemical isolation and structure identification analyses of putative metabolites involved in antimicrobial activities.

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

    PubMed

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

    2012-02-01

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

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

    PubMed

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

    1992-05-01

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

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

    PubMed

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

    2016-05-01

    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.

  14. Bioremediation potential of a tropical soil contaminated with a mixture of crude oil and production water.

    PubMed

    Alvarez, Vanessa Marques; Santos, Silvia Cristina Cunha Dos Santos; Casella, Renata da Costa; Vital, Ronalt Leite; Sebastin, Gina Vasquez; Seldin, Lucy

    2008-12-01

    A typical tropical soil from the northeast of Brazil, where an important terrestrial oil field is located, was accidentally contaminated with a mixture of oil and saline production water. To study the bioremediation potential in this area, molecular methods based on PCR-DGGE were used to determine the diversity of the bacterial communities in bulk and in contaminated soils. Bacterial fingerprints revealed that the bacterial communities were affected by the presence of the mixture of oil and production water, and different profiles were observed when the contaminated soils were compared with the control. Halotolerant strains capable of degrading crude oil were also isolated from enrichment cultures obtained from the contaminated soil samples. Twenty-two strains showing these features were characterized genetically by amplified ribosomal DNA restriction analysis (ARDRA) and phenotypically by their colonial morphology and tolerance to high NaCl concentrations. Fifteen ARDRA groups were formed. Selected strains were analyzed by 16S rDNA sequencing, and Actinobacteria was identified as the main group found. Strains were also tested for their growth capability in the presence of different oil derivatives (hexane, dodecane, hexadecane, diesel, gasoline, toluene, naphthalene, o-xylene, and p-xylene) and different degradation profiles were observed. PCR products were obtained from 12 of the 15 ARDRA representatives when they were screened for the presence of the alkane hydroxylase gene (alkB). Members of the genera Rhodococcus and Gordonia were identified as predominant in the soil studied. These genera are usually implicated in oil degradation processes and, as such, the potential for bioremediation in this area can be considered as feasible.

  15. 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

  16. 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.

  17. 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.

  18. Amyloid-Like Adhesins Produced by Floc-Forming and Filamentous Bacteria in Activated Sludge▿

    PubMed Central

    Larsen, Poul; Nielsen, Jeppe Lund; Otzen, Daniel; Nielsen, Per Halkjær

    2008-01-01

    Amyloid proteins (fimbriae or other microbial surface-associated structures) are expressed by many types of bacteria, not yet identified, in biofilms from various habitats, where they likely are of key importance to biofilm formation and biofilm properties. As these amyloids are potentially of great importance to the floc properties in activated sludge wastewater treatment plants (WWTP), the abundance of amyloid adhesins in activated sludge flocs from different WWTP and the identity of bacteria producing these were investigated. Amyloid adhesins were quantified using a combination of conformationally specific antibodies targeting amyloid fibrils, propidium iodide to target all fixed bacterial cells, confocal laser scanning microscopy, and digital image analysis. The biovolume fraction containing amyloid adhesins ranged from 10 to 40% in activated sludge from 10 different WWTP. The identity of bacteria producing amyloid adhesins was determined using fluorescence in situ hybridization with oligonucleotide probes in combination with antibodies or thioflavin T staining. Among the microcolony-forming bacteria, amyloids were primarily detected among Alpha- and Betaproteobacteria and Actinobacteria. A more detailed analysis revealed that many denitrifiers (from Thauera, Azoarcus, Zoogloea, and Aquaspirillum-related organisms) and Actinobacteria-related polyphosphate-accumulating organisms most likely produced amyloid adhesins, whereas nitrifiers did not. Many filamentous bacteria also expressed amyloid adhesins, including several Alphaproteobacteria (e.g., Meganema perideroedes), some Betaproteobacteria (e.g., Aquaspirillum-related filaments), Gammaproteobacteria (Thiothrix), Bacteroidetes, Chloroflexi (e.g., Eikelboom type 1851), and some foam-forming Actinobacteria (e.g., Gordonia amarae). The results show that amyloid adhesins were an abundant component of activated sludge extracellular polymeric substances and seem to have unexpected, divers functions. PMID:18192426

  19. 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

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

    PubMed

    Birke, Jakob; Röther, Wolf; Jendrossek, Dieter

    2015-06-01

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

  1. Identification and characterization of non-tuberculous mycobacteria isolated from tuberculosis suspects in Southern-central China.

    PubMed

    Yu, Xiao-li; Lu, Lian; Chen, Gao-zhan; Liu, Zhi-Guo; Lei, Hang; Song, Yan-zheng; Zhang, Shu-lin

    2014-01-01

    The incidence of non-tuberculous mycobacteria (NTM)-related death has increased globally recently. To obtain information of the species and characterization of pathogens involved in NTM pulmonary infection in Southern-central China, we identified 160 non-tuberculous infection cases from 3995 acid-fast bacilli (AFB)-positive tuberculous suspects. We then randomly selected 101 non-tuberculous patients, isolated bacteria from their sputa and genotyped the pathogens using the 16S rRNA gene and 16S-23S rRNA internal transcribed spacer sequences. M. intracellulare (32.67%, 33/101), M. abscessus (32.67%, 33/101) and M. fortuitum (7.92%, 8/101) are identified in these isolates. Surprisingly, non-mycobacteria including Gordonia (8.91%, 9/101), Nocardia (5.94%, 6/101) and Tsukamurella (0.99%, 1/101) are also discovered, and the case of Tsukamurella pulmonis infection is first discovered in Southern-central China. Moreover, species of M. mucogenicum group, M. chubuense, M. kansasii, M. gastri, M. avium, M. porcinum and M. smegmatis are identified. In addition, nine immune compromised cases (8.91%, 9/101), including type two diabetes mellitus and HIV/AIDS are found to be infected with non-tuberculous bacteria. This study revealed the distribution and characteristics of non-tuberculous AFB pathogen infection occurred in Southern-central China, and suggested that physicians should be alert of the emerging of NTM and non-mycobacteria infection in AFB positive cases and take caution when choosing chemotherapy for tuberculosis-like pulmonary infections. Generally, this study may help with the development of new strategy for the diagnosis and treatment of mycobacterial infection.

  2. Identification and Characterization of Non-Tuberculous Mycobacteria Isolated from Tuberculosis Suspects in Southern-Central China

    PubMed Central

    Yu, Xiao-li; Lu, Lian; Chen, Gao-zhan; Liu, Zhi-Guo; Lei, Hang; Song, Yan-zheng; Zhang, Shu-lin

    2014-01-01

    The incidence of non-tuberculous mycobacteria (NTM)-related death has increased globally recently. To obtain information of the species and characterization of pathogens involved in NTM pulmonary infection in Southern-central China, we identified 160 non-tuberculous infection cases from 3995 acid-fast bacilli (AFB)-positive tuberculous suspects. We then randomly selected 101 non-tuberculous patients, isolated bacteria from their sputa and genotyped the pathogens using the 16S rRNA gene and 16S-23S rRNA internal transcribed spacer sequences. M. intracellulare (32.67%, 33/101), M. abscessus (32.67%, 33/101) and M. fortuitum (7.92%, 8/101) are identified in these isolates. Surprisingly, non-mycobacteria including Gordonia (8.91%, 9/101), Nocardia (5.94%, 6/101) and Tsukamurella (0.99%, 1/101) are also discovered, and the case of Tsukamurella pulmonis infection is first discovered in Southern-central China. Moreover, species of M. mucogenicum group, M. chubuense, M. kansasii, M. gastri, M. avium, M. porcinum and M. smegmatis are identified. In addition, nine immune compromised cases (8.91%, 9/101), including type two diabetes mellitus and HIV/AIDS are found to be infected with non-tuberculous bacteria. This study revealed the distribution and characteristics of non-tuberculous AFB pathogen infection occurred in Southern-central China, and suggested that physicians should be alert of the emerging of NTM and non-mycobacteria infection in AFB positive cases and take caution when choosing chemotherapy for tuberculosis-like pulmonary infections. Generally, this study may help with the development of new strategy for the diagnosis and treatment of mycobacterial infection. PMID:25463697

  3. Sequence-Based Identification of Aerobic Actinomycetes

    PubMed Central

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

    2004-01-01

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

  4. 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

  5. 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.

  6. A synthesis of the structural geology of a major tectonic boundary between a 1000 m.y. mobile belt and a 3000 m.y. craton

    NASA Astrophysics Data System (ADS)

    van Bever Donker, J. M.

    1991-10-01

    On the boundary between the 3000 Ma Kaapvaal Craton and the ±1100 Ma Gordonia sub-province of the Namaqua Province situated west of the craton lies the Areachap Group, which mainly comprises amphibolitic and calc-silicate rich rocks. Various studies investigating the structural relationships between the adjacent terranes all reveal an intensely deformed area, where at least four phases of deformation can be defined, developing complex interference patterns which in turn have been displaced by a large number of shear zones. Geochemical evidence shows that the Areachap Group may represent a volcanic island arc. In order to explain the different orientations of the various phases of deformation, an oblique collision model with a rigid indentor is suggested. The model suggests that the initially pointed indentor caused thrusting in what is now described as the ± 2000 Ma Kheiss Province, situated on the edge of the craton. This event could have changed the shape of the indentor from pointed to flat, resulting in a differently oriented stress field thus causing the interference structures typical of this area. The structures resulting from this collision have been interpreted as the lateral ramp of a N-directed collision zone, causing thrusting to take place obliquely towards the northeast, so that the NW-trending shear zones can be considered frontal ramps. The NNW-trending shear zones have consequently been interpreted as oblique ramps. Careful analysis of fabric data and joint systems has led to the interpretation that σ1 was sub-perpendicular to the strike-slip zone, which together with compressive conditions is interpreted as a transpressive environment. Differential transport and the consequent rotation of σ1 caused the differential stresses responsible for the development of the en-echelon fault pattern with zones of reversed sense shearing.

  7. Stable-Isotope-Based Labeling of Styrene-Degrading Microorganisms in Biofilters†

    PubMed Central

    Alexandrino, Maria; Knief, Claudia; Lipski, André

    2001-01-01

    Deuterated styrene ([2H8]styrene) was used as a tracer in combination with phospholipid fatty acid (PLFA) analysis for characterization of styrene-degrading microbial populations of biofilters used for treatment of waste gases. Deuterated fatty acids were detected and quantified by gas chromatography-mass spectrometry. The method was evaluated with pure cultures of styrene-degrading bacteria and defined mixed cultures of styrene degraders and non-styrene-degrading organisms. Incubation of styrene degraders for 3 days with [2H8]styrene led to fatty acids consisting of up to 90% deuterated molecules. Mixed-culture experiments showed that specific labeling of styrene-degrading strains and only weak labeling of fatty acids of non-styrene-degrading organisms occurred after incubation with [2H8]styrene for up to 7 days. Analysis of actively degrading filter material from an experimental biofilter and a full-scale biofilter by this method showed that there were differences in the patterns of labeled fatty acids. For the experimental biofilter the fatty acids with largest amounts of labeled molecules were palmitic acid (16:0), 9,10-methylenehexadecanoic acid (17:0 cyclo9-10), and vaccenic acid (18:1 cis11). These lipid markers indicated that styrene was degraded by organisms with a Pseudomonas-like fatty acid profile. In contrast, the most intensively labeled fatty acids of the full-scale biofilter sample were palmitic acid and cis-11-hexadecenoic acid (16:1 cis11), indicating that an unknown styrene-degrading taxon was present. Iso-, anteiso-, and 10-methyl-branched fatty acids showed no or weak labeling. Therefore, we found no indication that styrene was degraded by organisms with methyl-branched fatty fatty acids, such as Xanthomonas, Bacillus, Streptomyces, or Gordonia spp. PMID:11571187

  8. 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.

  9. 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.

  10. Homology modeling and protein engineering of alkane monooxygenase in Burkholderia thailandensis MSMB121: in silico insights.

    PubMed

    Jain, Chakresh Kumar; Gupta, Money; Prasad, Yamuna; Wadhwa, Gulshan; Sharma, Sanjeev Kumar

    2014-07-01

    The degradation of hydrocarbons plays an important role in the eco-balancing of petroleum products, pesticides and other toxic products in the environment. The degradation of hydrocarbons by microbes such as Geobacillus thermodenitrificans, Burkhulderia, Gordonia sp. and Acinetobacter sp. has been studied intensively in the literature. The present study focused on the in silico protein engineering of alkane monooxygenase (ladA)-a protein involved in the alkane degradation pathway. We demonstrated the improvement in substrate binding energy with engineered ladA in Burkholderia thailandensis MSMB121. We identified an ortholog of ladA monooxygenase found in B. thailandensis MSMB121, and showed it to be an enzyme involved in an alkane degradation pathway studied extensively in Geobacillus thermodenitrificans. Homology modeling of the three-dimensional structure of ladA was performed with a crystal structure (protein databank ID: 3B9N) as a template in MODELLER 9v11, and further validated using PROCHECK, VERIFY-3D and WHATIF tools. Specific amino acids were substituted in the region corresponding to amino acids 305-370 of ladA protein, resulting in an enhancement of binding energy in different alkane chain molecules as compared to wild protein structures in the docking experiments. The substrate binding energy with the protein was calculated using Vina (Implemented in VEGAZZ). Molecular dynamics simulations were performed to study the dynamics of different alkane chain molecules inside the binding pockets of wild and mutated ladA. Here, we hypothesize an improvement in binding energies and accessibility of substrates towards engineered ladA enzyme, which could be further facilitated for wet laboratory-based experiments for validation of the alkane degradation pathway in this organism.

  11. Differential proteomic analysis of an engineered Streptomyces coelicolor strain reveals metabolic pathways supporting growth on n-hexadecane.

    PubMed

    Gallo, Giuseppe; Lo Piccolo, Luca; Renzone, Giovanni; La Rosa, Ruggero; Scaloni, Andrea; Quatrini, Paola; Puglia, Anna Maria

    2012-06-01

    The alkB gene, encoding an alkane monooxygenase in the actinomycete Gordonia sp. SoCg, was expressed in the non-alkane-degrading actinomycete Streptomyces coelicolor M145. The resulting engineered strain, M145-AH, can grow on n-hexadecane as sole carbon source. To unravel proteins associated with growth on n-alkanes, proteome of M145-AH after 6, 24, and 48 h of incubation in the Bushnell-Haas (BH) mineral medium containing n-hexadecane as sole carbon source (H condition) and in BH without any carbon source (0 condition) were compared using 2D-differential gel electrophoresis. Proteome analysis revealed significant changes only at 48 h, showing 48 differentially abundant proteins identified by mass spectrometry procedures. To asses if these proteins were specifically related to n-hexadecane metabolism, their expression was investigated, comparing H proteome with that of M145-AH incubated in BH with glucose as sole carbon source (G condition). Thus, protein expression profiles at 6, 24, and 48 h under H, 0, and G conditions were combined, revealing that M145-AH regulates in a temporally- and carbon source-dependent manner the expression of proteins involved in regulatory events, central carbon metabolism, respiration, β-oxidation, membrane transport, and amino acid and protein metabolism. Interestingly, 21 % of them, mostly involved in membrane transport and protein metabolism, showed a n-hexadecane-dependent regulation with regulatory proteins such as CRP likely to have a key role in M145-AH n-hexadecane growth. These results, expanding the knowledge on n-alkane utilization in Gram-positive bacteria, reveal genes to be targeted to develop an efficient S. coelicolor M145-AH-based bioremediation system.

  12. Hydrocarbonoclastic bacteria isolated from petroleum contaminated sites in Tunisia: isolation, identification and characterization of the biotechnological potential.

    PubMed

    Mahjoubi, Mouna; Jaouani, Atef; Guesmi, Amel; Ben Amor, Sonia; Jouini, Ahlem; Cherif, Hanen; Najjari, Afef; Boudabous, Abdellatif; Koubaa, Nedra; Cherif, Ameur

    2013-09-25

    Petroleum hydrocarbons are important energy resources used by industry and in our daily life, whose production contributes highly to environmental pollution. To control such risk, bioremediation constitutes an environmentally friendly alternative technology that has been established and applied. It constitutes the primary mechanism for the elimination of hydrocarbons from contaminated sites by natural existing populations of microorganisms. In this work, a collection of 125 strains, adapted to grow on minimal medium supplemented with crude oil, was obtained from contaminated sediments and seawater from a refinery harbor of the Bizerte coast in the North of Tunisia. The diversity of the bacterial collection was analyzed by amplification of the internal transcribed spacers between the 16S and the 23S rRNA genes (ITS-PCR) and by 16S rRNA sequencing. A total of 36 distinct ITS haplotypes were detected on agarose matrix. Partial 16S rRNA gene sequencing performed on 50 isolates showed high level of identity with known sequences. Strains were affiliated to Ochrabactrum, Sphingobium, Acinetobacter, Gordonia, Microbacterium, Brevundimonas, Novosphingobium, Stenotrophomonas, Luteibacter, Rhodococcus, Agrobacterium, Achromobacter, Bacilllus, Kocuria and Pseudomonas genera. Acinetobacter and Stenotrophomons were found to be the most abundant species characterized by a marked microdiversity as shown through ITS typing. Culture-independent approach (DGGE) showed high diversity in the microbial community in all the studied samples with a clear correlation with the hydrocarbon pollution rate. Sequencing of the DGGE bands revealed a high proportion of Proteobacteria represented by the Alpha and Gamma subclasses. The predominant bacterial detected by both dependent and independent approaches were the Proteobacteria. The biotechnological potential of the isolates revealed a significant production of biosurfactants with important emulsification activities useful in bioremediation

  13. Metabolism of the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in a contaminated vadose zone.

    PubMed

    Ronen, Zeev; Yanovich, Yuval; Goldin, Regina; Adar, Eilon

    2008-11-01

    The aim of this study was to explore biodegradation potential of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in a deep contaminated unsaturated zone over Israel's coastal aquifer. While anaerobic biodegradation potential was observed throughout the profile down to the water table at a depth of 45 m, aerobic biodegradation was limited to the surface of the unsaturated zone. Traces of nitroso-RDX intermediates were detected in the soil samples, indicating possible in situ activity. Polymerase chain reaction and denaturing gradient gel electrophoresis analysis revealed that the microbial population in the soil consisted of protobacteria, but no known RDX degraders were detected. However, a 16S rRNA gene sequence most similar to Sphingomonas sp. was detected at all depths. Biodegradation rates were faster in the surface (0 and 1m) versus deeper soil samples (22 and 45 m) and were not affected under anaerobic conditions by the presence of nitrate, indicating a concurrent reduction of both compounds. RDX half-life in the surface soil was mostly dependent on carbon content and to lesser extent on soil moisture. Biomineralization of RDX to CO(2) was confirmed by incubating surface soil with (14)C-labeled RDX. An aerobic RDX-degrading bacterium, identified as Gordonia sp., was isolated from the soil: it degraded RDX aerobically and produced 4-nitro-2,4-diazabutanal. This study, the first to explore RDX biodegradation in the deep vadoze zone, indicates biodegradation potential throughout the profile, which is likely to support natural attenuation.

  14. RDX degradation in bioaugmented model aquifer columns under aerobic and low oxygen conditions.

    PubMed

    Fuller, Mark E; Hatzinger, Paul B; Condee, Charles W; Andaya, Christina; Rezes, Rachel; Michalsen, Mandy M; Crocker, Fiona H; Indest, Karl J; Jung, Carina M; Alon Blakeney, G; Istok, Jonathan D; Hammett, Steven A

    2017-07-01

    Degradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in laboratory columns following biostimulation and bioaugmentation was investigated using sediment and groundwater from a contaminated aquifer at a US Navy facility. No RDX degradation was observed following aerobic biostimulation with either fructose or lactate (both 0.1 mM) prior to bioaugmentation. Replicate columns were then bioaugmented with either Gordonia sp. KTR9, Pseudomonas fluorescens I-C (Ps I-C), or both strains. Under aerobic conditions (influent dissolved oxygen (DO) >6 mg/L), RDX was degraded following the addition of fructose, and to a lesser extent with lactate, in columns bioaugmented with KTR9. No degradation was observed in columns bioaugmented with only Ps I-C under aerobic conditions, consistent with the known anaerobic RDX degradation pathway for this strain. When influent DO was reduced to <2 mg/L, good RDX degradation was observed in the KTR9-bioaugmented column, and some degradation was also observed in the Ps I-C-bioaugmented column. After DO levels were kept below 1 mg/L for more than a month, columns bioaugmented with KTR9 became unresponsive to fructose addition, while RDX degradation was still observed in the Ps I-C-bioaugmented columns. These results indicate that bioaugmentation with the aerobic RDX degrader KTR9 could be effective at sites where site geology or geochemistry allow higher DO levels to be maintained. Further, inclusion of strains capable of anoxic RDX degradation such as Ps I-C may facilitate bimodal RDX removal when DO levels decrease.

  15. 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.

  16. 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. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    PubMed

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

    2016-08-01

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

  18. 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

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

    PubMed

    Kaewkla, Onuma; Franco, Christopher M M

    2013-02-01

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

  20. Identification of three homologous latex-clearing protein (lcp) genes from the genome of Streptomyces sp. strain CFMR 7.

    PubMed

    Nanthini, Jayaram; Ong, Su Yean; Sudesh, Kumar

    2017-09-10

    Rubber materials have greatly contributed to human civilization. However, being a polymeric material does not decompose easily, it has caused huge environmental problems. On the other hand, only few bacteria are known to degrade rubber, with studies pertaining them being intensively focusing on the mechanism involved in microbial rubber degradation. The Streptomyces sp. strain CFMR 7, which was previously confirmed to possess rubber-degrading ability, was subjected to whole genome sequencing using the single molecule sequencing technology of the PacBio® RS II system. The genome was further analyzed and compared with previously reported rubber-degrading bacteria in order to identify the potential genes involved in rubber degradation. This led to the interesting discovery of three homologues of latex-clearing protein (Lcp) on the chromosome of this strain, which are probably responsible for rubber degrading activities. Genes encoding oxidoreductase α-subunit (oxiA) and oxidoreductase β-subunit (oxiB) were also found downstream of two lcp genes which are located adjacent to each other. In silico analysis reveals genes that have been identified to be involved in the microbial degradation of rubber in the Streptomyces sp. strain CFMR 7. This is the first whole genome sequence of a clear-zone-forming natural rubber- degrading Streptomyces sp., which harbours three Lcp homologous genes with the presence of oxiA and oxiB genes compared to the previously reported Gordonia polyisoprenivorans strain VH2 (with two Lcp homologous genes) and Nocardia nova SH22a (with only one Lcp gene). Copyright © 2017 Elsevier B.V. All rights reserved.

  1. 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

  2. Rhizosphere effects of PAH-contaminated soil phytoremediation using a special plant named Fire Phoenix.

    PubMed

    Liu, Rui; Xiao, Nan; Wei, Shuhe; Zhao, Lixing; An, Jing

    2014-03-01

    The rhizosphere effect of a special phytoremediating species known as Fire Phoenix on the degradation of polycyclic aromatic hydrocarbons (PAHs) was investigated, including changes of the enzymatic activity and microbial communities in rhizosphere soil. The study showed that the degradation rate of Σ8PAHs by Fire Phoenix was up to 99.40% after a 150-day culture. The activity of dehydrogenase (DHO), peroxidase (POD) and catalase (CAT) increased greatly, especially after a 60-day culture, followed by a gradual reduction with an increase in the planting time. The activity of these enzymes was strongly correlated to the higher degradation performance of Fire Phoenix growing in PAH-contaminated soils, although it was also affected by the basic characteristics of the plant species itself, such as the excessive, fibrous root systems, strong disease resistance, drought resistance, heat resistance, and resistance to barren soil. The activity of polyphenoloxidase (PPO) decreased during the whole growing period in this study, and the degradation rate of Σ8PAHs in the rhizosphere soil after having planted Fire Phoenix plants had a significant (R(2)=0.947) negative correlation with the change in the activity of PPO. Using an analysis of the microbial communities, the results indicated that the structure of microorganisms in the rhizosphere soil could be changed by planting Fire Phoenix plants, namely, there was an increase in microbial diversity compared with the unplanted soil. In addition, the primary advantage of Fire Phoenix was to promote the growth of flora genus Gordonia sp. as the major bacteria that can effectively degrade PAHs.

  3. 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.

  4. 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

  5. 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.

  6. Variation of the linkage of root function with root branch order.

    PubMed

    Long, Yingqian; Kong, Deliang; 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.

  7. 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

  8. 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

  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. 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

  11. 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

  12. Jerusalem artichoke as low-cost fructose-rich feedstock for fossil fuels desulphurization by a fructophilic bacterium.

    PubMed

    Silva, T P; Paixão, S M; Roseiro, J C; Alves, L

    2015-03-01

    Through biodesulphurization (BDS) is possible to remove the sulphur present in fossil fuels to carry out the very strict legislation. However, this biological process is limited by the cost of the culture medium, and thus, it is important to explore cheaper alternative carbon sources, such as Jerusalem artichoke (JA). These carbon sources usually contain sulphates which interfere with the BDS process. The goal of this work was to remove the sulphates from Jerusalem artichoke juice (JAJ) through BaCl2 precipitation viewing the optimization of dibenzothiophene (DBT) desulphurization by Gordonia alkanivorans strain 1B. Using a statistical design (Doehlert distribution), the effect of BaCl2 concentration (0.125-0.625%) and pH (5-9) was studied on sulphate concentration in hydrolysed JAJ. A validated surface response derived from data indicated that zero sulphates can be achieved with 0.5-0.55% (w/v) BaCl2 at pH 7; however, parallel BDS assays showed that the highest desulphurization was obtained with the juice treated with 0.5% (w/v) BaCl2 at pH 8.73. Further assays demonstrated that enhanced DBT desulphurization was achieved using hydrolysed JAJ treated in these optimal conditions. A total conversion of 400 μmol l(-1) DBT into 2-hydroxybiphenyl (2-HBP) in <90 h was observed, attaining a 2-HBP maximum production rate of 28.2 μmol l(-1) h(-1) and a specific production rate of 5.06 μmol(-1) g(-1) (DCW) h(-1) . These results highlight the efficacy of the treatment applied to JAJ in making this agromaterial a promising low-cost renewable feedstock for improved BDS by the fructophilic strain 1B. This study is a fundamental step viewing BDS application at the industrial level as it accounts a cost-effective production of the biocatalysts, one of the main drawbacks for BDS scale-up. © 2014 The Society for Applied Microbiology.

  13. A simple, rapid and cost-effective process for production of latex clearing protein to produce oligopolyisoprene molecules.

    PubMed

    Andler, R; Steinbüchel, A

    2017-01-10

    Aiming at finding feasible alternatives for rubber waste disposal, the partial enzymatic degradation of poly(cis-1,4-isoprene)-containing materials represents a potential solution. The use of rubber-degrading enzymes and the biotransformation of rubber into new materials is limited by the high costs associated with the production and purification of the enzyme and the complexity of the process. This study presents a simple and low-cost procedure to obtain purified latex clearing protein (Lcp), an enzyme capable of cleaving the double bonds of poly(cis-1,4-isoprene) in presence of oxygen to produce different size of oligomers with terminal aldehyde and ketone groups, respectively. The gene coding for Lcp1VH2 from Gordonia polyisoprenivorans strain VH2 was overexpressed in Escherichia coli C41 (DE3), and by using an auto-induction medium high protein yields were obtained. The cultivation process was described and compared with an IPTG-inducible medium previously used. Purification of the enzyme was performed using salting out precipitation with ammonium sulfate. Different salt concentrations and pH were tested in order to find the optimal for purification, obtaining a concentration of 60mg Lcp per l. The enzymatic activity of the purified enzyme was measured by an oxygen consumption assay in the presence of polyisoprene latex. Volumetric activities of 0.16Uml(-1) were obtained at optimal conditions of temperature and pH. The results showed an active and partial purified fraction of Lcp1VH2, able to cleave the backbone of poly(cis-1,4-isoprene) and to produce degradation products that were identified with staining methodologies (Schiff reagent for aldehyde groups and 2,4-DNPH for carbonyl groups) and characterized using nuclear magnetic resonance (NMR). Thirteen different storage conditions were tested for the purified enzyme analyzing the enzymatic activity after 1 and 3 months. Lcp1VH2, as an ammonium sulfate precipitate, was stable, easy to handle and sufficiently

  14. A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments

    PubMed Central

    Brinkman, Eva K.; Schipper, Kira; Bongaerts, Nadine; Voges, Mathias J.; Abate, Alessandro; Wahl, S. Aljoscha

    2012-01-01

    This work puts forward a toolkit that enables the conversion of alkanes by Escherichia coli and presents a proof of principle of its applicability. The toolkit consists of multiple standard interchangeable parts (BioBricks)9 addressing the conversion of alkanes, regulation of gene expression and survival in toxic hydrocarbon-rich environments. A three-step pathway for alkane degradation was implemented in E. coli to enable the conversion of medium- and long-chain alkanes to their respective alkanols, alkanals and ultimately alkanoic-acids. The latter were metabolized via the native β-oxidation pathway. To facilitate the oxidation of medium-chain alkanes (C5-C13) and cycloalkanes (C5-C8), four genes (alkB2, rubA3, rubA4and rubB) of the alkane hydroxylase system from Gordonia sp. TF68,21 were transformed into E. coli. For the conversion of long-chain alkanes (C15-C36), theladA gene from Geobacillus thermodenitrificans was implemented. For the required further steps of the degradation process, ADH and ALDH (originating from G. thermodenitrificans) were introduced10,11. The activity was measured by resting cell assays. For each oxidative step, enzyme activity was observed. To optimize the process efficiency, the expression was only induced under low glucose conditions: a substrate-regulated promoter, pCaiF, was used. pCaiF is present in E. coli K12 and regulates the expression of the genes involved in the degradation of non-glucose carbon sources. The last part of the toolkit - targeting survival - was implemented using solvent tolerance genes, PhPFDα and β, both from Pyrococcus horikoshii OT3. Organic solvents can induce cell stress and decreased survivability by negatively affecting protein folding. As chaperones, PhPFDα and β improve the protein folding process e.g. under the presence of alkanes. The expression of these genes led to an improved hydrocarbon tolerance shown by an increased growth rate (up to 50%) in the presences of 10% n-hexane in the culture

  15. 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

  16. Applying bacterial metallophores to mobilize gallium

    NASA Astrophysics Data System (ADS)

    Schwabe, Ringo; Obst, Britta; Mehnert, Marika; Tischler, Dirk; Wiche, Oliver

    2017-04-01

    Metallophores are produced by many organisms such as bacteria, fungi and plants in order to mobilize metals, especially iron (Greek: "siderophore" = iron carrier), to overcome limitations or stress. Respectively, it is well known these compounds loaded with relevant metal ions are used not only by the producing organism but also by others. Thus metallophores as metal carriers are relevant for many processes at various habitats (e.g. metal acquisition, pathogenic factors, antimicrobial activity, sensing). However, metallophores do also mobilize metals of industrial interest which have no critical role in the living world. Here we focused on gallium as industrial relevant metal and compared it to iron which is important for all organisms. The herein described mobilization of valuable metals such as gallium from soils provides first hints towards alternative strategies, such as phytomining, sensor development, or solvent extraction based on metallophores. Two produced metallophore preparations of soil bacteria (Gordonia rubripertincta CWB2 and Paracoccus denitrificans PD1222) and the commercially available metallophore desferrioxamine B were analyzed for iron binding activity by means of a standard chromazurol S assay and equal iron binding activities were employed to treat a soil sample. The pH was set constant to 6 in order to avoid pH related effects. Therefore, the metallophore was prepared in a special medium and control of water and medium were also applied onto the soil. The soil was washed and incubated with the mentioned preparations. The mobilization of iron and gallium was determined prior and after the treatment by means of ICP-MS. Water showed no effect and medium only a little on metal mobilization which is related to its ionic strength. All metallophores mobilized iron at a similar strength but showed significant differences in case of gallium. Here the metallophore mix produced by strain CWB2 showed best results and allowed to mobilize gallium 3-times

  17. 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

  18. Novel Diagnostic Algorithm for Identification of Mycobacteria Using Genus-Specific Amplification of the 16S-23S rRNA Gene Spacer and Restriction Endonucleases

    PubMed Central

    Roth, Andreas; Reischl, Udo; Streubel, Anna; Naumann, Ludmila; Kroppenstedt, Reiner M.; Habicht, Marion; Fischer, Marga; Mauch, Harald

    2000-01-01

    A novel genus-specific PCR for mycobacteria with simple identification to the species level by restriction fragment length polymorphism (RFLP) was established using the 16S-23S ribosomal RNA gene (rDNA) spacer as a target. Panspecificity of primers was demonstrated on the genus level by testing 811 bacterial strains (122 species in 37 genera from 286 reference strains and 525 clinical isolates). All mycobacterial isolates (678 strains among 48 defined species and 5 indeterminate taxons) were amplified by the new primers. Among nonmycobacterial isolates, only Gordonia terrae was amplified. The RFLP scheme devised involves estimation of variable PCR product sizes together with HaeIII and CfoI restriction analysis. It yielded 58 HaeIII patterns, of which 49 (84%) were unique on the species level. Hence, HaeIII digestion together with CfoI results was sufficient for correct identification of 39 of 54 mycobacterial taxons and one of three or four of seven RFLP genotypes found in Mycobacterium intracellulare and Mycobacterium kansasii, respectively. Following a clearly laid out diagnostic algorithm, the remaining unidentified organisms fell into five clusters of closely related species (i.e., the Mycobacterium avium complex or Mycobacterium chelonae-Mycobacterium abscessus) that were successfully separated using additional enzymes (TaqI, MspI, DdeI, or AvaII). Thus, next to slowly growing mycobacteria, all rapidly growing species studied, including M. abscessus, M. chelonae, Mycobacterium farcinogenes, Mycobacterium fortuitum, Mycobacterium peregrinum, and Mycobacterium senegalense (with a very high 16S rDNA sequence similarity) were correctly identified. A high intraspecies sequence stability and the good discriminative power of patterns indicate that this method is very suitable for rapid and cost-effective identification of a wide variety of mycobacterial species without the need for sequencing. Phylogenetically, spacer sequence data stand in good agreement with 16S r

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

    PubMed

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

    2010-05-01

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

  20. Production of ω-hydroxy palmitic acid using CYP153A35 and comparison of cytochrome P450 electron transfer system in vivo.

    PubMed

    Jung, Eunok; Park, Beom Gi; Ahsan, Md Murshidul; Kim, Joonwon; Yun, Hyungdon; Choi, Kwon-Young; Kim, Byung-Gee

    2016-12-01

    Bacterial cytochrome P450 enzymes in cytochrome P450 (CYP)153 family were recently reported as fatty acid ω-hydroxylase. Among them, CYP153As from Marinobacter aquaeolei VT8 (CYP153A33), Alcanivorax borkumensis SK2 (CYP153A13), and Gordonia alkanivorans (CYP153A35) were selected, and their specific activities and product yields of ω-hydroxy palmitic acid based on whole cell reactions toward palmitic acid were compared. Using CamAB as redox partner, CYP153A35 and CYP153A13 showed the highest product yields of ω-hydroxy palmitic acid in whole cell and in vitro reactions, respectively. Artificial self-sufficient CYP153A35-BMR was constructed by fusing it to the reductase domain of CYP102A1 (i.e., BM3) from Bacillus megaterium, and its catalytic activity was compared with CYP153A35 and CamAB systems. Unexpectedly, the system with CamAB resulted in a 1.5-fold higher yield of ω-hydroxy palmitic acid than that using A35-BMR in whole cell reactions, whereas the electron coupling efficiency of CYP153A35-BM3 reductase was 4-fold higher than that of CYP153A35 and CamAB system. Furthermore, various CamAB expression systems according to gene arrangements of the three proteins and promoter strength in their gene expression were compared in terms of product yields and productivities. Tricistronic expression of the three proteins in the order of putidaredoxin (CamB), CYP153A35, and putidaredoxin reductase (CamA), i.e., A35-AB2, showed the highest product yield from 5 mM palmitic acid for 9 h in batch reaction owing to the concentration of CamB, which is the rate-limiting factor for the activity of CYP153A35. However, in fed-batch reaction, A35-AB1, which expressed the three proteins individually using three T7 promoters, resulted with the highest product yield of 17.0 mM (4.6 g/L) ω-hydroxy palmitic acid from 20 mM (5.1 g/L) palmitic acid for 30 h.

  1. 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